ORCID Profile
0000-0002-0776-5861
Current Organisation
RMIT University
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Veterinary Microbiology (excl. Virology) | Animal Production | Animal Protection (Pests and Pathogens) | Infectious Agents | Veterinary Sciences | Food Packaging, Preservation and Safety |
Poultry | Veterinary Biological Preventatives (e.g. Vaccines) | Eggs | Expanding Knowledge in the Agricultural and Veterinary Sciences
Publisher: Elsevier BV
Date: 05-1993
Abstract: In retrovirus-induced tumors, proviral DNA is commonly found next to or within a cellular proto-oncogene such that transcription of the gene is influenced by the viral promoter or enhancer. Extensive surveys of naturally occurring tumors reveal that proviruses integrated on the 3' side of the gene are usually in the same transcriptional orientation, suggesting a model in which the bidirectional viral enhancer acts primarily on the closest promoters. Here we describe a virally induced mammary tumor that appears to contradict these ideas since the Wnt-1/int-1 and Fgf-3/int-2 proto-oncogenes have both been activated by mouse mammary tumor virus (MMTV) DNA integrated 3' of the gene in the opposite transcriptional orientation. However, by cloning the relevant DNAs, we show that these are not simple proviral insertions. In the Wnt-1 locus, there is an additional LTR immediately adjacent to the 3' end of the MMTV provirus, while in Fgf-3, the provirus has sustained a deletion that removes the 5' LTR, gag, and most of pol. These structural alterations can be reconciled with the enhancer insertion model by postulating that the viral enhancer can only function if it is not transcribed.
Publisher: Elsevier BV
Date: 12-2018
DOI: 10.1016/J.VETMIC.2018.10.022
Abstract: Clostridium perfringens is the etiological agent of necrotic enteritis in chickens. As necrotic enteritis is a gastrointestinal disease, the interactions of pathogenic C. perfringens strains with the complex microbiota of the gastrointestinal tract may influence disease development and severity of disease. In this study the interactions of a pathogenic strain of C. perfringens, WER-NE36, with the microbiota of broilers was investigated to determine whether the pre-existing microbiota could influence disease outcomes in the necrotic enteritis challenge model. Methods and approach: Faecal microbiota compositions were measured before and after C. perfringens challenge and caecal microbiota was also characterised at necropsy. The microbiota profiles from in idual birds were related back to the degree of necrotic enteritis that each bird developed. Under the experimental conditions used the pre-existing microbiota did not have an effect on disease outcomes. However, C. perfringens challenge was shown to have a significant effect on the microbiota of broilers, regardless of disease status, by displacement of commensal clostridia. The microbiota signature after challenge resembled that of lower productivity birds, supporting the finding that physically obvious disease (necrotic lesions), as well as dysbiosis, are associated with shifts in gut microbiota and affect broiler performance, increasing costs to the poultry industry.
Publisher: Public Library of Science (PLoS)
Date: 18-04-2011
Publisher: Public Library of Science (PLoS)
Date: 23-03-2018
Publisher: Wiley
Date: 07-2016
DOI: 10.1038/CTI.2016.41
Publisher: Public Library of Science (PLoS)
Date: 05-08-2021
DOI: 10.1371/JOURNAL.PONE.0255633
Abstract: Traditional s ling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative s ling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive s les (excreta, litter and poultry dust) are representative of invasive s les (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene licon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive s les were detected in non-invasive s les, the relative abundance of members of the microbial communities of these groups were different, as shown by beta ersity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes , and excreta as a proxy of caecal contents for the detection of Tenericutes . Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes . However, none of the non-invasive s les could be used to infer the overall abundance of OTUs observed in invasive s les. In conclusion, non-invasive s les could be used to detect the presence and absence of the majority of the OTUs found in invasive s les, but could not accurately reflect the microbial community structure of invasive s les.
Publisher: Informa UK Limited
Date: 22-11-2020
Publisher: Springer Science and Business Media LLC
Date: 22-05-2018
Publisher: Elsevier BV
Date: 12-2019
Publisher: SAGE Publications
Date: 26-01-2020
Abstract: Focal duodenal necrosis (FDN) is an intestinal disease of egg-layer chickens characterized by multifocal necrosis of the duodenal loop and proximal jejunum. Affected flocks usually have decreased egg weights and drops in egg production. Previous studies have associated this condition with Clostridium perfringens infection. We tried to reproduce FDN by experimental infection of egg-laying chickens using different netB-positive and netB-negative C. perfringens strains, and duodenal homogenate obtained from FDN lesions. Chickens challenged with C. perfringens and/or duodenal homogenate developed duodenitis after challenge. Gross lesions included mucosal erosions, hyperemia, mucosal hemorrhages, and watery intestinal content. Microscopic lesions included mild enterocyte degeneration and necrosis, and mild-to-moderate hemorrhage and lymphoplasmacytic and heterophilic infiltration of the lamina propria. Two netB-positive C. perfringens strains closely related to necrotic enteritis pathogenic strains, by genomic composition, were re-isolated from lesions. Necrosis of intestinal crypts was observed in chickens challenged with duodenal homogenate with or without C. perfringens coinfection. Characteristic microscopic FDN lesions with significant necrosis and loss of villus enterocytes were not reproduced.
Publisher: Springer Science and Business Media LLC
Date: 18-10-2017
DOI: 10.1038/NI1117-1271C
Abstract: This corrects the article DOI: 10.1038/ni.3713.
Publisher: Springer Science and Business Media LLC
Date: 23-06-2015
DOI: 10.1038/NCOMMS8320
Abstract: Asthma is prevalent in Western countries, and recent explanations have evoked the actions of the gut microbiota. Here we show that feeding mice a high-fibre diet yields a distinctive gut microbiota, which increases the levels of the short-chain fatty acid, acetate. High-fibre or acetate-feeding led to marked suppression of allergic airways disease (AAD, a model for human asthma), by enhancing T-regulatory cell numbers and function. Acetate increases acetylation at the Foxp3 promoter, likely through HDAC9 inhibition. Epigenetic effects of fibre/acetate in adult mice led us to examine the influence of maternal intake of fibre/acetate. High-fibre/acetate feeding of pregnant mice imparts on their adult offspring an inability to develop robust AAD. High fibre/acetate suppresses expression of certain genes in the mouse fetal lung linked to both human asthma and mouse AAD. Thus, diet acting on the gut microbiota profoundly influences airway responses, and may represent an approach to prevent asthma, including during pregnancy.
Publisher: Microbiology Society
Date: 20-04-2022
Abstract: A novel species of C ylobacter was isolated from bile s les of chickens with spotty liver disease in Australia, making it the second novel species isolated from chickens with the disease, after C ylobacter hepaticus was isolated and described in 2016. Six independently derived isolates were obtained. They were Gram-stain-negative, microaerobic, catalase-positive, oxidase-positive and urease-negative. Unlike most other species of the genus C ylobacter , more than half of the tested strains of this novel species hydrolysed hippurate and most of them could not reduce nitrate. Distinct from C. hepaticus , many of the isolates were sensitive to 2,3,5-triphenyltetrazolium chloride (0.04%) and metronidazole (4 mg ml −1 ), and all strains were sensitive to nalidixic acid. Phylogenetic analysis using 16S rRNA and hsp60 gene sequences demonstrated that the strains formed a robust clade that was clearly distinct from recognized C ylobacter species. Whole genome sequence analysis of the strains showed that the average nucleotide identity and the genome blast distance phylogeny values compared to other C ylobacter species were less than 86 and 66%, respectively, which are below the cut-off values generally recognized for isolates of the same species. The genome of the novel species has a DNA G+C content of 30.6 mol%, while that of C. hepaticus is 27.9 mol%. Electron microscopy showed that the cells were spiral-shaped, with bipolar unsheathed flagella. The protein spectra generated from matrix-assisted laser desorption/ionization time of flight analysis demonstrated that they are different from the most closely related C ylobacter species. These data indicate that the isolates belong to a novel C ylobacter species, for which the name C ylobacter bilis sp. nov. is proposed. The type strain is VicNov18 T (=ATCC TSD-231 T =NCTC 14611 T ).
Publisher: Elsevier BV
Date: 12-2018
Publisher: Burleigh Dodds Science Publishing
Date: 31-07-2017
Abstract: Poultry producers have been cautious in the application of probiotics, due to mixed experiences of their effectiveness and lack of knowledge regarding the scientific basis for their modes of action. Prebiotics have been more readily accepted because they can be added without any significant change to traditional practices. Recent research has increased our knowledge of the effects of both types of treatment, their possible modes of action, and the strengths and limitations of their use. We are beginning to understand why some products may give variable outcomes and what may be done to further validate the performance of existing products and develop a new generation of more reliable and effective probiotics and prebiotics.
Publisher: Informa UK Limited
Date: 14-03-2018
DOI: 10.1080/00071668.2018.1447083
Abstract: 1. Salmonella enterica subsp. salamae serovar sofia (S. sofia) is a prevalent strain of Salmonella in Australian broilers and has been isolated from broiler chickens, litter, dust, as well as pre- and post-processing carcasses, and retail chicken portions but has never been reported in commercial Australian layers or eggs. 2. To investigate whether a S. sofia isolate from a broiler could colonise layers, one-month-old Hyline brown layers were orally inoculated with S. sofia and colonisation was monitored for 2-4 weeks. 3. Overall, 30-40% of the chickens shed S. sofia from the cloaca between 6 and 14 d post-inoculation which then declined to 10% by d 21. Necropsy at 2 weeks post-inoculation revealed 80% of birds harboured S. sofia in the caecum, whilst, by 4 weeks post-infection, no chickens were colonised with S. sofia in the gastrointestinal tract, liver or spleen. Additionally, no aerosol 'bird to bird' transfer was evident. 4. This study demonstrated that laying hens can be colonised by broiler-derived S. sofia however, this colonisation was transient, reaching a peak at 14 d post-inoculation, and was completely cleared by 28 d post-inoculation. The transience of colonisation of S. sofia in layers could be a factor explaining why S. sofia has never been detected when screening for Salmonella serotypes found in Australian laying hens or eggs.
Publisher: American Society for Microbiology
Date: 27-09-2011
DOI: 10.1128/JB.05854-11
Publisher: Springer Science and Business Media LLC
Date: 12-01-2018
DOI: 10.1038/S41598-017-18904-8
Abstract: Recent work from our laboratory has provided evidence that indicates selective bacterial translocation from the host gut microbiota to peripheral tissues (i.e. lung) plays a key role in the development of post-stroke infections. Despite this, it is currently unknown whether mucosal bacteria that live on and interact closely with the host intestinal epithelium contribute in regulating bacterial translocation after stroke. Here, we found that the microbial communities within the mucosa of gastrointestinal tract (GIT) were significantly different between sham-operated and post-stroke mice at 24 h following surgery. The differences in microbiota composition were substantial in all sections of the GIT and were significant, even at the phylum level. The main characteristics of the stroke-induced shift in mucosal microbiota composition were an increased abundance of Akkermansia muciniphila and an excessive abundance of clostridial species. Furthermore, we analysed the predicted functional potential of the altered mucosal microbiota induced by stroke using PICRUSt and revealed significant increases in functions associated with infectious diseases, membrane transport and xenobiotic degradation. Our findings revealed stroke induces far-reaching and robust changes to the intestinal mucosal microbiota. A better understanding of the precise molecular events leading up to stroke-induced mucosal microbiota changes may represent novel therapy targets to improve patient outcomes.
Publisher: Elsevier BV
Date: 08-2015
Publisher: Springer Science and Business Media LLC
Date: 19-03-2014
DOI: 10.1007/S00253-014-5646-2
Abstract: Recent advances in the technology available for culture-independent methods for identification and enumeration of environmental bacteria have invigorated interest in the study of the role of chicken intestinal microbiota in health and productivity. Chickens harbour unique and erse bacterial communities that include human and animal pathogens. Increasing public concern about the use of antibiotics in the poultry industry has influenced the ways in which poultry producers are working towards improving birds' intestinal health. Effective means of antibiotic-independent pathogen control through competitive exclusion and promotion of good protective microbiota are being actively investigated. With the realisation that just about any change in environment influences the highly responsive microbial communities and with the abandonment of the notion that we can isolate and investigate a single species of interest outside of the community, came a flood of studies that have attempted to profile the intestinal microbiota of chickens under numerous conditions. This review aims to address the main issues in investigating chicken microbiota and to summarise the data acquired to date.
Publisher: Springer Science and Business Media LLC
Date: 27-02-2020
Publisher: PeerJ
Date: 05-05-2016
DOI: 10.7717/PEERJ.2002
Abstract: Organophosphate insecticides have been directly or indirectly implicated in avian populations declining worldwide. Birds in agricultural environments are commonly exposed to these insecticides, mainly through ingestion of invertebrates after insecticide application. Despite insecticide exposure in birds occurring mostly by ingestion, the impact of organophosphates on the avian digestive system has been poorly researched. In this work we used the Japanese quail ( Coturnix japonica ) as an avian model to study short-term microbial community responses to a single dose of trichlorfon at low concentration in three s le origins of the gastrointestinal tract (GIT): caecum, large intestine and faeces. Using next-generation sequencing of 16S rRNA gene licons as bacterial markers, the study showed that ingestion of insecticide caused significant changes in the GIT microbiome. Specifically, microbiota composition and ersity differed between treated and untreated quail. Insecticide-associated responses in the caecum showed differences between sexes which did not occur with the other s le types. In caecal microbiota, only treated females showed significant shifts in a number of genera within the Lachnospiraceae and the Enterobacteriaceae families. The major responses in the large intestine were a significant reduction in the genus Lactobacillus and increases in abundance of a number of Proteobacteria genera. All microbial shifts in faeces occurred in phylotypes that were represented at low relative abundances. In general, changes in microbiota possibly resulted from contrasting responses towards the insecticide, either positive (e.g., biodegrading bacteria) or negative (e.g., insecticide-susceptible bacteria). This study demonstrates the significant impact that organophosphate insecticides have on the avian gut microbiota showing that a single small dose of trichlorfon caused dysbiosis in the GIT of the Japanese quail. Further research is necessary to understand the implications on birds’ health, especially in females.
Publisher: MDPI AG
Date: 24-02-2020
DOI: 10.3390/MICROORGANISMS8020309
Abstract: The Cedecea genus is comprised of six rarely isolated species within the Enterobacteriaceae family. Representatives are Gram-negative motile bacilli, and are typically oxidase-negative, lipase-positive and resistant to colistin and cephalothin. In this study, a putative novel Cedecea species (designated strain ZA_0188T), isolated from the koala hindgut, was characterised using a polyphasic taxonomic approach. Maximum average nucleotide identity (ANI) and 16S ribosomal RNA (rRNA) similarity scores well below thresholds of species demarcation were reported, at 81.1% and 97.9%, respectively. Multilocus phylogenetic analysis indicated strain ZA_0188T was most similar to but ergent from recognised Cedecea species. The isolate’s genomic G+C content was determined as 53.0 mol%, % lower than previously reported in Cedecea. Phenotypically, strain ZA_0188T was distinct from recognised Cedecea species such as colistin- and cephalothin-sensitive, lipase-, sorbitol-, sucrose-, and Voges-Proskauer-negative, and melibiose-, arabinose-, arginine-, and rhamnose-positive. In preliminary experiments, strain ZA_0188T exhibited cellulase activity and high-level tolerance to eucalyptus oil compared to other enteric species surveyed. Collectively, these findings suggest that strain ZA_0188T represents a novel enteric species, for which the name Cedecea colo is proposed.
Publisher: Frontiers Media SA
Date: 21-12-2022
DOI: 10.3389/FVETS.2022.1082358
Abstract: C ylobacter hepaticus is the aetiological agent of Spotty Liver Disease (SLD). SLD can cause significant production loss and mortalities among layer hens at and around peak of lay. We previously developed an enzyme linked immunosorbent assay (ELISA), SLD-ELISA1, to detect C. hepaticus specific antibodies from bird sera using C. hepaticus total proteins and sera pre-absorbed with C ylobacter jejuni proteins. The high specificity achieved with SLD-ELISA1 indicated the presence of C. hepaticus specific antibodies in sera of infected birds. However, some of the reagents used in SLD-ELISA1 are time consuming to prepare and difficult to quality control. This understanding led to the search for C. hepaticus specific immunogenic proteins that could be used in recombinant forms as antibody capture antigens in immunoassay design. In this study, an immunoproteomic approach that combined bioinformatics analysis, western blotting, and LC MS/MS protein profiling was used, and a fragment of filamentous hemagglutinin adhesin (FHA), FHA 1,628−1,899 with C. hepaticus specific antigenicity was identified. Recombinant FHA 1,628−1,899 was used as antigen coating on ELISA plates to capture FHA 1,628−1,899 specific antibodies in sera of infected birds. SLD-ELISA2, based on the purified recombinant FHA fragment, is more user-friendly and standardizable than SLD-ELISA1 for screening antibody responses to C. hepaticus exposure in hens. This study is the first report of the use of FHA from a C ylobacter species in immunoassays, and it also opens future research directions to investigate the role of FHA in C. hepaticus pathogenesis and its effectiveness as a vaccine candidate.
Publisher: Public Library of Science (PLoS)
Date: 26-10-2012
Publisher: American Society for Microbiology
Date: 11-2011
Abstract: The pathogenesis of avian necrotic enteritis involves NetB, a pore-forming toxin produced by virulent avian isolates of Clostridium perfringens type A. To determine the location and mobility of the netB structural gene, we examined a derivative of the tetracycline-resistant necrotic enteritis strain EHE-NE18, in which netB was insertionally inactivated by the chlor henicol and thi henicol resistance gene catP . Both tetracycline and thi henicol resistance could be transferred either together or separately to a recipient strain in plate matings. The separate transconjugants could act as donors in subsequent matings, which demonstrated that the tetracycline resistance determinant and the netB gene were present on different conjugative elements. Large plasmids were isolated from the transconjugants and analyzed by high-throughput sequencing. Analysis of the resultant data indicated that there were actually three large conjugative plasmids present in the original strain, each with its own toxin or antibiotic resistance locus. Each plasmid contained a highly conserved 40-kb region that included plasmid replication and transfer regions that were closely related to the 47-kb conjugative tetracycline resistance plasmid pCW3 from C. perfringens . The plasmids were as follows: (i) a conjugative 49-kb tetracycline resistance plasmid that was very similar to pCW3, (ii) a conjugative 82-kb plasmid that contained the netB gene and other potential virulence genes, and (iii) a 70-kb plasmid that carried the cpb2 gene, which encodes a different pore-forming toxin, beta2 toxin. IMPORTANCE The anaerobic bacterium Clostridium perfringens can cause an avian gastrointestinal disease known as necrotic enteritis. Disease pathogenesis is not well understood, although the plasmid-encoded pore-forming toxin NetB, is an important virulence factor. In this work, we have shown that the plasmid that carries the netB gene is conjugative and has a 40-kb region that is very similar to replication and transfer regions found within each of the sequenced conjugative plasmids from C. perfringens . We also showed that this strain contained two additional large plasmids that were also conjugative and carried a similar 40-kb region. One of these plasmids encoded beta2 toxin, and the other encoded tetracycline resistance. To our knowledge, this is the first report of a bacterial strain that carries three closely related but different independently conjugative plasmids. These results have significant implications for our understanding of the transmission of virulence and antibiotic resistance genes in pathogenic bacteria.
Publisher: S. Karger AG
Date: 2007
DOI: 10.1159/000103176
Abstract: In recent years there has been a revolution in our understanding of genes and how they come to control the physical outcomes of development. Central to this has been the understanding of the cellular processes of RNA interference (RNAi), for which the Nobel Prize for Physiology or Medicine was awarded in 2006. Coupled with this has been the recognition that microRNAs are key mediators of this process within cells. RNAi whether mediated exogenously by synthetic oligonucleotides or vector-delivered double stranded RNA or endogenously by microRNAs can have a profound and specific effect on gene expression. Elucidating and understanding these processes in the chicken will provide critical information to enable more precise control over breeding strategies for improvement of traits in production poultry, either by direct or indirect means. It will also provide alternative strategies for the control and prevention of important avian diseases.
Publisher: Elsevier BV
Date: 14-10-1999
DOI: 10.1016/S0264-410X(99)00243-1
Abstract: A defined phospholipase D mutant of Corynebacterium pseudotuberculosis, designated Toxminus, was used as a live vector to express and deliver a range of candidate vaccine antigens to sheep. Expression levels of the foreign genes in Toxminus were evaluated when directed from a number of different promoters, both constitutively expressed and inducible, as fusions with expressed genes including a signal sequence, and from chromosomal and episomal loci. In general expression levels were low and it appeared that some of the recombinant proteins were tolerated by C. pseudotuberculosis Toxminus better than others. Gene expression was however sufficiently high for three of the genes to elicit antibody responses specific to the recombinant protein following a single dose of the live Toxminus vector vaccine. This work suggests that C. pseudotuberculosis Toxminus has potential for development as a live veterinary vaccine vector.
Publisher: Microbiology Society
Date: 07-2007
DOI: 10.1099/MIC.0.2007/005926-0
Abstract: Corynebacterium pseudotuberculosis is the aetiological agent of caseous lymphadenitis, a disease affecting sheep and goats. Phospholipase D (Pld), a major virulence determinant of C. pseudotuberculosis, is believed to play a critical role in dissemination of bacteria from the site of infection to the lymph nodes. Although the pld gene has been studied for some time, it is only recently that it has been identified as being down-regulated following heat shock from 37 to 43 degrees C. To gain insights into the mechanisms of Pld action, this study investigated how it was regulated under varying environmental conditions. Studies measuring pld mRNA levels or utilizing a reporter construct containing the pld promoter upstream of a gfp gene were performed. These showed that pld was upregulated in a cell-density-dependent manner, was regulated by heat shock at all cell-culture densities, and was highly expressed in a tissue-culture macrophage-infection model. Finally, the expression of Pld by intracellular C. pseudotuberculosis was shown to play a small but significant role in the reduction of macrophage viability following infection. This study demonstrates that the regulation of C. pseudotuberculosis pld is complex. This regulatory complexity may play an important role in allowing the pathogen to successfully adapt to the changing host environment during infection, migration, establishment and disease progression.
Publisher: American Society for Microbiology
Date: 17-06-2020
DOI: 10.1128/AEM.00600-20
Abstract: The microbiota plays a vital role in maintaining gut health and influences the overall performance of chickens. Most gut microbiota-related studies have been performed in broilers, which have different microbial communities compared to those of layers. The normal gut microbiota of laying chickens is dominated by Proteobacteria , Firmicutes , Bacteroidetes , Fusobacteria , and Actinobacteria at the phylum level. The composition of the gut microbiota changes with chicken age, genotype, and production system.
Publisher: Elsevier BV
Date: 12-2016
DOI: 10.1016/J.VETMIC.2016.10.028
Abstract: Necrotic enteritis of poultry is an emerging disease of substantial economic importance, but aspects of the pathogenesis of this multi-factorial disease are still unclear. We recently demonstrated that the ability of avian strains of the causative bacterium, Clostridium perfringens, to bind to specific collagen types correlated strongly with their virulence and we postulated that binding of the pathogen to collagen types IV and V and gelatin may involve the putative adhesin-encoding gene cnaA, which is found in the VR-10B locus. In this study we have used site-directed mutagenesis to demonstrate that disruption of the cnaA gene leads to a reduction in the expression of the three genes immediately downstream of cnaA and reduced adherence to collagen types IV and V and gelatin. In addition, a cnaA mutant of strain EHE-NE18 was no longer capable of causing necrotic enteritis in a chicken disease induction model and had a significantly reduced ability to colonise the chicken intestinal mucosa. These results were confirmed by generating and analysing a similar mutant in an independent necrotic enteritis causing C. perfringens strain. This study expands our understanding of the mechanisms involved in necrotic enteritis pathogenesis by demonstrating the importance of C. perfringens adherence to extracellular matrix proteins.
Publisher: Elsevier BV
Date: 03-1981
DOI: 10.1016/0147-619X(81)90021-4
Abstract: Most tumors are composed of a heterogeneous population of subclones. A more detailed insight into the subclonal evolution of these tumors can be helpful to study progression and treatment response. Problematically, tumor s les are typically very heterogeneous, making deconvolving in idual tumor subclones a major challenge. To overcome this limitation, reducing heterogeneity, such as by means of microdissections, coupled with targeted sequencing, is a viable approach. However, computational methods that enable reconstruction of the evolutionary relationships require unbiased read depth measurements, which are commonly challenging to obtain in this setting. We introduce TargetClone, a novel method to reconstruct the subclonal evolution tree of tumors from single-nucleotide polymorphism allele frequency and somatic single-nucleotide variant measurements. Furthermore, our method infers copy numbers, alleles and the fraction of the tumor component in each s le. TargetClone was specifically designed for targeted sequencing data obtained from microdissected s les. We demonstrate that our method obtains low error rates on simulated data. Additionally, we show that our method is able to reconstruct expected trees in a testicular germ cell cancer and ovarian cancer dataset. The TargetClone package including tree visualization is written in Python and is publicly available at github.com/UMCUGenetics/targetclone.
Publisher: Elsevier BV
Date: 08-2023
Publisher: Informa UK Limited
Date: 02-11-2017
Publisher: Springer Science and Business Media LLC
Date: 19-10-2019
DOI: 10.1007/S00253-019-10143-3
Abstract: The Australian saltwater crocodile (Crocodylus porosus) industry began commercially in the 1980s, producing skins for export and crocodile meat as a by-product. Industry research has thus far focused on strategies to improve production efficiency. In the current study, we utilised 16S rRNA sequencing to characterise the intestinal microbiome of Australian saltwater crocodiles. S les were collected from 13 commercially farmed crocodiles from six s le sites along the length of the intestinal tract. The results indicate a similar microbiome composition to that found in the freshwater alligator, with the dominate phyla represented by Firmicutes, primarily Clostridia, and Fusobacteria, which appears to be distinct from mammalian, fish, and other reptile phyla which are generally dominated by Firmicutes and Bacteroidetes. The high abundance of 'pathogenic' bacteria, with no apparent consequence to the host's health, is of great interest and warrants further additional investigation. This will enable expansion of the current understanding of host immune function and how it is modified by host and intestinal microbiome interactions.
Publisher: SAGE Publications
Date: 10-01-2020
Abstract: Two putative zinc metalloproteases encoded by Clostridium perfringens have been implicated in the pathogenesis of necrotic enteritis, an economically significant poultry disease that is caused by this anaerobic bacterium. These proteases have ~64% amino acid identity and are encoded by the zmpA and zmpB genes. We screened 83 C. perfringens isolates by PCR for the presence of these genes. The first gene, zmpB, is chromosomally located and was present in all screened strains of C. perfringens, regardless of their origin and virulence. The second gene, zmpA, is plasmid-borne and was only found in isolates derived from chickens with necrotic enteritis. We describe the generation of insertionally inactivated mutants of both zmpA and zmpB in a virulent C. perfringens isolate. For each mutant, a significant ( p 0.001) reduction in virulence was observed in a chicken necrotic enteritis disease model. Ex les of each mutant strain were characterized by whole genome sequencing, which showed that there were a few off-site mutations with the potential to affect the virulence of these strains. To confirm the importance of these genes, independently derived zmpA and zmpB mutants were constructed in different virulent C. perfringens isolates and shown to have reduced virulence in the experimental disease induction model. A zmpA–zmpB double mutant also was generated and shown to have significantly reduced virulence, to the same extent as the respective single mutants. Our results provide evidence that both putative zinc metalloproteases play an important role in disease pathogenesis.
Publisher: MDPI AG
Date: 23-07-2010
Publisher: Informa UK Limited
Date: 23-09-2020
Publisher: Frontiers Media SA
Date: 07-05-2018
Publisher: Cold Spring Harbor Laboratory
Date: 09-05-2008
Abstract: MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small regulatory RNAs characterized in chickens we used a deep sequencing approach developed by Solexa (now Illumina Inc.). We sequenced three small RNA libraries prepared from different developmental stages of the chicken embryo (days five, seven, and nine) to produce over 9.5 million short sequence reads. We developed a bioinformatics pipeline to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected almost all of the previously known chicken miRNAs and their respective miRNA* sequences. In addition we discovered 449 new chicken miRNAs including 88 miRNA candidates. Of these, 430 miRNAs appear to be specific to the avian lineage. Another six new miRNAs had evidence of evolutionary conservation in at least one vertebrate species outside of the bird lineage. The remaining 13 putative miRNAs appear to represent chicken orthologs of known vertebrate miRNAs. We discovered 39 additional putative miRNA candidates originating from miRNA generating intronic sequences known as mirtrons.
Publisher: BMJ
Date: 23-08-2016
Publisher: Springer Science and Business Media LLC
Date: 15-08-2020
DOI: 10.1186/S13568-020-01077-5
Abstract: Microbial colonisation of the gastrointestinal tract of newly hatched chicks starts at hatch, seeded from the immediate hatching environment, and quickly results in dense colonisation. The role of ecological factors in gut colonisation has been extensively investigated, as well as the role of micro- and macronutrients in supporting and selecting for bacterial species highly adapted for utilising those nutrients. However, the microbial community contained in poultry feed and its influence on colonisation and maturation of gut microbiota has not been directly addressed. In this study, we compared the microbiota found in poultry feed, with the microbiota of ileum, cecum and excreta, to identify substantial overlap in core microbiotas of the compared groups. We then investigated the microbiota present in raw feedstuffs: meat and bone meal, wheat, corn, canola, barley, soybean, millrun, sorghum, poultry oil, oats, limestone and bloodmeal from four geographically distinct feedstuff suppliers. Each of the feedstuffs had erse microbial communities. The meat and bone meal and bloodmeal s les had the most complex and distinct microbial populations. There was substantial overlap in the phylogenetic composition found in the grain and seed s les: barley, canola, corn, millrun, oats, sorghum, soybean meal and wheat. Issues related to methodology, viability of microbial communities in the gut and feed, and the implications for biosecurity are discussed.
Publisher: Frontiers Media SA
Date: 05-02-2019
Publisher: Springer Science and Business Media LLC
Date: 26-05-2010
Abstract: Fleece rot (FR) and body-strike of Merino sheep by the sheep blowfly Lucilia cuprina are major problems for the Australian wool industry, causing significant losses as a result of increased management costs coupled with reduced wool productivity and quality. In addition to direct effects on fleece quality, fleece rot is a major predisposing factor to blowfly strike on the body of sheep. In order to investigate the genetic drivers of resistance to fleece rot, we constructed a combined ovine-bovine cDNA microarray of almost 12,000 probes including 6,125 skin expressed sequence tags and 5,760 anonymous clones obtained from skin subtracted libraries derived from fleece rot resistant and susceptible animals. This microarray platform was used to profile the gene expression changes between skin s les of six resistant and six susceptible animals taken immediately before, during and after FR induction. Mixed-model equations were employed to normalize the data and 155 genes were found to be differentially expressed (DE). Ten DE genes were selected for validation using real-time PCR on independent skin s les. The genomic regions of a further 5 DE genes were surveyed to identify single nucleotide polymorphisms (SNP) that were genotyped across three populations for their associations with fleece rot resistance. The majority of the DE genes originated from the fleece rot subtracted libraries and over-representing gene ontology terms included defense response to bacterium and epidermis development, indicating a role of these processes in modulating the sheep's response to fleece rot. We focused on genes that contribute to the physical barrier function of skin, including keratins, collagens, fibulin and lipid proteins, to identify SNPs that were associated to fleece rot scores. We identified FBLN1 (fibulin) and FABP4 (fatty acid binding protein 4) as key factors in sheep's resistance to fleece rot. Validation of these markers in other populations could lead to vital tests for marker assisted selection that will ultimately increase the natural fleece rot resistance of Merino sheep.
Publisher: Public Library of Science (PLoS)
Date: 12-08-2020
Publisher: American Society for Microbiology
Date: 03-2013
Abstract: Clostridium perfringens is an anaerobic bacterium that causes numerous important human and animal diseases, primarily as a result of its ability to produce many different protein toxins. In chickens, C. perfringens causes necrotic enteritis, a disease of economic importance to the worldwide poultry industry. The secreted pore-forming toxin NetB is a key virulence factor in the pathogenesis of avian necrotic enteritis and is similar to alpha-hemolysin, a β-barrel pore-forming toxin from Staphylococcus aureus . To address the molecular mechanisms underlying NetB-mediated tissue damage, we determined the crystal structure of the monomeric form of NetB to 1.8 Å. Structural comparisons with other members of the alpha-hemolysin family revealed significant differences in the conformation of the membrane binding domain. These data suggested that NetB may recognize different membrane receptors or use a different mechanism for membrane-protein interactions. Consistent with this idea, electrophysiological experiments with planar lipid bilayers revealed that NetB formed pores with much larger single-channel conductance than alpha-hemolysin. Channel conductance varied with phospholipid net charge. Furthermore, NetB differed in its ion selectivity, preferring cations over anions. Using hemolysis as a screen, we carried out a random-mutagenesis study that identified several residues that are critical for NetB-induced cell lysis. Mapping of these residues onto the crystal structure revealed that they were clustered in regions predicted to be required for oligomerization or membrane binding. Together these data provide an insight into the mechanism of NetB-mediated pore formation and will contribute to our understanding of the mode of action of this important toxin. IMPORTANCE Necrotic enteritis is an economically important disease of the worldwide poultry industry and is mediated by Clostridium perfringens strains that produce NetB, a β-pore-forming toxin. We carried out structural and functional studies of NetB to provide a mechanistic insight into its mode of action and to assist in the development of a necrotic enteritis vaccine. We determined the structure of the monomeric form of NetB to 1.8 Å, used both site-directed and random mutagenesis to identify key residues that are required for its biological activity, and analyzed pore formation by NetB and its substitution-containing derivatives in planar lipid bilayers.
Publisher: Elsevier BV
Date: 10-2001
Publisher: Elsevier BV
Date: 10-2001
DOI: 10.1016/S0264-410X(01)00314-0
Abstract: Expression library immunization (ELI) has previously been used in a number of disease models in mice. Here, we describe the first ex le of the application of ELI to a large animal model with the immunization of pigs against enzootic pneumonia, a disease caused by Mycoplasma hyopneumoniae. The development of new plasmid vectors and library screening methods facilitated the application of ELI to this disease by allowing random libraries to be screened for clones expressing recombinant proteins. In this way the vast majority of clones in random libraries that are unproductive can be eliminated, meaning that libraries are more likely to give protection and are subsequently easier to further screen and analyze. By using this approach we have used one library screen and two animal trials to progress from an original library of 20,000 clones to a group of just 96 clones.
Publisher: Elsevier BV
Date: 11-2011
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 27-06-2013
DOI: 10.1007/S11248-013-9727-2
Abstract: Traditional methods of avian transgenesis involve complex manipulations involving either retroviral infection of blastoderms or the ex vivo manipulation of primordial germ cells (PGCs) followed by injection of the cells back into a recipient embryo. Unlike in mammalian systems, avian embryonic PGCs undergo a migration through the vasculature on their path to the gonad where they become the sperm or ova producing cells. In a development which simplifies the procedure of creating transgenic chickens we have shown that PGCs are directly transfectable in vivo using commonly available transfection reagents. We used Lipofectamine 2000 complexed with Tol2 transposon and transposase plasmids to stably transform PGCs in vivo generating transgenic offspring that express a reporter gene carried in the transposon. The process has been shown to be highly effective and as robust as the other methods used to create germ-line transgenic chickens while substantially reducing time, infrastructure and reagents required. The method described here defines a simple direct approach for transgenic chicken production, allowing researchers without extensive PGC culturing facilities or skills with retroviruses to produce transgenic chickens for wide-ranging applications in research, biotechnology and agriculture.
Publisher: Springer Science and Business Media LLC
Date: 03-10-2016
DOI: 10.1038/NM.4194
Abstract: Bacterial infection is highly prevalent in patients who have had a stroke. Despite the potential contribution of micro-aspiration in post-stroke pneumonia, we found that the majority of the microorganisms detected in the patients who developed infections after having a stroke were common commensal bacteria that normally reside in the intestinal tracts. In a mouse model of ischemic stroke, post-stroke infection was only observed in mice that were born and raised in specific-pathogen-free facilities this was not seen in mice that were born and raised in germ-free facilities. Using high-throughput 16S rRNA gene licon sequencing and bioinformatics analyses, we provide evidence demonstrating that the source of the bacteria forming the microbial community in the lungs of post-stroke mice was indeed the host small intestine. Additionally, stroke-induced gut barrier permeability and dysfunction preceded the dissemination of orally inoculated bacteria to peripheral tissues. This study identifies a novel pathway in which stroke promotes the translocation and dissemination of selective strains of bacteria that originated from the host gut microbiota.
Publisher: Springer Science and Business Media LLC
Date: 13-01-2016
DOI: 10.1007/S00253-015-7280-Z
Abstract: Microbiota in the gastrointestinal tract (GIT) plays an essential role in the health and well-being of the host. With the exception of chickens, this area has been poorly studied within birds. The avian GIT harbours unique microbial communities. Birds require rapid energy bursts to enable energy-intensive flying. The passage time of feed through the avian GIT is only 2-3.5 h, and thus requires the presence of microbiota that is extremely efficient in energy extraction. This investigation has used high-throughput 16S rRNA gene sequencing to explore the GIT microbiota of the flighted bird, the Japanese quail (Coturnix japonica). We are reporting, for the first time, the ersity of bacterial phylotypes inhabiting all major sections of the quail GIT including mouth, esophagus, crop, proventriculus, gizzard, duodenum, ileum, cecum, large intestine and feces. Nine phyla of bacteria were found in the quail GIT however, their distribution varied significantly between GIT sections. Cecal microbiota was the most highly differentiated from all the other communities and showed highest richness at an OTU level but lowest richness at all other taxonomic levels being comprised of only 15 of total 57 families in the quail GIT. Differences were observed in the presence and absence of specific phylotypes between sexes in most sections.
Publisher: Elsevier BV
Date: 2023
DOI: 10.1016/J.VETMIC.2022.109603
Abstract: Spotty Liver Disease (SLD) is a significant disease of commercial layer hens. It can cause up to 10 % flock mortalities and reduce egg production by 25 %. C ylobacter hepaticus has been identified as the main cause of the disease, although it also appears that predisposing factors, such as some form of stress, may increase the likelihood of clinical disease occurring. Recently, a newly identified species, C ylobacter bilis, was isolated from bile s les of clinical SLD affected chickens. To investigate the pathogenic potential of C. bilis two independent isolates were used in infection trials of layer hens. Within 6 days of oral challenge birds developed typical SLD liver lesions, demonstrating that both strains induced SLD. C. bilis could be recovered from all the challenged birds that developed SLD. Thus, each of the steps in Koch's postulates have been fulfilled, confirming that C. bilis is an additional cause of SLD. A PCR method was developed which can specifically detect C. bilis from s les with complex microbiota. The identification of this newly discovered C ylobacter species as a second cause of SLD and the provision of a rapid method to detect the SLD causing bacterium will help with SLD vaccine development and epidemiology, thus assisting in the control of this important disease of poultry.
Publisher: Oxford University Press (OUP)
Date: 25-04-2003
DOI: 10.1093/JAC/DKG229
Publisher: Springer Science and Business Media LLC
Date: 17-12-2018
DOI: 10.1007/S00253-017-8688-4
Abstract: The poultry industry aims to improve productivity while maintaining the health and welfare of flocks. Pathogen control has been achieved through biosecurity, vaccinations and the use of antibiotics. However, the emergence of antibiotic resistance, in animal and human pathogens, has prompted researchers and chicken growers alike to seek alternative approaches. The use of new and emerging approaches to combat pathogen activity including nanotechnology, in particular, silver nanoparticles (NPs), has been found to not only eradicate pathogenic bacteria but also include issues of toxicity and bioaccumulation effects. Other novel metal nanoparticles could provide this pathogen reducing property with a more tailored and biocompatible nanomaterial for the model used, something our study represents. This study investigated the benefits of nanomaterial delivery mechanisms coupled with important health constituents using selenium as a biocompatible metal to minimise toxicity properties. Selenium NPs were compared to two common forms of bulk selenium macronutrients already used in the poultry industry. An intermediate concentration of selenium nanoparticles (0.9 mg/kg) demonstrated the best performance, improving the gut health by increasing the abundance of beneficial bacteria, such as Lactobacillus and Faecalibacterium, and short-chain fatty acids (SCFAs), in particular butyric acid. SCFAs are metabolites produced by the intestinal tract and are used as an energy source for colonic cells and other important bodily functions. Selenium nanoparticles had no significant effect on live weight gain or abundance of potentially pathogenic bacteria.
Publisher: Springer Science and Business Media LLC
Date: 06-2005
DOI: 10.1007/S00284-005-4472-2
Abstract: The nucleotide sequence of the Brachyspira hyodysenteriae ftnA gene, encoding a putative ferritin protein (FtnA), was determined. Analysis of the sequence predicted that this gene encoded a protein of 180 amino acids. RT-PCR and Western blot showed that the ftnA gene was expressed in B. hyodysenteriae, and evidence suggests that FtnA stores iron rather than haem. ftnA was delivered as DNA and recombinant protein vaccines in a mouse model of B. hyodysenteriae infection. Vaccine efficacy was monitored by caecal pathology and quantification of B. hyodysenteriae numbers in the caeca of infected mice by real-time PCR.
Publisher: Elsevier BV
Date: 12-2016
Publisher: Frontiers Media SA
Date: 23-02-2021
DOI: 10.3389/FIMMU.2021.619366
Abstract: Ulcerative colitis is an inflammatory disease of the colon that is associated with colonic neutrophil accumulation. Recent evidence indicates that diet alters the composition of the gut microbiota and influences host–pathogen interactions. Specifically, bacterial fermentation of dietary fiber produces metabolites called short-chain fatty acids (SCFAs), which have been shown to protect against various inflammatory diseases. However, the effect of fiber deficiency on the key initial steps of inflammation, such as leukocyte–endothelial cell interactions, is unknown. Moreover, the impact of fiber deficiency on neutrophil recruitment under basal conditions and during inflammation in vivo is unknown. Herein, we hypothesized that a fiber-deficient diet promotes an inflammatory state in the colon at baseline and predisposes the host to more severe colitis pathology. Mice fed a no-fiber diet for 14 days showed significant changes in the gut microbiota and exhibited increased neutrophil-endothelial interactions in the colonic microvasculature. Although mice fed a no-fiber diet alone did not have observable colitis-associated symptoms, these animals were highly susceptible to low dose (0.5%) dextran sodium sulphate (DSS)-induced model of colitis. Supplementation of the most abundant SCFA, acetate, prevented no-fiber diet-mediated enrichment of colonic neutrophils and colitis pathology. Therefore, dietary fiber, possibly through the actions of acetate, plays an important role in regulating neutrophil recruitment and host protection against inflammatory colonic damage in an experimental model of colitis.
Publisher: Springer Science and Business Media LLC
Date: 11-05-2005
Abstract: The use of small interfering RNA (siRNA) molecules in animals to achieve double-stranded RNA-mediated interference (RNAi) has recently emerged as a powerful method of sequence-specific gene knockdown. As DNA-based expression of short hairpin RNA (shRNA) for RNAi may offer some advantages over chemical and in vitro synthesised siRNA, a number of vectors for expression of shRNA have been developed. These often feature polymerase III (pol. III) promoters of either mouse or human origin. To develop a shRNA expression vector specifically for bovine RNAi applications, we identified and characterised a novel bovine U6 small nuclear RNA (snRNA) promoter from bovine sequence data. This promoter is the putative bovine homologue of the human U6-8 snRNA promoter, and features a number of functional sequence elements that are characteristic of these types of pol. III promoters. A PCR based cloning strategy was used to incorporate this promoter sequence into plasmid vectors along with shRNA sequences for RNAi. The promoter was then used to express shRNAs, which resulted in the efficient knockdown of an exogenous reporter gene and an endogenous bovine gene. We have mined data from the bovine genome sequencing project to identify a functional bovine U6 promoter and used the promoter sequence to construct a shRNA expression vector. The use of this native bovine promoter in shRNA expression is an important component of our future development of RNAi therapeutic and transgenic applications in bovine species.
Publisher: PeerJ
Date: 16-10-2020
DOI: 10.7717/PEERJ.10117
Abstract: The widespread occurrence of pathogenic bacteria resistant to last-line antibiotics has resulted in significant challenges in human and veterinary medicine. There is an urgent need for new antimicrobial agents that can be used to control these life threating pathogens. We report the identification of antimicrobial activities, against a broad range of bacterial pathogens, from a collection of marine-derived spore-forming bacteria. Although marine environments have been previously investigated as sources of novel antibiotics, studies on such environments are still limited and there remain opportunities for further discoveries and this study has used resources derived from an under-exploited region, the Vietnam Sea. Antimicrobial activity was assessed against a panel of Gram-positive and Gram-negative bacteria, including several multi-drug resistant pathogens. From a total of 489 isolates, 16.4% had antimicrobial activity. Of 23 shortlisted isolates with the greatest antimicrobial activity, 22 were Bacillus spp. isolates and one was a Paenibacillus polymyxa isolate. Most of the antimicrobial compounds were sensitive to proteases, indicating that they were proteins rather than secondary metabolites. The study demonstrated that marine bacteria derived from the Vietnam Sea represent a rich resource, producing antimicrobial compounds with activity against a broad range of clinically relevant bacterial pathogens, including important antibiotic resistant pathogens. Several isolates were identified that have particularly broad range activities and produce antimicrobial compounds that may have value for future drug development.
Publisher: Elsevier BV
Date: 03-2022
DOI: 10.1016/J.VETMIC.2022.109341
Abstract: C ylobacter hepaticus causes Spotty Liver Disease (SLD) in layer hens, resulting in mortality and productivity losses. Like other C ylobacter species, C. hepaticus is a fastidious organism that requires microaerobic conditions to grow and efficiently replicate. Despite its apparent vulnerability to environmental conditions, it is suspected that there are environmental sources of C. hepaticus that cause infections in chickens newly placed in production houses. Although C. hepaticus DNA has been detected in insects, rodent and wild bird droppings, and in environmental s les such as water and soil, it has not been possible to culture C. hepaticus from these sources. Therefore, it is unclear whether these environments harbor viable bacteria or the remnants of dead bacteria. Determining the viability of C. hepaticus in challenging conditions has implications for understanding the potential relevance of environmental reservoirs and routes of transmission. Other C ylobacters are known to enter viable but nonculturable (VBNC) states that result in prolonged survival in hostile environmental conditions. This study has demonstrated that C. hepaticus can also enter a VBNC state when stored in water or a simple salt solution (Ringer's solution). Cells in the VBNC state could not be recovered on media normally used for primary isolation, but media modifications were tested, and a 'resuscitation' media was developed. VBNC cells could be recovered from Ringer's solution stored at 4 °C for up to 112 days. VBNC cells are postulated to play an important role in the epidemiology of SLD.
Publisher: Wiley
Date: 05-2007
DOI: 10.1042/BA20060207
Publisher: Public Library of Science (PLoS)
Date: 21-02-2012
Publisher: Frontiers Media SA
Date: 02-07-2019
Publisher: Informa UK Limited
Date: 03-05-2016
DOI: 10.1080/03079457.2016.1150587
Abstract: Necrotic enteritis in chickens develops as a result of infection with pathogenic strains of Clostridium perfringens and the presence of predisposing factors. Predisposing factors include elements that directly change the physical properties of the gut, either damaging the epithelial surface, inducing mucus production, or changing gut transit times factors that disrupt the gut microbiota and factors that alter the immune status of birds. In the past research into necrotic enteritis predisposing factors was directed by the simple hypothesis that low-level colonization of C. perfringens commonly occurred within the gut of healthy chickens and the predisposing factors lead to a proliferation of those bacteria to produce disease. More recently, with an increasing understanding of the major virulence factors of C. perfringens and the application of molecular techniques to define different clades of C. perfringens strains, it has become clear that the C. perfringens isolates commonly found in healthy chickens are generally not strains that have the potential to cause disease. Therefore, we need to re-evaluate hypotheses regarding the development of disease, the origin of disease causing isolates of C. perfringens, and the importance of interactions with other C. perfringens strains and with predisposing factors. Many predisposing factors that affect the physical and immunological characteristics of the gastrointestinal tract may also change the resident microbiota. Research directed towards defining the relative importance of each of these different actions of predisposing factors will improve the understanding of disease pathogenesis and may allow refinement of experiment disease models.
Publisher: Mary Ann Liebert Inc
Date: 07-2019
Abstract: Resistance to aminoglycoside antibiotics is now common in pathogenic bacteria, making treatment of infections difficult. The rapid spread of resistance is mainly related to the dissemination of genes encoding aminoglycoside-modifying enzymes (AMEs). Staphylococci and enterococci are opportunistic human pathogens capable of causing a wide range of infections. Isolates from clinical cases are often found to be resistant to aminoglycosides. The aim of the present study was to develop a bead-based xTAG assay for the simultaneous detection of five prevalent aminoglycoside resistance genes in staphylococci and enterococci, including
Publisher: Oxford University Press (OUP)
Date: 16-05-2017
DOI: 10.1111/JAM.13442
Abstract: Intestinal microbiota modulates the development of clinical conditions, including metabolic syndrome and obesity. Many of these conditions are influenced by nutritional and exercise behaviours. This study aimed to investigate the ability of exercise to re-shape the intestinal microbiota and the influence of the diet on the process. A rat model was used to examine the intestinal microbiota responses to four activity conditions, including: high-intensity interval training (HIIT), light-intensity training (LIT), sedentary and normal control, each containing two nutritional conditions: high-fat high-fructose diet (HF) and standard chow (SC) diet. No significant differences in microbiota were apparent between activity conditions in rats fed a HF diet but changes in the presence/absence of phylotypes were observed in the LIT and HIIT groups. In rats fed SC, significant differences in intestinal microbiota were evident between exercised and nonexercised rats. Both LIT and HIIT induced significant differences in intestinal microbiota in SC-fed rats compared to their respective SC-fed controls. Characterization of the exercise-induced bacterial phylotypes indicated an increase in bacteria likely capable of degrading resistant polysaccharides and an increase in short chain fatty acid producers. While a significant effect of exercise on microbiota composition occurred in SC-fed rats, the HF-fed rats microbiota showed little response. These data suggest that a HF diet prevented microbiota differentiation in response to exercise. The importance of diet-exercise interaction is extended to the level of intestinal bacteria and gut health.
Publisher: PeerJ
Date: 07-03-2017
DOI: 10.7717/PEERJ.3071
Abstract: This study compared the effects of wheat- and sorghum-based diets on broiler chickens. The growth performance and caecal microbial community of chickens were measured and correlations between productivity and specific gut microbes were observed. Cobb broilers 15 days of age were in idually caged and two dietary treatments were used, one with a wheat-based diet ( n = 48) and another one with a sorghum-based diet ( n = 48). Growth performance measurements were taken over a 10 day period and s les for microbiota analysis were taken at the end of that period. Caecal microbiota was characterised by sequencing of 16S bacterial rRNA gene licons. Overall, the results indicated that a sorghum-based diet produced higher apparent metabolisable energy (AME) and body-weight gain (BWG) values in chickens, compared to a wheat-based diet. Nevertheless, sorghum-fed birds had higher feed conversion ratio (FCR) values than wheat-fed birds, possibly because of some anti-nutritional factors in sorghum. Further analyses showed that caecal microbial community was significantly associated with AME values, but microbiota composition differed between dietary treatments. A number of bacteria were in idually correlated with growth performance measurements. Numerous OTUs assigned to strains of Lactobacillus crispatus and Lachnospiraceae, which were prevalent in sorghum-fed chickens, were correlated with high AME and BWG values, respectively. Additionally, a number of OTUs assigned to Clostridiales that were prevalent in wheat-fed chickens were correlated with low FCR values. Overall, these results suggest that between-diet variations in growth performance were partly associated with changes in the caecal microbiota.
Publisher: Elsevier BV
Date: 11-2021
Publisher: Elsevier BV
Date: 11-2015
DOI: 10.1016/J.VETMIC.2015.09.019
Abstract: This study investigated the ability of Clostridium perfringens isolates derived from chickens to bind to collagen types I-V and gelatin. In total 21 strains from three distinct backgrounds were studied: (i) virulent strains isolated from birds suffering from necrotic enteritis, (ii) avirulent strains isolated from birds suffering from necrotic enteritis and (iii) strains isolated from healthy birds. All strains isolated from diseased birds had been assessed for virulence in a disease induction model. The virulent isolates all displayed collagen binding ability. However, most strains in the other two classes showed negligible binding to collagen. The prevalence of a previously described C. perfringens putative collagen adhesin-encoding gene was investigated by PCR screening. It was found that five of the strains carried the putative collagen adhesin-encoding gene and that all of these strains were virulent isolates. Based on these studies it is postulated that collagen adhesion may play a role in the pathogenesis of necrotic enteritis.
Publisher: Oxford University Press (OUP)
Date: 03-2005
DOI: 10.1111/J.1365-2672.2004.02502.X
Abstract: To develop a method and plasmid vectors suitable for expression of class II bacteriocins from Escherichia coli. The expression vector pSuV1 was constructed by inserting the PelB secretion signal coding sequence and a number of restriction endonuclease sites for cloning, into pTYB1. Codon optimized genes encoding the active mature region of each bacteriocin were constructed and inserted into pSuV1. Transfer of these constructs to a host expressing T7 RNA polymerase allowed for expression of secreted mature or fusion forms of the bacteriocins. Generation of the fusion, to the adjacent intein-chitin-binding domain gene, was achieved by removal of a small intervening BseRI fragment. The bacteriocins BacR1, ercin V41, enterocin P, pediocin PA-1 and piscicolin 126 were expressed from this system. For piscicolin 126, expression levels of 200 microg l(-1) in the mature form and 1100 microg l(-1) when cleaved from the fusion partner were achieved. All expressed bacteriocins displayed antimicrobial activity. Several class II bacteriocins have been expressed in E. coli using purpose designed plasmid vectors described here. This method provides a common expression system capable of producing a range of different class II bacteriocins. It allows researchers to study class II bacteriocins without access to the original producer strain, the native bacteriocin gene, or highly specific heterologous producing strains. Resulting expression levels are as high or higher than those previously reported for related bacteriocins.
Publisher: Springer Science and Business Media LLC
Date: 08-2017
DOI: 10.1038/NI0817-951C
Publisher: Springer Science and Business Media LLC
Date: 28-02-2017
DOI: 10.1007/S00253-017-8193-9
Abstract: Unravelling the mechanisms of how antibiotics influence growth performance through changes in gut microbiota can lead to the identification of highly productive microbiota in animal production. Here we investigated the effect of zinc bacitracin and avilamycin on growth performance and caecal microbiota in chickens and analysed associations between in idual bacteria and growth performance. Two trials were undertaken each used 96 in idually caged 15-day-old Cobb broilers. Trial 1 had a control group (n = 48) and a zinc bacitracin (50 ppm) treatment group (n = 48). Trial 2 had a control group (n = 48) and an avilamycin (15 ppm) treatment group (n = 48). Chicken growth performance was evaluated over a 10-day period, and caecal microbiota was characterised by sequencing of bacterial 16S rRNA gene licons. Avilamycin produced no effect on growth performance and exhibited little significant disturbance of the microbiota structure. However, zinc bacitracin reduced the feed conversion ratio (FCR) in treated birds, changed the composition and increased the ersity of their caecal microbiota by reducing dominant species. Avilamycin only produced minor reductions in the abundance of two microbial taxa, whereas zinc bacitracin produced relatively large shifts in a number of taxa, primarily Lactobacillus species. Also, a number of phylotypes closely related to lactobacilli species were positively or negatively correlated with FCR values, suggesting contrasting effects of Lactobacillus spp. on chicken growth performance. By harnessing such bacteria, it may be possible to develop high-productivity strategies in poultry that rely on the use of probiotics and less on in-feed antibiotics.
Publisher: Elsevier BV
Date: 08-2017
DOI: 10.1016/J.VETMIC.2017.06.022
Abstract: Spotty liver disease (SLD) causes significant egg production losses and mortality in chickens and is therefore a disease of concern for some sectors of the poultry industry. Although the first reports of the disease came from the United States in the 1950s it is only recently that the organism that causes the disease was identified, isolated, and characterised as a new bacterial species, C ylobacter hepaticus. The first isolations of C. hepaticus were from the livers and bile of SLD affected birds. Isolates could only be recovered from s les that had a monoculture of C. hepaticus in the tissues, as a selective culturing method has not yet been developed. In non-selective growth conditions the slow growing C. hepaticus is quickly outgrown by many other members of the chicken microbiota. Therefore, it is currently not possible to use a culturing approach to evaluate C. hepaticus carriage in tissues, such as the gastrointestinal tract (GIT), that also carry complex microbial populations. As it is suspected that birds become infected via the faecal-oral route it is important that pathogen carriage in the GIT is investigated. In the present study, a specific and sensitive quantitative real-time PCR assay, based on the glycerol kinase gene of C. hepaticus, was developed. The assay facilitated the detection and quantification of C. hepaticus in tissue s les from clinical cases of SLD. It was shown that in infected birds C. hepaticus colonises the small intestine, increasing in abundance from duodenum to ileum, and is at highest levels within the ceaca. C. hepaticus was also readily detected in cloacal swabs, indicating that thecl-oral infection.
Publisher: CSIRO Publishing
Date: 1995
DOI: 10.1071/WR9950253
Abstract: An experiment compared effectiveness, cost and cost-efficiency of factorial combinations of the four commonly used methods of rabbit control on grazing properties in the Southern Tablelands of eastern Australia. Sixteen different treatment combinations were applied to 32 sites. The treatments comprised initial control, applied over four months, followed by repeated maintenance control on half the replicates, applied after intervals of 2,6 and 12 months. Initial control comprised no treatment, or poisoning (P) with sodium monofluoroacetate (1080), or warren-ripping (R), or chloropicrin pressure fumigation (F), or combinations of these (P+R, P+F, R+F, P+R+F). Maintenance control consisted of phosphine-diffusion fumigation (M). Indices of rabbit abundance were compared one month before treatments were implemented. Treatment effects were assessed one month after completion of the initial control, and one and 5-6 months after the three maintenance controls, and additionally nine months after the second maintenance control. Control combinations that were highly effective and cost-efficient included both warren-ripping and maintenance treatment. Poisoning prior to warren-ripping, or fumigating subsequently, or both, improved effectiveness and cost-efficiency. Warren-ripping interacted positively with one or more subsequent fumigations, improving effectiveness and cost-efficiency non-additively. Control combinations that excluded warren-ripping were ineffective and cost-inefficient, and one combination interacted negatively. Single treatments of poisoning or fumigation were cost-inefficient, allowing rabbits to recolonise rapidly to densities higher than original. Only multiple combination treatments or repeated applications were highly effective and cost-efficient single applications of any method were inefficient and costly. The most effective and cost-efficient combination comprised the maximum six applications including ripping and maintenance treatment, namely P+R+F+M. The high effort and expenditure on the initial control resulted in high effectiveness and cost-efficiency, which maintenance control sustained at low cost. Maintenance treatments sustained or achieved effective control of rabbits the cost of maintenance treatments halved on each repetition.
Publisher: Wiley
Date: 06-02-2010
Publisher: Elsevier BV
Date: 06-2023
Publisher: American Society for Microbiology
Date: 11-05-2021
DOI: 10.1128/AEM.00392-21
Abstract: Therapeutic proteins such as antigens can be used to prevent infectious diseases in poultry. However, traditional vaccine delivery by intramuscular or subcutaneous injection generally has not proven effective for mucosa-dwelling microorganisms that live within the gastrointestinal tract.
Publisher: Hindawi Limited
Date: 04-1985
DOI: 10.1017/S0016672300022114
Abstract: By physical and genetic analysis of deletion mutants of the narrow host range IncP-10 P. aeruginosa conjugative plasmid R91–5 it has been shown that the phenotypes related to its transfer, namely the inhibition of the replication of the phage G101, entry exclusion and the fertility inhibition of the wide host range plasmid R18 map at kilobase coordinates 19·7–20·7, 18·5–19·7, 28·8–30·15 and/or 34·9–36·15, respectively. These locations have been confirmed by cloning restriction enzyme generated DNA fragments of R91–5 into a small broad host range, multicopy non-conjugative plasmid.
Publisher: Public Library of Science (PLoS)
Date: 10-12-2019
Publisher: PeerJ
Date: 20-07-2017
DOI: 10.7717/PEERJ.3587
Abstract: The microbial populations that inhabit the gastrointestinal tract (GIT) are known to influence the health and growth performance of the host. Clean hatcheries and machine-based incubation practices in the commercial poultry industry can lead to the acquisition of aberrant microbiota in the GIT of chickens and a very high level of bird-to-bird variation. The lack of microbial profile flock uniformity presents challenges for harnessing and manipulating intestinal bacteria to better serve the host. Cecal contents from high or low performing chickens were used to inoculate the surface of eggs prior to hatching and then the initial gut colonisation was monitored and subsequent changes in gut microbiota composition were followed over time. Two different cecal treatment groups were compared to an untreated control group ( n = 32). Bacterial communities were characterised using high-throughput 16S rRNA gene sequencing techniques. Cecal microbiota transfer via egg surface application did not transfer the performance profile of the donors to the recipient birds. One of the cecal inoculations provided a more uniform gut microbiota, but this was not reproduced in the second group with a different inoculum. Development of the intestinal community was reproducible in all three groups with some genera like Lactobacillus showing no change, others like Faecalibacterium increased in abundance slowly and steadily over time and others like Enterobacter were abundant only in the first days of life. The cecal treatment reduced bird-to-bird variation in microbiota composition. Although the high FCR performance of donor birds was not transferred with the cecal microbiota, all three groups, including the control, performed better than standard for the breed. The pattern of microbiota development was similar in all three flocks, indicating that the normal processes of microbiota acquisition largely sw ed any effect of the cecal material applied to eggs.
Publisher: American Society for Microbiology
Date: 15-12-2017
DOI: 10.1128/AEM.01814-17
Abstract: Clostridium perfringens is a gastrointestinal pathogen capable of causing disease in a variety of hosts. Necrotic enteritis in chickens is caused by C. perfringens strains that produce the pore-forming toxin NetB, the major virulence factor for this disease. Like many other C. perfringens toxins and antibiotic resistance genes, NetB is encoded on a conjugative plasmid. Conjugative transfer of the netB -containing plasmid pJIR3535 has been demonstrated in vitro with a netB -null mutant. This study has investigated the effect of plasmid transfer on disease pathogenesis, with two genetically distinct transconjugants constructed under in vitro conditions, within the intestinal tract of chickens. This study also demonstrates that plasmid transfer can occur naturally in the host gut environment without the need for antibiotic selective pressure to be applied. The demonstration of plasmid transfer within the chicken host may have implications for the progression and pathogenesis of C. perfringens -mediated disease. Such horizontal gene transfer events are likely to be common in the clostridia and may be a key factor in strain evolution, both within animals and in the wider environment. IMPORTANCE Clostridium perfringens is a major gastrointestinal pathogen of poultry. C. perfringens strains that express the NetB pore-forming toxin, which is encoded on a conjugative plasmid, cause necrotic enteritis. This study demonstrated that the conjugative transfer of the netB -containing plasmid to two different nonpathogenic strains converted them into disease-causing strains with disease-causing capability similar to that of the donor strain. Plasmid transfer of netB and antibiotic resistance was also demonstrated to occur within the gastrointestinal tract of chickens, with approximately 14% of the isolates recovered comprising three distinct, in vivo -derived, transconjugant types. The demonstration of in vivo plasmid transfer indicates the potential importance of strain plasticity and the contribution of plasmids to strain virulence.
Publisher: American Society for Microbiology
Date: 07-2010
DOI: 10.1128/IAI.00123-10
Abstract: Clostridium perfringens causes several diseases in domestic livestock, including necrotic enteritis in chickens, which is of concern to the poultry industry due to its health implications and associated economic cost. The novel pore-forming toxin NetB is a critical virulence factor in the pathogenesis of this disease. In this study, we have examined the regulation of NetB toxin production. In C. perfringens , the quorum sensing-dependent VirSR two-component signal transduction system regulates genes encoding several toxins and extracellular enzymes. Analysis of the sequence upstream of the netB gene revealed the presence of potential DNA binding sites, or VirR boxes, that are recognized by the VirR response regulator. In vitro binding experiments showed that purified VirR was able to recognize and bind to these netB -associated VirR boxes. Furthermore, using a reporter gene assay, the netB VirR boxes were shown to be functional. Mutation of the virR gene in two avian C. perfringens strains was shown to significantly reduce the production of the NetB toxin culture supernatants derived from these strains were no longer cytotoxic to Leghorn male hepatoma cells. Complementation with the virRS operon restored the toxin phenotypes to wild type. The results also showed that the VirSR two-component system regulates the expression of netB at the level of transcription. We postulate that in the gastrointestinal tract of infected birds, NetB production is upregulated when the population of C. perfringens cells reaches a threshold level that leads to activation of the VirSR system.
Publisher: Elsevier BV
Date: 05-2004
Publisher: Elsevier BV
Date: 09-2020
Publisher: American Society for Microbiology
Date: 10-2010
DOI: 10.1128/AEM.01137-10
Abstract: Lactobacilli are autochthonous residents in the chicken gastrointestinal tract, where they may potentially be used as probiotics, competitive exclusion agents, or delivery vehicles. The aim of this study was to use an in vivo model to investigate the effect of diet and competing lactic acid bacteria on the colonization of inoculated Lactobacillus strains, with the goal of identifying strains which can consistently colonize or persist for an extended period of several weeks. Chicken-derived Lactobacillus strains were genetically marked with rif in resistance and administered on day 0 to chickens fed either a normal commercial diet or a specially formulated high-protein diet. Chickens fed the high-protein diet were also coinoculated with two different mixes of additional lactic acid bacteria. Enterobacterial repetitive intergenic consensus sequence-based PCR (ERIC-PCR) was used to identify rif in-resistant isolates recovered from chickens. Three strains, belonging to the species Lactobacillus agilis , Lactobacillus crispatus , and Lactobacillus vaginalis , were commonly reisolated from the chickens on both diets at days 21 and 42. The ability of these strains to persist was confirmed in a second chicken trial. All three strains persisted throughout the production period in the chickens fed a commercial diet, while only the L. agilis and L. vaginalis strains persisted in the chickens fed the high-protein diet. In both in vivo trials, competing lactic acid bacteria modified representation of the strains recovered, with all three stains capable of competing in the presence of one or both mixes of coinoculated strains. The in vivo model successfully identified three persistent strains that will be characterized further.
Publisher: Springer Science and Business Media LLC
Date: 27-02-2015
Publisher: Frontiers Media SA
Date: 14-05-2019
Publisher: Frontiers Media SA
Date: 28-10-2022
DOI: 10.3389/FVETS.2022.1039774
Abstract: Spotty Liver Disease (SLD) is a serious infectious disease which occurs mainly in laying chickens in free range production systems. SLD outbreaks can increase mortality and decrease egg production of chickens, adversely impact welfare and cause economic hardship for poultry producers. The bacterium C ylobacter hepaticus is the primary cause of the disease. This study aimed to identify the effects of C. hepaticus on chicken gut microbiota and gut structure. Three C. hepaticus strains (HV10 T , NSW44L and QLD19L), isolated from different states of Australia, were used in the study. Chickens at 26-weeks post-hatch were orally dosed with one of the C. hepaticus strains (challenged groups) or Brucella broth (unchallenged or control group). Six days after the challenge, birds were necropsied to assess liver damage, and caecal content and tissue s les were collected for histology, microbiology, and 16S rRNA gene licon sequencing to characterize the composition of the bacterial microbiota. Strain C. hepaticus NSW44L produced significantly more disease compared to the other C. hepaticus strains and this coincided with more adverse changes observed in the caecal microbiota of the birds challenged with this strain compared to the control group. Microbial ersity determined by Shannon and Simpson alpha ersity indices was lower in the NSW44L challenged groups compared to the control group ( p = 0.009 and 0.0233 respectively, at genus level). Short-chain fatty acids (SCFAs) producing bacteria Faecalibacterium, Bifidobacterium and Megamonas were significantly reduced in the challenged groups compared to the unchallenged control group. Although SLD-induction affected the gut microbiota of chickens, their small intestine morphology was not noticeably affected as there were no significant differences in the villus height or ratio of villus height and crypt depth. As gut health plays a pivotal role in the overall health and productivity of chickens, approaches to improve the gut health of the birds during SLD outbreaks such as through diet and keeping the causes of stress to a minimum, may represent significant ways to alleviate the impact of SLD.
Publisher: Elsevier BV
Date: 1995
DOI: 10.1016/0264-410X(95)00144-P
Abstract: Vaccines for ovine caseous lymphadenitis (CLA) are currently formulated using partially purified, formalin inactivated phospholipase D (PLD) derived from Corynebacterium pseudotuberculosis culture supernatants. Chemical treatment has been a common and effective way of inactivating bacterial toxins for use in toxoid vaccines. Genetic inactivation of toxin genes using site-specific mutagenesis has the potential to improve this process by providing a safer and more cost-effective product. In the present study amino acid substitutions at the putative catalytic site and metal binding domain of the PLD protein had a profound affect upon PLD activity and secretion from C. pseudotuberculosis. Two mutated PLD analogues that were secreted to a level of 40% compared to the wild-type and retained minimal activity showed promise for development as recombinant CLA vaccines. Further work will be required to establish their suitability for commercialization.
Publisher: Frontiers Media SA
Date: 07-12-2020
DOI: 10.3389/FVETS.2020.582297
Abstract: Escherichia coli is frequently associated with mastitis in cattle. “Pathogenic” and “commensal” isolates appear to be genetically similar. With a few exceptions, no notable genotypic differences have been found between commensal and mastitis-associated E. coli . In this study, 24 E. coli strains were isolated from dairy cows with clinical mastitis in three geographic regions of Australia (North Queensland, South Queensland, and Victoria), sequenced, then genomically surveyed. There was no observed relationship between sequence type (ST) and region ( p = 0.51). The most common Multi Locus Sequence Type was ST10 (38%), then ST4429 (13%). Pangenomic analysis revealed a soft-core genome of 3,463 genes, including genes associated with antibiotic resistance, chemotaxis, motility, adhesion, biofilm formation, and pili. A total of 36 different plasmids were identified and generally found to have local distributions ( p = 0.02). Only 2 plasmids contained antibiotic resistance genes, a p1303_5-like plasmid encoding multidrug-resistance (trimethoprim, quaternary ammonium, beta-lactam, streptomycin, sulfonamide, and kanamycin) from two North Queensland isolates on the same farm, while three Victorian isolates from the same farm contained a pCFSAN004177P_01-like plasmid encoding tetracycline-resistance. This pattern is consistent with a local spread of antibiotic resistance through plasmids of bovine mastitis cases. Notably, co-occurrence of plasmids containing virulence factors/antibiotic resistance with putative mobilization was rare, though the multidrug resistant p1303_5-like plasmid was predicted to be conjugative and is of some concern. This survey has provided greater understanding of antibiotic resistance within E. coli -associated bovine mastitis which will allow greater prediction and improved decision making in disease management.
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.VACCINE.2022.08.059
Abstract: Vaccines are very effective in providing protection against many infectious diseases. However, it has proven difficult to develop highly efficacious vaccines against some pathogens and so there is a continuing need to improve vaccine technologies. The first successful and widely used vaccines were based on attenuated pathogens (e.g., laboratory passaged Pasteurella multocida to vaccinate against fowl cholera) or closely related non-pathogenic organisms (e.g., cowpox to vaccinate against smallpox). Subsequently, live vaccines, either attenuated pathogens or non-pathogenic microorganisms modified to deliver heterologous antigens, have been successfully used to induce protective immune responses against many pathogens. Unlike conventional killed and subunit vaccines, live vaccines can deliver antigens to mucosal surfaces in a similar manner and context as the natural infection and hence can often produce a more appropriate and protective immune response. Despite these advantages, there is still a need to improve the immunogenicity of some live vaccines. The efficacy of injectable killed and subunit vaccines is usually enhanced using adjuvants such mineral salts, oils, and saponin, but such adjuvants cannot be used with live vaccines. Instead, live vaccines can be engineered to produce immunomodulatory molecules that can stimulate the immune system to induce more robust and long-lasting adaptive immune responses. This review focuses on research that has been undertaken to engineer live vaccines to produce immunomodulatory molecules that act as adjuvants to increase immunogenicity. Adjuvant strategies with varying mechanisms of action (inflammatory, antibody-mediated, cell-mediated) and delivery modes (oral, intramuscular, intranasal) have been investigated, with varying degrees of success. The goal of such research is to define adjuvant strategies that can be adapted to enhance live vaccine efficacy by triggering strong innate and adaptive immune responses and produce vaccines against a wider range of pathogens.
Publisher: CSIRO Publishing
Date: 2005
DOI: 10.1071/EA05070
Abstract: Chickens have undergone intensive selection to produce highly productive strains with excellent growth rates and feed conversion ratios. There does not appear to be any reduction in the rate of strain improvement. The recently completed chicken genome sequencing project and adjunct projects cataloging single nucleotide polymorphisms demonstrate that there is still a high level of genetic variation present in modern breeds. The information provided by genome and transcriptome studies furnishes the chicken biologist with powerful tools for the functional analysis of gene networks. Gene microarrays have been constructed and used to investigate gene expression patterns associated with certain production traits and changes in expression induced by pathogen challenge. Such studies have the potential to identify important genes involved in biological processes influencing animal productivity and health. Fundamental regulatory mechanisms controlled by non-coding RNAs, such as microRNAs, can now be studied following the identification of many potential genes by homology with previously identified genes from other organisms. We demonstrate here that microarrays and northern blotting can be used to detect expression of microRNAs in chicken tissue. Other tools are being used for functional genomic analysis including the production of transgenic birds, still a difficult process, and the use of gene silencing. Gene silencing via RNA interference is having a large impact in many areas of functional genomics and we and others have shown that the mechanisms needed for its action are functional in chickens. The chicken genome sequence has revealed a large number of immune related genes that had not previously been identified in chickens. Functional analysis of these genes is likely to lead to applications aimed at improving chicken health and productivity.
Publisher: Inter-Research Science Center
Date: 02-07-2020
DOI: 10.3354/ESR01042
Abstract: The microbiota of metazoans can be influenced by a variety of factors including diet, environment and genetics. In this study we s led multiple populations from 2 host species that do not overlap in distribution, in order to test whether their bacterial microbiotas are species-specific or more variable. Intestinal swabs were collected from loggerhead turtles originating from Florida, USA, and Queensland, Australia, as well as from flatback turtles from Crab Island, Queensland, and Port Hedland, Western Australia. We then manually extracted bacterial DNA and used 16S rRNA sequencing to explore bacterial microbial community composition and structure. Our investigation showed that the bacterial microbiota of sea turtles is heavily influenced by geography, with loggerhead turtles originating from the USA and Australia harbouring significantly different bacterial microbial populations in terms of composition. Similarly, we also found that flatback turtles from Crab Island had significantly less erse microbiotas, with a predominance of the bacterial phylum Firmicutes , in comparison to their genetically similar counterparts from Port Hedland. Factors that may explain these observed differences between populations include host genetics, differences in foraging habitat quality and differences in migratory distance (and thus durations of inappetence) between foraging and breeding grounds. The mechanisms by which these factors may influence bacterial microbial composition of sea turtle gastrointestinal tracts warrants further investigation. The results of this study highlight the importance of interpreting microbiota data of wild animals in the context of geography.
Publisher: Wiley
Date: 25-08-2017
Publisher: SAGE Publications
Date: 03-2004
DOI: 10.1177/019027250406700106
Abstract: Standardized survey interviewing is a form of institutional talk whose special constraints often conflict with ordinary conversational practices. Although survey manuals tend to recognize the conflict between standardization and respondents' requests for clarification, an alternative strategy for managing troubles in answering—“projective reporting”—is largely missing from the literature. Respondents may report circumstances in response to fixed-choice questions rather than providing an answer option. Such reports invite the interviewer to infer its relevance for an answer. Respondents use projective reporting in two different ways: to account for particular answers and to defer judgments in answering. Speakers and recipients in ordinary conversation have a variety of options for dealing with the upshots of projective reportings, but some of these options are prohibited in standardized interviews. When respondents use reporting to defer judgment, ordinary conversation and standardized interviewing can conflict.
Publisher: CSIRO Publishing
Date: 2007
DOI: 10.1071/EA07012
Abstract: The ability of cattle to resist tick infestations is partly genetically determined. In order to better define the nature of Bos taurus resistance to the cattle tick Boophilus microplus, skin gene expression was studied using a cattle skin derived cDNA microarray. Expression profiles were determined in skin biopsies s led from three highly tick resistant animals (HR) and two animals with lower tick resistance (LR) at time 0, immediately before challenge, and again 24 h after challenge. The analysis of the resulting expression data addressed two biological questions: first, for any animal exposed to ticks, which genes are differentially expressed in the 24 h following challenge and second, which genes are differentially expressed between animals of high and low resistance at 24 h after challenge? In total, 214 genes were found to be differentially expressed in response to larval challenge across all the animals. Seventy-two genes were upregulated and 76 were downregulated at 24 h after challenge. Genes with significantly altered gene expression levels following tick infestation were predominantly keratin genes or mitochondrial genes, as well as odorant binding protein (OBP) and Bos taurus major allergen BDA20. In addition, we identified 66 genes with differential expression between HR and LR animals at 24 h. Of these, genes representing the extracellular matrix and immunoglobulin gene expression pathways were overrepresented. Three differentially expressed genes, OBP, Bos taurus major allergen BDA20 and dendritic cell protein HFL-B5 were further analysed by quantitative reverse transcription PCR (qRT-PCR). The qRT-PCR assay results closely mirrored the expression profiles found in the microarray experiment.
Publisher: Elsevier BV
Date: 12-2012
DOI: 10.1016/J.YGENO.2012.08.006
Abstract: MicroRNAs (miRNAs) are small non-coding RNAs that play a role in post-transcriptional regulation of gene expression in most eukaryotes. They help in fine-tuning gene expression by targeting messenger RNAs (mRNA). The interactions of miRNAs and mRNAs are sequence specific and computational tools have been developed to predict miRNA target sites on mRNAs, but miRNA research has been mainly focused on target sites within 3' untranslated regions (UTRs) of genes. There is a need for an easily accessible repository of genome wide full length mRNA - miRNA target predictions with versatile search capabilities and visualization tools. We have created a web accessible database of miRNA target predictions for human, mouse, cow, chicken, Zebra fish, fruit fly and Caenorhabditis elegans using two different target prediction algorithms, The database has target predictions for miRNA's on 5' UTRs, coding region and 3' UTRs of all mRNAs. This database can be freely accessed at mamsap.it.deakin.edu.au/mirna_targets/.
Publisher: Elsevier BV
Date: 2009
DOI: 10.1016/J.TIM.2008.09.005
Abstract: For decades, low doses of antibiotics have been used widely in animal production to promote growth. However, there is a trend to reduce this use of antibiotics in feedstuffs, and legislation is now in place in Europe to prohibit their use in this way. As a consequence, economically important diseases, such as necrotic enteritis (NE) of chickens, that are caused by Clostridium perfringens have become more prevalent. Recent research is creating a paradigm shift in our understanding of the pathogenesis of NE and is now providing information that will be necessary to monitor and control the incidence of NE in poultry.
Publisher: Springer Science and Business Media LLC
Date: 02-10-2021
DOI: 10.1186/S42523-021-00127-Y
Abstract: A major focus of research on the gut microbiota of poultry has been to define signatures of a healthy gut and identify microbiota components that correlate with feed conversion. However, there is a high variation in in idual gut microbiota profiles and their association with performance. Population level s les such as dust and pooled excreta could be useful to investigate bacterial signatures associated with productivity at the flock-level. This study was designed to investigate the bacterial signatures of high and low-performing commercial meat chicken farms in dust and pooled excreta s les. Poultry house dust and fresh pooled excreta were collected at days 7, 14, 21, 28 and 35 of age from 8 farms of two Australian integrator companies and 389 s les assessed by 16S ribosomal RNA gene licon sequencing. The farms were ranked as low (n = 4) or high performers (n = 4) based on feed conversion rate corrected by body weight. Permutational analysis of variance based on Bray–Curtis dissimilarities using abundance data for bacterial community structure results showed that company explained the highest variation in the bacterial community structure in excreta (R 2 = 0.21, p = 0.001) while age explained the highest variation in the bacterial community structure in dust (R 2 = 0.13, p = 0.001). Farm performance explained the least variation in the bacterial community structure in both dust (R 2 = 0.03, p = 0.001) and excreta (R 2 = 0.01, p = 0.001) s les. However, specific bacterial taxa were found to be associated with high and low performance in both dust and excreta. The bacteria taxa associated with high-performing farms in dust or excreta found in this study were Enterococcus and Candidatus Arthromitus whereas bacterial taxa associated with low-performing farms included Nocardia , Lapillococcus , Brachybacterium , Ruania , Dietzia , Brevibacterium , Jeotgalicoccus, Corynebacterium and Aerococcus. Dust and excreta could be useful for investigating bacterial signatures associated with high and low performance in commercial poultry farms . Further studies on a larger number of farms are needed to determine if the bacterial signatures found in this study are reproducible.
Publisher: Springer Science and Business Media LLC
Date: 21-10-2021
DOI: 10.1038/S41598-021-00277-8
Abstract: C ylobacter hepaticus causes Spotty Liver Disease (SLD) in chickens. C. hepaticus is fastidious and slow-growing, presenting difficulties when growing this bacterium for the preparation of bacterin vaccines and experimental disease challenge trials. This study applied genomic analysis and in vitro experiments to develop an enhanced C. hepaticus liquid culture method. In silico analysis of the anabolic pathways encoded by C. hepaticus revealed that the bacterium is unable to biosynthesise l- cysteine, l- lysine and l- arginine. It was found that l -cysteine added to Brucella broth, significantly enhanced the growth of C. hepaticus , but l- lysine or l- arginine addition did not enhance growth. Brucella broth supplemented with l- cysteine (0.4 mM), l- glutamine (4 mM), and sodium pyruvate (10 mM) gave high-density growth of C. hepaticus and resulted in an almost tenfold increase in culture density compared to the growth in Brucella broth alone (log10 = 9.3 vs 8.4 CFU/mL). The type of culture flask used also significantly affected C. hepaticus culture density. An SLD challenge trial demonstrated that C. hepaticus grown in the enhanced culture conditions retained full virulence. The enhanced liquid culture method developed in this study enables the efficient production of bacterial biomass and therefore facilitates further studies of SLD biology and vaccine development.
Publisher: Springer Science and Business Media LLC
Date: 20-05-2021
Publisher: Elsevier BV
Date: 04-2007
DOI: 10.1016/J.RESMIC.2006.12.006
Abstract: Heat shock response genes have been characterised in many organisms. Such genes are often induced not only following heat stress but also following a range of other stresses. In pathogenic bacteria, the common heat shock genes are usually induced during the initial infection process. The identification of other genes regulated during heat shock, besides the classical heat shock genes such as those of the dnaK and groEL operons, may provide information about other cellular responses such as membrane remodelling and nutrient scavenging that may be important in the early stages of infection. In this study, macroarray analysis has been used to identify a number of genes of Corynebacterium pseudotuberculosis that are either upregulated (e.g. clpB, dnaK) or downregulated (e.g. fagC, fas) in vitro following a heat shock. The major virulence factor, phospholipase D, was found to be highly downregulated.
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.VETMIC.2014.01.007
Abstract: It is widely established that a high-protein fishmeal supplemented starter diet and Eimeria infection can predispose birds to the development of clinical necrotic enteritis symptoms following Clostridium perfringens infection. However, it has not been clearly established what changes these treatments cause to predispose birds to succumb to necrotic enteritis. We analysed caecal microbiota of 4 groups of broilers (n=12) using deep pyrosequencing of 16S rDNA licons: (1) control chicks fed a control diet, (2) Eimeria infected chicks fed control diet, (3) chicks fed fishmeal supplemented diet and lastly (4) both fishmeal fed and Eimeria infected chicks. We found that the high-protein fishmeal diet had a strong effect on the intestinal microbiota similar to the previously reported effect of C. perfringens infection. We noted major changes in the prevalence of various lactobacilli while the total culturable Lactobacillus counts remained stable. The Ruminococcaceae, Lachnospiraceae, unknown Clostridiales and Lactobacillaceae families were most affected by fishmeal with increases in a number of operational taxonomic units (OTUs) that had previously been linked to Crohn's disease and reductions in OTUs known to be butyrate producers. Eimeria induced very different changes in microbiota Ruminococcaceae groups were reduced in number and three unknown Clostridium species were increased in abundance. Additionally, Eimeria did not significantly influence changes in pH, formic, propionic or isobutyric acid while fishmeal induced dramatic changes in all these measures. Both fishmeal feeding and Eimeria infection induced significant changes in the gut microbiota these changes may play an important role in predisposing birds to necrotic enteritis.
Publisher: Public Library of Science (PLoS)
Date: 08-02-2008
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1016/J.VETMIC.2012.03.032
Abstract: Necrotic enteritis is a disease of considerable economic importance to the global poultry industry. Clostridium perfringens has long been recognised as the etiological agent of the disease. However, disease initiation and progression is complex and appears to be precipitated by a range of predisposing factors. The present study investigated microbial interactions in the caecum of birds challenged with C. perfringens that developed necrotic enteritis. Bacterial populations of healthy and diseased birds, across two independent animal trials, were characterised by pyrosequencing of the V1-V3 region of 16S rRNA genes. Significant changes in the microbiota of infected birds were detected. Most of the affected bacterial species, including a number of butyrate producers, were reduced in abundance in infected birds compared to uninfected controls and a number of phylotypes, classified as Weissella species, were also more abundant in healthy birds. Conversely, some bacterial groups were more abundant in the C. perfringens-infected birds, for ex le, members of an unclassified order of Mollicutes showed a 3.7-fold increase in abundance in infected birds. Representative sequences from this novel order shared 99% identity with sequences previously detected in intestinal microbiota of chickens and humans, and have previously been shown to be represented in a number of s les originating from irritable bowel syndrome disease patients. We speculate that these newly identified perturbations in the composition of caecal microflora may play a role in the development and manifestation of necrotic enteritis.
Publisher: Springer Science and Business Media LLC
Date: 27-08-2018
DOI: 10.1007/S00253-018-9281-1
Abstract: Immune function is influenced by the ersity and stability of the intestinal microbiota. A likely trade-off of immune function for growth has been demonstrated in heavier breeds of poultry that have been genetically selected for growth and feed efficiency traits. We investigated the expression of selected innate immune genes and genes encoding products involved in intestinal barrier function to determine whether function changes could be consistently linked to the phenotypic expression of feed conversion ratio (FCR), a common measure of performance within poultry broiler flocks. In addition, we compared in idual cecal microbial composition with innate immune gene expression. S les were utilised from two replicate trials termed P1E1 and P1E2. High (n = 12) and low (n = 12) performing birds were selected based on their in idual FCR data from each replicate and combined for microbiota phylogenetic composition and immune gene expression analysis. Toll-like receptor 1 (TLR1La) and zonula occludens 1 (ZO1) were differentially expressed between high- and low-performing broilers. Several taxa were correlated with FCR of these, unclassified YS2 and ZO1 were also positively correlated with each other. Interactions between taxa and differentially expressed innate immune genes between P1E1 and P1E2 were much greater compared to relationships between high- and low-performing birds. At the level of phylum, reciprocal correlations between tight junction proteins and Toll-like receptors with Bacteroidetes and Firmicutes were evident, as were correlations at the genus level.
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.MICRES.2016.11.006
Abstract: According to the World Health Organisation, antibiotics are rapidly losing potency in every country of the world. Poultry are currently perceived as a major source of pathogens and antimicrobial resistance. There is an urgent need for new and natural ways to control pathogens in poultry and humans alike. Porous, cation rich, aluminosilicate minerals, zeolites can be used as a feed additive in poultry rations, demonstrating multiple productivity benefits. Next generation sequencing of the 16S rRNA marker gene was used to phylogenetically characterize the fecal microbiota and thus investigate the ability and dose dependency of zeolite in terms of anti-pathogenic effects. A natural zeolite was used as a feed additive in laying hens at 1, 2, and 4% w/w for a 23 week period. At the end of this period cloacal swabs were collected to s le faecal microbial communities. A significant reduction in carriage of bacteria within the phylum Proteobacteria, especially in members of the pathogen-rich family Enterobacteriaceae, was noted across all three concentrations of zeolite. Zeolite supplementation of feed resulted in a reduction in the carriage of a number of poultry pathogens without disturbing beneficial bacteria. This effect was, in some phylotypes, correlated with the zeolite concentration. This result is relevant to zeolite feeding in other animal production systems, and for human pathogenesis.
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.MCP.2018.08.006
Abstract: Theiler's murine encephalomyelitis virus (TMEV) is one of the most common viral pathogens that circulate widely in captive mouse colonies. A molecular biology detection method would be a useful tool to use in an integrated program to monitor and prevent TMEV infection and transmission. Thus, a reverse transcription recombinase polymerase lification (RT-RPA) assay was developed to detect TMEV infection. The sensitivity of the RT-RPA assay approached 8 copies per reaction, which is equivalent to the sensitivity of RT-qPCR reactions. This assay did not detect RNA extracts from other murine pathogens included in this study or TMEV negative s les. Brain tissues and contaminated biological materials were used to assess the clinical performance of the RT-RPA. The detection results of RT-RPA and RT-qPCR were very similar, except that a contaminated biological material s le which was positive by RT-qPCR, with a CT value of 38, was negative by RT-RPA. In summary, the developed RT-RPA assay offers a rapid, sensitive and specific alternative method for monitoring of TMEV, especially in resource-limited conditions.
Publisher: Oxford University Press (OUP)
Date: 1986
Abstract: The provirus of mouse mammary tumour virus (MMTV) is reputed to contain sequences within the viral gag gene that prevent or inhibit its propagation as a recombinant DNA clone in Escherichia coli. Here we report the successful isolation of several lambda and plasmid clones comprising the 5' virus-host DNA junction fragments from integrated MMTV proviruses in BR6 mice. Although the lambda clones appeared intact, almost all of the plasmids were found to contain the bacterial insertion sequences IS1 or IS2 within a small region of the gag gene. One nondisrupted clone was recovered which had undergone multiple G to A transitions, some of which created stop codons in gag. These results have provided more precise information as to the location of the poison sequences and are discussed in relation to possible explanations for the phenomenon.
Publisher: Informa UK Limited
Date: 03-05-2016
DOI: 10.1080/03079457.2016.1152625
Abstract: An outbreak of necrotic enteritis (NE) is a complex process requiring one or a number of predisposing factors rather than just the presence of pathogenic Clostridium perfringens. Ex les are dietary influences, such as high levels of non-starch polysaccharides and fishmeal, and factors that evoke epithelial cell damage, such as Fusarium mycotoxins in feed and Eimeria infections. Recent studies have shown that different predisposing factors induce similar shifts in the intestinal microbiota composition. Butyrate-producing-strains of the Ruminococcaceae family are decreased in abundance by both fishmeal and Eimeria. Similarly, a decreased abundance of butyrate-producing-strains belonging to the Lachnospiraceae family has been induced by fishmeal. Also shifts are observed in the lactic acid-producing bacteria, such as decreased abundance of Lactobacillus johnsonii or Weissella confusa, when broilers were fed a fishmeal-based diet or a Fusarium mycotoxin contaminated diet. Finally, the abundance of Candidatus Savagella was decreased in broilers following Eimeria challenge or feeding a fumonisins contaminated diet. The nature of the microbiota shifts indicate that immune modulatory actions of the intestinal microbiota may play a critical role in the effect on the necrosis inducing activity of C. perfringens. Indeed, colonization with butyrate-producing bacteria plays a key role in counteracting inflammation in the gut and preserving intestinal integrity, while Candidatus Savagella is involved in stimulating Th17 and immunoglobulin A responses. Lactic acid bacteria stimulate colonization of lactate-utilizing and butyrate-producing Lachnospiraceae. Future research needs to clarify the role of the microbiota changes in the pathogenesis of NE.
Publisher: American Society for Microbiology
Date: 11-2006
DOI: 10.1128/IAI.00806-06
Abstract: The Clostridium perfringens alpha-toxin has previously been implicated as the major virulence factor in necrotic enteritis in chickens, although definitive proof has not been reported. In this study an alpha-toxin mutant was constructed in a virulent chicken isolate and shown to retain full virulence in a chicken disease model. These results demonstrated that alpha-toxin is not an essential virulence factor in the pathogenesis of necrotic enteritis in chickens.
Publisher: Informa UK Limited
Date: 03-05-2016
DOI: 10.1080/03079457.2016.1153799
Abstract: The investigation of genomic variation between Clostridium perfringens isolates from poultry has been an important tool to enhance our understanding of the genetic basis of strain pathogenicity and the epidemiology of virulent and avirulent strains within the context of necrotic enteritis (NE). The earliest studies used whole genome profiling techniques such as pulsed-field gel electrophoresis to differentiate isolates and determine their relative levels of relatedness. DNA sequencing has been used to investigate genetic variation in (a) in idual genes, such as those encoding the alpha and NetB toxins (b) panels of housekeeping genes for multi-locus sequence typing and (c) most recently whole genome sequencing to build a more complete picture of genomic differences between isolates. Conclusions drawn from these studies include: differential carriage of large conjugative plasmids accounts for a large proportion of inter-strain differences plasmid-encoded genes are more highly conserved than chromosomal genes, perhaps indicating a relatively recent origin for the plasmids isolates from NE-affected birds fall into three distinct sequence-based clades while non-pathogenic isolates from healthy birds tend to be more genomically erse. Overall, the NE causing strains are closely related to C. perfringens isolates from other birds and other diseases whereas the non-pathogenic poultry strains are generally more remotely related to either the pathogenic strains or the strains from other birds. Genomic analysis has indicated that genes in addition to netB are associated with NE pathogenic isolates. Collectively, this work has resulted in a deeper understanding of the pathogenesis of this important poultry disease.
Publisher: Springer Science and Business Media LLC
Date: 11-2014
Publisher: Future Medicine Ltd
Date: 03-2014
DOI: 10.2217/FMB.13.168
Abstract: ABSTRACT: Clostridium perfringens uses its arsenal of toxins to cause histotoxic and intestinal infections in humans and animals. It has been unclear why this bacterium produces so many different toxins, especially since many target the plasma membrane of host cells. However, it is now established that C. perfringens uses chromosomally encoded alpha toxin (a phospholipase C) and perfringolysin O (a pore-forming toxin) during histotoxic infections. In contrast, this bacterium causes intestinal disease by employing toxins encoded by mobile genetic elements, including C. perfringens enterotoxin, necrotic enteritis toxin B-like, epsilon toxin and beta toxin. Like perfringolysin O, the toxins with established roles in intestinal disease form membrane pores. However, the intestinal disease-associated toxins vary in their target specificity, when they are produced (sporulation vs vegetative growth), and in their sensitivity to intestinal proteases. Producing many toxins with erse characteristics likely imparts virulence flexibility to C. perfringens so it can cause an array of diseases.
Publisher: Microbiology Society
Date: 11-2016
Abstract: Ten strains of an unknown C ylobacter species were isolated from the livers of chickens with spotty liver disease in Australia. The strains were Gram-stain-negative, microaerobic, catalase- and oxidase-positive and urease-negative. Unlike most other species of the genus C ylobacter, most of the tested strains of this novel species hydrolysed hippurate and half of them could not reduce nitrate. All strains showed resistance, or intermediate resistance, to nalidixic acid and most of them were resistant to cephalothin. Examination of negatively stained cells under transmission electron microscopy revealed that they were S-shaped, with bipolar unsheathed flagella. Phylogenetic analyses based on the 16S rRNA gene and the heat shock protein 60 (hsp60) gene sequences indicated that the strains formed a robust clade that was clearly distinct from recognized C ylobacter species. Unusually, they had a DNA G+C content of 27.9 mol%, lower than any previously described C ylobacter species, and they showed less than 84 % average nucleotide identity to the nearest sequenced species. Taken together, these data indicate that the strains belong to a novel C ylobacter species, for which the name C ylobacter hepaticus sp. nov. is proposed. The type strain is HV10T (=NCTC 13823T=CIP 111092T).
Publisher: Springer Science and Business Media LLC
Date: 20-05-2020
DOI: 10.1038/S41598-020-65321-5
Abstract: The microbiota is considered critical for normal vertebrate homeostasis and it may exert its effects at a local level within the gastrointestinal tract, or systemically through the production of bacterial metabolites. To date, investigations into the role that the microbiota plays in reptile physiology are rare. To address this knowledge gap, we explored the relationship between differences in microbial communities to see if they accounted for differences in haematology and biochemistry values, in different populations of nesting flatback turtles ( Natator depressus ). We found that microbiota composition was not correlated to any of the blood analytes we measured in flatbacks. This study is the first of its kind in reptiles and highlights the need for further investigations to determine mechanisms by which the microbiota influences the physiology and health of reptiles.
Publisher: Springer Science and Business Media LLC
Date: 05-01-2023
DOI: 10.1038/S41598-022-26532-0
Abstract: C ylobacter hepaticus is an important pathogen which causes Spotty Liver Disease (SLD) in layer chickens. SLD results in an increase in mortality and a significant decrease in egg production and therefore is an important economic concern of the global poultry industry. The human pathogen C ylobacter jejuni encodes an N -linked glycosylation system that plays fundamental roles in host colonization and pathogenicity. While N -linked glycosylation has been extensively studied in C. jejuni and is now known to occur in a range of C ylobacter species, little is known about C. hepaticus glycosylation. In this study glycoproteomic analysis was used to confirm the functionality of the C. hepaticus N- glycosylation system. It was shown that C. hepaticus HV10 T modifies 35 proteins with an N -linked heptasaccharide glycan. C. hepaticus shares highly conserved glycoproteins with C. jejuni that are involved in host colonisation and also possesses unique glycoproteins which may contribute to its ability to survive in challenging host environments. C. hepaticus N- glycosylation may function as an important virulence factor, providing an opportunity to investigate and develop a better understanding the system’s role in poultry infection.
Publisher: Springer Science and Business Media LLC
Date: 27-03-2017
DOI: 10.1038/NI.3713
Abstract: Gut dysbiosis might underlie the pathogenesis of type 1 diabetes. In mice of the non-obese diabetic (NOD) strain, we found that key features of disease correlated inversely with blood and fecal concentrations of the microbial metabolites acetate and butyrate. We therefore fed NOD mice specialized diets designed to release large amounts of acetate or butyrate after bacterial fermentation in the colon. Each diet provided a high degree of protection from diabetes, even when administered after breakdown of immunotolerance. Feeding mice a combined acetate- and butyrate-yielding diet provided complete protection, which suggested that acetate and butyrate might operate through distinct mechanisms. Acetate markedly decreased the frequency of autoreactive T cells in lymphoid tissues, through effects on B cells and their ability to expand populations of autoreactive T cells. A diet containing butyrate boosted the number and function of regulatory T cells, whereas acetate- and butyrate-yielding diets enhanced gut integrity and decreased serum concentration of diabetogenic cytokines such as IL-21. Medicinal foods or metabolites might represent an effective and natural approach for countering the numerous immunological defects that contribute to T cell-dependent autoimmune diseases.
Publisher: Hindawi Limited
Date: 04-1985
DOI: 10.1017/S0016672300022059
Abstract: The transcriptional organization of the Tra2 region controlling conjugation by the narrow host range plasmid R91–5 of Pseudomonas aeruginosa has been determined. This region of 15·2 kilobase pairs of DNA encodes ten cistrons and specifies the synthesis and functionality of sex pili. The order of the cistrons was previously shown to be traW , ( S, Z ), U , ( V, R ), Q, T, Y, X (those within parentheses could not be ordered with respect to each other). The organization was determined by complementation tests for the restoration of plasmid transfer between transposon Tn 7 or Tn 501 induced insertion mutants and point mutants representative of the ten cistrons. Polarity mutations induced by Tn 7 permitted the identification of three operons. Cistrons traW, Z, S, U, V, R and Q formed a large operon with transcription postulated to be in that order. The second consisted of tra T and tra Y also in that order and the third consisted of only one cistron, traX . Polarity was not observed with Tn 501 insertions as they still permitted full expression of cistrons distal to the site of insertion with respect to the proposed promoter. Despite the unexpected behaviour of this transposon it nevertheless led to the identification of two previously unidentified cistrons, traO and traP being between traZ and S and traR and V , respectively.
Publisher: American Society for Microbiology
Date: 31-05-2019
DOI: 10.1128/MICROBIOLSPEC.GPP3-0033-2018
Abstract: Whole-genome sequences are now available for all the clinically important clostridia and many of the lesser or opportunistically pathogenic clostridia. The complex clade structures of C. difficile , C. perfringens , and the species that produce botulinum toxins have been delineated by whole-genome sequence analysis. The true clostridia of cluster I show relatively low levels of gross genomic rearrangements within species, in contrast to the species of cluster XI, notably C. difficile , which have been found to have very plastic genomes with significant levels of chromosomal rearrangement. Throughout the clostridial phylotypes, a large proportion of the strain ersity is driven by the acquisition and loss of mobile elements, including phages, plasmids, insertion sequences, and transposons. Genomic analysis has been used to investigate the ersity and spread of C. difficile within hospital settings, the zoonotic transfer of isolates, and the emergence, origins, and geographic spread of epidemic ribotypes. In C. perfringens the clades defined by chromosomal sequence analysis show no indications of clustering based on host species or geographical location. Whole-genome sequence analysis helps to define the different survival and pathogenesis strategies that the clostridia use. Some, such as C. botulinum , produce toxins which rapidly act to kill the host, whereas others, such as C. perfringens and C. difficile , produce less lethal toxins which can damage tissue but do not rapidly kill the host. The genomes provide a resource that can be mined to identify potential vaccine antigens and targets for other forms of therapeutic intervention.
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/MA15041
Abstract: Clostridium perfringens, a spore-forming, Gram-positive, anaerobic bacterium, causes a variety of diseases throughout the animal kingdom. Each disease in each animal species tends to be caused by particular strains of C. perfringens and is defined by the tissue tropism and toxin profile of the bacteria. In chickens toxinotype A strains cause necrotic enteritis a disease characterised by tissue damage to the proximal regions of the small intestine. In extreme cases the disease can be lethal but is more commonly seen as a sub-clinical disease that causes welfare issues and productivity losses within the poultry industry. The disease is currently well controlled in Australia by good management practices and, for some poultry producers, the use of antibiotics in the feed. However, the disease does cause significant issues in other regions including North America and Europe. In Europe there was a spike of necrotic enteritis disease when antibiotics were withdrawn from animal feeds. It is probable that the disease will become more of an issue in the Australian poultry industry as in-feed antibiotic use is reduced. Therefore, other methods of disease control are under investigation, including the development of vaccines.
Publisher: Public Library of Science (PLoS)
Date: 26-04-2016
Publisher: American Society for Microbiology
Date: 2011
DOI: 10.1128/AEM.02006-10
Abstract: Lactobacilli are naturally found in the gastrointestinal tract of chickens, and there is interest in utilizing autochthonous strains for the delivery of therapeutic proteins. Previously we identified three chicken-derived Lactobacillus strains, Lactobacillus agilis La3, Lactobacillus vaginalis Lv5, and Lactobacillus crispatus Lc9, which persist in the gastrointestinal tract of chickens fed either a commercial or high-protein diet. In the current study, we investigated the ability to electrotransform these strains, determined plasmid vector stability, and compared reporter gene expression directed by several different promoters. The La3 and Lv5 strains were reproducibly transformed with efficiencies of 10 8 and 10 6 transformants per microgram of plasmid DNA, respectively. The third strain tested, L. crispatus Lc9, was recalcitrant to all transformation protocols examined. The plasmid vectors pTRK563 and pTRKH2 were maintained over 100 generations in La3 and Lv5, respectively. The ability of La3 and Lv5 to express the heterologous reporter gene gfp was analyzed using heterologous and homologous promoters. Transformants of both La3 and Lv5 containing the La3 ldhL promoter were the most fluorescent. To our knowledge, this is the first report of successful transformation and heterologous protein expression in L. agilis and L. vaginalis . The ability of these strains to express heterologous proteins in vitro indicates their potential utility as in vivo delivery vectors for therapeutic peptides to the chicken gastrointestinal tract.
Publisher: American Society for Microbiology
Date: 11-2009
DOI: 10.1128/AEM.01150-09
Abstract: Three repetitive-element PCR techniques were evaluated for the ability to type strains of Lactobacillus species commonly identified in the chicken gastrointestinal tract. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) produced species- and strain-specific profiles for Lactobacillus crispatus , Lactobacillus gallinarum , Lactobacillus johnsonii , and Lactobacillus reuteri isolates. The technique typed strains within these species equally as well as pulsed-field gel electrophoresis. DNA concentration and quality did not affect the ERIC-PCR profiles, indicating that this method, unlike other high-resolution methods, can be adapted to high-throughput analysis of isolates. Subsequently, ERIC-PCR was used to type Lactobacillus species ersity of a large collection of isolates derived from chickens grown under commercial and necrotic enteritis disease induction conditions. This study has illustrated, for the first time, that there is great strain ersity within each Lactobacillus species present and has revealed that chickens raised under commercial conditions harbor greater species and strain ersity than chickens raised under necrotic enteritis disease induction conditions.
Publisher: Elsevier BV
Date: 10-2019
Publisher: Oxford University Press (OUP)
Date: 11-08-2020
DOI: 10.1093/JNCI/DJAA114
Abstract: ASPirin in Reducing Events in the Elderly, a randomized, double-blind, placebo-controlled trial of daily low-dose aspirin (100 mg) in older adults, showed an increase in all-cause mortality, primarily due to cancer. In contrast, prior randomized controlled trials, mainly involving younger in iduals, demonstrated a delayed cancer benefit with aspirin. We now report a detailed analysis of cancer incidence and mortality. 19 114 Australian and US community-dwelling participants aged 70 years and older (US minorities 65 years and older) without cardiovascular disease, dementia, or physical disability were randomly assigned and followed for a median of 4.7 years. Fatal and nonfatal cancer events, a prespecified secondary endpoint, were adjudicated based on clinical records. 981 cancer events occurred in the aspirin and 952 in the placebo groups. There was no statistically significant difference between groups for all incident cancers (hazard ratio [HR] = 1.04, 95% confidence interval [CI] = 0.95 to 1.14), hematological cancer (HR = 0.98, 95% CI = 0.73 to 1.30), or all solid cancers (HR = 1.05, 95% CI = 0.95 to 1.15), including by specific tumor type. However, aspirin was associated with an increased risk of incident cancer that had metastasized (HR = 1.19, 95% CI = 1.00 to 1.43) or was stage 4 at diagnosis (HR = 1.22, 95% CI = 1.02 to 1.45), and with higher risk of death for cancers that presented at stages 3 (HR = 2.11, 95% CI = 1.03 to 4.33) or 4 (HR = 1.31, 95% CI = 1.04 to 1.64). In older adults, aspirin treatment had an adverse effect on later stages of cancer evolution. These findings suggest that in older persons, aspirin may accelerate the progression of cancer and, thus, suggest caution with its use in this age group.
Publisher: Springer Science and Business Media LLC
Date: 31-08-2007
Publisher: Frontiers Media SA
Date: 14-11-2022
DOI: 10.3389/FVETS.2022.1058110
Abstract: Spotty liver disease (SLD) caused by C ylobacter hepaticus affects the health and productivity of layer hens and is a disease of concern in poultry. In this study, blood and cloacal swab s les were collected from 709 birds across 11 free-range layer farms from different regions of Australia. The prevalence of C. hepaticus specific antibodies and DNA was assessed using a C. hepaticus specific ELISA and PCR and its correlation with mortalities and changes in egg production was analyzed to better understand the seroprevalence of C. hepaticus in Australian free-range layer farms. C. hepaticus specific antibodies were detected from birds in four of the five farms that had no history of SLD with seroprevalence as high as 41% in one of the farms. Seroprevalence of anti- C. hepaticus antibodies among flocks that had an active or previous SLD outbreak varied between 2 and 64%. C. hepaticus DNA was detected from birds in three farms with no known SLD history and five farms with confirmed SLD outbreaks. A good correlation was observed between the ELISA and PCR results with a Pearson correlation coefficient value of 0.85 ( p -value = 0.001). No correlation was observed between the flock size or flock age and ELISA or PCR outcomes, and no significant difference between the seroprevalence of anti- C. hepaticus antibodies among flocks with or without a known history of SLD was established ( p = 0.143). This study demonstrates the usefulness of C. hepaticus specific ELISA and PCR in identifying the occurrence of mild or sub-clinical SLD and provides a broader and more complete understanding of SLD epidemiology that will inform future research aimed at the development of methods to control SLD, such as appropriate biosecurity measures, vaccines, and feed additives.
Publisher: Elsevier BV
Date: 2007
DOI: 10.1016/J.VETMIC.2006.09.008
Abstract: Bovine viral diarrhea virus (BVDV) is a ubiquitous viral pathogen that affects cattle herds' worldwide causing significant economic loss. The current strategies to control BVDV infection include vaccination (modified-live or killed) and control of virus spread by enhanced biosecurity management, however, the disease remains prevalent. With the discovery of the sequence-specific method of gene silencing known as RNA interference (RNAi), a new era in antiviral therapies has begun. Here we report the efficient inhibition of BVDV replication by small interfering (siRNA) and short hairpin RNA (shRNA)-mediated gene silencing. siRNAs were generated to target the 5' non-translated (NTR) region and the regions encoding the C, NS4B and NS5A proteins of the BVDV genome. The siRNAs were first validated using an EGFP/BVDV reporter system and were then shown to suppress BVDV-induced cytopathic effects and viral titers in cell culture with surprisingly different activities compared to the reporter system. Efficient viral suppression was then achieved by bovine 7SK-expressed BVDV-specific shRNAs. Overall, our results demonstrated the use of siRNA and shRNA-mediated gene silencing to achieve efficient inhibition of the replication of this virus in cell culture.
Publisher: Elsevier BV
Date: 09-2021
Publisher: Springer Science and Business Media LLC
Date: 04-2015
DOI: 10.1038/NCOMMS7734
Abstract: Diet and the gut microbiota may underpin numerous human diseases. A major metabolic product of commensal bacteria are short-chain fatty acids (SCFAs) that derive from fermentation of dietary fibre. Here we show that diets deficient or low in fibre exacerbate colitis development, while very high intake of dietary fibre or the SCFA acetate protects against colitis. SCFAs binding to the 'metabolite-sensing' receptors GPR43 and GPR109A in non-haematopoietic cells mediate these protective effects. The inflammasome pathway has hitherto been reported as a principal pathway promoting gut epithelial integrity. SCFAs binding to GPR43 on colonic epithelial cells stimulates K(+) efflux and hyperpolarization, which lead to NLRP3 inflammasome activation. Dietary fibre also shapes gut bacterial ecology, resulting in bacterial species that are more effective for inflammasome activation. SCFAs and metabolite receptors thus explain health benefits of dietary fibre, and how metabolite signals feed through to a major pathway for gut homeostasis.
Publisher: Elsevier BV
Date: 2020
Publisher: Frontiers Media SA
Date: 22-12-2022
DOI: 10.3389/FVETS.2022.1058115
Abstract: Bacteriophages are viral predators of bacteria and are common in nature. Their host-specific infections against specific bacteria make them an attractive natural agent to control bacterial pathogens. Interest in the potential of bacteriophages as antibacterial agents in the production animal industries has increased. A total of 18 bacteriophages were isolated from Australian commercial poultry environments, from which three highly active phages were chosen for enrichment. Sequencing libraries were prepared using a Nextera XT kit (Illumina) and sequenced on an Illumina MiSeq instrument using 2 × 300 bp paired-end chemistry. The sequence data were then assembled and aligned with a2 bacteriophage as the reference. An animal trial was performed by oral gavaging Clostridium perfringens netB containing strain EHE-NE18 to the Ross 308 broiler chickens prior inoculation with Eimeria species. The chickens were raised following the management guide for Ross 308 from d 0 to d 21 and fed with starter and grower diets met the specific breed nutrient requirements. Body weight gain and feed intake were measured on d 9 and d 21 and FCR adjusted with mortality was calculated. The isolated bacteriophages only had only 96.7% similarity to the most closely related, previously characterized, Clostridium bacteriophage indicated that they might represent a novel strain of bacteriophage. A “cocktail” containing the three bacteriophages was capable of lysing four known disease-inducing C. perfringens strains in vitro . Oral administration of the bacteriophages cocktail to broilers challenged with necrotic enteritis markedly alleviated intestinal necrotic lesions in the duodenum and jejunum on day 16 post-hatch. The phage treatment significantly reduced the lesion scores of birds challenged with NE ( P & 0.01), and the lesion scores between birds treated with the bacteriophages and the unchallenged birds were not statistically different ( P & 0.05). However, no effect on the growth performance was observed during the recorded period of days 9-21. These findings suggest that bacteriophage treatment is a promising approach to protect intestinal health from C. perfringens induced necrotic enteritis. Further research will be required on the dosing, route of administration, and large scale validation studies to further advance this approach to pathogen control.
Publisher: Public Library of Science (PLoS)
Date: 28-08-2014
Publisher: CSIRO Publishing
Date: 2013
DOI: 10.1071/AN12426
Abstract: Among the terrestrial production animals, chickens are the most efficient users of energy. Apparent metabolisable energy (AME) is a measure of energy utilisation efficiency representing the difference between energy consumed and energy lost via the excreta. There are significant differences in the energy utilisation capability of in idual birds that have a similar genetic background and are raised under identical conditions. It would be of benefit to poultry producers if the basis of these differences could be understood and the differences minimised. We analysed duodenal gene expression and microbiota differences in birds with different energy utilisation efficiencies. Using microarray analysis, significant differences were found in duodenal gene expression between high- and low-AME birds, indicating that level of cell turnover may distinguish different groups of birds. High-throughput sequencing of bacterial 16S rRNA genes indicated that duodenal microbiota was dominated by Lactobacillus species and two operational taxonomic units, identified as lactobacilli species, were found to be more abundant (P 0.05) in low-AME birds. The present study has identified gene expression and microbiota properties that correlate with differences in AME further studies will be required to investigate the causal relationships.
Publisher: Informa UK Limited
Date: 12-04-2019
Publisher: Springer Science and Business Media LLC
Date: 02-1989
DOI: 10.1007/BF00427038
Publisher: Frontiers Media SA
Date: 15-01-2020
Publisher: Morressier
Date: 30-03-2016
Publisher: Frontiers Media SA
Date: 04-11-2021
DOI: 10.3389/FVETS.2021.743725
Abstract: Mastitis is the most common disease in dairy cattle worldwide. The objectives of this study were to estimate the prevalence of different bacterial species associated with mastitis from dairy herds located in geographically and climatically distinct zones in Australia, and to evaluate the antimicrobial susceptibility of the isolated bacteria. Quarter-level milk s les ( n = 419) were collected from 151 mastitis cases and 268 healthy controls originating from 18 dairy herds located in tropical (Northern Queensland), subtropical (Southeast Queensland) and temperate zones (Victoria) between March and June 2019. Milk s les were cultured, and the isolated bacteria were grouped into six groups: Enterobacteriaceae spp. Streptococcus spp. Staphylococcus aureus , non-aureus staphylococci (NAS) Bacillus spp. and Others. Mixed effects conditional logistic regression models were applied to quantify the association between the prevalence of each bacterial group and the herd zone and bulk milk tank somatic cell counts (BMTSCC). Of the 205 isolates, 102 (50%) originated from mastitis cases, and 103 (50%) from controls. Staphylococci were the most prevalent (NAS 32% and S. aureus 11%). Contagious mastitis bacteria were more prevalent in Victoria compared to Queensland dairy herds. NAS species ( P & 0.001) were less prevalent in herds with BMTSCC & ,000 cells/mL compared with herds with low BMTSCC ≤150,000 cells/mL. Enterobacteriaceae and Streptococcus spp. groups showed high resistance rates to 1 (51 and 47%, respectively), and 2 (11 and 23%, respectively), antimicrobials. More than one third of the Enterobacteriaceae (48%) and Others (43%) groups spp. were resistant to at least three antimicrobials. This study provided a unique opportunity to investigate the prevalence of mastitis-associated bacteria in clinical cases and in apparently healthy controls. The findings of this study help inform mastitis control and antimicrobial stewardship programs aimed to reduce the prevalence of mastitis and antimicrobial resistance in dairy herds.
Publisher: Springer Science and Business Media LLC
Date: 09-2013
Abstract: In this report we have explored the genomic and microbiological basis for a sustained increase in bloodstream infections at a major Australian hospital caused by Enterococcus faecium multi-locus sequence type (ST) 203, an outbreak strain that has largely replaced a predecessor ST17 sequence type. To establish a ST203 reference sequence we fully assembled and annotated the genome of Aus0085, a 2009 vancomycin-resistant Enterococcus faecium (VREfm) bloodstream isolate, and the first ex le of a completed ST203 genome. Aus0085 has a 3.2 Mb genome, comprising a 2.9 Mb circular chromosome and six circular plasmids (2 kb–130 kb). Twelve percent of the 3222 coding sequences (CDS) in Aus0085 are not present in ST17 E. faecium Aus0004 and ST18 E. faecium TX16. Extending this comparison to an additional 12 ST17 and 14 ST203 E. faecium hospital isolate genomes revealed only six genomic regions spanning 41 kb that were present in all ST203 and absent from all ST17 genomes. The 40 CDS have predicted functions that include ion transport, riboflavin metabolism and two phosphotransferase systems. Comparison of the vancomycin resistance-conferring Tn 1549 transposon between Aus0004 and Aus0085 revealed differences in transposon length and insertion site, and van locus sequence variation that correlated with a higher vancomycin MIC in Aus0085. Additional phenotype comparisons between ST17 and ST203 isolates showed that while there were no differences in biofilm-formation and killing of Galleria mellonella , ST203 isolates grew significantly faster and out-competed ST17 isolates in growth assays. Here we have fully assembled and annotated the first ST203 genome, and then characterized the genomic differences between ST17 and ST203 E. faecium . We also show that ST203 E. faecium are faster growing and can out-compete ST17 E. faecium . While a causal genetic basis for these phenotype differences is not provided here, this study revealed conserved genetic differences between the two clones, differences that can now be tested to explain the molecular basis for the success and emergence of ST203 E. faecium .
Publisher: MDPI AG
Date: 27-04-2020
DOI: 10.3390/MICROORGANISMS8050635
Abstract: Microbiota in the kangaroo gut degrade cellulose, contributing to the kangaroo’s energy and survival. In this preliminary study, to discover more about the gut microbes that contribute to the survival of kangaroos, cellulose-degrading bacteria were isolated from kangaroo scats by selection on solidified media containing carboxymethyl cellulose as the main carbon source. One frequently occurring aerobic bacterium was Siccibacter turicensis, a microbe previously isolated in fruit powder and from a patient with angular cheilitis. The whole genome sequence of the kangaroo isolate was obtained using the Illumina MiSeq platform. Its sequence shared 97.98% identity of the S. turicensis Type strain, and the ability of the Type strain to degrade cellulose was confirmed. Analysis of the genomic data focused on the cellulose operon. In addition to genes from the operon, we suggest that a gene following the operon may have an important role in regulating cellulose metabolism by signal transduction. This is the first report of S. turicensis found within microbiota of the animal gut. Because of its frequent presence in the kangaroo gut, we suggest that S. turicensis plays a role in cellulose digestion for kangaroos.
Publisher: Wiley
Date: 20-06-2006
DOI: 10.1111/J.1365-2052.2006.01468.X
Abstract: RNA interference (RNAi) mediated by DNA-based expression of short hairpin RNA (shRNA) is a powerful method of sequence-specific gene knockdown. A number of vectors for expression of shRNA have been developed that feature promoters from RNA polymerase III (pol III)-transcribed genes of mouse or human origin. To advance the use of RNAi as a tool for functional genomic research and for future development of specific therapeutics in the bovine species, we have developed shRNA expression vectors that feature novel bovine RNA pol III promoters. We characterized two bovine U6 small nuclear RNA (snRNA) promoters (bU6-2 and bU6-3) and a bovine 7SK snRNA promoter (b7SK). We compared the efficiency of each of these promoters to express shRNA molecules. Promoter activity was measured in the context of RNAi by targeting and suppressing the reporter gene encoding enhanced green fluorescent protein. Results show that the b7SK promoter induced the greatest level of suppression in a range of cell lines. The comparison of these bovine promoters in shRNA expression is an important component for the future development of bovine-specific RNAi-based research.
Publisher: EDP Sciences
Date: 25-11-2009
Publisher: Wiley
Date: 2021
DOI: 10.1002/CTI2.1233
Publisher: Public Library of Science (PLoS)
Date: 03-04-2019
Publisher: Informa UK Limited
Date: 04-07-2007
DOI: 10.1080/10495390600867515
Abstract: RNA interference (RNAi) is a powerful method of sequence-specific gene knockdown that can be mediated by DNA-based expression of short hairpin RNA (shRNA) molecules. A number of vectors for expression of shRNA have been developed with promoters for a small group of RNA polymerase III (pol III) transcripts of either mouse or human origin. To advance the use of RNAi as a tool for functional genomic research and future development of specific therapeutics in the chicken species, we have developed shRNA expression vectors featuring chicken U6 small nuclear RNA (snRNA) promoters. These sequences were identified based on the presence of promoter element sequence motifs upstream of matching snRNA sequences that are characteristic of these types of pol III promoters. To develop suitable shRNA expression vectors specifically for chicken functional genomic RNAi applications, we compared the efficiency of each of these promoters to express shRNA molecules. Promoter activity was measured in the context of RNAi by targeting and silencing the reporter gene encoding the enhanced green fluorescent protein (EGFP). Plasmids containing one of four identified chicken U6 promoters gave a similar degree of knockdown in DF-1 cells (chicken) although, there was some variability in Vero cells (monkey). Because the chicken promoters were not stronger than the benchmark mouse U6 promoter, we suggest that the promoter sequence and structure is more important in determining efficiency in vitro rather than its species origin.
Publisher: Elsevier BV
Date: 10-2005
DOI: 10.1016/J.MICINF.2005.05.002
Abstract: Corynebacterium pseudotuberculosis is the etiological agent of the sheep disease caseous lymphadenitis. We have developed a promoter reporter system for this organism based on expression of the green fluorescent protein (gfp) gene from Aequorea victoria. A promoterless vector, pSM20, containing the gfp gene was constructed, and promoters were inserted upstream of the gfp gene. Upon transformation into C. pseudotuberculosis, fluorescence could be visualised by fluorescence microscopy, and relative promoter strength measured by flow cytometry. The usefulness of this system for measuring changes in gene expression was demonstrated by measuring fluorescence levels of heat shocked C. pseudotuberculosis carrying a dnaK promoter construct. Replication of C. pseudotuberculosis within J774 macrophages could be monitored by fluorescence microscopy. The establishment of the system allowed the use of differential fluorescence to identify genes that showed up-regulation following macrophage infection. Genes coding for a non-ribosomal peptide synthetase and the beta chain of a propionyl CoA carboxylase were identified as possessing promoters that demonstrated enhanced activity following macrophage infection by C. pseudotuberculosis.
Publisher: Springer Science and Business Media LLC
Date: 04-02-2021
DOI: 10.1038/S41598-021-82357-3
Abstract: Streptococcus uberis is one of the most frequent mastitis-causing pathogens isolated from dairy cows. Further understanding of S. uberis genetics may help elucidate the disease pathogenesis. We compared the genomes of S. uberis isolates cultured from dairy cows located in distinctly different geographic regions of Australia. All isolates had novel multi locus sequence types (MLST) indicating a highly erse population of S. uberis . Global clonal complexes (GCC) were more conserved. GCC ST86 and GCC ST143 represented 30% of the total isolates ( n = 27) and were clustered within different geographic regions. Core genome phylogeny revealed low phylogenetic clustering by region, isolation source, and MLST. Identification of putative sortase ( srtA ) substrates and generation of a custom putative virulence factor database revealed genes which may explain the affinity of S. uberis for mammary tissue, evasion of antimicrobial efforts and disease pathogenesis. Of 27 isolates, four contained antibiotic resistance genes including an antimicrobial resistance cluster containing mel / mef ( A ), mrsE , vatD , lnuD , and transposon-mediated lnuC was also identified. These are novel genes for S. uberis , which suggests interspecies lateral gene transfer. The presence of resistance genes across the two geographic regions tested within one country supports the need for a careful, tailored, implementation and monitoring of antimicrobial stewardship.
Publisher: Informa UK Limited
Date: 03-05-2016
DOI: 10.1080/03079457.2016.1158781
Abstract: Clostridium perfringens is the primary causative agent of avian necrotic enteritis. Our understanding of the pathogenesis of this economically important disease has been enhanced by the discovery of C. perfringens NetB toxin, which belongs to the α-haemolysin family of β-pore-forming toxins. In a chicken disease model, the analysis of an isogenic set of strains comprising the wild type, a netB mutant, and its complemented derivative, fulfilled molecular Koch's postulates and revealed that NetB was essential for disease. These results were consistent with epidemiological surveys, which generally found that there was a higher prevalence of netB carriage in C. perfringens isolates from diseased poultry compared to healthy birds. The netB gene has been shown to be located on large conjugative plasmids that are closely related to other toxin plasmids from C. perfringens, which has potential implications for the epidemiology of necrotic enteritis infections. The crystal structures of both monomeric NetB and the heptameric NetB pore have been determined, the latter revealed a central pore diameter of approximately 26 Å. Finally, it has been shown that vaccine preparations that include NetB can protect chickens against disease and a series of single amino acid substitution derivatives of NetB that have potential value for vaccine formulations have been isolated and analysed. It is likely that NetB will be an important antigen to include in an effective, commercially viable, necrotic enteritis vaccine.
Publisher: American Society for Microbiology
Date: 03-2004
DOI: 10.1128/JCM.42.3.1345-1347.2003
Abstract: Clostridium perfringens causes necrotic enteritis in chickens, and alpha-toxin has been suggested to be a key virulence determinant. Analysis of the alpha-toxin of 25 chicken-derived C. perfringens strains demonstrated high homology to mammal-derived strains rather than to the only avian-derived C. perfringens alpha-toxin sequence reported previously.
Publisher: Elsevier BV
Date: 10-2020
Publisher: MDPI AG
Date: 29-01-2019
Abstract: Clostridium perfringens causes a wide range of diseases in a variety of hosts, due to the production of a erse set of toxins and extracellular enzymes. The C. perfringens toxins play an important role in pathogenesis, such that the presence and absence of the toxins is used as a typing scheme for the species. In recent years, several new toxins have been discovered that have been shown to be essential or highly correlated to diseases these include binary enterotoxin (BecAB), NetB and NetF. In the current study, genome sequence analysis of C. perfringens isolates from erse sources revealed several putative novel toxin homologs, some of which appeared to be associated with potential mobile genetic elements, including transposons and plasmids. Four novel toxin homologs encoding proteins related to the pore-forming Leukocidin/Hemolysin family were found in type A and G isolates. Two novel toxin homologs encoding proteins related to the epsilon aerolysin-like toxin family were identified in Type A and F isolates from humans, contaminated food and turkeys. A novel set of proteins related to clostridial binary toxins was also identified. While phenotypic characterisation is required before any of these homologs can be established as functional toxins, the in silico identification of these novel homologs on mobile genetic elements suggests the potential toxin reservoir of C. perfringens may be much larger than previously thought.
Publisher: Elsevier BV
Date: 10-2018
Publisher: American Society for Microbiology
Date: 12-10-2017
Abstract: Lactobacillus plantarum strain A6, a strong acid producer, was isolated from a Vietnamese fermented sausage (nem chua). Here, we report the genome sequence of this strain (3,368,579 bp).
Publisher: Mary Ann Liebert Inc
Date: 08-2018
Abstract: C ylobacter jejuni and C ylobacter coli play a major role in bacteria-related foodborne illness in humans. Recently, a newly identified species, C ylobacter hepaticus, was shown to be the causative agent of spotty liver disease in chickens. The pathogenic potential of C. hepaticus in humans is unknown. This new species contains genes usually used to detect C. jejuni and C. coli in DNA-based detection methods, such as the hippuricase (hipO) gene and the glyA (serine hydroxymethyltransferase) gene, with a high degree of similarity. Therefore, polymerase chain reaction (PCR) primers used to detect these species need to be evaluated carefully to prevent misidentification of these important C ylobacter species. A multiplex PCR was developed and optimized to simultaneously and specifically identify the presence of C. jejuni, C. coli, and C. hepaticus in chicken s les containing high-complexity microbiota. The assay represents a new diagnostic tool for investigating the epidemiology of C ylobacter colonization in poultry and environmental s les. It may also be applicable to the investigation of C ylobacter contamination in food and in outbreaks of c ylobacteriosis.
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Elsevier BV
Date: 02-2017
DOI: 10.1016/J.VETMIC.2016.12.033
Abstract: Spotty liver disease (SLD) in chickens can present with variable impacts on mortality and production, ranging from sporadic mortalities of in idual birds and no notable impact on production to severe reduction in egg output and increased mortality in layer flocks of greater than 1% per day. It was first described over 60 years ago and there have been sporadic reports of the disease throughout the intervening decades, particularly in the US, UK and Germany. Recently it has become of increasing concern as outbreaks of the disease have occurred more frequently, particularly in the Australian poultry industry. An understanding of the causes of the disease has proven elusive. However, recent studies of SLD have strongly implicated a novel C ylobacter species, C ylobacter hepaticus, as the causative agent. Here we demonstrate that C. hepaticus is highly invasive in LMH cells, an immortalised chicken hepatoma cell line, and can induce disease when orally delivered to mature layer birds. Challenged birds developed liver lesions, typical of those seen in field clinical cases, within 5days of challenge. The bacterium used to challenge the birds could be recovered from the diseased liver and from bile, thus demonstrating that C. hepaticus is the causative agent of chicken SLD.
Publisher: American Society for Microbiology
Date: 21-11-2014
DOI: 10.1128/MICROBIOLSPEC.PLAS-0024-2014
Abstract: Plasmid-encoded virulence factors are important in the pathogenesis of diseases caused by spore-forming bacteria. Unlike many other bacteria, the most common virulence factors encoded by plasmids in Clostridium and Bacillus species are protein toxins. Clostridium perfringens causes several histotoxic and enterotoxin diseases in both humans and animals and produces a broad range of toxins, including many pore-forming toxins such as C. perfringens enterotoxin, epsilon-toxin, beta-toxin, and NetB. Genetic studies have led to the determination of the role of these toxins in disease pathogenesis. The genes for these toxins are generally carried on large conjugative plasmids that have common core replication, maintenance, and conjugation regions. There is considerable functional information available about the unique tcp conjugation locus carried by these plasmids, but less is known about plasmid maintenance. The latter is intriguing because many C. perfringens isolates stably maintain up to four different, but closely related, toxin plasmids. Toxin genes may also be plasmid-encoded in the neurotoxic clostridia. The tetanus toxin gene is located on a plasmid in Clostridium tetani , but the botulinum toxin genes may be chromosomal, plasmid-determined, or located on bacteriophages in Clostridium botulinum . In Bacillus anthracis it is well established that virulence is plasmid determined, with anthrax toxin genes located on pXO1 and capsule genes on a separate plasmid, pXO2. Orthologs of these plasmids are also found in other members of the Bacillus cereus group such as B. cereus and Bacillus thuringiensis . In B. thuringiensis these plasmids may carry genes encoding one or more insecticidal toxins.
Publisher: Public Library of Science (PLoS)
Date: 31-12-2013
Publisher: Frontiers Media SA
Date: 19-02-2016
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: American Association of Avian Pathologists (AAAP)
Date: 03-2015
DOI: 10.1637/10774-011614-REG.1
Abstract: Necrotic enteritis (NE) is an important infectious disease in chickens. Predisposing factors play critical roles both in disease outbreaks in the field and in models for experimental induction of disease. Systematic manipulation and study of predisposing factors help to optimize methods for the experimental reproduction of disease. The nature of such factors may play a confounding role in challenge models and, therefore, warrant investigation to determine their importance in industry-relevant NE reproduction models. In the present study, we examined the roles of dietary fishmeal inclusion, Eimeria inoculation (E), and Clostridium perfringens challenge (C) on broiler growth performance and induction of NE infection. The results showed that E, preceding C, greatly increased the severity of NE induced in broiler chickens, but fishmeal addition played only a marginal role in the challenge model. Bird performance was significantly affected by all three factors during the 35-day experimental period. Fishmeal increased body weight, but statistically significant effects of fishmeal were not observed on feed conversion ratio (FCR) and feed intake. Both Eimeria and C. perfringens significantly reduced body weight gain and feed intake. E but not C led to significantly poorer FCR. These findings indicate that dietary fishmeal may be removed from the model to allow the performance results of challenged chicks to be equivalent to the performance of chicks in the field. In conclusion, the present study demonstrates that an NE challenge model without fishmeal is valid and removes bird performance bias in the model introduced by feeding high fishmeal diets, refining the model to facilitate the yield of more commercially relevant results.
Publisher: Springer Science and Business Media LLC
Date: 12-11-2020
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: Australia
Start Date: 11-2020
End Date: 11-2023
Amount: $390,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 12-2016
End Date: 02-2022
Amount: $450,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 06-2021
End Date: 06-2025
Amount: $989,000.00
Funder: Australian Research Council
View Funded Activity