ORCID Profile
0000-0003-4054-1947
Current Organisation
South Australian Health and Medical Research Institute
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Springer Science and Business Media LLC
Date: 17-11-2015
DOI: 10.1038/SREP16350
Abstract: Sequencing-based studies of the human faecal microbiota are increasingly common. Appropriate storage of s le material is essential to avoid the introduction of post-collection bias in microbial community composition. Rapid freezing to −80 °C is commonly considered to be best-practice. However, this is not feasible in many studies, particularly those involving s le collection in participants’ homes. We determined the extent to which a range of stabilisation and storage strategies maintained the composition of faecal microbial community structure relative to freezing to −80 °C. Refrigeration at 4 °C, storage at ambient temperature and the use of several common preservative buffers (RNAlater, OMNIgene.GUT, Tris-EDTA) were assessed relative to freezing. Following 72 hours of storage, faecal microbial composition was assessed by 16 S rRNA licon sequencing. Refrigeration was associated with no significant alteration in faecal microbiota ersity or composition. However, s les stored using other conditions showed substantial ergence compared to −80 °C control s les. Aside from refrigeration, the use of OMNIgene.GUT resulted in the least alteration, while the greatest change was seen in s les stored in Tris-EDTA buffer. The commercially available OMNIgene.GUT kit may provide an important alternative where refrigeration and cold chain transportation is not available.
Publisher: Frontiers Media SA
Date: 26-06-2019
Publisher: Walter de Gruyter GmbH
Date: 2010
DOI: 10.1515/JPM.2010.026
Abstract: Although premature infants are increasingly surviving the neonatal period, up to one-third develop bronchopulmonary dysplasia (BPD). Despite evidence that bacterial colonization of the neonatal respiratory tract by certain bacteria may be a risk factor in BPD development, little is known about the role these bacteria play. The aim of this study was to investigate the use of culture-independent molecular profiling methodologies to identify potential etiological agents in neonatal airway secretions. This study used terminal restriction fragment length polymorphism (T-RFLP) and clone sequence analyses to characterize bacterial species in endo-tracheal (ET) aspirates from eight intubated pre-term infants. A wide range of different bacteria was identified in the s les. Forty-seven T-RF band lengths were resolved in the s le set, with a range of 0-15 separate species in each patient. Clone sequence analyses confirmed the identity of in idual species detected by T-RFLP. We speculate that the identification of known opportunistic pathogens including S. aureus, Enterobacter sp., Moraxella catarrhalis, Pseudomonas aeruginosa and Streptococcus sp., within the airways of pre-term infants, might be causally related to the subsequent development of BPD. Further, we suggest that culture-independent techniques, such as T-RFLP, hold important potential for the characterization of neonatal conditions, such as BPD.
Publisher: Elsevier BV
Date: 09-2015
DOI: 10.1016/J.IJPORL.2015.07.013
Abstract: Indigenous Australian children have a high prevalence of otitis media with effusion (OME) and associated conductive hearing loss. Only three microbiological studies of middle ear fluid (MEF) from Indigenous Australian children with OME have been reported. All of these were reliant on culture or species-specific PCR assays. The aim of this study was to characterise the middle ear fluid (MEF), adenoid and nasopharyngeal (NP) microbiomes of Indigenous Australian children, using culture-independent 16S rRNA gene sequencing. MEF, NP swabs and adenoid specimens were collected from 11 children in the Alice Springs region of Central Australia. Bacterial communities in these specimens were characterised using 16S rRNA gene sequencing. The microbiota in MEF s les were dominated (>50% relative abundance) by operational taxonomic units (OTUs) consistent with Alloiococcus otitidis (6/11), Haemophilus influenzae (3/11) or Streptococcus sp. (specifically, Mitis group streptococci which includes Streptococcus pneumoniae) (1/11). Anatomical site selectivity was indicated by the presence of a single conserved Haemophilus OTU in 7/11 MEF s les. In comparison, there were ten distinct Haemophilus OTUs observed across the NP and adenoid s les. Despite significant differences between the MEF and NP/adenoid microbiomes, Streptococcus sp., H. influenzae and Moraxella catarrhalis OTUs were common to all s le types. Co-occurrence of classical otopathogens in paired MEF and NP/Adenoid s les is consistent with earlier culture-based studies. These data highlight the need to further assess H. influenzae traits important in otitis media and to understand the role of canal flora, especially A. otitidis, in populations with a high prevalence of tympanic membrane perforation.
Publisher: American Society for Microbiology
Date: 29-10-2019
Abstract: Dietary flavonoids, which have been implicated in lowering chronic disease risk and improving blood pressure, represent a erse group of polyphenolic compounds found in many commonly consumed foods such as tea, red wine, apples, and berries. The bioactivity and bioavailability of more dietary flavonoids can be influenced by gastrointestinal microbiome metabolism. With demonstrated prebiotic and antimicrobial effects in in vitro and in animal models, it is surprising that there are not many human studies investigating the role dietary flavonoids play in shaping the gastrointestinal microbiome. Our analysis revealed patterns of community assembly that uniquely and independently characterize an in idual’s exposure to various flavonoid compounds. Furthermore, this study confirmed, independent from effects of other dietary and lifestyle factors included in the multivariate-adjusted model, that flavonoid intake is associated with microbial community assembly.
Publisher: Elsevier BV
Date: 09-2011
Publisher: Elsevier BV
Date: 08-2010
Publisher: Proceedings of the National Academy of Sciences
Date: 16-09-2019
Abstract: The gut microbiome is an established regulator of aspects of host metabolism, such as glucose handling. Despite the known impacts of the gut microbiota on host glucose homeostasis, the underlying mechanisms are unknown. The gut microbiome is also a potent mediator of gut-derived serotonin synthesis, and this peripheral source of serotonin is itself a regulator of glucose homeostasis. Here, we determined whether the gut microbiome influences glucose homeostasis through effects on gut-derived serotonin. Using both pharmacological inhibition and genetic deletion of gut-derived serotonin synthesis, we find that the improvements in host glucose handling caused by antibiotic-induced changes in microbiota composition are dependent on the synthesis of peripheral serotonin.
Publisher: Elsevier BV
Date: 03-2019
Publisher: American Society for Microbiology
Date: 11-2004
DOI: 10.1128/JCM.42.11.5176-5183.2004
Abstract: Progressive loss of lung function resulting from the inflammatory response to bacterial colonization is the leading cause of mortality in cystic fibrosis (CF) patients. A greater understanding of these bacterial infections is needed to improve lung disease management. As culture-based diagnoses are associated with fundamental drawbacks, we used terminal restriction fragment (T-RF) length polymorphism profiling and 16S rRNA clone data to characterize, without prior cultivation, the bacterial community in 71 sputa from 34 adult CF patients. Nineteen species from 15 genera were identified in 53 16S rRNA clones from three patients. Of these, 15 species have not previously been reported in CF lung infections and many were species requiring strict anaerobic conditions for growth. The species richness and evenness were determined from the T-RF length and volume for the 71 profiles. Species richness was on average 13.3 ± 7.9 per s le and 13.4 ± 6.7 per patient. On average, the T-RF bands of the lowest and highest volumes represented 0.6 and 59.2% of the total volume in each profile, respectively. The second through fifth most dominant T-RF bands represented 15.3, 7.5, 4.7, and 2.8% of the total profile volume, respectively. On average, the remaining T-RF bands represented 10.2% of the total profile volume. The T-RF band corresponding to Pseudomonas aeruginosa had the highest volume in 61.1% of the s les. However, 18 other T-RF band lengths were dominant in at least one s le. In conclusion, this reveals the enormous complexity of bacteria within the CF lung. Although their significance is yet to be determined, these findings alter our perception of CF lung infections.
Publisher: Elsevier BV
Date: 05-2018
DOI: 10.1016/J.TIM.2017.10.009
Abstract: The global spread of antibiotic-resistant pathogens threatens to increase the mortality of cancer patients significantly. We propose that chemotherapy contributes to the emergence of antibiotic-resistant bacteria within the gut and, in combination with antibiotics, drives pathogen overgrowth and translocation into the bloodstream. In our model, these processes are mediated by the effects of chemotherapy on bacterial mutagenesis and horizontal gene transfer, the disruption of commensal gut microbiology, and alterations to host physiology. Clinically, this model manifests as a cycle of recurrent sepsis, with each episode involving ever more resistant organisms and requiring increasingly broad-spectrum antimicrobial therapy. Therapies that restore the gut microbiota following chemotherapy or antibiotics could provide a means to break this cycle of infection and treatment failure.
Publisher: Oxford University Press (OUP)
Date: 16-10-2015
DOI: 10.1093/CID/CIU813
Publisher: Elsevier BV
Date: 04-2019
DOI: 10.1016/J.CLNESP.2018.12.088
Abstract: Almonds are a rich source of bioactive components. This study examined the effects of daily almond consumption on glycaemic regulation, liver fat concentration and function, adiposity, systemic inflammation and cardiometabolic health. 76 adults with elevated risk of type 2 diabetes (T2D) or T2D (age: 60.7 ± 7.7 years, body mass index: 33.8 ± 5.6 kg/m No group differential effects were observed on HbA1c, GV, body weight and composition, liver fat and aminotransferases, cardio-metabolic health and inflammatory markers (all P > 0.05). For serum TC/HDL-C ratio a significant gender × treatment × time interaction occurred (P < 0.01), such that in women TC/HDL-C ratio was significantly reduced after AS compared to BS (-0.36 [0.26] mmol/L [n = 14] vs. -0.14 [0.32] mmol/L [n = 17] P = 0.05), but not in men (P = 0.52). Compared to BS, AS consumed between meals did not substantially alter glycaemic regulation, liver fat or function, adiposity, and metabolic health and inflammatory markers. Serum TC/HDL-C ratio improved in women, but not in men with AS but as this sub-analysis was not defined a priori the results should be interpreted with caution. Further research should examine the longer-term health effects of regular almond consumption and differential gender responses. Australia New Zealand Clinical Trial Registry: ACTRN12616000571471 (www.anzctr.org.au).
Publisher: American Society for Microbiology
Date: 2010
DOI: 10.1128/JCM.01324-09
Abstract: S ling of the lower airways of the adult cystic fibrosis (CF) lung has received insufficient detailed consideration, with the importance of s ling strategies for bacteriological outcome not known. Although spontaneously expectorated sputum (SES) s les are often used for diagnostic bacteriological analysis, induced sputum (IS) methods have advantages. This study examined whether significant differences in bacterial content were detected when using a culture-independent, molecular profiling technique to analyze SES or IS s les. Moreover, this work examined what trends relating to bacterial species distributions and reproducibility were found in sequentially induced sputum s les and what implications this has for pathogen detection. Terminal restriction fragment length polymorphism (T-RFLP) analysis was performed on a SES s le and 4 subsequent IS s les taken at 5-min intervals from 10 clinically stable, adult CF patients. This was repeated over 3 s ling days, with variability between s les, induction periods, and s ling days determined. A erse range of bacterial species, including potentially novel pathogens, was found. No significant difference in bacterial content was observed for either SES or serial IS s les. On average, the analysis of a single s le from any time point resolved ∼58% of total bacterial ersity achieved by analysis of an SES s le and 4 subsequent IS s les. The reliance on analysis of a single respiratory s le was not sufficient for the detection of recognized CF pathogens in all instances. Close correlation between T-RFLP and microbiological data in the detection of key species indicates the importance of these findings in routine diagnostics for the detection of recognized and novel CF pathogens.
Publisher: American Society for Microbiology
Date: 17-08-2017
Abstract: Enterobacter cloacae is a common member of the gut microbiota in healthy in iduals. However, it is also an opportunistic pathogen, capable of causing bacteremia. We report the draft genomes of two Enterobacter cloacae subspecies cloacae strains isolated from hematology patients with bacteremia. Both isolates carry genes encoding extended-spectrum β-lactamases.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 11-2017
Publisher: Public Library of Science (PLoS)
Date: 17-03-2015
Publisher: American Thoracic Society
Date: 08-2019
Publisher: Public Library of Science (PLoS)
Date: 25-09-2013
Publisher: SAGE Publications
Date: 07-2011
DOI: 10.2500/AJRA.2011.25.3628
Abstract: Chronic rhinosinusitis (CRS) with or without polyps is a common chronic upper airway condition of multifactorial origin. Fundamental to effective treatment of any infection is the ability to accurately characterize the underlying cause. Many studies have shown that only a small fraction of the total range of bacterial species present in CRS is detected through conventional culture-dependent techniques. Consequently, culture data are often unrepresentative of the true ersity of the microbial community within the s le. These drawbacks, along with the length of time required to complete the analysis, strongly support the development of alternative means of assessing which bacterial species are present. As such, molecular microbiological approaches that assess the content of clinical s les in a culture-independent manner could significantly enhance the range and quality of data obtained routinely from such s les. We aimed to characterize the bacterial ersity present in tissue and mucus s les taken from the CRS setting using molecular nonculture-dependent techniques. Through 16S ribosomal RNA (rRNA) gene clone sequencing and terminal restriction fragment length polymorphism (T-RFLP) analysis, the bacteria present in 70 clinical s les from 43 CRS patients undergoing endoscopic sinus surgery were characterized. Bacterial T-RFLP profiles were generated for 70 of 73 s les and a total of 48 separate bands were detected. Species belonging to 34 genera were identified as present by clone sequence analysis. Of the species detected, those within the genera Pseudomonas, Citrobacter, Haemophilus, Propionibacterium, Staphylococcus, and Streptococcus were found numerically dominant, with Pseudomonas aeruginosa the most frequently detected species. This study has validated the use of the culture-independent technique T-RFLP in sinonasal s les. Preliminary characterization of the microbial ersity in CRS suggests a complex range of common and novel bacterial species within the upper airway in CRS, providing further evidence for the polymicrobial etiology of CRS.
Publisher: Public Library of Science (PLoS)
Date: 23-06-2014
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 2018
Publisher: Informa UK Limited
Date: 04-01-2019
Publisher: Springer Science and Business Media LLC
Date: 10-11-2015
Publisher: Public Library of Science (PLoS)
Date: 05-2014
Publisher: Frontiers Media SA
Date: 16-04-2019
Publisher: Oxford University Press (OUP)
Date: 12-2009
DOI: 10.1002/IBD.21022
Abstract: Pouchitis is believed to occur as a reaction to dysbiosis. In this study we assessed differences between mucosal bacterial communities cultured from noninflamed and inflamed ileal pouches. Thirty-two ileal pouch patients, 22 with ulcerative colitis (UC) and 10 with familial adenomatous polyposis (FAP), underwent symptomatic, endoscopic, and histological assessment. The Objective Pouchitis Score (OPS) and the Pouch Disease Activity Index (PDAI) were used to diagnose pouchitis. Seven UC patients had pouchitis (UC+), 15 had a noninflamed pouch (UC-), 9 had a noninflamed pouch (FAP-), and 1 FAP patient had pouchitis (FAP+). Biopsies taken from the ileal mucosa of the pouch were cultured under aerobic and anaerobic conditions. Following standardized DNA extraction a polymerase chain reaction (PCR) was performed to generate 16S rRNA gene products. A "fingerprint" of the bacterial community within each s le was created using terminal-restriction fragment length polymorphism (T-RFLP) profiling. Species richness and evenness were determined using T-RF band lengths and relative band intensities. From the 64 DNA s les, 834 bands were detected, of which 179 represented different species (operational taxonomic units [OTUs]). The average species richness for the FAP-, FAP+, UC-, and UC+ groups was 26, 35, 23.9, and 29.6 per patient, with the average species ersity within the groups of 10.6, 29, 8.3, and 11.4, respectively. Similar trends were observed when the anaerobic and aerobic-derived bacterial groups were analyzed separately. No significant differences were found between the bacterial cultures derived from any of the clinical groups or between pouchitis and nonpouchitis patients.
Publisher: Elsevier BV
Date: 05-2015
Publisher: BMJ
Date: 19-11-2012
Publisher: Elsevier BV
Date: 09-2017
Publisher: Elsevier BV
Date: 11-2010
DOI: 10.1111/J.1469-0691.2010.03189.X
Abstract: The DNA-based techniques used to detect bacteria in clinical s les are unable to discriminate between live bacteria, dead bacteria, and extracellular DNA. This failure to limit analysis to viable bacterial cells represents a significant problem, leading to false-positive results, as well as a failure to resolve the impact of antimicrobial therapy. The use of propidium monoazide treatment significantly reduces the contribution of dead cells and extracellular DNA to such culture-independent analyses. Here, the increased ability to resolve the impact of antibiotic therapy on Pseudomonas aeruginosa load in cystic fibrosis respiratory s les reveals statistically significant changes that would otherwise go undetected.
Publisher: Springer Science and Business Media LLC
Date: 05-05-2013
Publisher: Elsevier BV
Date: 02-2018
Publisher: Wiley
Date: 25-01-2012
Publisher: BMJ
Date: 15-06-2012
Publisher: BMJ
Date: 17-07-2015
Publisher: Springer Science and Business Media LLC
Date: 18-03-2010
DOI: 10.1007/S10096-010-0891-5
Abstract: Spontaneous bacterial peritonitis (SBP) is a severe complication of liver disease. A significant proportion of patients have culture-negative ascites, despite having similar signs, symptoms and mortality to those with SBP. Therefore, empirical antibiotic treatment for infection is often started without knowledge of the causative organisms. Here, we investigated the potential of molecular techniques to provide rapid and accurate characterisation of the bacteria present in ascitic fluid. Ascites s les were obtained from 29 cirrhotic patients undergoing clinically indicated therapeutic paracentesis. Bacterial content was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis, quantitative polymerase chain reaction (PCR) and 16S ribosomal clone sequence analysis. Bacterial signal was detected in all s les, compared to three out of ten using standard methods. Bacterial loads ranged from 5.5 x 10(2) to 5.4 x 10(7) cfu/ml, with a mean value of 1.9 x 10(6) cfu/ml (standard deviation +/- 9.6 x 10(6) cfu/ml). In all but one instance, bacterial species identified by culture were also confirmed by molecular analyses. Preliminary data presented here suggests that culture-independent, molecular analyses could provide rapid characterisation of the bacterial content of ascites fluid, providing a basis for the investigation of SBP development and allowing early and targeted antibiotic intervention.
Publisher: Informa UK Limited
Date: 03-2010
DOI: 10.1586/ERM.09.81
Abstract: Lower respiratory tract bacterial infections, such as those associated with cystic fibrosis lung disease, represent a major healthcare burden. Treatment strategies are currently informed by culture-based routine diagnostics whose limitations, including an inability to isolate all potentially clinically significant bacterial species present in a s le, are well documented. Some advances have resulted from the introduction of culture-independent molecular assays for the detection of specific pathogens. However, the application of bacterial community profiling techniques to the characterization of these infections has revealed much higher levels of microbial ersity than previously recognized. These findings are leading to a fundamental shift in the way such infections are considered. Increasingly, polymicrobial infections are being viewed as complex communities of interacting organisms, with dynamic processes key to their pathogenicity. Such a model requires an analytical strategy that provides insight into the interactions of all members of the infective community. The rapid advance in sequencing technology, along with protocols that limit analysis to viable bacterial cells, are for the first time providing an opportunity to gain such insight.
Publisher: Elsevier BV
Date: 08-2019
DOI: 10.1016/J.DIAGMICROBIO.2019.02.016
Abstract: Staphylococcus aureus in blood cultures is rarely considered a contaminant. We report a case of intra-laboratory contamination between blood culture bottles which was confirmed by whole genome sequencing, highlighting the importance of molecular analysis in the clinical laboratory setting.
Publisher: Informa UK Limited
Date: 03-2011
DOI: 10.1586/ERM.10.117
Publisher: Springer Science and Business Media LLC
Date: 25-06-2014
DOI: 10.1038/SREP05437
Publisher: Elsevier BV
Date: 12-2017
DOI: 10.1016/J.JPEDS.2017.08.070
Abstract: To assess whether features of the infant intestinal microbiome, including the carriage of toxigenic bacteria, are associated with sudden infant death syndrome (SIDS). We undertook a case-controlled analysis of fecal microbiology in SIDS. Fecal material was obtained from 44 cases and 44 aged-matched controls. Microbiota composition was determined by 16S ribosomal RNA gene licon sequencing and comparisons between cases and controls made based on both bacterial alpha ersity measures and unconstrained ordination. Specific quantitative polymerase chain reaction assays were used to determine intestinal carriage of Staphylococcus aureus, toxigenic Clostridium difficile, and pathogenic and nonpathogenic Escherichia coli. The microbial composition for the study population as a whole was consistent with previous studies of infants <12 months of age, with a correlation between alpha ersity and age (r We found no evidence of an association between altered intestinal microbiology and SIDS, or to support the development of strategies to reduce the incidence of SIDS that target intestinal microbiology.
Publisher: Oxford University Press (OUP)
Date: 26-04-2013
DOI: 10.1093/CID/CIT270
Publisher: Elsevier BV
Date: 07-2015
Publisher: Springer Science and Business Media LLC
Date: 19-04-2016
DOI: 10.1038/MP.2016.46
Publisher: Springer Science and Business Media LLC
Date: 29-11-2012
Publisher: Springer Science and Business Media LLC
Date: 23-04-2019
DOI: 10.1038/S41598-018-38055-8
Abstract: Converging evidence supports the involvement of pro-inflammatory pathways and the gut microbiome in major depressive disorder (MDD). Pre-clinical and clinical studies suggest that decreasing pro-inflammatory signaling may provide clinical benefit in MDD. In this study, we used the chronic unpredictable stress (CUS) paradigm to assess whether mice lacking the pro-inflammatory caspase 1, interferon gamma-receptor, and nitric oxide synthase ( Casp1, Ifngr, Nos2 ) −/− present altered depressive- and anxiety-like behaviour at baseline and in response to CUS. In comparison to wild-type (wt) mice, ( Casp1, Ifngr, Nos2 ) −/− mice displayed decreased depressive- and anxiety-like behaviour, and increased hedonic-like behaviour and locomotor activity at baseline, and resistance to developing anhedonic-like behaviour and a heightened emotional state following stress. Plasma levels of ACTH and CORT did not differ between the triple knockout and wt mice following stress. The faecal microbiome of ( Casp1, Ifngr, Nos2 ) −/− mice differed from that of wt mice at baseline and displayed reduced changes in response to chronic stress. Our results demonstrate that simultaneous deficit in multiple pro-inflammatory pathways has antidepressant-like effects at baseline, and confers resilience to stress-induced anhedonic-like behaviour. Moreover, accompanying changes in the gut microbiome composition suggest that CASP1, IFNGR and NOS2 play a role in maintaining microbiome homeostasis.
Publisher: Springer Science and Business Media LLC
Date: 06-2005
Publisher: American Thoracic Society
Date: 05-2014
Publisher: Informa UK Limited
Date: 03-2010
Publisher: Wiley
Date: 23-09-2016
DOI: 10.1002/PPUL.23544
Publisher: Elsevier BV
Date: 04-2019
Publisher: Springer Science and Business Media LLC
Date: 12-2010
DOI: 10.1007/BF03256391
Publisher: American Society for Microbiology
Date: 12-2013
DOI: 10.1128/JCM.02164-13
Abstract: Primary ciliary dyskinesia (PCD) is a genetic disease characterized by abnormalities in ciliary function, leading to compromised airway clearance and chronic bacterial infection of the upper and lower airways. The compositions of these infections and the relationships between their characteristics and disease presentation are poorly defined. We describe here the first systematic culture-independent evaluation of lower airway bacteriology in PCD. Thirty-three airway s les (26 from sputum, 7 from bronchoalveolar lavage [BAL] fluid) were collected from 24 PCD patients aged 4 to 73 years. 16S rRNA quantitative PCR and pyrosequencing were used to determine the bacterial loads and community compositions of the s les. Bacterial loads, which ranged from 1.3 × 10 4 to 5.2 × 10 9 CFU/ml, were positively correlated with age ( P = 0.002) but not lung function. An analysis of ∼7,000 16S rRNA sequences per s le identified bacterial species belonging to 128 genera. The concurrently collected paired s les showed high bacterial community similarity. The mean relative abundance of the dominant genera was 64.5% (standard deviation [SD], 24.5), including taxa reported through standard diagnostic microbiology (members of the genera Pseudomonas , Haemophilus , and Streptococcus ) and those requiring specific ex vivo growth conditions (members of the genera Prevotella and Porphyromonas ). The significant correlations observed included a positive relationship between Pseudomonas aeruginosa relative abundance and age and a negative relationship between P. aeruginosa relative abundance and lung function. Members of the genus Ralstonia were also found to contribute substantially to the bacterial communities in a number of patients. Follow-up s les from a subset of patients revealed high levels of bacterial community temporal stability. The detailed microbiological characterization presented here provides a basis for the reassessment of the clinical management of PCD airway infections.
Publisher: Elsevier BV
Date: 02-2019
Publisher: Springer Science and Business Media LLC
Date: 19-04-2016
DOI: 10.1038/MP.2016.50
Publisher: American Society for Microbiology
Date: 31-12-2012
Abstract: Recent studies have greatly extended our understanding of the microbiota present in and on the human body. Here, advanced sequencing strategies have provided unprecedented analytical power. The important implications that the emerging data have for human health emphasize the need to intensify research in this area (D. A. Relman, Nature 486:194-195, 2012). It is already clear from these studies that the microbiotas characterized in different body locations of healthy in iduals are both complex and erse (The Human Microbiome Project Consortium, Nature 486:215-221). These studies also provide a point of contrast for investigations that aim to characterize the microbiota present in disease conditions. In this regard, Madan et al. (mBio 3(4):e00251-12, 2012) monitored the development over time of microbiota in the oropharynges and feces of neonates with cystic fibrosis and explored the potential for interactions between these complex microbial systems.
Publisher: Springer Science and Business Media LLC
Date: 18-07-2014
Publisher: Springer Science and Business Media LLC
Date: 15-08-2008
Publisher: Elsevier BV
Date: 05-2014
Publisher: Elsevier BV
Date: 2018
DOI: 10.1016/J.JACI.2017.03.044
Abstract: Asthma pathophysiology and treatment responsiveness are predicted by inflammatory phenotype. However, the relationship between airway microbiology and asthma phenotype is poorly understood. We aimed to characterize the airway microbiota in patients with symptomatic stable asthma and relate composition to airway inflammatory phenotype and other phenotypic characteristics. The microbial composition of induced sputum specimens collected from adult patients screened for a multicenter randomized controlled trial was determined by using 16S rRNA gene sequencing. Inflammatory phenotypes were defined by sputum neutrophil and eosinophil cell proportions. Microbiota were defined by using α- and β- ersity measures, and interphenotype differences were identified by using similarity of percentages, network analysis, and taxon fold change. Phenotypic predictors of airway microbiology were identified by using multivariate linear regression. Microbiota composition was determined in 167 participants and classified as eosinophilic (n = 84), neutrophilic (n = 14), paucigranulocytic (n = 60), or mixed neutrophilic-eosinophilic (n = 9) asthma phenotypes. Airway microbiology was significantly less erse (P = .022) and more dissimilar (P = .005) in neutrophilic compared with eosinophilic participants. Sputum neutrophil proportions, but not eosinophil proportions, correlated significantly with these ersity measures (α- ersity: Spearman r = -0.374, P < .001 β- ersity: r = 0.238, P = .002). Interphenotype differences were characterized by a greater frequency of pathogenic taxa at high relative abundance and reduced Streptococcus, Gemella, and Porphyromonas taxa relative abundance in patients with neutrophilic asthma. Multivariate regression confirmed that sputum neutrophil proportion was the strongest predictor of microbiota composition. Neutrophilic asthma is associated with airway microbiology that is significantly different from that seen in patients with other inflammatory phenotypes, particularly eosinophilic asthma. Differences in microbiota composition might influence the response to antimicrobial and steroid therapies and the risk of lung infection.
Publisher: Microbiology Society
Date: 11-2009
Abstract: The ability to characterize accurately the cause of infection is fundamental to effective treatment. The impact of any antimicrobial agents used to treat infection will, however, always be constrained by both the appropriateness of their use and our ability to determine their effectiveness. Traditional culture-based diagnostic microbiology is, in many cases, unable to provide this information. Molecular microbiological approaches that assess the content of clinical s les in a culture-independent manner promise to change dramatically the types of data that are obtained routinely from clinical s les. We argue that, in addition to the technical advance that these methodologies offer, a conceptual advance in the way that we reflect on the information generated is also required. Through the development of both of these advances, our understanding of infection, as well as the ways in which infections can be treated, may be improved. In the analysis of the microbiological content of certain clinical s les, such as blood, cerebrospinal fluid, brain and bone biopsy, culture-independent approaches have been well documented. Herein, we discuss how extensions to such studies can shape our understanding of infection at the many sites of the human body where a mixed flora, or in more ecological terms, a community of microbes, is present. To do this, we consider the underlying principles that underpin diagnostic systems, describe the ways in which these systems can be applied to community characterization, and discuss the significance of the data generated. We propose that at all locations within the human body where infection is routinely initiated within the context of a community of microbes, the same principles will apply. To consider this further, we take insights from areas such as the gut, oral cavity and skin. The main focus here is understanding respiratory tract infection, and specifically the infections of the cystic fibrosis lung. The impact that the use of culture-independent, molecular analyses will have on the way we approach the treatment of infections is also considered.
Publisher: Elsevier BV
Date: 12-2011
Publisher: Oxford University Press (OUP)
Date: 08-2015
DOI: 10.1136/POSTGRADMEDJ-2014-205826REP
Abstract: Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially h ering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
Publisher: Springer Science and Business Media LLC
Date: 09-12-2010
Publisher: Elsevier BV
Date: 10-2008
DOI: 10.1016/J.DIAGMICROBIO.2008.06.011
Abstract: Identification of bacteria in clinical s les is fundamental to combating infections. Modern molecular genetic approaches exploit nucleic acids signals from clinical s les. However, DNA-derived signals can originate from nonviable bacterial cells and, therefore, generate data that could be misinterpreted. Terminal restriction fragment length polymorphism profiling of cystic fibrosis sputum s les was combined with propidium monoazide (PMA) photo-induced cross-linking. PMA is highly membrane impermeant and is excluded from viable bacteria but readily penetrates dead cells. Exposure to a light source renders DNA in permeable cells incapable of contributing to polymerase chain reaction. PMA treatment was shown to effectively prevent dead bacteria, spiked into sputum s les, from contributing to profiles. Comparison of treated and untreated clinical s les indicated that dead bacterial cells significantly bias untreated profiles. These findings highlight the significant contribution that nonviable bacteria can make to DNA-based diagnostic analysis of clinical s les while providing a simple and effective means of avoiding such bias.
Publisher: Springer Science and Business Media LLC
Date: 05-05-2015
Publisher: Elsevier BV
Date: 08-2017
Publisher: Elsevier BV
Date: 08-2019
Publisher: Elsevier BV
Date: 12-2014
Publisher: BMJ
Date: 06-04-2013
Publisher: Elsevier BV
Date: 05-2019
Publisher: Springer Science and Business Media LLC
Date: 15-04-2009
Abstract: Drawing from previous studies, the traditional routine diagnostic microbiology evaluation of s les from chronic respiratory conditions may provide an incomplete picture of the bacteria present in airways disease. Here, the aim was to determine the extent to which routine diagnostic microbiology gave a different assessment of the species present in sputa when analysed by using culture-independent assessment. Six different media used in routine diagnostic microbiology were inoculated with sputum from twelve patients. Bacterial growth on these plates was harvested and both RNA and DNA extracted. DNA and RNA were also extracted directly from the same s le of sputum. All nucleic acids served as templates for PCR and reverse transcriptase-PCR lification of "broad range" bacterial 16S rRNA gene regions. The regions lified were separated by Terminal Restriction Fragment Length Polymorphism (T-RFLP) profiling and compared to assess the degree of overlap between approaches. A mean of 16.3 (SD 10.0) separate T-RF band lengths in the profiles from each sputum s le by Direct Molecular Analysis, with a mean of 8.8 (SD 5.8) resolved by DNA profiling and 13.3 (SD 8.0) resolved by RNA profiling. In comparison, 8.8 (SD 4.4) T-RF bands were resolved in profiles generated by Culture-derived Molecular Analysis. There were a total of 184 instances of T-RF bands detected in the direct sputum profiles but not in the corresponding culture-derived profiles, representing 83 different T-RF band lengths. Amongst these were fifteen instances where the T-RF band represented more than 10% of the total band volume (with a mean value of 23.6%). Eight different T-RF band lengths were resolved as the dominant band in profiles generated directly from sputum. Of these, only three were detected in profiles generated from the corresponding set of cultures. Due to their focus on isolation of a small group of recognised pathogens, the use of culture-dependent methods to analyse s les from chronic respiratory infections can provide a restricted understanding of the bacterial species present. The use of a culture-independent molecular approach here identifies that there are many bacterial species in s les from CF and COPD patients that may be clinically relevant.
Publisher: Elsevier BV
Date: 06-2013
Publisher: Wiley
Date: 09-2015
DOI: 10.1111/IMJ.12650
Abstract: There is a growing appreciation of the importance of the human microbiome to our normal physiology. This complex microbial ecosystem plays a range of roles, including influencing the development and function of our immune systems, providing essential nutrients, regulating metabolism and protecting us from opportunistic infections. Our increasing understanding of these processes is due, to a large extent, to the development of high-throughput sequencing technologies, providing for the first time a means by which complex microbial dynamics can be detailed. There is also a growing recognition that disruption of commensal microbiota, a phenomenon known as dysbiosis, is associated with several common disorders, including inflammatory bowel disease, type 2 diabetes and oncogenesis. Further, where innate immunity fails to protect us, the microbial communities that colonise the external surfaces of our bodies represent a ready source of infection. This review discusses the mechanisms that govern our interaction with our resident microbiota, both in health and disease, the technological advances that allow us to gain insight into these relationships, and the way in which our growing understanding can inform clinical practice.
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.JCF.2017.08.002
Abstract: G551D is a class III mutation of the cystic fibrosis transmembrane regulator (CFTR) that results in impaired chloride channel function in cystic fibrosis (CF). Ivacaftor, a CFTR-potentiating agent improves sweat chloride, weight, lung function, and pulmonary exacerbation rate in CF patients with G551D mutations, but its effect on the airway microbiome remains poorly characterised. Twenty CF patients with at least one G551D mutation from a single centre were recruited to a 4month double-blind, placebo-controlled, crossover study of ivacaftor with 28days of active treatment. Sputum microbiota composition was assessed by 16S rRNA gene licon sequencing and quantitative PCR at five key time points, along with regular clinical review, respiratory function assessment, and peripheral blood testing. No significant difference in microbiota composition was observed in subjects following ivacaftor treatment or placebo (PERMANOVA P=0.95, square root ECV=-4.94, 9479 permutations). Microbiota composition variance was significantly greater between subjects, than within subjects over time (P<0.0001, Mann Whitney U test), and an additional within-patient paired assessment of microbiota similarity was therefore performed. Again, change in microbiota composition was not significantly greater during treatment with ivacaftor compared to placebo (Wilcoxon test, P=0.51). A significant change in microbiota composition was however associated with any change in antibiotic exposure, regardless of whether ivacaftor or placebo was administered (P=0.006). In a small, subgroup analysis of subjects whose antibiotic exposure did not change within the study period, a significant reduction in total bacterial load was observed during treatment with ivacaftor (P=0.004, two-tailed paired Student's t-test). The short-term impact of ivacaftor therapy on sputum microbiota composition in patients with G551D mutations are modest compared to those resulting from antibiotic exposure, and may be masked by changes in antibiotic treatment regimen.
Publisher: American Society for Microbiology
Date: 08-2014
DOI: 10.1128/JCM.00764-14
Abstract: Spontaneously expectorated sputum is traditionally used as the s ling method for the investigation of lower airway infections. While guidelines exist for the handling of these s les for culture-based diagnostic microbiology, there is no comparable consensus on their handling prior to culture-independent analysis. The increasing incorporation of culture-independent approaches in diagnostic microbiology means that it is of critical importance to assess potential biases. The aim of this study was to assess the impact of delayed freezing on culture-independent microbiological analyses and to identify acceptable parameters for s le handling. Sputum s les from eight adult cystic fibrosis (CF) patients were collected and aliquoted into sterile Bijou bottles. Aliquots were stored at room temperature before being frozen at −80°C for increasing intervals, up to a 72-h period. S les were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions. Substantial variation was observed in s les with high- ersity bacterial communities over time, whereas little variation was observed in low- ersity communities dominated by recognized CF pathogens, regardless of time to freezing. Partitioning into common and rare species demonstrated that the rare species drove changes in similarity. The percentage abundance of anaerobes over the study significantly decreased after 12 h at room temperature ( P = 0.008). Failure to stabilize s les at −80°C within 12 h of collection results in significant changes in the detected community composition.
Publisher: Cambridge University Press (CUP)
Date: 05-06-2013
DOI: 10.1017/S0950268813001362
Abstract: The incidence, morbidity, and mortality associated with Clostridium difficile gastrointestinal infections has increased greatly over recent years, reaching epidemic proportions a trend due, in part, to the emergence of hypervirulent and antibiotic-resistant strains. The need to identify alternative, non-antibiotic, treatment strategies is therefore urgent. The ability of bacteria in faecal matter transplanted from healthy in iduals to displace pathogen populations is well recognized. Further, there is growing evidence that such faecal microbiota transplantation can be of benefit in a wide range of conditions associated with gut dysbiosis. Recent technical advances have greatly increased our ability to understand the processes that underpin the beneficial changes in bacterial community composition, as well as to characterize their extent and duration. However, while much of the research into faecal microbiota transplantation focuses currently on achieving clinical efficacy, the potential for such therapies to contribute to the transmission of infective agents also requires careful consideration.
Publisher: American Thoracic Society
Date: 05-2015
Publisher: Elsevier BV
Date: 06-2021
DOI: 10.1016/J.CLNESP.2021.02.022
Abstract: Dyslipidemia is a major cardiovascular disease risk factor. Research has proposed mechanisms whereby yogurt may improve circulating lipid concentrations. However, at the population level, the association of yogurt, as distinct from other dairy foods, with these important risk factors is poorly understood. This study aimed to determine whether the circulating lipid profile associated with yogurt is different to the circulating lipid profile that is associated with non-yogurt dairy products, specifically milk and cheese. The current study included the 192,564 US Veterans enrolled in the Million Veteran Program who reported frequency of yogurt consumption (assessed via food frequency questionnaire) and had lipid concentrations assessed. Trends were evaluated with linear regression. Mean age was 65 (SD = 11) years [20, 100 years]. A one serve/day higher yogurt consumption was positively associated (coefficient ± SE) with the concentration of high-density lipoprotein cholesterol (HDLC) in in iduals who were not (0.26 ± 0.12 mg/dL, P value = 0.025), and who were (0.25 ± 0.09, P value = 0.004), using antilipemic agents. Furthermore, higher yogurt consumption was inversely associated with the concentration of triglycerides, but only in in iduals who were not using antilipemic agents (-1.46 ± 0.58, P value = 0.012). These apparent beneficial associations of yogurt with HDLC and triglycerides were independent of consumption of non-yogurt dairy foods and were not observed for consumption of either milk or cheese. In this prospective cohort study of U.S. Veterans, we found a beneficial relationship between higher frequency of yogurt consumption with circulating HDLC and triglyceride concentrations that was distinct from non-yogurt dairy foods.
Publisher: European Respiratory Society (ERS)
Date: 29-09-2021
DOI: 10.1183/13993003.01293-2021
Abstract: Chronic airway inflammation is the main driver of pathogenesis in respiratory diseases such as severe asthma, chronic obstructive pulmonary disease, cystic fibrosis (CF) and bronchiectasis. While the role of common pathogens in airway inflammation is widely recognised, the influence of other microbiota members is still poorly understood. We hypothesised that the lung microbiota contains bacteria with immunomodulatory activity which modulate net levels of immune activation by key respiratory pathogens. Therefore, we assessed the immunomodulatory effect of several members of the lung microbiota frequently reported as present in CF lower respiratory tract s les. We show that Rothia mucilaginosa , a common resident of the oral cavity that is also often detectable in the lower airways in chronic disease, has an inhibitory effect on pathogen- or lipopolysaccharide-induced pro-inflammatory responses, in vitro (three-dimensional cell culture model) and in vivo (mouse model). Furthermore, in a cohort of adults with bronchiectasis, the abundance of Rothia species was negatively correlated with pro-inflammatory markers (interleukin (IL)-8 and IL-1β) and matrix metalloproteinase (MMP)-1, MMP-8 and MMP-9 in sputum. Mechanistic studies revealed that R. mucilaginosa inhibits NF-κB pathway activation by reducing the phosphorylation of IκBα and consequently the expression of NF-κB target genes. These findings indicate that the presence of R. mucilaginosa in the lower airways potentially mitigates inflammation, which could in turn influence the severity and progression of chronic respiratory disorders.
Publisher: American Society for Microbiology
Date: 2011
DOI: 10.1128/JCM.01650-10
Abstract: The aim of this study was to determine whether geographical differences impact the composition of bacterial communities present in the airways of cystic fibrosis (CF) patients attending CF centers in the United States or United Kingdom. Thirty-eight patients were matched on the basis of clinical parameters into 19 pairs comprised of one U.S. and one United Kingdom patient. Analysis was performed to determine what, if any, bacterial correlates could be identified. Two culture-independent strategies were used: terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA clone sequencing. Overall, 73 different terminal restriction fragment lengths were detected, ranging from 2 to 10 for U.S. and 2 to 15 for United Kingdom patients. The statistical analysis of T-RFLP data indicated that patient pairing was successful and revealed substantial transatlantic similarities in the bacterial communities. A small number of bands was present in the vast majority of patients in both locations, indicating that these are species common to the CF lung. Clone sequence analysis also revealed that a number of species not traditionally associated with the CF lung were present in both s le groups. The species number per s le was similar, but differences in species presence were observed between s le groups. Cluster analysis revealed geographical differences in bacterial presence and relative species abundance. Overall, the U.S. s les showed tighter clustering with each other compared to that of United Kingdom s les, which may reflect the lower ersity detected in the U.S. s le group. The impact of cross-infection and biogeography is considered, and the implications for treating CF lung infections also are discussed.
Publisher: American Thoracic Society
Date: 09-2014
Publisher: Elsevier BV
Date: 05-2020
Publisher: Springer Science and Business Media LLC
Date: 02-03-2022
DOI: 10.1038/S41380-022-01479-W
Abstract: The gut microbiome exerts a considerable influence on human neurophysiology and mental health. Interactions between intestinal microbiology and host regulatory systems have now been implicated both in the development of psychiatric conditions and in the efficacy of many common therapies. With the growing acceptance of the role played by the gut microbiome in mental health outcomes, the focus of research is now beginning to shift from identifying relationships between intestinal microbiology and pathophysiology, and towards using this newfound insight to improve clinical outcomes. Here, we review recent advances in our understanding of gut microbiome-brain interactions, the mechanistic underpinnings of these relationships, and the ongoing challenge of distinguishing association and causation. We set out an overarching model of the evolution of microbiome-CNS interaction and examine how a growing knowledge of these complex systems can be used to determine disease susceptibility and reduce risk in a targeted manner.
Publisher: CRC Press
Date: 24-07-2015
DOI: 10.1201/B18629-18
Publisher: Springer Science and Business Media LLC
Date: 08-2015
DOI: 10.1038/NM.3916
Publisher: Springer International Publishing
Date: 2021
Publisher: American Society for Microbiology
Date: 30-10-2019
Abstract: Recent molecular-based studies have suggested that a erse middle ear microbiome in adults and children can exist in the absence of disease. These studies have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. While 16S rRNA gene licon sequencing has proven to be a highly informative technique in many clinical contexts, it is susceptible to spurious signal arising from sequencing reagent contaminants where s le biomass is low. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. In finding no evidence of viable bacterial cells in middle ear s les, our study further underlines the importance of careful consideration of licon sequence data derived from very-low-biomass contexts and the value of analytical approaches that combine culture and molecular techniques.
Publisher: BMJ
Date: 08-08-2017
DOI: 10.1136/THORAXJNL-2016-208775
Abstract: To assess whether Induced sputum s les were obtained from 112 adult patients with high-resolution CT scan-proven bronchiectasis and at least two exacerbations in the previous year, as part of an unrelated randomised control trial. Presence of null Patients were grouped by ACTRN12609000578202 (anzctr.org.au) Pre-results.
Publisher: Wiley
Date: 14-07-2021
DOI: 10.1111/CEA.13979
Abstract: A high fruit and vegetable (F& V) diet reduces asthma exacerbations in adults this has not been examined in children to date. To investigate the effect of a 6‐month, high F& V diet on the time to first asthma exacerbation in children with asthma, in a parallel‐group, randomized, controlled trial. Children (aged 3–11 years) with asthma, history of exacerbations and usual low F& V intake (≤3 serves/day) were randomized to the intervention (high F& V diet) or control group (usual diet) for 6 months. The primary outcome was time to first exacerbation requiring medical intervention. Secondary outcomes included exacerbation rate, lung function, plasma TNF‐α, CRP, and IL‐6, faecal microbiota and peripheral blood mononuclear cell (PBMC) histone deacetylase (HDAC) activity and G‐protein coupled receptor (GPR) 41/43 and HDAC (1–11) expression. 67 children were randomized between September 2015 and July 2018. F& V intake (difference in change (∆): 3.5 serves/day, 95% CI: [2.6, 4.4] p 0.001) and plasma total carotenoids (∆: 0.44 µg/ml [0.19, 0.70] p = 0.001) increased after 6 months (intervention vs control). Time to first exacerbation (HR: 0.81, 95% CI: [0.38, 1.69], p = 0.569 control vs. intervention) and exacerbation rate (IRR: 0.84, [0.47, 1.49], p = 0.553 control vs. intervention) were similar between groups. In per‐protocol analysis, airway reactance z‐scores increased in the intervention versus control group ( X 5 ∆: 0.76 [0.04, 1.48] p = 0.038, X 20 ∆: 0.93 [0.23, 1.64] p = 0.009) and changes in faecal microbiota were observed though there was no difference between groups in systemic inflammation or molecular mechanisms. In the control group, CRP and HDAC enzyme activity increased, while GPR41 expression decreased. No adverse events attributable to the interventions were observed. A high F& V diet did not affect asthma exacerbations over the 6‐month intervention, though warrants further investigation as a strategy for improving lung function and protecting against systemic inflammation in children with asthma.
Publisher: American Society for Microbiology
Date: 08-2003
DOI: 10.1128/JCM.41.8.3548-3558.2003
Abstract: The leading cause of morbidity and mortality in cystic fibrosis (CF) patients stems from repeated bacterial respiratory infections. Many bacterial species have been cultured from CF specimens and so are associated with lung disease. Despite this, much remains to be determined. In the present study, we characterized without prior cultivation the total bacterial community present in specimens taken from adult CF patients, extracting DNA directly from 14 bronchoscopy or sputum s les. Bacterial 16S ribosomal DNA (rRNA) gene PCR products were lified from extracted nucleic acids, with analyses by terminal restriction fragment length polymorphism (T-RFLP), length heterogeneity PCR (LH-PCR), and sequencing of in idual cloned PCR products to characterize these communities. Using the same loading of PCR products, 12 distinct T-RFLP profiles were identified that had between 3 and 32 T-RFLP bands. Nine distinct LH-PCR profiles were identified containing between one and four bands. T-RFLP bands were detected in certain s les at positions that corresponded to pathogens cultured from CF s les, e.g., Burkholderia cepacia and Haemophilus influenzae . In every s le studied, one T-RFLP band was identified that corresponded to that produced by Pseudomonas aeruginosa. A total of 103 16S rRNA gene clones were examined from five patients. P. aeruginosa was the most commonly identified species (59% of clones). Stenotrophomonas species were also common, with eight other (typically anaerobic) bacterial species identified within the remaining 17 clones. In conclusion, T-RFLP analysis coupled with 16S rRNA gene sequencing is a powerful means of analyzing the composition and ersity of the bacterial community in specimens s led from CF patients.
Publisher: Hindawi Limited
Date: 21-04-2016
DOI: 10.1111/CMI.12589
Abstract: Respiratory infection is a leading cause of global morbidity and mortality. Understanding the factors that influence risk and outcome of these infections is essential to improving care. We increasingly understand that interactions between the microbial residents of our mucosal surfaces and host regulatory systems is fundamental to shaping local and systemic immunity. These mechanisms are most well defined in the gastrointestinal tract, however analogous systems also occur in the airways. Moreover, we now appreciate that the host-microbiota interactions at a given mucosal surface influence systemic host processes, in turn, affecting the course of infection at other anatomical sites. This review discusses the mechanisms by which the respiratory microbiome influences acute and chronic airway disease and examines the contribution of cross-talk between the gastrointestinal and respiratory compartments to microbe-mucosa interactions.
Publisher: Frontiers Media SA
Date: 11-04-2017
Publisher: American Society for Microbiology
Date: 09-2016
DOI: 10.1128/JCM.01410-16
Abstract: Culture-based detection of nontuberculous Mycobacteria (NTM) in respiratory s les is time consuming and can be subject to overgrowth by nonmycobacterial bacteria. We describe a single-reaction TaqMan quantitative PCR assay for the direct detection of NTM species in clinical s les that is specific, sensitive, and robust.
Publisher: The Endocrine Society
Date: 03-2017
DOI: 10.1210/EN.2016-1839
Abstract: Serotonin (5-hydroxytryptamine or 5-HT) is a multifunctional bioamine with important signaling roles in a range of physiological pathways. Almost all of the 5-HT in our bodies is synthesized in specialized enteroendocrine cells within the gastrointestinal (GI) mucosa called enterochromaffin (EC) cells. These cells provide all of our circulating 5-HT. We have long appreciated the important contributions of 5-HT within the gut, including its role in modulating GI motility. However, evidence of the physiological and clinical significance of gut-derived 5-HT outside of the gut has recently emerged, implicating 5-HT in regulation of glucose homeostasis, lipid metabolism, bone density, and diseases associated with metabolic syndrome, such as obesity and type 2 diabetes. Although a new picture has developed in the last decade regarding the various metabolic roles of peripheral serotonin, so too has our understanding of the physiology of EC cells. Given that they are scattered throughout the lining of the GI tract within the epithelial cell layer, these cells are typically difficult to study. Advances in isolation procedures now allow the study of pure EC-cell cultures and single cells, enabling studies of EC-cell physiology to occur. EC cells are sensory cells that are capable of integrating cues from ingested nutrients, the enteric nervous system, and the gut microbiome. Thus, levels of peripheral 5-HT can be modulated by a multitude of factors, resulting in both local and systemic effects for the regulation of a raft of physiological pathways related to metabolism and obesity.
Publisher: American Society for Microbiology
Date: 07-2006
DOI: 10.1128/JCM.02282-05
Abstract: The bacterial communities present in the oral cavity and the lungs of 19 adult cystic fibrosis (CF) patients were compared by using terminal restriction fragment length polymorphism analysis of 16S rRNA gene PCR products lified from nucleic acids extracted directly from bacteria in clinical s les. Sputum s les were not found to be subject to profound contamination by oral cavity bacteria. Evidence of colonization of the CF lung by certain oral bacterial species was found.
Publisher: Elsevier BV
Date: 2016
Publisher: European Respiratory Society (ERS)
Date: 11-2017
Publisher: Elsevier BV
Date: 05-2013
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: Australia
Start Date: 2016
End Date: 2017
Funder: Bill and Melinda Gates Foundation
View Funded ActivityStart Date: 2015
End Date: 2016
Funder: Flinders University
View Funded ActivityStart Date: 2016
End Date: 2017
Funder: Almond Board of California
View Funded ActivityStart Date: 2018
End Date: 2019
Funder: Flinders University
View Funded ActivityStart Date: 2016
End Date: 2019
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 2018
End Date: 2020
Funder: Hospital Research Foundation
View Funded ActivityStart Date: 2016
End Date: 2019
Funder: National Health and Medical Research Council
View Funded ActivityStart Date: 2013
End Date: 2015
Funder: National Health and Medical Research Council
View Funded Activity