ORCID Profile
0000-0002-5341-312X
Current Organisations
University of Newcastle Australia
,
Australian BioCommons
,
Griffith University
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Publisher: Wiley
Date: 12-11-2012
Abstract: The gut microbiota of mammals underpins the metabolic capacity and health of the host. Our understanding of what influences the composition of this community has been limited primarily to evidence from captive and terrestrial mammals. Therefore, the gut microbiota of southern elephant seals, Mirounga leonina, and leopard seals, Hydrurga leptonyx, inhabiting Antarctica were compared with captive leopard seals. Each seal exhibited a gut microbiota dominated by four phyla: Firmicutes (41.5 ± 4.0%), Fusobacteria (25.6 ± 3.9%), Proteobacteria (17.0 ± 3.2%) and Bacteroidetes (14.1 ± 1.7%). Species, age, sex and captivity were strong drivers of the composition of the gut microbiota, which can be attributed to differences in diet, gut length and physiology and social interactions. Differences in particular prey items consumed by seal species could contribute to the observed differences in the gut microbiota. The longer gut of the southern elephant seal provides a habitat reduced in available oxygen and more suitable to members of the phyla Bacteroidetes compared with other hosts. Among wild seals, 16 'core' bacterial community members were present in the gut of at least 50% of in iduals. As identified between southern elephant seal mother-pup pairs, 'core' members are passed on via vertical transmission from a young age and persist through to adulthood. Our study suggests that these hosts have co-evolved with their gut microbiota and core members may provide some benefit to the host, such as developing the immune system. Further evidence of their strong evolutionary history is provided with the presence of 18 shared 'core' members in the gut microbiota of related seals living in the Arctic. The influence of diet and other factors, particularly in captivity, influences the composition of the community considerably. This study suggests that the gut microbiota has co-evolved with wild mammals as is evident in the shared presence of 'core' members.
Publisher: Springer Science and Business Media LLC
Date: 14-03-2017
DOI: 10.1038/SREP44423
Abstract: Human parechovirus types 1–16 (HPeV1–16) are positive strand RNA viruses in the family Picornaviridae . We investigated a 2015 outbreak of HPeV3 causing illness in infants in Victoria, Australia. Virus genome was extracted from clinical material and isolates and sequenced using a combination of next generation and Sanger sequencing. The HPeV3 outbreak genome was 98.7% similar to the HPeV3 Yamagata 2011 lineage for the region encoding the structural proteins up to nucleotide position 3115, but downstream of that the genome varied from known HPeV sequences with a similarity of 85% or less. Analysis indicated that recombination had occurred, may have involved multiple types of HPeV and that the recombination event/s occurred between March 2012 and November 2013. However the origin of the genome downstream of the recombination site is unknown. Overall, the capsid of this virus is highly conserved, but recombination provided a different non-structural protein coding region that may convey an evolutionary advantage. The indication that the capsid encoding region is highly conserved at the amino acid level may be helpful in directing energy towards the development of a preventive vaccine for expecting mothers or antibody treatment of young infants with severe disease.
Publisher: Springer Science and Business Media LLC
Date: 16-01-2018
DOI: 10.1038/S41598-017-14943-3
Abstract: Cigarette smoking has been associated with both the diagnosis of bacterial vaginosis (BV) and a vaginal microbiota lacking protective Lactobacillus spp. As the mechanism linking smoking with vaginal microbiota and BV is unclear, we sought to compare the vaginal metabolomes of smokers and non-smokers (17 smokers/19 non-smokers). Metabolomic profiles were determined by gas and liquid chromatography mass spectrometry in a cross-sectional study. Analysis of the 16S rRNA gene populations revealed s les clustered into three community state types (CSTs) ---- CST-I ( L . crispatus -dominated), CST-III ( L . iners -dominated) or CST-IV (low- Lactobacillus ). We identified 607 metabolites, including 12 that differed significantly (q-value 0.05) between smokers and non-smokers. Nicotine, and the breakdown metabolites cotinine and hydroxycotinine were substantially higher in smokers, as expected. Among women categorized to CST-IV, biogenic amines, including agmatine, cadaverine, putrescine, tryptamine and tyramine were substantially higher in smokers, while dipeptides were lower in smokers. These biogenic amines are known to affect the virulence of infective pathogens and contribute to vaginal malodor. Our data suggest that cigarette smoking is associated with differences in important vaginal metabolites, and women who smoke, and particularly women who are also depauperate for Lactobacillus spp., may have increased susceptibilities to urogenital infections and increased malodor.
Publisher: Springer Science and Business Media LLC
Date: 24-04-2023
DOI: 10.1007/S00248-023-02222-W
Abstract: Bacteria residing in the guts of pollinating insects play a key role in nutrient acquisition, digestion, and resistance to pests and diseases. Imbalances in microbial flora in response to environmental change and stress can therefore impact insect health and resilience. This study is aimed at defining the core gut microbiome of the Australian native stingless bee, Tetragonula carbonaria , and exploring the impact of colony transplantation on gut health. The gut microbiomes of nine forager bees from natural (log) and manufactured (box) hives were examined via 16S rRNA gene licon sequencing. Some differences were observed at the ASV level between the microbiomes of log and box hive bees. However, a core microbiome, dominated by Lactobacillus spp., unclassified Acetobacteraceae spp., and Bombella spp., was maintained. Further, the inferred functional potential of the microbiomes was consistent across all in iduals. This study highlights that although hive transplantation has an impact on the overall ersity of stingless bee gut microbiomes, it is unlikely to have a significant negative impact on the overall health and resilience of the colony.
Publisher: Springer Science and Business Media LLC
Date: 17-07-2018
Abstract: Sustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Bio ersity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic licon sequencing data describing Bacteria , Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. S les are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30 ° of latitude and ~38 ° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 s les are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 s les are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/MA15004
Publisher: Springer Science and Business Media LLC
Date: 06-06-2018
DOI: 10.1038/S41598-018-26851-1
Abstract: We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses. Initial evaluation included both spiked and non-spiked bird faecal s les as well as non-spiked human faecal s les. From the non-spiked bird s les (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal s les. We then present a detailed analysis of selected virus sequences in the avian s les that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for ex le, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses. Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the “ribosomal activity microbiome” of gut parasites and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.
Publisher: Wiley
Date: 27-07-2020
DOI: 10.1111/GCB.15257
Publisher: Springer Science and Business Media LLC
Date: 20-06-2017
DOI: 10.1038/S41598-017-04145-2
Abstract: We present the near complete virus genome sequences with phylogenetic and network analyses of potential transmission networks of a total of 18 Australian cases of human parechovirus type 3 (HPeV3) infection in infants in the period from 2012–2015. Overall the results support our previous finding that the Australian outbreak strain/lineage is a result of a major recombination event that took place between March 2012 and November 2013 followed by further virus evolution and possibly recombination. While the nonstructural coding region of unknown provenance appears to evolve significantly both at the nucleotide and amino acid level, the capsid encoding region derived from the Yamagata 2011 lineage of HPeV3 appears to be very stable, particularly at the amino acid level. The phylogenetic and network analyses performed support a temporal evolution from the first Australian recombinant virus sequence from November 2013 to March/April 2014, onto the 2015 outbreak. The 2015 outbreak s les fall into two separate clusters with a possible common ancestor between March/April 2014 and September 2015, with each cluster further evolving in the period from September to November/December 2015.
Publisher: Wiley
Date: 19-02-2020
Abstract: Noninvasive s ling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive s ling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal s ling methods in adult hibians. In this study, we compare microbiomes from two noninvasive s le types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal s ling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher ersity. Our results indicate that cloacal swabs were more similar to large intestine s les than were faecal s les, and small intestine s les were significantly different from both nonlethal s le types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal s ling of hibian gut microbiota.
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/MF16033
Abstract: Bacterial communities in floodplain and wetland soils cycle elements essential for flora and fauna. The coastal habitats of northern Australia are threatened with increasing saltwater intrusion (SWI) events that will destroy freshwater habitats. The effect of the impending SWI on bacterial communities is unknown. Here, we examined the bacterial communities of a tropical river floodplain located in World Heritage Kakadu National Park. Using 16S rRNA gene pyrosequencing, we measured the baseline bacterial communities from three morphologically distinct regions of the floodplain (lower, upper and backwater sw ), within three zones of the South Alligator River (upstream, cuspate and estuarine funnel or sinuous). Significant differences in the bacterial community were observed at each category of floodplain morphology and river zone. The greatest differences were due to pH and salinity. Large changes in bacterial compositions are predicted to occur with increases in salinity and pH. Saltwater intrusion is predicted to increase substantially in the next decades with sea-level rise, and is likely to cause large and significant changes to the bacterial community with unknown consequences for biogeochemical cycling. Kakadu National Park may benefit from incorporating bacteria into routine studies, because we have shown here that they are sensitive indicators of change, even across small ranges of abiotic variables.
Publisher: Cold Spring Harbor Laboratory
Date: 17-11-2020
DOI: 10.1101/2020.11.16.385690
Abstract: Gut bacterial communities influence, and are influenced by, the behaviour and ecology of their hosts. Those interactions have been studied primarily in humans and model organisms, but we need field research to understand the relationship between an organism’s gut bacteria and its ecological challenges, such as those imposed by rapid range expansion (as in invasive species) and the presence of host-manipulating parasites. Cane toads ( Rhinella marina ) provide an excellent model system in this respect, because the species’ ongoing colonization of Australia has enforced major changes in phenotypic traits (including behaviour), and lungworm parasites ( Rhabdias pseudosphaerocephala ) modify host gut function in ways that enhance the viability of lungworm larvae. We collected female toads from across the species’ invasive range and studied their morphology, behaviour, parasite infection status and gut bacterial community. Range-core versus range-edge toads differed in morphology, behaviour, gut bacterial composition and predicted gut bacterial function but did not differ in the occurrence of parasite infection nor in the intensity of infection. Toads infected with lungworms differed from uninfected conspecifics in gut bacterial composition and ersity. Our study demonstrates strong associations between gut bacterial community and host ecology and behaviour.
Publisher: Springer Science and Business Media LLC
Date: 13-04-2018
DOI: 10.1038/S41598-018-24407-X
Abstract: We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird s les collected during 2016–17. Coronaviruses were detected in 141 s les (15.3%) from species of ducks, shorebirds and herons and from multiple s ling locations. Sequencing of selected positive s les found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive s les. Sequencing of the relatively conserved Orf1 PCR licons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.
Publisher: Public Library of Science (PLoS)
Date: 30-12-2013
Publisher: Wiley
Date: 21-03-2022
DOI: 10.1111/GBI.12489
Abstract: Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, ersity and metabolic potential of bacterial communities from different microbialite‐forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat s les. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria‐rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite‐forming mats in the five South Australian lakes and reinforce the concept that ‘who’ is in the community is not as critical as their net metabolic capacity.
Publisher: Wiley
Date: 29-06-2022
Abstract: The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or ‘biocrusts’. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi‐arid Australian continent. Yet, their distribution and the parameters that shape their microbial composition have not been investigated. We present here the first detailed description of Australia's biocrust microbiome assessed from 15 sites across the continent using 16S rRNA sequencing. The most abundant bacterial phyla from all sites were Cyanobacteria, Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Cyanobacterial communities from northern regions were more erse and unclassified cyanobacteria were a noticeable feature of northern biocrusts. Segregation between northern and southern regions was largely due to the differential abundance of Microcoleus spp., with M . paludosus dominating in the north and M . vaginatus dominating in the south. The geographical shifts in bacterial composition and ersity were correlated to seasonal temperatures and summer rainfall. Our findings provide an initial reference for s ling strategies to maximize access to bacterial genetic ersity. As hubs for essential ecosystem services, further investigation into biocrusts in arid and semi‐arid regions may yield discoveries of genetic mechanisms that combat increases in warming due to climate change.
Publisher: Elsevier BV
Date: 12-2016
Publisher: Frontiers Media SA
Date: 29-09-2015
Publisher: Elsevier BV
Date: 2015
DOI: 10.1016/J.SCITOTENV.2014.08.109
Abstract: Saltwater intrusion (SWI) can result in the loss of dominant vegetation from freshwater habitats. In northern Australia, sea level is predicted to rise 17-50 cm by 2030-2070. This will exacerbate the impact of SWI, threatening Ramsar-listed habitats. Soil bacteria in these habitats play a significant role in biogeochemical cycling, regulating availability of essential nutrients such as nitrogen to vegetation. However, there is limited understanding as to how SWI will impact these soil bacteria. Floodplain soil s les were collected from the South Alligator River floodplain in Northern Australia from sites with contrasting histories of SWI. A SWI event was simulated over 7 days with treatments of saltwater and freshwater. Bacterial community composition before and after treatment were measured using next generation sequencing of bacterial DNA. Sites with no history of SWI showed no significant changes in community taxonomic composition following treatments, suggesting the community at these sites have broad functional capacity which may be due to their historic conditioning over many years. Sites with a history of SWI showed a significant response to both treatments. Following saltwater treatment, there was an increase in sulfate-reducing bacteria, which are known to have an impact on carbon and nitrogen cycling. We suggest that the impact of SWI causes a shift in the soil bacteria which alters the community to one which is more specialised, with implications for the cycling of essential elements and nutrients.
Publisher: BMJ Publishing Group Ltd
Date: 07-2017
No related grants have been discovered for Tiffanie Nelson.