Dr Tiffanie Nelson

(1) Background: Individuals with diabetes and chronic kidney disease display gut dysbiosis when compared to healthy controls. However, it is unknown whether there is a change in dysbiosis across the stages of diabetic chronic kidney disease. We investigated a cross-sectional study of patients with early and late diabetes associated chronic kidney disease to identify possible microbial differences between these two groups and across each of the stages of diabetic chronic kidney disease. (2) Methods: This cross-sectional study recruited 95 adults. DNA extracted from collected stool samples were used for 16S rRNA sequencing to identify the bacterial community in the gut. (3) Results: The phylum Firmicutes was the most abundant and its mean relative abundance was similar in the early and late chronic kidney disease group, 45.99 ± 0.58% and 49.39 ± 0.55%, respectively. The mean relative abundance for family Bacteroidaceae, was also similar in the early and late group, 29.15 ± 2.02% and 29.16 ± 1.70%, respectively. The lower abundance of Prevotellaceae remained similar across both the early 3.87 ± 1.66% and late 3.36 ± 0.98% diabetic chronic kidney disease groups. (4) Conclusions: The data arising from our cohort of individuals with diabetes associated chronic kidney disease show a predominance of phyla Firmicutes and Bacteroidetes. The families Ruminococcaceae and Bacteroidaceae represent the highest abundance, while the beneficial Prevotellaceae family were reduced in abundance. The most interesting observation is that the relative abundance of these gut microbes does not change across the early and late stages of diabetic chronic kidney disease, suggesting that this is an early event in the development of diabetes associated chronic kidney disease. We hypothesise that the dysbiotic microbiome acquired during the early stages of diabetic chronic kidney disease remains relatively stable and is only one of many risk factors that influence progressive kidney dysfunction.

A wines¿ terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.

Objective: Characterise the vaginal metabolome of cervical HPV-infected and uninfected women. Design: Cross-sectional. Setting: The Center for Health Behavior Research at the University of Maryland School of Public Health. Sample: Thirty-nine participants, 13 categorised as HPV-negative and 26 as HPV-positive (any genotype; HPV+), 14 of whom were positive with at least one high-risk HPV strain (hrHPV). Method: Self-collected mid-vaginal swabs were profiled for bacterial composition by 16S rRNA gene amplicon sequencing, metabolites by both gas and liquid chromatography mass spectrometry, and 37 types of HPV DNA. Main outcome measures: Metabolite abundances. Results: Vaginal microbiota clustered into Community State Type (CST) I (Lactobacillus¿crispatus-dominated), CST III (Lactobacillus¿iners-dominated), and CST IV (low-Lactobacillus, ¿molecular-BV¿). HPV+ women had higher biogenic amine and phospholipid concentrations compared with HPV¿ women after adjustment for CST and cigarette smoking. Metabolomic profiles of HPV+ and HPV- women differed in strata of CST. In CST III, there were higher concentrations of biogenic amines and glycogen-related metabolites in HPV+ women than in HPV¿ women. In CST IV, there were lower concentrations of glutathione, glycogen, and phospholipid-related metabolites in HPV+ participants than in HPV¿participants. Across all CSTs, women with hrHPV strains had lower concentrations of amino acids, lipids, and peptides compared with women who had only low-risk HPV (lrHPV). Conclusions: The vaginal metabolome of HPV+ women differed from HPV- women in terms of several metabolites, including biogenic amines, glutathione, and lipid-related metabolites. If the temporal relation between increased levels of reduced glutathione and oxidised glutathione and HPV incidence/persistence is confirmed in future studies, anti-oxidant therapies may be considered as a non-surgical HPV control intervention. Tweetable abstract: Metabolomics study: Vaginal microenvironment of HPV+ women may be informative for non-surgical interventions.

Buruli ulcer (BU) is a subcutaneous necrotic infection of the skin caused by Mycobacterium ulcerans. It is the third most common human mycobacterial disease after tuberculosis (TB) and leprosy. The available methods for detection of the bacilli in lesions are microscopic detection, isolation and cultivation of the bacterium, histopathology, and polymerase chain reaction (PCR). These methods, although approved by the World Health Organization (WHO), have infrastructural and resource challenges in medical centres and cell-mediated immunity (CMI) and/or serology-based tests have been suggested as easier and more appropriate for accurate assessment of the disease, especially in remote or underdeveloped areas. This study system-atically reviewed and conducted a meta-analysis for all research aimed at developing cell-medi-ated immunity (CMI) and/or serology-based tests for M. ulcerans disease. Information for this review was searched through PubMed and Web of Science databases and identified up to June 2019. References from relevant articles and reports from the WHO Annual Meeting of the Global Buruli Ulcer Initiative were also used. Twelve studies beginning in 1952, that attempted to develop CMI and/or serology-based tests for the disease were identified. These studies addressed issues of specificity and sensitivity in context of antigen composition as well as study heterogeneity and bias. The two main types of antigenic preparations considered were pathogen-derived and recombinant protein preparations. There was slight difference in test performance when M. ulcerans recombinant proteins [positivity: 67.5%; 32.5%] or pathogen-derived [positivity: 76.0%; 24.0%] preparations were used as test antigens among BU patients. However, pathogen-derived preparations were better at differentiating between patients and control groups [odds ratio (OR) of 27.92, 95%CI: 5.05¿154.28]. This was followed by tests with the recombinant proteins [OR = 1.23, 95%CI: 0.27¿5.62]. Overall, study heterogeneity index, I2 was 92.4% (p = 0.000). It is apparent from this review that standardisation is needed in any future CMI and/or serology-based tests used for M. ulcerans disease.

The number of social contacts of mammals is positively correlated with the diversity of their gut microbes. There is some evidence that sociality also affects microbes in the respiratory tract. We tested whether the airway microbiota of cetacean species differ depending on the whales' level of sociality. We sampled the blow of blue (Balaenoptera musculus), grey (Eschrichtius robustus), humpback (Megaptera novaeangliae) and long-finned pilot whales (PWs) (Globicephala melas) and analysed the blow microbiota by barcode tag sequencing targeting the V4 region of the bacterial 16S rRNA gene. Humpback whales (HWs) show higher levels of sociality than blue (BW) and grey (GW), while PWs are the most gregarious among the four species. The blow samples of the HWs showed the highest richness and diversity. HWs were also the only species with a species-specific clustering of their microbial community composition and a relatively large number of core taxa. Therefore, we conclude that it cannot be sociality alone shaping the diversity and composition of airway microbiota. We suggest the whale species' lung volume and size of the plume of exhaled air as an additional factor impacting the transmission potential of blow microbiota from one individual whale to another.

Humpback whales endure several months of fasting while undertaking one of the longest annual migrations of any mammal, which depletes the whales¿ energy stores and likely compromises their physiological state. Airway microbiota are linked to respiratory health in mammals. To illuminate the dynamics of airway microbiota in a physiologically challenged mammal, we investigated the bacterial communities in the blow of East Australian humpback whales at two stages of their migration: at the beginning (n = 20) and several months into their migration (n = 20), using barcoded tag sequencing of the bacterial 16S rRNA gene. We show that early in the fasting the whale blow samples had a higher diversity and richness combined with a larger number of core taxa and a different bacterial composition than later in the fasting. This study provides some evidence that the rich blow microbiota at the beginning of their fasting might reflect the whales¿ uncompromised physiology and that changes in the microbiota occur during the whales¿ migration.

Infectious diseases contribute to the vulnerable status of marine mammals, including respiratory illnesses. This study aimed to capture exhaled breath condensate (blow) for microbial identification from wild Indo-Pacific bottlenose dolphins Tursiops aduncus. Individual dolphins were sampled by holding a funnel connected to a 50 ml centrifuge tube over the blowhole of the animal near shore in Shark Bay (SB), Western Australia. Four individuals were sampled on 2 occasions along with seawater samples. Comparative blow and pool water samples were collected from 4 individual common bottlenose dolphins Tursiops truncatus housed in the National Aquarium (NA), Baltimore, Maryland, USA. Bacteria were identified using the V4 region of the 16S rRNA gene from extracted DNA. We identified bacteria independent of seawater in SB dolphins, which included the classes Alphaproteobacteria (26.1%) and Gammaproteobacteria (25.8%); the phyla Bacteroidetes (15.6%) and Fusobacteria (7.2%); and the genera Pseudomonas (11.5%), Pedomicrobium (4.5%), Streptobacillus (3.7%), Phenylobacterium (2.2%) and Sphingomonas (2.1%). There were broad similarities in phyla between SB and NA dolphins yet there were differences between lower taxonomic groups. A number of operational taxonomic units (OTUs) were shared between dolphin individuals, which may be a result of their genetic lineage (siblings or parentage), shared living and social interactions. A number of genera were observed in SB dolphins which have species known to be infectious in marine mammals such as Pseudomonas, Mycoplasma and Streptococcus. This study successfully characterised bacteria from DNA captured in blow from wild dolphins. The ability to capture these communities from individuals in the wild provides a novel health indicator.

An emerging novel therapeutic agent for major depressive disorder, minocycline, has the potential to influence both gut microbiome and inflammatory status. The present study showed that chronic high fat diet feeding led to changes in both behaviour and the gut microbiome in male mice, without an overt inflammatory response. The diet-induced behavioural changes were characterised as increased immobility in the forced swim test and changes in locomotor activities in the open field test. Minocycline significantly altered the gut microbiome, rendering a community distinctly different to both untreated healthy and diet-affected states. In contrast, minocycline did not reverse high fat diet-induced changes in behaviour.

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 swamp), 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.

Forecasted climate-change models predict that much of northern Australia's coastal habitats will be in retreat because of saltwater intrusion (SWI) from sea-level rise. A region of primary concern is the nutrient-rich and biodiverse floodplains of world heritage-listed Kakadu National Park (KNP). To understand the implications of SWI, we need fundamental baseline information for floodplain biota from the South Alligator River, KNP, northern Australia, and informative data on how increased and prolonged exposure to salt is likely to shape the eukaryotic community. To assist in addressing these key knowledge gaps, we used amplicon sequencing to examine the composition of eukaryotic soil communities from the South Alligator River floodplain, an ecologically important area at the 'coalface' of sea-level rise. Samples were obtained from three river zones and three floodplain morphologies, capturing a wide range of habitats and episodic exposures to both saltwater and freshwater. We found that both the floodplain morphology and positioning along the river significantly influenced eukaryotic composition. However, the influence of these variables varied greatly among the floodplain morphologies, with correlative evidence suggesting that both salinity and pH played a dominant role in shaping communities within lower parts of the floodplain, with this being particularly evident in those regions subjected to major tidal influence (estuarine funnel and sinuous, and cuspate).

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 individuals. 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. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness. © 2013 Nelson et al.