Differences In Community Membership Research Articles

The Effect of Dietary Synbiotics in Actively Racing Standardbred Horses Receiving Trimethoprim/Sulfadiazine.

Synbiotics are often provided to horses receiving antibiotics to protect against microbiome disturbances, despite a lack of evidence for efficacy. The purpose of this study was to evaluate the effect of a synbiotic product in horses receiving antibiotics. Sixteen actively racing Standardbred horses were randomly allocated (four-way crossover) to one of four groups: antibiotics (10 days; AB), synbiotics (28 days; PROBIOPlusTM; PBP), PBP + AB, or Control. The fecal microbiome was investigated using 16S rRNA sequencing, and fecal dry matter (DM; %), pH, and scores (FS; 0-9) were measured. Data were analyzed with two-way ANOVA. Results found microbiota differences in community membership between PBP + AB and all other treatments during and after antibiotic treatment. During antibiotic treatment, AB and PBP + AB were significantly different from Control. After antibiotic treatment, PBP + AB was significantly different from all other treatments. The few differences found in relative abundance of phyla or predominant genera were mostly in fiber degrading bacteria. The Fibrobacter population was significantly higher in AB and PBP + AB horses than Control. Unclassified Ruminococcaceae was significantly higher in Control than AB and PBP. After antibiotic treatment, PBP + AB horses were significantly higher than PBP horses. In conclusion, these data provide support for the ability of PROBIOPlus™ to maintain healthy gastrointestinal microbiome during antibiotic treatment.

How do people understand inequality in Chile? A study through attitude network analysis

This article constitutes the first application of the attitude network approach to peoples' views on inequality. We adopt a network model in which nodes represent survey variables and edges their conditional associations. This allows us to conceptualize perceptions, beliefs, and judgments about inequality as a network of connected evaluative reactions. We analyze data from the 2019 ISSP Social Inequality Module for Chile, one of the most unequal countries in the world. Relying on a network approach, we systematically analyze the wide-ranging indicators measuring subjective inequality. Results show that conceptions regarding inequality, redistribution, taxation, and wages form a moderately connected unified belief system with a small-world structure. In addition, we stratify the sample by education, income, and social class, obtaining six attitude networks. We compare the structures of these networks, investigating differences in community membership, node centrality, and network connectivity, evidencing that people in lower social positions have a more multidimensional understanding of inequality. Our work contributes to social justice research by proposing an innovative conceptualization of these attitudes and providing evidence of their structural variation across different socioeconomic groups.

Convergent Microbial Community Formation in Replicate Anaerobic Reactors Inoculated from Different Sources and Treating Ersatz Crew Waste.

Future manned space travel will require efficient recycling of nutrients from organic waste back into food production. Microbial systems are a low-energy, efficient means of nutrient recycling, but their use in a life support system requires predictability and reproducibility in community formation and reactor performance. To assess the reproducibility of microbial community formation in fixed-film reactors, we inoculated replicate anaerobic reactors from two methanogenic inocula: a lab-scale fixed-film, plug-flow anaerobic reactor and an acidic transitional fen. Reactors were operated under identical conditions, and we assessed reactor performance and used 16s rDNA amplicon sequencing to determine microbial community formation. Reactor microbial communities were dominated by similar groups, but differences in community membership persisted in reactors inoculated from different sources. Reactor performance overlapped, suggesting a convergence of both reactor communities and organic matter mineralization. The results of this study suggest an optimized microbial community could be preserved and used to start new, or restart failed, anaerobic reactors in a life support system with predictable reactor performance.

The Antarctic mite, Alaskozetes antarcticus, shares bacterial microbiome community membership but not abundance between adults and tritonymphs

The Antarctic mite (Alaskozetes antarcticus) is widely distributed on sub-Antarctic islands and throughout the Antarctic Peninsula, making it one of the most abundant terrestrial arthropods in the region. Despite the impressive ability of A. antarcticus to thrive in harsh Antarctic conditions, little is known about the biology of this species. In this study, we performed 16S rRNA gene sequencing to examine the microbiome of the final immature instar (tritonymph) and both male and female adults. The microbiome included a limited number of microbial classes and genera, with few differences in community membership noted among the different stages. However, the abundances of taxa that composed the microbial community differed between adults and tritonymphs. Five classes—Actinobacteria, Flavobacteriia, Sphingobacteriia, Gammaproteobacteria, and Betaproteobacteria—comprised ~ 82.0% of the microbial composition, and five (identified) genera—Dermacoccus, Pedobacter, Chryseobacterium, Pseudomonas, and Flavobacterium—accounted for ~ 68.0% of the total composition. The core microbiome present in all surveyed A. antarcticus was dominated by the families Flavobacteriaceae, Comamonadaceae, Sphingobacteriaceae, Chitinophagaceae and Cytophagaceae, but the majority of the core consisted of operational taxonomic units of low abundance. This comprehensive analysis reveals a diverse microbiome among individuals of different stages, with overlap likely due to their shared habitat and common feeding preferences as herbivores and detritivores. The microbiome of the Antarctic mite shows considerably more diversity than observed in mite species from lower latitudes.

Rotavirus-mediated alteration of gut microbiota and its correlation with physiological characteristics in neonatal calves.

Diarrhea is a fatal disease to neonatal calves, and rotavirus is the main pathogen associated with neonatal calf diarrhea. Although previous studies have reported that the gut microbiota is changed in calves during diarrhea, less is known about whether rotavirus infection alters the structure of the gut microbiota. Here, we characterized fecal microbial communities and identified possible relationships between the gut microbiota profiles and physiological parameters. Five fecal specimens of rotavirus-infected calves from 1 to 30 days after birth and five fecal specimens of age-matched healthy calves were used for the microbial community analysis using the Illumina MiSeq sequencer. Rotavirus infection was associated with reduced rotavirus infection significantly reduced the richness and diversity of the bacterial community. Weighted unique fraction metric analysis exhibited significant differences in community membership and structure between healthy and rotavirus-infected calves. Based on relative abundance analysis and linear discriminant analysis effect size, we found that the representative genera from Lactobacillus, Subdoligranulum, Blautia, and Bacteroides were closely related to healthy calves, while the genera Escherichia and Clostridium were closely affiliated to rotavirus-infected calves. Furthermore, canonical correlation analysis and Pearson correlation coefficient results revealed that the increased relative abundances of Lactobacillus, Subdoligranulum, and Bacteroides were correlated with normal levels of physiological characteristics such as white blood cells, blood urea nitrogen, serum amyloid protein A, and glucose concentration in serum. These results suggest that rotavirus infection alters the structure of the gut microbiota, correlating changes in physiological parameters. This study provides new information on the relationship between gut microbiota and the physiological parameters of rotavirus-mediated diarrheic calves.

The fecal bacterial microbiota of bats; Slovenia.

MethodsFecal samples were collected from 92 bats in Slovenia, consisting of 12 different species, and the bacterial microbiota was assessed via next generation sequencing of the 16S rRNA gene V4 region.ResultsSequences were assigned to 28 different phyla, but only Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria accounted for ≥1% of sequences. One phylum (Proteobacteria), one class (Gammaproteobacteria), three orders (Pseudomonadales, Lactobacillales, Bacillales), four families (Enterobacteriaceae, Pseudomonadaceae, Staphylococcaceae, Carnobacteriaceae), and five genera (Pseudomonas, Staphylococcus, Carnobacterium, an unclassified Enterobacteriaceae, Acinetobacter) accounted for 50% of sequences. There were no significant differences in the relative abundances of any phyla between bat species, but various differences were noted at lower taxonomic levels, such as Enterobacteriaceae (P = 0.007, most abundant in M. blythii), Pseudomonadaceae (P = 0.007, most abundant in Rhinolophus hipposideros) and Chlamydiaceae (P = 0.04, most abundant in Myotis myotis). There were significant differences in richness between species in both adults and juveniles/subadults, but there was no impact of sex on any alpha diversity index. When only adults are considered, there were significant differences in community membership between M. blythii and M. emarginatus (P = 0.011), and M. blythii and R. hipposideros (P = 0.004). There were also significant differences in community structure between M. blythii and M. emarginatus (P = 0.025), and M. blythii and R. hipposideros (P = 0.026). When adults of the four main species were compared, 14 OTUs were identified as differentially abundant using LEfSe. Only one difference was identified when comparing R. hipposideros adults and juvenile/subadults, with Klebsiella over-represented in the younger bats.ConclusionsBats have a complex and diverse microbiota with a high relative abundance of Proteobacteria. The relevance of this difference is unclear and requires further study. Differences in the microbiota were observed between bat species, perhaps reflecting different diets and environmental exposures.

Microbiota of field-collected Ixodes scapularis and Dermacentor variabilis from eastern and southern Ontario, Canada

The microbiota of hard ticks has been an area of growing interest due to the potential role that the broader microbial community may play in pathogen carriage and transmission. In the last two decades, Ontario, Canada has experienced rapid changes in the risk of tick-borne disease, primarily due to the range expansion of Ixodes scapularis. Another human-biter, Dermacentor variabilis, is a longstanding resident of the province, but currently poses minimal risk of pathogen transmission. To examine the microbiota of these two species, we collected adult and nymphal I. scapularis and D. variabilis from the eastern and southern regions of the province via tick dragging, and conducted next generation sequencing of 19 samples (composed of 45 ticks) via Illumina MiSeq. A total of 1400469 sequences were detected (median 69118/sample; range 23350–155227). The most abundant families of bacteria were unclassified Clostridiales and Ruminococcaceae for both I. scapularis and D. variabilis. No significant differences in the relative abundances of any phylum, class, order, family or genus were detected between locations (east vs south), sex, life stage or tick species. There were no differences in community membership or structure based on unifrac and AMOVA analyses. Female and male ticks had lower microbial diversity when compared to nymphs, based on the Simpson’s index and Shannon evenness index. The findings of our study differ from previous studies of these tick species conducted in other geographic areas, and highlight the potential role geography and related ecological factors may have in shaping the tick microbiota.

Implementation of an algorithm for selection of antimicrobial therapy for diarrhoeic calves: Impact on antimicrobial treatment rates, health and faecal microbiota

This study evaluated the impact of an algorithm targeting antimicrobial therapy of diarrhoeic calves on the incidence of diarrhoea, antimicrobial treatment rates, overall mortality, mortality of diarrhoeic calves and changes in the faecal microbiota. The algorithm was designed to target antimicrobial therapy in systemically ill calves from on two dairy farms. Retrospective (farm 1: 529 calves; farm 2: 639 calves) and prospective (farm 1: 639 calves; farm 2: 842 calves) cohorts were examined for 12 months before and after implementation of the algorithm. The Mantel–Haenszel test and Kaplan–Meier survival curves were used to assess the cumulative incidence risk (CIR) and time to development of each outcome before and after implementation of the algorithm. The CIR of antimicrobial treatment rates was 80% lower after implementation of the algorithm on both farms (CIR 0.19, 95% confidence interval 0.17–0.21). There was no difference in the CIR of overall mortality, but the CRI for mortality of diarrhoeic calves was lower in the period after implementation of the algorithm on one farm. The faecal microbiota of 15 healthy calves from both farms at each time period were characterised using a sequencing platform targeting the V4 region of the 16S rRNA gene. On both farms, there were significant differences in community membership and structure (parsimony P<0.001). Use of the algorithm for treatment of diarrhoeic calves reduced antimicrobial treatment rates without a negative impact on the health of calves. However, the experimental design did not take into account the potential confounding effects of dietary changes between the study periods.

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves.

BackgroundNeonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population‐based studies of cattle have investigated how the microbiota is impacted during diarrhea.ObjectivesTo characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.MethodsFifteen diarrheic calves between the ages of 1 and 30 days and 15 age‐matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high‐throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).ResultsSignificant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.Clinical RelevanceThe fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.

Detecting state changes for ecosystem conservation with long-term monitoring of species composition.

Effective conservation requires an understanding not only of contemporary vegetation distributions in the landscape, but also cognizance of vegetation transitions over time with the goal of maintaining persistence of all states within the landscape. Using a state and transition model framework, we investigated temporal transitions over 31years in species composition among five upland swamp vegetation communities in southeastern Australia. We applied fuzzy clustering to document transitions across communities; evaluated the resilience and resistance of communities to change; and explored the relationship between ecosystem states and major environmental factors posited to structure the system. We also evaluated the predictive ability of an established vegetation dynamics model. We found that community composition remained stable or underwent reversible or directional transitions depending on the vegetation type. Wetter communities (Ti-tree thicket and Cyperoid heath) were more stable (i.e., resistant) while drier communities showed a greater propensity to transition (i.e., had lower resistance) under the observed disturbance regime (low variance fire intervals). The resilience of drier communities differed under this regime, with Banksia thicket showing reversible compositional change, while Restioid heath and Sedgeland showed directional change. In accord with an established conceptual model, we found that communities were distributed along a hydrological gradient. In addition, vegetation structure, along with light penetration to ground level, differentiated communities. However, internal dynamics of drier communities were complex: differences in fire regime (penultimate fire interval in 2014 and number of fires since 1965) were unable to predict differences in community membership among sites. Aspects of the fire regime are expected to be more important predictors if fire intervals vary more strongly among sites in the future. Fuzzy clustering of compositional data allows managers to track community transitions over time and facilitates planned interventions for conservation purposes.

Disruption of the microbiota across multiple body sites in critically ill children.

BackgroundDespite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a pediatric ICU (PICU). Standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets.ResultsBacterial 16S rRNA gene sequences were analyzed from 71 total tongue swabs, 50 skin swabs, and 77 stool samples or rectal swabs. The mean age of the PICU patients was 2.9 years (range 1–9 years), and many were chronically ill children that had previously been hospitalized in the PICU. Relative to healthy adults and children, alpha diversity was decreased in PICU GI and tongue but not skin samples. Measures of beta diversity indicated differences in community membership at each body site between PICU, adult, and pediatric groups. Taxonomic alterations in the PICU included enrichment of gut pathogens such as Enterococcus and Staphylococcus at multiple body sites and depletion of commensals such as Faecalibacterium and Ruminococcus from GI samples. Alpha and beta diversity were unstable over time in patients followed longitudinally. We observed the frequent presence of “dominant” pathogens in PICU samples at relative abundance >50%. PICU samples were characterized by loss of site specificity, with individual taxa commonly present simultaneously at three sample sites on a single individual. Some pathogens identified by culture of tracheal aspirates were commonly observed in skin samples from the same patient.ConclusionsWe conclude that the microbiota in critically ill children differs sharply from the microbiota of healthy children and adults. Acknowledgement of dysbiosis associated with critical illness could provide opportunities to modulate the microbiota with precision and thereby improve patient outcomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0211-0) contains supplementary material, which is available to authorized users.

Dysbiosis Across Multiple Body Sites in Critically Ill Adult Surgical Patients.

The microbiota of critically ill patients likely undergoes dramatic changes but has not been rigorously studied with a culture-independent high-throughput approach. The aim of this study was to characterize spatial and temporal variation in the microbiota of critically ill patients. Trauma and acute surgery patients admitted to the intensive care unit (ICU) were sampled at five body sites (stool, tongue, skin, trachea, urine) every 3 to 4 days. A mean of 10.8 samples was collected from 32 patients with a mean sampling period of 8.8 days. Bacterial 16S rRNA sequences were amplified and sequenced for microbiota analyses. Results were compared to data from unhospitalized adult participants in the American Gut and Human Microbiome Projects. Relative to healthy adults, alpha diversity was decreased in ICU gut and skin samples at all time points. Diversity in tongue swabs decreased over time. Beta diversity measures indicated differences in community membership between critically ill and healthy adults at each body site. Taxonomic alterations in the ICU included depletion of important commensal bacteria such as Faecalibacterium in GI samples and Corynebacterium in skin swabs and enrichment with pathogens such as Enterococcus, Mycoplasma, and Staphylococcus. A high proportion of ICU sample sets contained pathogens present simultaneously at three body sites indicating widespread colonization. In several cases, clinically relevant airway infections were preceded by the appearance of the causative pathogen in tracheal microbiome profiles. These results demonstrate that the microbiome of critically ill patients undergoes a loss of diversity, loss of site specificity, and a shift toward dominant pathogens. These changes may provide opportunities to precisely modulate the microbiome and thereby improve patient outcomes.

Assessment of the Fecal Microbiota in Beef Calves.

BackgroundThere is increasing interest in the fecal microbiota, but study in calves has been limited.Hypothesis/ObjectivesTo evaluate the fecal microbiota of beef calves and cows on different farms, and to preliminarily explore the impact of antimicrobial exposure.AnimalsA total of 172 animals, 156 (91%) calves and 16 (9.3%) cows, were enrolled from 5 cow‐calf farms.MethodsThe fecal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V4 region) amplicons.ResultsThere were significant differences in the relative abundances of numerous phyla between calves on different farms. Farms could be separated into 2 groups: 1 (farms B and C) dominated by Firmicutes and 1 (farms A, D, and E) with predominance of Proteobacteria and Actinobacteria. Richness (median 2,974 versus 1,477, P = .008), diversity (51.4 versus 29.1, P = .0029), and evenness (0.73 versus 0.68, P = .006) were higher in cows. Over‐represented operational taxonomic units (OTUs) in cows tended to be from the classes Bacilli and Bacteroidia, whereas Clostridia and Actinobacteria were most prominently over‐represented in calves. There were differences in community membership (P = .028) and structure (P = .029) in calves that had a history of antimicrobial exposure compared those that did not. Eight (89%) over‐represented OTUs in the untreated group were Firmicutes (7 from the order Clostridiales), compared to only 3 (38%) (2 Clostridiales) in the untreated group.Conclusions and Clinical ImportanceInterfarm variation should be investigated to determine the causes and potential implications for health and production. Antimicrobial exposure may have an impact on the fecal microbiota at individual and farm levels.

Development of the faecal microbiota in foals.

The intestinal microbiota is a complex polymicrobial ecosystem that exerts extremely important roles in the development and maintenance of health. Recently, as new sequencing technologies have become more available, there has been a revolution in the understanding of the equine intestinal microbiota. However, studies characterising the pioneer intestinal bacteria colonising foals and its development over time are still limited. The objectives of this study were to characterise the intestinal bacterial colonisation of newborn foals and to follow individual animals over time until age 9 months. Longitudinal study. Eleven pregnant mares from one farm were enrolled and faecal samples were collected longitudinally from mares and foals during their first day post partum and again periodically until foals were age 9 months. The V4 region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Newborn foals had a rich and diverse bacterial community, which was mainly comprised of the Firmicutes phylum with several low abundant genera being unique at this age. Foals aged 2-30 days had significantly decreased diversity compared to older animals, with the majority of organisms classified as Akkermansia spp. After 60 days of life, the intestinal microbiota structure tended to remain stable, but differences in community membership were still present between 9-month-old animals and mature mares. Several differences at the phylum level were observed between different ages, including a higher abundance of Fibrobacteres after weaning. The intestinal microbiota of the equine newborn is already complex by the first day of life. Microbiota adaptation occurs during the first month and the microbiota of foals older than 60 days resemble the mother's microbiota, although differences in community membership are still present.

The rectal microbiota of cats infected with feline immunodeficiency virus infection and uninfected controls

Rectal swabs were collected from 31 cats, 16 with FIV infection and 15 uninfected controls, to evaluate and compare the rectal bacterial microbiota in cats with feline immunodeficiency virus (FIV) infection and uninfected controls. The rectal microbiota was characterized via next generation sequencing of 16S rRNA gene (V4 region) polymerase chain reaction products.Eighteen different phyla were identified. Firmicutes dominated in both groups, followed by Proteobacteria and Actinobacteria, but there were no significant differences between groups. When predominant orders are compared, FIV-infected cats had significant higher median relative abundances of Bifidobacteriales (P=0.022), Lactobacillales (P=0.022) and Aeromonadales (P=0.043). No differences were identified in the 50 most common genera when adjusted for false discovery rate. There were significant differences in community membership (Jaccard index, unifrac P=0.008, AMOVA P<0.001) and community structure (Yue&Clayton index, unifrac P=0.03, AMOVA P=0.005) between groups. However, only one metacommunity (enterotype) was identified.The rectal microbiota differed between cats with FIV infection and uninfected controls. Some of the changes that were noted have been associated with ‘dysbiosis’ and proinflammatory states in other species, so it is possible that subclinical alteration in the intestinal microbiota could influence the health of FIV-infected cats. Evaluation of the reasons for microbiota alteration and the potential impact on cat health is required.

Mo1711 Interleukin 35 and 37 Intestinal Expression and Peripheral Synthesis by Subsets of Regulatory Cells in Patients With Inflammatory Bowel Disease

Background: Primary sclerosing cholangitis (PSC) is a progressive disease of the biliary tree characterised by inflammation, fibrosis and stenoses. Inflammatory bowel disease (IBD) in patients with primary sclerosing cholangitis (PSC IBD) is considered to be a distinct phenotype of IBD with a multi factorial origin where microbiota most likely have a substantial role. In our pilot study, our aim was to compare the microbiota composition in PSC and/or IBD groups with ulcerative colitis (UC) and healthy controls. Methods: Total number of 15 individuals was used in presented study: 4 control healthy samples, 4 UC patients, 4 PSC-IBD patients and 3 PSC (without IBD). Fecal microbiota composition was assesed by sequencing of variable V4 and V5 region of 16S rRNA gene on Personal Genome Machine platform (Fisher Scientific). Library preparation, template preparation and template sequencing was performed according to manufacturer's protocols. Obtained data were filtered by quality and length and processed for alpha and beta diversity analyses using QIIME software package. Results: Following significant changes in bacterial numbers were observed among tested groups: PSC versus PSC-IBD: Higher Bifidobacterium sp. (18 vs 2.71 %), Lachnospira (4.58 vs 0,68 %) and Dorea sp (5.7 vs 1.55 %) and lower Enterococcus sp. (0 vs 9.14 %), Faecallibacterium sp. (1.31 vs 4.12 %) and Prevotella/ Paraprevotella sp. (0 vs 9.71 %) numbers. PSC-IBD versus UC: Higher Bacteroides sp. (17.13 vs. 4.86 %), Enterococcus sp. (9.14 vs 0 %) and Prevotella/Paraprevotella sp. (9.71 vs 2.13 %) and lower Bifidobacterium sp (2.71 vs 12.95 %) and Faecallibacterium sp. (4.12 vs 16.4 %) numbers. The clustering of samples according to the type is stronger with the unweighted UniFrac metric than with the weighted metric, suggesting that differences in community membership (rather than community structure) discriminate better among groups. Conclusions: Members of genus Faecallibacterium and Prevotella showed highest variations with regards to PSC /PSC-IBD/UC groups comparison. Control samples showed higher species richness than patients samples. Our data suggest that microbiota composition differs among patients with PSC (without IBD), PSC IBD and UC. Presented data should be considered as preliminary, as more samples are needed for statistical analyses to support detected observations.

Spatially resolved sampling reveals dynamic microbial communities in rising hydrothermal plumes across a back-arc basin.

Within hydrothermal plumes, chemosynthetic processes and microbe-mineral interactions drive primary productivity in deep-ocean food webs and may influence transport of elements such as iron. However, the source of microorganisms in plumes and the factors governing how these communities assemble are poorly understood, in part due to lack of data from early stages of plume formation. In this study, we examined microbial community composition of rising hydrothermal plumes from five vent fields along the Eastern Lau Spreading Center. Seafloor and plume microbial communities were significantly dissimilar and shared few phylotypes. Plume communities were highly similar to each other with significant differences in community membership only between Kilo Moana and Mariner, two vents that are separated by extremes in depth, latitude and geochemistry. Systematic sampling of waters surrounding the vents revealed that species richness and phylogenetic diversity was typically highest near the vent orifice, implying mixing of microbial communities from the surrounding habitats. Above-plume background communities were primarily dominated by SAR11, SAR324 and MG-I Archaea, while SUP05, Sulfurovum, Sulfurimonas, SAR324 and Alteromonas were abundant in plume and near-bottom background communities. These results show that the ubiquitous water-column microorganisms populate plume communities, and that the composition of background seawater exerts primary influence on plume community composition, with secondary influence from geochemical and/or physical properties of vents. Many of these pervasive deep-ocean organisms are capable of lithotrophy, suggesting that they are poised to use inorganic electron donors encountered in hydrothermal plumes.

Evaluation of the impact of refrigeration on next generation sequencing-based assessment of the canine and feline fecal microbiota.

BackgroundEvaluation of factors that might impact microbiota assessment is important to avoid spurious results, particularly in field and multicenter studies where sample collection may occur distant from the laboratory. This study evaluated the impact of refrigeration on next generation sequence-based assessment of the canine and feline fecal microbiota. Fecal samples were collected from seven dogs and ten cats, and analysed at baseline and after 3, 7, 10 and 14 days of storage at 4°C.ResultsThere were no differences in community membership or population structure between timepoints for either dogs or cats, nor were there any differences in richness, diversity and evenness. There were few differences in relative abundance of phyla or predominant genera, with the only differences being significant increases in Actinobacteria between Days 0-14 (P = 0.0184) and 1-14 (P = 0.0182) for canine samples, and a decrease in Erysipelotrichaceae incertae sedis between Day 0 and Day 7 (median 4.9 vs 2.2%, P = 0.046) in feline samples.Linear discriminant analysis effect size and indicator analysis identified a small number of genera that were over-represented in, or defining characteristics of, Day 14 samples. These were predominantly Proteobacteria and Actinobacteria, with Psychrobacter and Arthrobacter enriched in both canine and feline Day 14 samples.ConclusionsStorage for at least 14 days at 4°C has limited impact on culture-independent assessment of the canine and feline fecal microbiota, although changes in some individual groups may occur.

Transplantation-associated long-term immunosuppression promotes oral colonization by potentially opportunistic pathogens without impacting other members of the salivary bacteriome.

Solid-organ transplant recipients rely on pharmacological immunosuppression to prevent allograft rejection. The effect of such chronic immunosuppression on the microflora at mucosal surfaces is not known. We evaluated the salivary bacterial microbiome of 20 transplant recipients and 19 nonimmunosuppressed controls via 454 pyrosequencing of 16S rRNA gene amplicons. Alpha-diversity and global community structure did not differ between transplant and control subjects. However, principal coordinate analysis showed differences in community membership. Taxa more prevalent in transplant subjects included operational taxonomic units (OTUs) of potentially opportunistic Gammaproteobacteria such as Klebsiella pneumoniae, Pseudomonas fluorescens, Acinetobacter species, Vibrio species, Enterobacteriaceae species, and the genera Acinetobacter and Klebsiella. Transplant subjects also had increased proportions of Pseudomonas aeruginosa, Acinetobacter species, Enterobacteriaceae species, and Enterococcus faecalis, among other OTUs, while genera with increased proportions included Klebsiella, Acinetobacter, Staphylococcus, and Enterococcus. Furthermore, in transplant subjects, the dose of the immunosuppressant prednisone positively correlated with bacterial richness, while prednisone and mycophenolate mofetil doses positively correlated with the prevalence and proportions of transplant-associated taxa. Correlation network analysis of OTU relative abundance revealed a cluster containing potentially opportunistic pathogens as transplant associated. This cluster positively correlated with serum levels of C-reactive protein, suggesting a link between the resident flora at mucosal compartments and systemic inflammation. Network connectivity analysis revealed opportunistic pathogens as highly connected to each other and to common oral commensals, pointing to bacterial interactions that may influence colonization. This work demonstrates that immunosuppression aimed at limiting T-cell-mediated responses creates a more permissive oral environment for potentially opportunistic pathogens without affecting other members of the salivary bacteriome.