Sandy or permeable sediment deposits cover the majority of the shallow ocean seafloor, and yet the associated bacterial communities remain poorly described. The objective of this study was to expand the characterization of bacterial community diversity in permeable sediment impacted by advective pore water exchange and to assess effects of spatial, temporal, hydrodynamic, and geochemical gradients. Terminal restriction fragment length polymorphism (TRFLP) was used to analyze nearly 100 sediment samples collected from two northeastern Gulf of Mexico subtidal sites that primarily differed in their hydrodynamic conditions. Communities were described across multiple taxonomic levels using universal bacterial small subunit (SSU) rRNA targets (RNA-and DNA-based) and functional markers for nitrification (amoA) and denitrification (nosZ). Clonal analysis of SSU rRNA targets identified several taxa not previously detected in sandy sediments (i.e., Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Firmicutes). Sequence diversity was high among the overall bacterial and denitrifying communities, with members of the Alphaproteobacteria predominant in both. Diversity of bacterial nitrifiers (amoA) remained comparatively low and did not covary with the other gene targets. TRFLP fingerprinting revealed changes in sequence diversity from the family to species level across sediment depth and study site. The high diversity of facultative denitrifiers was consistent with the high permeability, deeper oxygen penetration, and high rates of aerobic respiration determined in these sediments. The high relative abundance of Gammaproteobacteria in RNA clone libraries suggests that this group may be poised to respond to short-term periodic pulses of growth substrates, and this observation warrants further investigation.

Intestinal barrier immaturity, or “leaky gut,” is the proximate cause of susceptibility to necrotizing enterocolitis in preterm neonates. However, the impact of intestinal microbiota development on intestinal mucosal barrier maturation has not been evaluated in this population. In this study, we investigated a longitudinally sampled cohort of 38 preterm infants < 33 weeks gestation monitored for intestinal permeability (IP) and fecal microbiota during the first 2 weeks of life. Rapid decrease in IP indicating intestinal barrier function maturation correlated with significant increase in community diversity. In particular, members of the Clostridiales and Bifidobacterium were highly transcriptionally active, and progressively increasing abundance in Clostridiales was significantly associated with decreased intestinal permeability. Further, neonatal factors previously identified to promote intestinal barrier maturation, including early exclusive breastmilk feeding and shorter duration antibiotic exposure, associate with the early colonization of the intestinal microbiota by members of the Clostridiales, which altogether are associated with improved intestinal barrier function in preterm infants.

Background: Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed Community State Types (CSTs). This approach is advantageous because collapsing a hyper dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epidemiological studies and statistical modeling. Vaginal communities are typically assigned to CSTs based on the results of hierarchical clustering of the pairwise distances between samples. However, this approach is problematic because it complicates between-study comparisons and because the results are entirely dependent on the particular set of samples that were analyzed. We sought to standardize and advance the assignment of samples to CSTs.Results: We developed VALENCIA (VAginaL community state typE Nearest CentroId clAssifier), a nearest centroid based tool which classifies samples based on their similarity to a set of reference centroids. The references were defined using a comprehensive set of 13,160 taxonomic profiles from 1,975 women in the United States. This large dataset allowed us to comprehensively identify, define, and characterize vaginal CSTs common to reproductive age women, and expand upon the CSTs that had been defined in previous studies. We validated the broad applicability of VALENCIA for the classification of vaginal microbial communities by using it to classify three test datasets which included reproductive age African women, adolescent girls, and menopausal women. VALENCIA performed well on all three datasets despite the substantial variations in sequencing strategies and bioinformatics pipelines, indicating its broad application to vaginal microbiota. We further describe the relationships between community characteristics (vaginal pH, Nugent score) and participant demographics (race, age) and the CSTs defined by VALENCIA. Conclusion: VALENCIA provides a much-needed solution for the robust and reproducible assignment of vaginal community state types. This will allow unbiased analysis of both small and large vaginal microbiota datasets, comparisons between datasets and meta-analyses that combine multiple datasets.

We identified microbial taxa that catalyze phytodetritus degradation and denitrification in permeable coastal sediments of the northeast Gulf of Mexico. Stable isotope probing experiments were used to track the assimilation of isotopically labeled substrate into bacterial deoxyribonucleic acid (DNA) and directly link the taxonomic identification of benthic microorganisms with particulate organic matter degradation and denitrification activity. Phytodetritus deposition events were simulated in the laboratory by the addition of 13 C-enriched, heat-killed Spirulina cells to intact sediment core incubations. Immediate increases in O 2 consumption (3-fold), N 2 efflux (16-fold), and dissolved inorganic nitrogen efflux were observed after phytodetritus addition relative to unamended treatments, suggesting that the benthic microbial community was poised to immediately begin oxidizing deposited organic matter. Analyses of 16S ribosomal ribonucleic acid gene sequences amplified from 13 C-enriched DNA fractions demonstrated that members of the Gammaproteobacteria (Vibrionales and Alteromonadales), Deltaproteobacteria, Actinobacteria, Verrucomicrobia, and Planctomycetes metabolized the phytodetritus amendment. Terminal restriction length polymorphism analyses showed increases in the relative abundance of Gammaproteobacteria, Planctomycetes, and Bacteroidetes with phytodetritus addition. Alphaproteobacteria were identified as metabolically active denitrifiers by phylogenetic analysis of nitrous oxide reductase gene sequences from 13 C-enriched DNA fractions. This study provides the first identification of microorganisms responsible for organic matter degradation in marine sediments by DNA sequence analysis. Microbial assemblages recognized for high-molecular-weight organic matter oxidation in the marine water column were important in catalyzing these processes in permeable sediments.

We characterized the composition and structure of the vaginal microbiota in a cohort of 149 women with genital Chlamydia trachomatis infection at baseline who were followed quarterly for 9 months after antibiotic treatment. At time of diagnosis, the vaginal microbiota was dominated by Lactobacillus iners or a diverse array of bacterial vaginosis–associated bacteria including Gardnerella vaginalis. Interestingly, L. iners–dominated communities were most common after azithromycin treatment (1 g monodose), consistent with the observed relative resistance of L. iners to azithromycin. Lactobacillus iners–dominated communities have been associated with increased risk of C. trachomatis infection, suggesting that the impact of antibiotic treatment on the vaginal microbiota could favor reinfections. These results provide support for the dual need to account for the potential perturbing effect(s) of antibiotic treatment on the vaginal microbiota, and to develop strategies to protect and restore optimal vaginal microbiota.