The genus Prevotella includes more than fifty characterized species occurring in very different natural habitats, yet the majority have been associated with the human host. In the human microbiome, Prevotella species are highly abundant in different body-sites where they are key players in the balance between health and disease. Host factors related with diet, lifestyle, and geography are fundamental in affecting Prevotella species-and strain-level diversity in the human microbiome. These factors, along with the ecological relationship of Prevotella with other members of the microbiome, likely determine the extent of Prevotella contribution to human metabolism and health. Here we review the diversity, prevalence and impact of Prevotella spp. in the human host highlighting how genomics has improved, and will further help framing its ecological role. We also provide suggestions for future research to better understand their possible functions and the role of Westernisation in the host-Prevotella symbiotic relationship in the context of maintaining human health. genomes genome length (Mb) (perc) P. copri complex 106 3.65±0.21 44.93±0.23 human gut P. intermedia 33 2.79±0.13 43.45±0.15 human oral,empyema P. ruminicola 9 3.53±0.3 47.69±0.71 ruminant rumen P. bivia 8 2.49±0.08 39.79±0.17 human vagina P. denticola 7 3.06±0.11 50.04±0.18 human vagina,oral P. disiens 7 2.86±0.13 39.93±0.21 human vagina,gut,bartholin abscess P. timonensis 7 3.09±0.16 42.41±0.16 human vagina,breast abscess P. bryantii 6 3.41±0.14 38.8±0.19 ruminant rumen P. amnii 5 2.4±0.03 36.52±0.08 human vagina,amniotic fluid P. melaninogenica 5 3.14±0.12 41.02±0.23 human vagina,oral,sputum P. nigrescens 5 2.85±0.16 42.64±0.11 human oral P. oralis 5 2.87±0.07 44.54±0.09 human vagina,gut,oral P. oris 5 3.18±0.12 43.86±0.09 human oral,airways P. pectinovora 5 3.17±0.12 47.74±0.25 swine gut P. buccae 4 3.22±0.12 51.15±0.19 human oral P. buccalis 4 2.99±0.2 45.5±0.18 human vagina P. baroniae 3 3.09±0.06 53.1±0.17 human oral P. corporis 3 2.81±0.04 44.1±0.1 human vagina P. histicola 3 3.0±0.06 41.2±0.0 human vagina,oral P. loescheii 3 3.49±0.02 46.6±0.0 human oral P. maculosa 3 3.25±0.09 47.5±0.17 human oral P. micans 3 2.45±0.03 45.5±0.0 human oral P. oulorum 3 2.82±0.02 46.8±0.0 human oral P. pallens 3 3.1±0.04 37.47±0.06 human oral P. salivae 3 3.22±0.1 41.5±0.17 human gut,oral P. scopos 3 3.23±0.06 40.7±0.0 human oral P. stercorea 3 3.11±0.01 48.93±0.06 human gut P. veroralis 3 2.89±0.09 41.83±0.06 human oral 130 Prevotella in humans: different key species in different body-sitesEven within a given host, Prevotella species are stratified in different body locations. Specifically in humans and similarly to other genera 41 , distinct Prevotella species have been identified and isolated from the oral cavity and respiratory tract, vagina, skin and intestine. Surveying the 135 prevalence and abundance of the known characterised Prevotella species in over 9,500 individuals from multiple integrated datasets 15 , reveals that with the exception of vaginal Prevotel...

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

BackgroundVariation in induced models of autoimmunity has been attributed to the housing environment and its effect on the gut microbiota. In Graves’ disease (GD), autoantibodies to the thyrotropin receptor (TSHR) cause autoimmune hyperthyroidism. Many GD patients develop Graves’ orbitopathy or ophthalmopathy (GO) characterized by orbital tissue remodeling including adipogenesis. Murine models of GD/GO would help delineate pathogenetic mechanisms, and although several have been reported, most lack reproducibility. A model comprising immunization of female BALBc mice with a TSHR expression plasmid using in vivo electroporation was reproduced in two independent laboratories. Similar orbital disease was induced in both centers, but differences were apparent (e.g., hyperthyroidism in Center 1 but not Center 2). We hypothesized a role for the gut microbiota influencing the outcome and reproducibility of induced GO.ResultsWe combined metataxonomics (16S rRNA gene sequencing) and traditional microbial culture of the intestinal contents from the GO murine model, to analyze the gut microbiota in the two centers. We observed significant differences in alpha and beta diversity and in the taxonomic profiles, e.g., operational taxonomic units (OTUs) from the genus Lactobacillus were more abundant in Center 2, and Bacteroides and Bifidobacterium counts were more abundant in Center 1 where we also observed a negative correlation between the OTUs of the genus Intestinimonas and TSHR autoantibodies. Traditional microbiology largely confirmed the metataxonomics data and indicated significantly higher yeast counts in Center 1 TSHR-immunized mice. We also compared the gut microbiota between immunization groups within Center 2, comprising the TSHR- or βgal control-immunized mice and naïve untreated mice. We observed a shift of the TSHR-immunized mice bacterial communities described by the beta diversity weighted Unifrac. Furthermore, we observed a significant positive correlation between the presence of Firmicutes and orbital-adipogenesis specifically in TSHR-immunized mice.ConclusionsThe significant differences observed in microbiota composition from BALBc mice undergoing the same immunization protocol in comparable specific-pathogen-free (SPF) units in different centers support a role for the gut microbiota in modulating the induced response. The gut microbiota might also contribute to the heterogeneity of induced response since we report potential disease-associated microbial taxonomies and correlation with ocular disease.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0478-4) contains supplementary material, which is available to authorized users.

The rumen microbiome is fundamental for the productivity and health of dairy cattle and diet is known to influence the rumen microbiota composition. In this study, grape-pomace, a natural source of polyphenols, and copper sulfate were provided as feed supplementation in 15 Holstein-Friesian calves, including 5 controls. After 75 days of supplementation, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the composition of the rumen microbiota. From this, the rumen metagenome was predicted to obtain the associated gene functions and metabolic pathways in a cost-effective manner. Results showed that feed supplementations did alter the rumen microbiome of calves. Copper and grape-pomace increased the diversity of the rumen microbiota: the Shannon’s and Fisher’s alpha indices were significantly different across groups (p-values 0.045 and 0.039), and Bray-Curtis distances could separate grape-pomace calves from the other two groups. Differentially abundant taxa were identified: in particular, an uncultured Bacteroidales UCG-001 genus and OTUs from genus Sarcina were the most differentially abundant in pomace-supplemented calves compared to controls (p-values 0.003 and 0.0002, respectively). Enriched taxonomies such as Ruminiclostridium and Eubacterium sp., whose functions are related to degradation of the grape- pomace constituents (e.g. flavonoids or xyloglucan) have been described (p-values 0.027/0.028 and 0.040/0.022 in Pomace vs Copper and Controls, respectively). The most abundant predicted metagenomic genes belonged to the arginine and proline metabolism and the two- component (sensor/responder) regulatory system, which were increased in the supplemented groups. Interestingly, the lipopolysaccharide biosynthetic pathway was decreased in the two supplemented groups, possibly as a result of antimicrobial effects. Methanogenic taxa also responded to the feed supplementation, and methane metabolism in the rumen was the second most different pathway (up-regulated by feed supplementations) between experimental groups.

in an exploratory, block-randomised, parallel, double-blind, single-centre, placebo-controlled superiority study (ISRCTN12562026, funded by Cultech Ltd), 220 Bulgarian participants (30 to 65 years old) with BMI 25-34.9 kg/m 2 received Lab4P probiotic (50 billion/day) or a matched placebo for 6 months. Participants maintained their normal diet and lifestyle. primary outcomes were changes in body weight, BMi, waist circumference (WC), waist-to-height ratio (WtHR), blood pressure and plasma lipids. Secondary outcomes were changes in plasma C-reactive protein (CRP), the diversity of the faecal microbiota, quality of life (QoL) assessments and the incidence of upper respiratory tract infection (URTI). Significant between group decreases in body weight (1.3 kg, p < 0.0001), BMI (0.045 kg/m 2 , p < 0.0001), WC (0.94 cm, p < 0.0001) and WtHR (0.006, p < 0.0001) were in favour of the probiotic. Stratification identified greater body weight reductions in overweight subjects (1.88%, p < 0.0001) and in females (1.62%, p = 0.0005). Greatest weight losses were among probiotic hypercholesterolaemic participants (−2.5%, p < 0.0001) alongside a significant between group reduction in small dense LDL-cholesterol (0.2 mmol/L, p = 0.0241). Improvements in QoL and the incidence rate ratio of URTI (0.60, p < 0.0001) were recorded for the probiotic group. No adverse events were recorded. Six months supplementation with Lab4P probiotic resulted in significant weight reduction and improved small dense low-density lipoprotein-cholesterol (sdLDL-C) profiles, QoL and URTI incidence outcomes in overweight/obese individuals. World Health Organisation (WHO) global estimates indicate that 39% of adults are overweight and 13% are obese and trends suggest that levels will continue to rise as a result of current dietary habits and sedentary lifestyles 1. The burden of obesity on primary healthcare providers is substantial and it is estimated that, in England alone in 2013, excess body weight in women cost £2.2 billion in consultations and £1.9 billion for prescription medications 2. One of the consequences of obesity is the increased incidence of Metabolic Syndrome (MetS)-an umbrella term used for a cluster of interrelated metabolic conditions linked with obesity including hypercholesterolaemia,