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Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes were strongly associated with long-term diets, particularly protein and animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study of 10 subjects showed that microbiome composition changed detectably within 24 hours of initiating a high-fat/low-fiber or low-fat/high-fiber diet, but that enterotype identity remained stable during the 10-day study. Thus, alternative enterotype states are associated with long-term diet.

To further understand how diets containing high levels of fibre protect against colorectal cancer, we examined the effects of diets high in nonstarch polysaccharides (NSP) or high in NSP plus resistant starch (RS) on the composition of the faecal microbial community in 46 healthy adults in a randomized crossover intervention study. Changes in bacterial populations were examined using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Bacterial profiles demonstrated changes in response to the consumption of both RS and NSP diets [analysis of similarities (ANOSIM): R=0.341-0.507, P<0.01]. A number of different DGGE bands with increased intensity in response to dietary intervention were attributed to as-yet uncultivated bacteria closely related to Ruminococcus bromii. A real-time PCR assay specific to the R. bromii group was applied to faecal samples from the dietary study and this group was found to comprise a significant proportion of the total community when individuals consumed their normal diets (4.4±2.6% of total 16S rRNA gene abundance) and numbers increased significantly (±67%, P<0.05) with the RS, but not the NSP, dietary intervention. This study indicates that R. bromii-related bacteria are abundant in humans and may be significant in the fermentation of complex carbohydrates in the large bowel.

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii , previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.

Mammalian gut microbial communities form intricate mutualisms with their hosts, which have profound implications on overall health. One group of important gut microbial mutualists are bacteria in the genus Ruminococcus , which serve to degrade and convert complex polysaccharides into a variety of nutrients for their hosts. Isolated decades ago from the bovine rumen, ruminococci have since been cultured from other ruminant and non-ruminant sources, and next-generation sequencing has further shown their distribution to be widespread in a diversity of animal hosts. While most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic, nonruminant-associated species, such as those found in humans. Furthermore, a mechanistic understanding of the role of Ruminococcus spp. in their respective hosts is still a work in progress. This review highlights the broad work done on species within the genus Ruminococcus with respect to their physiology, phylogenetic relatedness, and their potential impact on host health.

An anaerobic isolate, strain AT7T, was cultivated from a stool sample of a morbidly obese French woman using a microbial culturomics approach. The 16S rRNA gene sequence analysis showed that strain AT7T exhibited 96% nucleotide sequence similarity with Ruminococcus torques strain JCM 6553T (= ATCC 27756T = VPI B2-51T), currently the closest related species with a validly published name. The strain was observed to be a Gram-stain positive, non-motile, asporogenous and coccobacillary-shaped bacterium. It was found to be catalase positive and oxidase negative. Its major fatty acids were identified as C16:0 (54%) and C18:1n9 (30%). The draft genome of strain AT7T is 3,069,882 bp long with 42.4% G+C content. 2925 genes were predicted, including 2867 protein-coding genes and 58 RNAs. Based on phenotypic, biochemical, phylogenetic and genomic evidence, we propose the creation of the new genus Mediterraneibacter and species, Mediterraneibacter massiliensis, that contains strain AT7T (= CSUR P2086T = DSM 100837T), and the reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus, Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., with type strain Eg2T (= KCTC 5757T = JCM15917T), Mediterraneibacter lactaris comb. nov., with type strain ATCC 29176T (= VPI X6-29T), Mediterraneibacter torques comb. nov., with type strain ATCC 27756T (= VPI B2-51T), Mediterraneibacter gnavus comb. nov., with type strain ATCC 29149T (= VPI C7-9T) and Mediterraneibacter glycyrrhizinilyticus comb. nov., with type strain ZM35T (= JCM 13368T = DSM 17593T), respectively.

Background: A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels. Methodology/Principal Findings: Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin-and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37). Conclusions/Significance: Our comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.

Background The human microbiome plays an important role in cancer. Accumulating evidence indicates that commensal microbiome-derived DNA may be represented in minute quantities in the cell-free DNA of human blood and could possibly be harnessed as a new cancer biomarker. However, there has been limited use of rigorous experimental controls to account for contamination, which invariably affects low-biomass microbiome studies. Results We apply a combination of 16S-rRNA-gene sequencing and droplet digital PCR to determine if the specific detection of cell-free microbial DNA (cfmDNA) is possible in metastatic melanoma patients. Compared to matched stool and saliva samples, the absolute concentration of cfmDNA is low but significantly above the levels detected from negative controls. The microbial community of plasma is strongly influenced by laboratory and reagent contaminants introduced during the DNA extraction and sequencing processes. Through the application of an in silico decontamination strategy including the filtering of amplicon sequence variants (ASVs) with batch dependent abundances and those with a higher prevalence in negative controls, we identify known gut commensal bacteria, such as Faecalibacterium , Bacteroides and Ruminococcus , and also other uncharacterised ASVs. We analyse additional plasma samples, highlighting the potential of this framework to identify differences in cfmDNA between healthy and cancer patients. Conclusions Together, these observations indicate that plasma can harbour a low yet detectable level of cfmDNA. The results highlight the importance of accounting for contamination and provide an analytical decontamination framework to allow the accurate detection of cfmDNA for future biomarker studies in cancer and other diseases.

Bacteria in the genus Ruminococcus are important and ubiquitous members of mammalian guts. In particular, ruminococci are key contributors to the rumen ecosystem because they are capable of digesting a wide range of plant cell wall polysaccharides. In bovines, Ruminococcus albus 7 is a primary cellulose degrader that ferments acetate, a nutrient usable by its host. Moreover, it is one of the few organisms that ferments cellulose to ethanol at mesophilic temperatures in vitro. The mechanism of cellulose degradation by R. albus 7 is not well-defined and is thought to involve pilin-like proteins, unique carbohydrate-binding domains, a thick glycocalyx, and cellulosomes. We compared the genome sequence for R. albus 7 with other Clostridiales known to utilize cellulosomes, in addition to other non-fibrolytic clostridia. We found that R. albus 7 does not encode for cellulosomal components. We further probed the fibrolytic capabilities of R. albus 7 using a combination of fermentation analyses and RNA-seq-based transcriptomics. We found that R. albus 7 is capable of fermenting a wide range of fibrous substrates into ethanol. When grown on cellulose in a chemostat, R. albus 7 utilized a carbohydrate-degrading strategy that involves overexpression of the rare CBM37 domain and the tryptophan biosynthetic operon. Our findings contribute to the understanding of carbohydrate degradation by this organism, which may enhance industrial cellulose fermentation efforts, in addition to providing insight into the role of ruminococci as key members of the mamalian gut microbiota.

Dysbiosis, or imbalance in the gut microbiome, has been implicated in auto-immune, inflammatory, neurological diseases as well as in cancers. More recently it has also been shown to be associated with ocular diseases. In the present study, the association of gut microbiome dysbiosis with bacterial Keratitis, an inflammatory eye disease which significantly contributes to corneal blindness, was investigated. Bacterial and fungal gut microbiomes were analysed using fecal samples of healthy controls (HC, n = 21) and bacterial Keratitis patients (BK, n = 19). An increase in abundance of several anti-inflammatory organisms including Dialister, Megasphaera, Faecalibacterium, Lachnospira, Ruminococcus and Mitsuokella and members of Firmicutes, Veillonellaceae, Ruminococcaceae and Lachnospiraceae was observed in HC compared to BK patients in the bacterial microbiome. In the fungal microbiome, a decrease in the abundance of Mortierella, Rhizopus, Kluyveromyces, Embellisia and Haematonectria and an increase in the abundance of pathogenic fungi Aspergillus and Malassezia were observed in BK patients compared to HC. In addition, heatmaps, PCoA plots and inferred functional profiles also indicated significant variations between the HC and BK microbiomes, which strongly suggest dysbiosis in the gut microbiome of BK patients. This is the first study demonstrating the association of gut microbiome with the pathophysiology of BK and thus supports the gut–eye axis hypothesis. Considering that Keratitis affects about 1 million people annually across the globe, the data could be the basis for developing alternate strategies for treatment like use of probiotics or fecal transplantation to restore the healthy microbiome as a treatment protocol for Keratitis.

Background Gut microbiota plays an important role in many metabolic diseases such as diabetes and atherosclerosis. Apolipoprotein E (apoE) knock-out (KO) mice are frequently used for the study of hyperlipidemia and atherosclerosis. However, it is unknown whether apoE KO mice have altered gut microbiota when challenged with a Western diet. Methods In the current study, we assessed the gut microbiota profiling of apoE KO mice and compared with wild-type mice fed either a normal chow or Western diet for 12 weeks using 16S pyrosequencing. Results On a western diet, the gut microbiota diversity was significantly decreased in apoE KO mice compared with wild type (WT) mice. Firmicutes and Erysipelotrichaceae were significantly increased in WT mice but Erysipelotrichaceae was unchanged in apoE KO mice on a Western diet. The weighted UniFrac principal coordinate analysis exhibited clear separation between WT and apoE KO mice on the first vector (58.6%) with significant changes of two dominant phyla ( Bacteroidetes and Firmicutes ) and seven dominant families ( Porphyromonadaceae , Lachnospiraceae, Ruminococcaceae, Desulfovibrionaceae, Helicobacteraceae, Erysipelotrichaceae and Veillonellaceae ). Lachnospiraceae was significantly enriched in apoE KO mice on a Western diet. In addition, Lachnospiraceae and Ruminococcaceae were positively correlated with relative atherosclerosis lesion size in apoE KO. Conclusions Collectively, our study showed that there are marked changes in the gut microbiota of apoE KO mice, particularly challenged with a Western diet and these alterations may be possibly associated with atherosclerosis.