A new genomic blueprint of the human gut microbiota

Abstract

The composition of the human gut microbiota is linked to health and disease, but knowledge of individual microbial species is needed to decipher their biological roles. Despite extensive culturing and sequencing efforts, the complete bacterial repertoire of the human gut microbiota remains undefined. Here we identify 1,952 uncultured candidate bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut microbiomes. These uncultured genomes substantially expand the known species repertoire of the collective human gut microbiota, with a 281% increase in phylogenetic diversity. Although the newly identified species are less prevalent in well-studied populations compared to reference isolate genomes, they improve classification of understudied African and South American samples by more than 200%. These candidate species encode hundreds of newly identified biosynthetic gene clusters and possess a distinctive functional capacity that might explain their elusive nature. Our work expands the known diversity of uncultured gut bacteria, which provides unprecedented resolution for taxonomic and functional characterization of the intestinal microbiota.

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

“…Despite the genomes assembled from metagenomes are not free from assembly problems [64,65] and should be considered for complementing rather than substituting those obtained from isolate sequencing, large-scale metagenomic assembly efforts to mine available metagenomic data showed to be crucial to uncover the whole diversity of environment-specific microbiomes [11,66,67], especially in these under-investigated hosts. Indeed, given the efficiency of metagenomic assembly pipelines [67,68] and the availability of complementary tools to explore the microbial diversity in a microbiome [69,70], the limiting factor appears to be the technical difficulties in sampling primates in the wild.…”

The Role of Lung and Gut Microbiota in the Pathology of Asthma

“…Bacteria within the gut confer several functions to the host, including vitamin production, absorption of ions, protection against pathogens, histological development, enhanced immune functions, and fermentation of food (Hillman et al, 2017). They are typically dominated by five phyla; Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, and Tenericutes (Desai and Oppenheimer, 2016;Almeida et al, 2019), whereas Bacteroides, Faecalibacterium, and Bifidobacterium are the most prevalent genera in healthy adults (Marsland et al, 2015). The oral cavity is mainly colonized by bacteria from the Streptococcaceae, Pasteurellaceae, Veillonellaceae, Prevotellaeace, and Neisseriaceae families and Gemella genus; the stomach mostly contains bacteria from the Lactobacillaceae family; the small intestine is dominated by Lactobacillaceae, Enterobacteriaceae, and Streptococcaceae; and the most densely colonized large intestine contains bacteria from the families of Enterococcaceae, Clostridiaceae, Enterobacteriaceae, Bacteroidaceae, Bifidobacteriaceae, Fusobacteriaceae, Lactobacillaceae, Peptostreptococcaceae, Peptococcaceae, Prevotellaeace, Lachnospiraceae, Ruminococcaceae, Rikenelleace, and the phylum Verrucomimicrobia (Hillman et al, 2017;Pereira and Berry, 2017).…”

Transplant associated infections—The role of the gastrointestinal microbiota and potential therapeutic options

“…There have been a plethora of clinical studies that have illustrated the gastrointestinal microbiota's role with respect to immune regulation, metabolic modulation, angiogenesis promotion, maintenance of gastrointestinal epithelial health, as well as food digestion, distribution and metabolism . Adverse changes in the gastrointestinal microbiota have been implicated in the pathogenesis of various diseases such as inflammatory bowel disease, irritable bowel syndrome, rheumatoid arthritis, ankylosing spondylitis, cognitive impairment, metabolic syndrome and more recently in anxiety and depression . With respect to chronic kidney disease, the increased production of uraemic toxins such as indoxyl sulfate and p‐cresyl sulfate has been hypothesised to lead to intestinal inflammation, renal tubulointerstitial fibrosis and progression to kidney disease …”

“…24 Adverse changes in the gastrointestinal microbiota have been implicated in the pathogenesis of various diseases such as inflammatory bowel disease, irritable bowel syndrome, rheumatoid arthritis, ankylosing spondylitis, cognitive impairment, metabolic syndrome and more recently in anxiety and depression. [25][26][27][28][29] With respect to chronic kidney disease, the increased production of uraemic toxins such as indoxyl sulfate and p-cresyl sulfate has been hypothesised to lead to intestinal inflammation, renal tubulointerstitial fibrosis and progression to kidney disease. 30 The gut microbiome patterns in patients with dialysis-dependent end-stage kidney disease have been well documented in the literature.…”