A new genomic blueprint of the human gut microbiota

By Alexandre Almeida, Alex L. Mitchell, M. Boland, S. Forster, G. Gloor, Aleksandra Tarkowska, T. Lawley, Robert D. Finn. Nature, 2019

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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. The known species repertoire of the collective human gut microbiota is substantially expanded with the discovery of 1,952 uncultured bacterial species that greatly improve classification of understudied African and South American samples.

Subfields: Food Science, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b51a6b9d92d9dfbc955f605b0268c71ca6363888

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Citations in the corpus

Benchmarking Metagenomics Tools for Taxonomic Classification. (2019, background): “These tools have recently identified thousands of novel metagenome assembled genomes in the human microbiome (Almeida et al., 2019; Nayfach et al., 2019; Pasolli et al., 2019) One of the biggest performance challenges for many classifiers is that they often report large numbers of low abundance…”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, background): “…in the laboratory pervades host-associated and (especially) environmental metagenomes (Parks et al., 2017) , with most communities containing a plurality, majority, or sometimes supermajority of novel and/or uncharacterized sequences (Almeida et al., 2019; Pasolli et al., 2019) .”
Short chain fatty acids in human gut and metabolic health. (2020, positive): “The phylogenetic core, dynamics and stability of this ecosystem have been intensively studied by high throughput 16S ribosomal RNA gene sequencing-based technologies (see recent reviews (Almeida et al. , 2019; Falony et al. , 2016; Hornung et al. , 2018; Shetty et al. , 2017).”
Critical Assessment of Metagenome Interpretation: the second round of challenges (2021, methodology): “For multi-sample metagenome datasets, common assembly strategies are pooling samples (coassembly) and single-sample assembly 10,20,35 .”
Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health (2020, background): “19 Various studies have indicated the existence of a core gut microbiota, comprising prevalent gut microbial populations, genes and essential functions for bacterial life in the ecosystem, which are observed in most individuals and persist over time.”
The microbiome and human cancer (2021, background): “1 to 1% are archaea and eukarya (including fungi) (27, 48).”
Linking metagenomics to aquatic microbial ecology and biogeochemical cycles (2019, background): “…20 years after the term “metagenomics” was coined (Handelsman et al. 1998), metagenomics can now be considered a mature technology, where enormous data sets (Sunagawa et al. 2015; Almeida et al. 2019) and an extensive set of analysis tools are accessible to many researchers (Mitchell et al. 2017).”
Gut Microbiome: Profound Implications for Diet and Disease (2019, background): “Shotgun metagenomic sequencing analysis discovered 1952 unclassified bacteria species in the human gut microbiome in addition to the 553 bacteria previously cultured from the gut [6].”