New insights from uncultivated genomes of the global human gut microbiome

By Stephen Nayfach, Z. Shi, Rekha Seshadri, Katherine S. Pollard, Nikos Kyrpides. Nature, 2019

616 citations recorded by the source corpus.

The genome sequences of many species of the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, from geographically and phenotypically diverse humans. These genomes provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over the previously known phylogenetic diversity of sequenced gut bacteria. On average, the newly identified OTUs comprise 33% of richness and 28% of species abundance per individual, and are enriched in humans from rural populations. A meta-analysis of clinical gut-microbiome studies pinpointed numerous disease associations for the newly identified OTUs, which have the potential to improve predictive models. Finally, our analysis revealed that uncultured gut species have undergone genome reduction that has resulted in the loss of certain biosynthetic pathways, which may offer clues for improving cultivation strategies in the future. Draft prokaryotic genomes from faecal metagenomes of diverse human populations enrich our understanding of the human gut microbiome by identifying over two thousand new species-level taxa that have numerous disease associations.

Subfields: Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a2a581ca4340a50515ce65a5491ce4745a25d523

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Citations in the corpus

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 (2023, methodology): “While the repository can be used for genome-based studies at a larger scale than what has been described so far 40–42 ,45, From this SGB genome catalog, we built the pangenome of each SGB (collection of all gene families found in at least one genome in identify and quantify the known taxa and genes…”
Likelihood Ratios for Out-of-Distribution Detection (2019, background): “Different bacterial classes continue to be discovered gradually over the years (see Figure S4 in Appendix C.1) and it is estimated that 60%-80% of genomic sequences belong to as yet unknown bacteria (Zhu et al., 2018; Eckburg et al., 2005; Nayfach et al., 2019).”
Trends in insulin resistance: insights into mechanisms and therapeutic strategy (2022, background): “The microbes living in the human gut are key contributors to host metabolism and immune function through mediating the interaction between the host and environment, or releasing metabolites and cytokines.(281) In 2012, the Human Microbiome Project Consortium began to show that the gut microbial phyl”
A genomic catalog of Earth’s microbiomes (2020, background): “With that said, MAGs from Porifera (307) Bioremediation (317) Microbial (371) Animal (437) Annelida (439) Modeled (462) Solid waste (836) Algae (924) Fungi (926) Insecta (1,293) Arthropoda (1,481) Bioreactor (1,910) Mammals (2,234) Lab enrichment (2,457) Wastewater (4,508) Plants (6,696) Built envir”
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…”