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Gone with a trace: cataloguing the disappearing gut microbes

Nature Reviews Microbiology volume 21, page 704 (2023)Cite this article

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This month’s Genome Watch highlights the use of high-depth genome-centric approaches to further our understanding of the human gut microbiome within the context of industrialized and non-industrialized lifestyles.

Poor gut health and the rise of non-communicable chronic diseases (NCCDs) such as cardiovascular disease and diabetes have been increasingly linked to dietary trends within industrialized societies such as calorie-dense, nutrient-poor processed foods, and a lack of dietary fibre1,2,3. To better understand the relationship between diet and the composition of the gut microbiota, Carter et al.4 used genome-resolved metagenomics to compare the gut microbiomes of a unique group of hunter–gatherers in Tanzania with the microbiomes of individuals in Nepal and California (representing non-industrial, transitional and industrial lifestyles, respectively). The authors applied ultra-deep metagenomic sequencing to faecal samples from 351 Hadza, 56 Nepali and 12 Californian individuals, and recovered more than 48,000 metagenome-assembled genomes (MAGs) spanning all domains of life. This massive MAG dataset comprised 2,400 bacterial and archaeal species, 13,600 bacteriophage species, 7 distinct eukaryotic species and 8.4 million protein families, half of which were absent from the Unified Human Gastrointestinal Protein (UHGP)-95 protein database. The authors also isolated and sequenced 52 bacterial strains from the same sample set. These strains were composed of 31 distinct species, 18 of which had no cultured representative and 9 without a database representative. Furthermore, these 52 cultivated strains were close phylogenetic relatives to the Hadza MAGs, indicating that these strains were representative of the Hadza gut metagenomes.

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  1. DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Robert M. Bowers

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  1. Robert M. Bowers
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Correspondence to Robert M. Bowers.

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Bowers, R.M. Gone with a trace: cataloguing the disappearing gut microbes. Nat Rev Microbiol 21, 704 (2023). https://doi.org/10.1038/s41579-023-00968-1

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  • DOI: https://doi.org/10.1038/s41579-023-00968-1

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