A metagenomic perspective on the microbial prokaryotic genome census

Wu, Dongying; Seshadri, Rekha; Kyrpides, Nikos C.; Ivanova, Natalia N.

doi:10.1126/sciadv.adq2166

A metagenomic perspective on the microbial prokaryotic genome census

Journal Article · Fri Jan 17 04:00:00 EST 2025 · Science Advances

DOI:https://doi.org/10.1126/sciadv.adq2166· OSTI ID:2528033

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USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2528033

Journal Information:: Science Advances, Journal Name: Science Advances Journal Issue: 3 Vol. 11; ISSN 2375-2548

Publisher:: AAASCopyright Statement

Country of Publication:: United States

Language:: English

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