A genomic catalog of Earth’s microbiomes

By Stephen Nayfach, Simon Roux, Rekha Seshadri, D. Udwary, Neha J. Varghese, Frederik Schulz, Dongying Wu, David Páez-Espino, I-Min A. Chen, Marcel Huntemann and 257 more. Nature Biotechnology, 2020

743 citations recorded by the source corpus.

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes. Cataloging microbial genomes from Earth’s environments expands the known phylogenetic diversity of bacteria and archaea.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5f38a4f91221e74116c8e4bc0a10d14f3fff5ac0

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Citations in the corpus

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy (2021, background): “The quality of MAGs is an ongoing concern and we are evaluating methods for decontaminating MAGs (39) and identifying and removing MAGs that may contribute to phylogenetic instability (40).”
Insights into Plant Interactions and the Biogeochemical Role of the Globally Widespread Acidobacteriota Phylum (2023, methodology): “We retrieved 758 MAGs from the publicly available GEM catalog (https://portal.nersc.gov/GEM/) (Nayfach et al., 2021b) that were taxonomically affiliated with the phylum Acidobacteriota.”
The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics (2024, background): “, to measure the biodiversity of earth’s and human gut microbiomes [16, 17]).”
Petabase-scale sequence alignment catalyses viral discovery (2020, background): “The ‘metagenomics revolution’ of virus discovery is accelerating 7,11 .”
iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria (2023, positive): “To verify whether iPHoP host predictions linked viruses from each main biome to host taxa consistently found in the same biomes, the GEM dataset [36] was used to evaluate the biome distribution of individual host genera.”
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters (2022, positive): “For example, it has been used to estimate the potential for biosynthetic novelty in large-scale microbiome studies (11,12), to identify conserved amino acids playing key roles in catalytic activities across enzyme families (13), to help guide natural product discovery efforts towards high-potential ”
Assessment of global health risk of antibiotic resistance genes (2022, background): “We appreciate Nayfach et al. (2020)28 for their work on the genomic catalog of Earth’s microbiomes and its publication as a public resource, and Almeida (2021)40 for their work on the human gut genome and its publication as a public resource.”
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses (2020, methodology): “2% of correct host prediction at the order, family, and genus ranks respectively, consistent with previous benchmarks (29).”