Towards the biogeography of prokaryotic genes

Luis Pedro Coelho (), Renato Alves, Álvaro Rodríguez Río, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquín Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjørn Nielsen, Jaime Huerta-Cepas () and Peer Bork ()
Additional contact information
Luis Pedro Coelho: Fudan University
Renato Alves: European Molecular Biology Laboratory
Álvaro Rodríguez Río: Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)
Pernille Neve Myers: Technical University of Denmark
Carlos P. Cantalapiedra: Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)
Joaquín Giner-Lamia: Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)
Thomas Sebastian Schmidt: European Molecular Biology Laboratory
Daniel R. Mende: European Molecular Biology Laboratory
Askarbek Orakov: European Molecular Biology Laboratory
Ivica Letunic: biobyte solutions GmbH
Falk Hildebrand: European Molecular Biology Laboratory
Thea Rossum: European Molecular Biology Laboratory
Sofia K. Forslund: European Molecular Biology Laboratory
Supriya Khedkar: European Molecular Biology Laboratory
Oleksandr M. Maistrenko: European Molecular Biology Laboratory
Shaojun Pan: Fudan University
Longhao Jia: Fudan University
Pamela Ferretti: European Molecular Biology Laboratory
Shinichi Sunagawa: European Molecular Biology Laboratory
Xing-Ming Zhao: Fudan University
Henrik Bjørn Nielsen: Clinical Microbiomics A/S
Jaime Huerta-Cepas: European Molecular Biology Laboratory
Peer Bork: European Molecular Biology Laboratory

Nature, 2022, vol. 601, issue 7892, 252-256

Abstract: Abstract Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats1–3, little is known about the distribution of genes across the global biosphere, with implications for human and planetary health. Here we constructed a non-redundant gene catalogue of 303 million species-level genes (clustered at 95% nucleotide identity) from 13,174 publicly available metagenomes across 14 major habitats and use it to show that most genes are specific to a single habitat. The small fraction of genes found in multiple habitats is enriched in antibiotic-resistance genes and markers for mobile genetic elements. By further clustering these species-level genes into 32 million protein families, we observed that a small fraction of these families contain the majority of the genes (0.6% of families account for 50% of the genes). The majority of species-level genes and protein families are rare. Furthermore, species-level genes, and in particular the rare ones, show low rates of positive (adaptive) selection, supporting a model in which most genetic variability observed within each protein family is neutral or nearly neutral.

Date: 2022
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DOI: 10.1038/s41586-021-04233-4

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