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, 178 (5), 1245-1259.e14

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

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Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

Hila Sberro et al. Cell.

Abstract

Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ∼30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.

Keywords: annotation; bacteria; bioinformatics; domain; genome; microbe; microbiome; phage; prediction; small open reading frame; small proteins.

Conflict of interest statement

DECLARATION OF INTERESTS

N.G. is an employee and shareholder of One Codex. M.P.S. is a cofounder of Personalis, SensOmics, January, Filtricine, Akna, Qbio; he is on the advisory board of the companies he cofounded, along with Genapsys and Jupiter. A.S.B. is on the advisory board of Caribou Biosciences, January, and ArcBio. The authors declare no other competing financial interests.

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