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

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. • A genomic approach finds >4,000 conserved small proteins in human microbiomes • The majority of these proteins have no known function or domain • A database provides insights into potential function of these proteins • Over 30% of the small proteins are predicted to be involved in cell-cell communication Computational identification and characterization of thousands of conserved small ORFs from human microbiome sequences spanning multiple anatomical sites suggests a diversity of unknown protein domains and families with diverse functions. [ABSTRACT FROM AUTHOR]