Thousands of small, novel genes predicted in global phage genomes

Cell Reports · 2022 · 55 citations

• Biology
• Computational biology
• Genetics

Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Author Correction: A genomic catalog of Earth’s microbiomes

Nature Biotechnology · 2021 · 19 citations

• Computer Science
• Computational biology
• Biology

A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.

A genomic catalog of Earth’s microbiomes

Nature Biotechnology · 2020 · 963 citations

• Biology
• Evolutionary biology
• Ecology

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.

Publisher Correction: A genomic catalog of Earth’s microbiomes

Nature Biotechnology · 2020 · 26 citations

• Computer Science
• Computational biology
• Biology

An amendment to this paper has been published and can be accessed via a link at the top of the paper.