2020
Al-Shayeb, Basem; Sachdeva, Rohan; Chen, Lin-Xing; Ward, Fred; Munk, Patrick; Devoto, Audra; Castelle, Cindy J.; Olm, Matthew R.; Bouma-Gregson, Keith; Amano, Yuki; He, Christine; Méheust, Raphaël; Brooks, Brandon; Thomas, Alex; Lavy, Adi; Matheus-Carnevali, Paula; Sun, Christine; Goltsman, Daniela S. A.; Borton, Mikayla A.; Sharrar, Allison; Jaffe, Alexander L.; Nelson, Tara C.; Kantor, Rose; Keren, Ray; Lane, Katherine R.; Farag, Ibrahim F.; Lei, Shufei; Finstad, Kari; Amundson, Ronald; Anantharaman, Karthik; Zhou, Jinglie; Probst, Alexander J.; Power, Mary E.; Tringe, Susannah G.; Li, Wen-Jun; Wrighton, Kelly; Harrison, Sue; Morowitz, Michael; Relman, David A.; Doudna, Jennifer A.; Lehours, Anne-Catherine; Warren, Lesley; Cate, Jamie H. D.; Santini, Joanne M.; Banfield, Jillian F.
Clades of huge phages from across Earth’s ecosystems Journal Article
In: Nature, vol. 578, pp. 425-431, 2020.
Abstract | Links | BibTeX | Tags: bacteriophage, ERCZO, metagenomes, metagenomic sequencing
@article{Al-Shayeb2020,
title = {Clades of huge phages from across Earth’s ecosystems},
author = {Basem Al-Shayeb and Rohan Sachdeva and Lin-Xing Chen and Fred Ward and Patrick Munk and Audra Devoto and Cindy J. Castelle and Matthew R. Olm and Keith Bouma-Gregson and Yuki Amano and Christine He and Raphaël Méheust and Brandon Brooks and Alex Thomas and Adi Lavy and Paula Matheus-Carnevali and Christine Sun and Daniela S. A. Goltsman and Mikayla A. Borton and Allison Sharrar and Alexander L. Jaffe and Tara C. Nelson and Rose Kantor and Ray Keren and Katherine R. Lane and Ibrahim F. Farag and Shufei Lei and Kari Finstad and Ronald Amundson and Karthik Anantharaman and Jinglie Zhou and Alexander J. Probst and Mary E. Power and Susannah G. Tringe and Wen-Jun Li and Kelly Wrighton and Sue Harrison and Michael Morowitz and David A. Relman and Jennifer A. Doudna and Anne-Catherine Lehours and Lesley Warren and Jamie H. D. Cate and Joanne M. Santini and Jillian F. Banfield},
doi = {10.1038/s41586-020-2007-4},
year = {2020},
date = {2020-02-12},
journal = {Nature},
volume = {578},
pages = {425-431},
abstract = {Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.},
keywords = {bacteriophage, ERCZO, metagenomes, metagenomic sequencing},
pubstate = {published},
tppubtype = {article}
}
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.
2018
Crits-Christoph, Alexander; Diamond, Spencer; Butterfield, Cristina N.; Thomas, Brian C.; Banfield, Jillian F.
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis Journal Article
In: Nature, vol. 558, pp. 440-444, 2018.
Abstract | Links | BibTeX | Tags: ERCZO, metagenomic sequencing, soil microbes
@article{Crits-Christoph2018,
title = {Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis},
author = {Alexander Crits-Christoph and Spencer Diamond and Cristina N. Butterfield and Brian C. Thomas and Jillian F. Banfield},
doi = {10.1038/s41586-018-0207-y},
year = {2018},
date = {2018-06-13},
journal = {Nature},
volume = {558},
pages = {440-444},
abstract = {In soil ecosystems, microorganisms produce diverse secondary metabolites such as antibiotics, antifungals and siderophores that mediate communication, competition and interactions with other organisms and the environment. Most known antibiotics are derived from a few culturable microbial taxa, and the biosynthetic potential of the vast majority of bacteria in soil has rarely been investigated. Here we reconstruct hundreds of near-complete genomes from grassland soil metagenomes and identify microorganisms from previously understudied phyla that encode diverse polyketide and nonribosomal peptide biosynthetic gene clusters that are divergent from well-studied clusters. These biosynthetic loci are encoded by newly identified members of the Acidobacteria, Verrucomicobia and Gemmatimonadetes, and the candidate phylum Rokubacteria. Bacteria from these groups are highly abundant in soils, but have not previously been genomically linked to secondary metabolite production with confidence. In particular, large numbers of biosynthetic genes were characterized in newly identified members of the Acidobacteria, which is the most abundant bacterial phylum across soil biomes5. We identify two acidobacterial genomes from divergent lineages, each of which encodes an unusually large repertoire of biosynthetic genes with up to fifteen large polyketide and nonribosomal peptide biosynthetic loci per genome. To track gene expression of genes encoding polyketide synthases and nonribosomal peptide synthetases in the soil ecosystem that we studied, we sampled 120 time points in a microcosm manipulation experiment and, using metatranscriptomics, found that gene clusters were differentially co-expressed in response to environmental perturbations. Transcriptional co-expression networks for specific organisms associated biosynthetic genes with two-component systems, transcriptional activation, putative antimicrobial resistance and iron regulation, linking metabolite biosynthesis to processes of environmental sensing and ecological competition. We conclude that the biosynthetic potential of abundant and phylogenetically diverse soil microorganisms has previously been underestimated. These organisms may represent a source of natural products that can address needs for new antibiotics and other pharmaceutical compounds.},
keywords = {ERCZO, metagenomic sequencing, soil microbes},
pubstate = {published},
tppubtype = {article}
}
In soil ecosystems, microorganisms produce diverse secondary metabolites such as antibiotics, antifungals and siderophores that mediate communication, competition and interactions with other organisms and the environment. Most known antibiotics are derived from a few culturable microbial taxa, and the biosynthetic potential of the vast majority of bacteria in soil has rarely been investigated. Here we reconstruct hundreds of near-complete genomes from grassland soil metagenomes and identify microorganisms from previously understudied phyla that encode diverse polyketide and nonribosomal peptide biosynthetic gene clusters that are divergent from well-studied clusters. These biosynthetic loci are encoded by newly identified members of the Acidobacteria, Verrucomicobia and Gemmatimonadetes, and the candidate phylum Rokubacteria. Bacteria from these groups are highly abundant in soils, but have not previously been genomically linked to secondary metabolite production with confidence. In particular, large numbers of biosynthetic genes were characterized in newly identified members of the Acidobacteria, which is the most abundant bacterial phylum across soil biomes5. We identify two acidobacterial genomes from divergent lineages, each of which encodes an unusually large repertoire of biosynthetic genes with up to fifteen large polyketide and nonribosomal peptide biosynthetic loci per genome. To track gene expression of genes encoding polyketide synthases and nonribosomal peptide synthetases in the soil ecosystem that we studied, we sampled 120 time points in a microcosm manipulation experiment and, using metatranscriptomics, found that gene clusters were differentially co-expressed in response to environmental perturbations. Transcriptional co-expression networks for specific organisms associated biosynthetic genes with two-component systems, transcriptional activation, putative antimicrobial resistance and iron regulation, linking metabolite biosynthesis to processes of environmental sensing and ecological competition. We conclude that the biosynthetic potential of abundant and phylogenetically diverse soil microorganisms has previously been underestimated. These organisms may represent a source of natural products that can address needs for new antibiotics and other pharmaceutical compounds.