Megaphages infect Prevotella and variants are widespread in gut microbiomes

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

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Megaphages infect Prevotella and variants are widespread in gut microbiomes. / Devoto, Audra E.; Santini, Joanne M.; Olm, Matthew R.; Anantharaman, Karthik; Munk, Patrick; Tung, Jenny; Archie, Elizabeth A.; Turnbaugh, Peter J.; Seed, Kimberley D.; Blekhman, Ran; Møller Aarestrup, Frank ; Thomas, Brian C.; Banfield, Jillian F.

In: Nature Microbiology, Vol. 4, 2019, p. 693-700.

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

Harvard

Devoto, AE, Santini, JM, Olm, MR, Anantharaman, K, Munk, P, Tung, J, Archie, EA, Turnbaugh, PJ, Seed, KD, Blekhman, R, Møller Aarestrup, F, Thomas, BC & Banfield, JF 2019, 'Megaphages infect Prevotella and variants are widespread in gut microbiomes', Nature Microbiology, vol. 4, pp. 693-700. https://doi.org/10.1038/s41564-018-0338-9

APA

Devoto, A. E., Santini, J. M., Olm, M. R., Anantharaman, K., Munk, P., Tung, J., ... Banfield, J. F. (2019). Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nature Microbiology, 4, 693-700. https://doi.org/10.1038/s41564-018-0338-9

CBE

Devoto AE, Santini JM, Olm MR, Anantharaman K, Munk P, Tung J, Archie EA, Turnbaugh PJ, Seed KD, Blekhman R, Møller Aarestrup F, Thomas BC, Banfield JF. 2019. Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nature Microbiology. 4:693-700. https://doi.org/10.1038/s41564-018-0338-9

MLA

Vancouver

Author

Devoto, Audra E. ; Santini, Joanne M. ; Olm, Matthew R. ; Anantharaman, Karthik ; Munk, Patrick ; Tung, Jenny ; Archie, Elizabeth A. ; Turnbaugh, Peter J. ; Seed, Kimberley D. ; Blekhman, Ran ; Møller Aarestrup, Frank ; Thomas, Brian C. ; Banfield, Jillian F. / Megaphages infect Prevotella and variants are widespread in gut microbiomes. In: Nature Microbiology. 2019 ; Vol. 4. pp. 693-700.

Bibtex

@article{fedc27b5d39d4249a2913f78f70bd7dc,
title = "Megaphages infect Prevotella and variants are widespread in gut microbiomes",
abstract = "Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.",
author = "Devoto, {Audra E.} and Santini, {Joanne M.} and Olm, {Matthew R.} and Karthik Anantharaman and Patrick Munk and Jenny Tung and Archie, {Elizabeth A.} and Turnbaugh, {Peter J.} and Seed, {Kimberley D.} and Ran Blekhman and {M{\o}ller Aarestrup}, Frank and Thomas, {Brian C.} and Banfield, {Jillian F.}",
year = "2019",
doi = "10.1038/s41564-018-0338-9",
language = "English",
volume = "4",
pages = "693--700",
journal = "Nature Microbiology",
issn = "2058-5276",
publisher = "Nature Publishing Group",

}

RIS

TY - JOUR

T1 - Megaphages infect Prevotella and variants are widespread in gut microbiomes

AU - Devoto, Audra E.

AU - Santini, Joanne M.

AU - Olm, Matthew R.

AU - Anantharaman, Karthik

AU - Munk, Patrick

AU - Tung, Jenny

AU - Archie, Elizabeth A.

AU - Turnbaugh, Peter J.

AU - Seed, Kimberley D.

AU - Blekhman, Ran

AU - Møller Aarestrup, Frank

AU - Thomas, Brian C.

AU - Banfield, Jillian F.

PY - 2019

Y1 - 2019

N2 - Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.

AB - Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.

U2 - 10.1038/s41564-018-0338-9

DO - 10.1038/s41564-018-0338-9

M3 - Journal article

VL - 4

SP - 693

EP - 700

JO - Nature Microbiology

JF - Nature Microbiology

SN - 2058-5276

ER -