Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus

Da Silva Morais, Emilene ; Grimaud, Ghjuvan Micaelu LU orcid ; Warda, Alicja ; Stanton, Catherine and Ross, Paul (2024) In Scientific Reports 14(1).
Abstract
Phocaeicola dorei and Phocaeicola vulgatus are very common
and abundant members of the human gut microbiome and play an important
role in the infant gut microbiome. These species are closely related and
often confused for one another; yet, their genome comparison,
interspecific diversity, and evolutionary relationships have not been
studied in detail so far. Here, we perform phylogenetic analysis and
comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic... (More)
Phocaeicola dorei and Phocaeicola vulgatus are very common
and abundant members of the human gut microbiome and play an important
role in the infant gut microbiome. These species are closely related and
often confused for one another; yet, their genome comparison,
interspecific diversity, and evolutionary relationships have not been
studied in detail so far. Here, we perform phylogenetic analysis and
comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus
have very different functional and carbohydrate utilisation profiles,
hinting at different ecological strategies, yet they present similar
antimicrobial resistance profiles. (Less)
Please use this url to cite or link to this publication:
author
; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Comparative genomics, Gut microbiome, Horizontal gene transfer, Pangenome, Phocaeicola
in
Scientific Reports
volume
14
issue
1
article number
10109
pages
11 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:85192007215
  • pmid:38698002
ISSN
2045-2322
DOI
10.1038/s41598-024-59148-7
language
English
LU publication?
no
additional info
Publisher Copyright: © The Author(s) 2024.
id
29511e3a-4793-4d25-aba7-292a6b898acf
date added to LUP
2024-11-25 16:07:46
date last changed
2025-07-08 10:29:41
@article{29511e3a-4793-4d25-aba7-292a6b898acf,
  abstract     = {{<i>Phocaeicola dorei</i> and <i>Phocaeicola vulgatus</i> are very common<br>
 and abundant members of the human gut microbiome and play an important <br>
role in the infant gut microbiome. These species are closely related and<br>
 often confused for one another; yet, their genome comparison, <br>
interspecific diversity, and evolutionary relationships have not been <br>
studied in detail so far. Here, we perform phylogenetic analysis and <br>
comparative genomic analyses of these two <i>Phocaeicola</i> species. We report that <i>P. dorei</i> has a larger genome yet a smaller pan-genome than <i>P. vulgatus</i>. We found that this is likely because <i>P. vulgatus</i> is more plastic than <i>P. dorei</i>, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that <i>P. dorei</i> directly descends from a clade of <i>P. vulgatus</i>¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, <i>P. dorei</i> and <i>P. vulgatus</i><br>
 have very different functional and carbohydrate utilisation profiles, <br>
hinting at different ecological strategies, yet they present similar <br>
antimicrobial resistance profiles.}},
  author       = {{Da Silva Morais, Emilene and Grimaud, Ghjuvan Micaelu and Warda, Alicja and Stanton, Catherine and Ross, Paul}},
  issn         = {{2045-2322}},
  keywords     = {{Comparative genomics; Gut microbiome; Horizontal gene transfer; Pangenome; Phocaeicola}},
  language     = {{eng}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Scientific Reports}},
  title        = {{Genome plasticity shapes the ecology and evolution of <i>Phocaeicola dorei</i> and <i>Phocaeicola vulgatus</i>}},
  url          = {{http://dx.doi.org/10.1038/s41598-024-59148-7}},
  doi          = {{10.1038/s41598-024-59148-7}},
  volume       = {{14}},
  year         = {{2024}},
}