Anatomy promotes neutral coexistence of strains in the human skin microbiome.
bacterial evolution
bacterial genomics
ecology
genomics
human microbiome
microbiome
molecular evolution
skin microbiome
Journal
Cell host & microbe
ISSN: 1934-6069
Titre abrégé: Cell Host Microbe
Pays: United States
ID NLM: 101302316
Informations de publication
Date de publication:
09 02 2022
09 02 2022
Historique:
received:
07
07
2021
revised:
18
10
2021
accepted:
09
12
2021
pubmed:
8
1
2022
medline:
17
3
2022
entrez:
7
1
2022
Statut:
ppublish
Résumé
What enables strains of the same species to coexist in a microbiome? Here, we investigate whether host anatomy can explain strain co-residence of Cutibacterium acnes, the most abundant species on human skin. We reconstruct on-person evolution and migration using whole-genome sequencing of C. acnes colonies acquired from healthy subjects, including from individual skin pores, and find considerable spatial structure at the level of pores. Although lineages (sets of colonies separated by <100 mutations) with in vitro fitness differences coexist within centimeter-scale regions, each pore is dominated by a single lineage. Moreover, colonies from a pore typically have identical genomes. An absence of adaptive signatures suggests a genotype-independent source of low within-pore diversity. We therefore propose that pore anatomy imposes random single-cell bottlenecks; the resulting population fragmentation reduces competition and promotes coexistence. Our findings suggest that therapeutic interventions involving pore-dwelling species might focus on removing resident populations over optimizing probiotic fitness.
Identifiants
pubmed: 34995483
pii: S1931-3128(21)00578-3
doi: 10.1016/j.chom.2021.12.007
pmc: PMC8831475
mid: NIHMS1769935
pii:
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
171-182.e7Subventions
Organisme : NIGMS NIH HHS
ID : DP2 GM140922
Pays : United States
Commentaires et corrections
Type : CommentIn
Informations de copyright
Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
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