Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice.

Yilmaz, Bahtiyar; Mooser, Catherine; Keller, Irene; Li, Hai; Zimmermann, Jakob; Bosshard, Lars; Fuhrer, Tobias; Gomez de Agüero, Mercedes; Fernandez Trigo, Nerea; Tschanz-Lischer, Heidi; Limenitakis, Julien P.; Hardt, Wolf-Dietrich; McCoy, Kathleen; Stecher, Bärbel; Excoffier, Laurent; Sauer, Uwe; Ganal-Vonarburg, Stephanie C.; Macpherson, Andrew J. (2021). Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Cell host & microbe, 29(4), 650-663.e9. Cell Press 10.1016/j.chom.2021.02.001

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Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand microbiota evolution in these models, we carried out a 6-year experiment in mice colonized with 12 representative taxa. Increased non-synonymous to synonymous mutation rates indicate positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that evolved within a single taxon can stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts trigger rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains are also rapidly altered after dietary shift. This indicates that microbial taxa within a mouse colony adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Department of Gastro-intestinal, Liver and Lung Disorders (DMLL) > Clinic of Visceral Surgery and Medicine > Gastroenterology
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR)
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DBMR Forschung Mu35 > Forschungsgruppe Gastroenterologie / Mukosale Immunologie
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DBMR Forschung Mu35 > Forschungsgruppe Gastroenterologie / Mukosale Immunologie

08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE) > Population Genetics

UniBE Contributor:

Yilmaz, Bahtiyar; Mooser, Catherine; Keller, Irene; Li, Hai; Zimmermann, Jakob; Bosshard, Lars; Gomez de Agüero Tamargo, Maria de la Mercedes; Fernandez Trigo, Nerea; Tschanz-Lischer, Heidi Erika Lisa; Limenitakis, Julien Periclis Jean; McCoy, Kathleen; Excoffier, Laurent; Ganal-Vonarburg, Stephanie Christine and Macpherson, Andrew

Subjects:

500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

ISSN:

1931-3128

Publisher:

Cell Press

Language:

English

Submitter:

Rahel Fuhrer

Date Deposited:

16 Sep 2021 10:08

Last Modified:

16 Sep 2021 10:08

Publisher DOI:

10.1016/j.chom.2021.02.001

PubMed ID:

33662276

Uncontrolled Keywords:

dietary shifts microbiota evolution niche partitioning stable animal model sub-strains

BORIS DOI:

10.48350/159008

URI:

https://boris.unibe.ch/id/eprint/159008

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