Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model.

TitleStochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model.
Publication TypeJournal Article
Year of Publication2013
AuthorsMcCafferty J, Mühlbauer M, Gharaibeh RZ, Arthur JC, Perez-Chanona E, Sha W, Jobin C, Fodor AA
JournalISME J
Volume7
Issue11
Pagination2116-25
Date Published2013 Nov
ISSN1751-7370
KeywordsAnimals, Biodiversity, Environmental Microbiology, Founder Effect, Gastrointestinal Tract, Housing, Animal, Mice, RNA, Ribosomal, 16S, Time Factors
Abstract

<p>Maternal transmission and cage effects are powerful confounding factors in microbiome studies. To assess the consequences of cage microenvironment on the mouse gut microbiome, two groups of germ-free (GF) wild-type (WT) mice, one gavaged with a microbiota harvested from adult WT mice and another allowed to acquire the microbiome from the cage microenvironment, were monitored using Illumina 16S rRNA sequencing over a period of 8 weeks. Our results revealed that cage effects in WT mice moved from GF to specific pathogen free (SPF) conditions take several weeks to develop and are not eliminated by the initial gavage treatment. Initial gavage influenced, but did not eliminate a successional pattern in which Proteobacteria became less abundant over time. An analysis in which 16S rRNA sequences are mapped to the closest sequenced whole genome suggests that the functional potential of microbial genomes changes significantly over time shifting from an emphasis on pathogenesis and motility early in community assembly to metabolic processes at later time points. Functionally, mice allowed to naturally acquire a microbial community from their cage, but not mice gavaged with a common biome, exhibit a cage effect in Dextran Sulfate Sodium-induced inflammation. Our results argue that while there are long-term effects of the founding community, these effects are mitigated by cage microenvironment and successional community assembly over time, which must both be explicitly considered in the interpretation of microbiome mouse experiments.</p>

DOI10.1038/ismej.2013.106
Alternate JournalISME J
PubMed ID23823492
PubMed Central IDPMC3806260
Grant ListR01 DK073338 / DK / NIDDK NIH HHS / United States
R01 DK047700 / DK / NIDDK NIH HHS / United States
P30 DK034987 / DK / NIDDK NIH HHS / United States
P40 R018603 / / PHS HHS / United States
R01 DK47700 / DK / NIDDK NIH HHS / United States
R01 DK73338 / DK / NIDDK NIH HHS / United States