Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity

Abstract

Gut microbial community properties of mammals are thought to be partly shaped by a combination of host immunity and environmental factors, but their relative importance is not firmly established. To address this gap, we first characterized the faecal bacteria of mice with a functioning immune system (wild-type, WT), mice with defective immune responses (CD45), mice lacking an adaptive immune system (RAG), and mice with both immune dysfunctions (45RAG). Using fingerprinting of 16S rRNA genes, we observed significant differences in gut microbiota composition across all mouse strains (P < 0.001) and identified several mouse strain-specific genera via pyrosequencing, including Turicibacter sp. (in WT mice) and Allobaculum sp. (in CD45-deficient animals). To define the role of the host immune system in constraining gut microbiota stability after perturbation, we cohoused CD45-deficient and WT mice and monitored gut bacterial community dynamics during 8 weeks. Cohousing caused the WT bacterial communities to become indistinguishable from those of CD45 mice (P > 0.05). Time-series analysis indicated that the communities of cohoused mice changed directionally as opposed to the relatively stable communities of non-cohoused controls. When we considered only taxonomic membership, it was the communities of CD45 non-cohoused mice that experienced the highest rate of change. Rather than be governed by fluctuations in the relative abundance of taxa, we suggest that CD45-regulated immune responses either are stimulated by the presence of bacteria per se or promote temporal stability by selecting for the occurrence of specific taxa.

Host adaptive immunity alters gut microbiota

“…À / À mice (Dimitriu et al, 2013), but a direct effect of adaptive immunity on microbiota was not demonstrated through adoptive transfer. In addition, whether the microbiota differences between mouse strains were affected by animal age and sampling site was unknown.…”

T lymphocytes control microbial composition by regulating the abundance of Vibrio in the zebrafish gut

“…22 In addition, Dimitriu et al also reported differences in bacterial community composition in faeces between WT mice and mice lacking adaptive immunity (CD45, RAG and 45RAG double knock-out) as analyzed by Principal coordinates analysis (PCoA) plots of bacterial community composition (T-RFLP fingerprints). 36 Interestingly, some bacterial species (and possible pathobionts) were only detected in the CD45 knockout mice, such as Alcaligenaceae and Helicobacteraceae. 36 In contrast, thymectomy of tadpoles (Xenopus laevis), a model in between zebrafish and higher vertebrates, did not result in differences in microbial composition.…”

“…36 Interestingly, some bacterial species (and possible pathobionts) were only detected in the CD45 knockout mice, such as Alcaligenaceae and Helicobacteraceae. 36 In contrast, thymectomy of tadpoles (Xenopus laevis), a model in between zebrafish and higher vertebrates, did not result in differences in microbial composition. 37 Although, Rag-deficiency and thymectomy cannot directly be compared, further investigation into this difference might yield clues concerning the mechanism by which T cells regulate microbial composition independently of B cells in zebrafish.…”

Technical note: A pilot study using a mouse mastitis model to study differences between bovine associated coagulase-negative staphylococci

“…Remarkably, sham-inoculated glands were only occasionally sterile. Molecular identification of the bacteria isolated from these glands suggests they originate from the pups, as they are closely related to the commensal microbiota (Martin et al, 2004) from the murine gut and respiratory system (Rodrigue and Lavoie, 1996;Shim et al, 2009;Dimitriu et al, 2013). These bacteria were retrieved in limited number compared with the inoculum and are therefore not considered to have influenced our results to a large extent.…”