The gut microbiota and mucosal homeostasis: colonized at birth or at adulthood, does it matter?

Abstract

The intimate interplay between the gut microbiota and the host may contribute to health and disease in the host. Experiments using conventionalized and conventionally raised animal models have illustrated the role of the intestinal microbiota in shaping and maintaining the host immune system. However, it is still unclear whether colonization at birth or at adulthood induces different host responses. Here, we perform comparative transcriptome analyses to elucidate the impact of the gut microbiota on the development and maintenance of the immune system in adult conventionalized (after 16 and 30 days of colonization) and conventionally raised mice, which were obtained in two independent laboratories. Transcriptional profiles of jejunum, ileum and colon were compared between germfree, conventionally raised mice and conventionalized mice. Germfree mice from the two different facilities clustered together, establishing the validity of the comparative analysis. Nevertheless, significant spatial differences were detected along the gut; the jejunum and colon exhibited a transient response (conventionalized mice) that eventually returned to a homeostatic level (conventionally raised). In contrast, the ileal response to microbiota was similar in conventionalized and conventionally raised mice. Overall, this comparative analysis supports the hypothesis that co-development of the gut microbiota and its host initiates at early stage of development and indicates that despite the achieved homeostasis, immune development is substantially different in mice conventionalized in adulthood. These findings imply that colonization during development is required to meet the window of opportunity where the gut microbiota can imprint the host's mucosal immune-homeostasis in a way that cannot be achieved at later stages in life.

Keywords: comparative analysis; conventionalized mice; conventionally raised mice; germfree adult mice; microbiota; transcriptome.

Figure 1. Region-specific clustering distinguishes conventionalized and conventionally raised adult mice. Dendogram using Ward clustering on the Pearson distance measure of the transcriptome data obtained from the two animal experiments under comparison; exp1; (see ref. 13) and exp2; (see ref. 5). The dendogram shows that the germfree animals grouped together and did not cluster based on the experiment, diet used or animal age, establishing the validity of the comparative analysis performed here. Convr = conventionally raised mice, Convd-D16 = day 16 of conventionalization, Convd-D30 = day 30 of conventionalization.

Figure 2. Temporal and spatial immune features of the conventionalized in contrast to conventionally raised mice. Ingenuity biological processes that were significantly modulated in the gut tissue of conventionalized mice as well as conventionally raised mice compared with the germfree control. Significance was calculated via a one-tailed Fisher’s Exact test in IPA and is represented as –log (p value); -log values exceeding 1.30 were significant p < 0.05, (n = 4−5 mice/time point).

Figure 3. Transcriptome signature for the colonic responses of conventionalized and conventionally raised adult mice to the gut microbiota. (A) Heat map of the genes that constitute the core regulatory protein-protein interaction network (B) derived by plotting STEM output genes (see Fig. S1) of the temporal expression profiles involved in immune response. Transcriptional data was projected onto the interaction map. Red arrows refer to genes associated with inflammatory bowel disease (n = 4−6/ group).

Figure 4. Dot plots represent the expression levels of transcriptional signatures identified for colonic tissues of conventionalized mice and were previously shown to be age-sensitive and regulated through epigenetic mechanisms.^,, Significant differences between time points are indicated by distinctive characters above the measurement groups (p < 0.05; n = 4−6 / group).