A large body of evidences have established a strong link of low-level vitamin D to high risk of colon cancer and colonic inflammatory disease. Epidemiologic studies have shown that decreased vitamin D levels may influence the onset of IBD [
8], increase clinical disease activity [
7,
23,
24] and have a higher risk of malignant transformation [
25,
26]. We and others also documented that in mice models, 1,25(OH)
2D
3 deficiency or VDR knockout was correlated with an increased risk of colitis and 1,25(OH)
2D
3 supplement ameliorated DSS-induced colitis [
3,
9‐
11]. In the present study, 1,25(OH)
2D
3 supplement was able to rescue the inflammation occurred in
Cyp27b1−/− mice (Fig.
4f). While the underlying mechanism is still unclear, accumulating evidences indicate that vitamin D play a preventive role in IBD development via regulating immune response, modulating the release of inflammatory cytokines [
27,
28], improving intestinal epithelial barrier function by increasing the expression of some tight junction proteins such as Occludin, Zo-1, Zo-2, Vinculin and Claudins [
29,
30], inducing colon cells senescence to secret senescence-associated inflammatory cytokines [
11], and increasing antimicrobial peptide synthesis and secretion [
31]. Metagenomic studies have shown that vitamin D deficient diet or VDR knockout could impact the gut microbiome [
20,
32].
Inflammatory bowel disease has been associated with dysbiotic microbiota due to a balance switch between commensal and pathogenic microorganisms [
33‐
35]. For instance, the phylum
Firmicutes is often less colonies in the feces of patients with Crohn’s disease [
35,
36] whereas members of the Proteobacteria phylum such as
Escherichia coli are commonly more abundant in patients with IBD as compared with healthy subjects [
36,
37]. Bowdish and his colleagues found that alterations in age-related microbiota influenced intestinal permeability, caused age-associated inflammation, and decreased macrophage function [
38]. Microbiome genome-wide association studies have discovered that defects in many human genes involving IBD are associated with an aberrant composition of the gut microbiome [
39]. For example, knockout of Nod2 in mice predisposed them to colitis with lower levels of antimicrobial defensins and a higher bacterial load as compared with the control mice [
40]. In the present study, we compared the microbiome composition between 1,25(OH)
2D
3 deficient
Cyp27b1−/− mice and WT mice via 16S rRNA sequencing. Our results demonstrated that the microbiomes established in WT and
Cyp27b1−/− were distinct (Fig.
2a), suggesting that 1,25(OH)
2D
3 did modulate the composition of the gut microbiota. While these associations are well fit with the roles of the gut microbiota in IBD pathogenesis, the exact mechanism underlying dysbiosis remains to be fully elucidated.
A mucus layer in the gut tract is generally considered as a protective barrier against pathogenic micro-organisms and various chemical, enzymic or physical damage. Mucus produced by goblet cells is a viscous gel that mainly consists of high-molecular-mass glycoproteins, named as mucins [
41]. During evolution some mucolytic bacterial species may gain the capacity of utilizing this nutrient source [
42]. Therefore, the integrity of the mucus layer is leveraged between degradation by gut bacteria and replenishment by goblet cells. The Gram-negative
A. muciniphila is a strictly anaerobic bacterium and abundant in the human gut with the capability of degrading mucin [
41]. Seregin and his colleagues found that NLRP6, which is a member of Nod-like receptor (NLR) family and are involved in the formation of inflammasomes [
43], its deficiency can increase the susceptibility to DSS-induced colitis [
44] and induced the enrichment of
Akkermansia muciniphila that could function as a pathobiont by promoting colitis in a genetically-susceptible host [
45]. In contrast, Lemire et al. [
46] and Mamantopoulos et al. [
47] found that NLRP6 did not significantly influence the intestinal microbiota at homeostasis. These differences may be resulted from several factors including the mouse lineages (NLRP6 conditional knock-out versus NLRP6 conventional knock-out) and location of mouse facilities. 1,25(OH)
2D
3 has been reported to be involved in the inflammasome [
48], whether 1,25(OH)
2D
3 has a function on NLRP6 is worthy of further investigation. It has also been reported that fiber-free dietary promoted enrichment of mucus-degrading bacteria including
A. muciniphila and
B. caccae [
49]. Consistently, our data showed that
A. muciniphila was significantly enriched in
Cyp27b1−/− mice as compared to WT mice (Fig.
2b, c), and supplement of 1,25(OH)
2D
3 could reduce its enrichment (Fig.
4d). This indicated that 1,25(OH)
2D
3 could limit the colonization of
A. muciniphila. However, vitamin D deficient high fat diet has been shown to decrease the abundance of
A. muciniphila in ileum [
21]. Such discrepancy might be due to the different mouse model and location site of
A. muciniphila. In our study,
Cyp27b1−/− mice showed the long-time status of 1,25(OH)
2D
3 deficiency while 1,25(OH)
2D
3 deficient diet indicated the short-time 1,25(OH)
2D
3 deficiency, which might result in the different effects on gut microbiota. The role of
A. muciniphila in colitis is not very clear. Some studies showed that it could promote colitis. For example, one study found that occurrence of colitis was substantially increased in SPF IL10
−/− mice administered with repeated oral gavage of
A. muciniphila [
45]. In the presence of
A. muciniphila, Salmonella-induced colitis was worsen and ulcerative colitis patients was accompanied by active pouchitis and the IBD patients presented with treatment failure [
50‐
52]. The mechanism underlying
A. muciniphila-promoted colitis might be due to the degradation of the mucus layer that allows a greater microbial access to the gut mucosa. However, some studies showed that colitis was associated with a reduction in
Akkermansia muciniphila in IBD patients [
53,
54]. Therefore, a large scale of studies is needed to confirm the clinical relation of colitis and
A. muciniphila. In fact, we found a thinner mucus layer in
Cyp27b1−/− mice with alterations in bacterial species such as higher amount of
A. muciniphila (Fig.
3a) and an increase of total bacterial translocation (Fig.
1c) leading to the inflammation (Fig.
1d). Our results also showed no significant changes in the number of goblets and the compositions of mucins such as Muc1 and Muc3 between WT and
Cyp27b1−/− mice (Fig.
3b, c). Since the proliferation of goblet cells and the expression of mucin genes were not significantly altered, it is reasonable to conceive that thinner mucus layer in
Cyp27b1−/− mice may result from faster degradation of mucus layer due to the enrichment of mucin-degraded A. muciniphila in the gut rather than a reduction of mucin production itself. We further found that 1,25(OH)
2D
3 supplement reversed the amount of
A. muciniphila, recovered the mucus layer and relieved the colonic inflammation (Fig.
4d–f). These findings indicate that 1,25(OH)
2D
3 could limit the colonization of
A. muciniphila in gut. We and others have shown that 1,25(OH)
2D
3 is an important regulator of immune systems that could elicit Th2 immune responses and decrease pro-inflammatory cytokines such as IL-1, IL-6, IL-8, IFNγ and TNFα [
11]. 1,25(OH)
2D
3 could also increase Tregs, downregulate T cell-driven IgG production, inhibit DC differentiation, and enhance protective innate immune responses [
55]. Moreover, it has also been reported that 1,25(OH)
2D
3 promotes the production of anti-microbial peptides (AMPs), including β-defensins and cathelicidin [
56,
57]. Although the mechanism was unclear, we speculated that 1,25(OH)
2D
3-reduced colonization of
A. muciniphila in gut might result from activation of immune response by 1,25(OH)
2D
3 or antimicrobial peptide induced by 1,25(OH)
2D
3. In order to exclude the influence of age on
A. muciniphila, we checked the colon phenotype and
A. muciniphila abundance between the young
Cyp27b1−/− and WT mice of 10–12 weeks. Our data demonstrated that even in young mice, 1,25(OH)
2D
3 deficiency led to a higher
A. muciniphila abundance in fecal sample (Fig.
4a) and increased the translocation of bacterial to MLNs and thinner mucus layer in
Cyp27b1−/− mice (Fig.
4b, c). It may be noteworthy that the inflammation was not significant in
Cyp27b1−/− mice (data not shown), which was in concert with our prior study showing that 1,25(OH)
2D
3 deficiency could induce colon inflammation with aging [
11]. Our present study suggests that 1,25(OH)
2D
3 deficiency-induced higher
A. muciniphila location in gut was gene associated but not age-related.