Host-microbial interactions in the mammalian colon are complex and incompletely understood, yet they play a central role in maintaining intestinal and immune homeostasis and providing the nimbleness to respond to physiological anomalies 
. For host-microbial interaction to occur, a dynamic mutualistic relationship must exist between host and microbes, where assembly and function of specific microbes are modulated by host factors and vice versa to achieve a state of stability and mutual benefit. In this study, we demonstrate an almost inseparable relationship between mucosa-associated microbiota and mucosal TLR expression. We observed, for instance, that cecal microbiota transferred to germ-free recipient mice can fully restore the pattern of regional mucosa-associated microbiota, a finding that has several important implications. First, cecal microbiota, which has the greatest diversity of the GI tract, is the source for most, if not all mucosa-associated microbiota of the proximal and distal colon. Second, as the cecal microbiota move distally, local conditional factors play a major role in determining the assembly rules that dictate which microbes are selected to become part of the more stable community of mucosa-associated microbiota. In the proximal colon, the host factors are similar to those in the cecum, as the microbiota in these two regions cluster closely. In contrast, host conditions of the distal colon are different, resulting in a less diverse mucosa-associated microbiota that cluster separately from those found in the cecum, proximal colon, distal colonic lumen and stool. Examples of host factors that can determine region-specific differences in mucosa-associated microbiota mucus composition, nutrient availability, motility, blood flow, and immune factors such as the regional expression of TLRs in both immune and epithelial cell compartments.
We found the profile of mucosa-associated microbiota from the proximal colon was relatively similar to feces in the rectal vault (essentially luminal microbiota of the distal colon). Thus, as stool forms in the transverse colon, most of these microorganisms are retained and sequestered in the stool. There appears to be little contribution to stool microbes by distal colonic mucosa-associated microbiota and vice versa. While the enteric microbiota of these regions varied considerably among different litters of in-house and Jackson Laboratory bred mice, the clustering of regional patterns remained consistent, i.e. proximal colonic mucosa-associated and rectal vault stool samples were similar, but both were significantly different from that in the distal colon. Analysis of microbiota richness showed that distal colonic mucosa-associated microbiota was consistently less diverse than that of proximal colon, cecal.
Once assembled, the mucosa-associated microbiota of the proximal and distal colon play an important role in regulating host gene expression and cellular functions 
. Our data support this notion because the exposure of the distal colonic mucosa to cecal microbiota induces TLR2 expression. Thus, the gradients of TLR2 and TLR4 expression along the length of the colon are not caused by inherent limitations in tissue response to microbial stimulus. Rather, it appears that regional TLR2 and TLR4 expression are determined by the overlying mucosa-associated microbiota.
Our finding of differences in regional TLR2 and TLR4 expression along the length of the colon confirm observations by Kinoshita and colleagues 
. However, similar patterns of expression are found among several other host genes whose expression are regulated by microbial signals, including peroxisome proliferator-activated receptors 
, TGF-B activators 
, inducible heat shock proteins (unpublished data) and vitamin D receptor 
. Many of these genes are involved in the regulation of immune/inflammatory responses, cell growth and differentiation, cytoprotection, and barrier function in the mammalian colon. Their region-specific expression is likely due to differences in region-specific mucosa-associated microbiota, but also imparts specialized functions that are inherently important to host physiology or maintenance of intestinal homeostasis.
While this study does not address the purpose of region-specific TLR expression, we offer two possibilities for consideration. First, the microbiota-induced expression profile of TLRs may be a self-reinforcing mechanism to further stabilize the existing mucosa-associated microbiota or deter non-compatible microbes from colonization through negative selection. In support of this possibility is the observation that NOD mice deficient in MyD88 gene expression have a distinct colonic microbiota profile from their heterozygote counterparts 
, ultimately influencing the clinical outcome of experimental type I diabetes. Another possibility for the region-specific, microbe-dependent TLR expression is that TLR2 can dimerize with either TLR1 or TLR6, resulting in skewing of naïve T cells towards either an immunogenic or tolerating immune response 
. Thus, the greater expression of TLR2 in the proximal colon may provide a more adaptable immune response capable of dealing with a microbial population of greater diversity and abundance.
Regional differences in colonic microbiota and microbiota-dependent host gene expression could also influence the pattern and presentation of certain bowel diseases. Inflammatory bowel diseases, for instance, have very characteristic presentations and patterns to their mucosal inflammation, suggesting a role for topical factors such as mucosa-associated microbiota. Among different individuals, for example, the extent of ulcerative colitis can vary, but the disease invariably starts in the rectum. A similar pattern of inflammation is seen in DSS-induced experimental murine colitis where the inflammation is predominantly found in the distal colon and rectum 
. We speculate that the composition and less diverse nature of the distal colonic mucosa-associated microbiota could favor the emergence of disease-promoting microbes. Alternatively, we raise the possibility that the declining proximal-distal gradient of host factors important for maintaining immune and intestinal homeostasis (e.g. TLR2, heat shock proteins, vitamin D receptor) could render the distal colon more susceptible to injury and the development of ulcerative colitis.
In summary, we find regional heterogeneity in mucosa-associated microbiota and TLR2 and TLR4 expression which appear to be interdependent. The findings also underscore a specific role of mucosa-associated microbiota that is distinct from the more transient population of luminal microbiota. Furthermore, our study raises the question as to whether the prevailing practice of sampling just luminal or stool microbiota is sufficient or appropriate for understanding the role of the enteric microbiome in health and disease. Finally, we believe the region-specific differences in mucosa-associated microbiota and their dependent host gene expression play an important role in contributing to the specific physiological functions of different parts of the mammalian colon.