ReviewAnalyzing the molecular foundations of commensalism in the mouse intestine
Introduction
Bacteria have been part of our planet’s biota from at least the late Archean eon 1, 2. These microorganisms colonize an amazingly wide variety of habitats, including ecosystems where nutrients are extraordinarily scarce and where environmental stresses are extreme (e.g. 3•, 4, 5). The human body is home to a remarkable consortium of bacteria. In healthy adults, microbial cells have been estimated to outnumber somatic and germ cells by a ratio of 10:1 [6]. As in most natural habitats, it appears that the vast majority of our microbial partners can not be cultured with available techniques, and identification by rDNA genotyping has not been systematically applied 7, 8, 9••.
An encompassing genetic overview of Homo sapiens, as a life form, should include the genes in our genome and in the genomes of our microbial partners. At present, we have a limited understanding of how much of our genetic makeup reflects our need to co-exist with our affiliated microbes. Similarly, we have only a few insights about how these organisms have co-evolved with us and how this co-evolution has affected their genotypes and phenotypes [10•].
Our intestinal tract is more densely populated with microbes than any of our other ecosystems. The microflora of an individual varies along the length and across the diameter of their gut, and as a function of development and environmental factors. At any given moment, the ‘assembled’ community consists of some components that are rapidly passing through with water and food, and other components that are relatively persistent [6]. These variations in the microflora occur in the setting of temporal and spatial variations in the differentiation programs of the intestine’s four continuously renewing epithelial cell lineages, and in its mucosal immune system. The interplay between the microflora, the epithelium, and the underlying gut-associated lymphoid tissue (GALT) is undoubtedly dynamic, reciprocal, and very intricate 11•, 12•.
Understanding how we establish and sustain mutualistic relationships with the components of our gut microflora is important in understanding the basis of health (e.g. 13, 14), as well as the origins of a variety of diseases [9••]. Comparisons of germ-free and conventionally raised transgenic rats or knockout mice have established that the ‘normal’ microflora is an important contributor to the development of inflammatory bowel diseases 15, 16, 17. Graft-versus-host reactions can be avoided in mice if the transplant recipient is germ-free, or if the normal intestinal microflora has been selectively depleted with antibiotics prior to transplantation [18]. Aggressive decontamination of the gut also helps prevent graft-versus-host disease in human recipients of bone marrow transplants [19]. Other recent work supports the idea that structural similarities between microbial epitopes and epitopes normally expressed in host cell lineages can, under the ‘right’ circumstances, lead to self-directed immunity [9••]. This may explain the association between Chlamydia spp. and heart disease [20•], or Campylobacter jejuni infection and Guillain-Barre syndrome [21•], or why Helicobacter pylori colonization of the stomach of some individuals leads to parietal cell loss, chronic atrophic gastritis, and an increased risk of gastric cancer [22•].
The study of how mutualistic relationships (symbiotic or commensal) are established between a microbe and its mammalian host represents an emerging field. One obstacle to defining the molecular foundations of mutualistic relationships has been the complexities of the ecosystems where such relationships are negotiated. This is particularly true in the intestine, where identifying a ‘conversation’ involving one or more of its resident commensals is difficult, because so many discussions are occurring at the same time and because we do not even know what ‘words’ to listen for. In this article we highlight recent progress in creating simplified and genetically manipulatable gnotobiotic models of the intestinal ecosystem. These models permit experimental analysis of how both host and microbe actively collaborate in shaping and manipulating the gut’s nutrient foundation. The approaches used, and the results obtained, are likely to be applicable to other mammalian ecosystems.
Section snippets
Evidence for microbial programming of a nutrient foundation in the mouse distal small intestine
A number of differences have been noted between the intestines of germ-free and conventionally raised mice [12•]. One of these differences involves a subset of fucosylated glycans in the distal small intestinal (ileal) epithelium. As discussed below, understanding the molecular basis for this difference has led to the conclusion that at least one component of the normal weaning microflora uses a clever and economical signaling mechanism to instruct the host to present a source of fucose that
Identification of a bacterial protein that regulates microbial fucose utilization and host fucosylated glycan production
The transposon in Fu-4 disrupts the gene encoding L-fucose isomerase (FucI) [28••]. This gene is part of a cluster of five genes encoding proteins required for uptake and breakdown of L-fucose. Four of these genes (i.e. fucR, fucI, fucA, and fucK) form an operon [28••] (Figure 2a). fucR encodes a transcriptional repressor of this operon. This dimeric protein belongs to the gluconate family of bacterial repressors [30]. fucI encodes the enzyme that converts L-fucose to L-fuculose, the first step
The benefits of collaboration
Engineering production of its own nutrient source in the intestinal epithelium makes sense for an organism such as B. thetaiotaomicron. It colonizes the intestine at weaning, when this ecosystem is already densely populated with an entrenched pre-weaning microflora, At this developmental stage, nutrient sources are likely to be limited by microbial consumption and competition. A preformed pool of Fucα1,2Gal-glycans in scattered ileal villi at the beginning of weaning may provide sufficient
The host response
Even in the simplified ecosystem provided by B. thetaiotaomicron colonization of germ-free mice, the microbial signal and the host response to this signal remain undefined. The intestinal epithelium undergoes continuous and rapid replacement of its four epithelial lineages. This renewal is fueled by multipotent stem cells located in mucosal invaginations (crypts of Lieberkühn) that surround the base of each villus (Figure 2b). As noted above, Fucα1,2Gal-producing enterocytes first appear in
Microbial responses: questions in need of answers
Many questions about the microbial response to colonization remain unanswered. An obvious question is the nature of the signal exported from B. thetaiotaomicron to the host. Does the signal bind to a known cell surface receptor? Does it have physicochemical properties that would allow it to diffuse across a host cell membrane? Is it a physiological ligand for an orphan nuclear receptor?
A comprehensive analysis of the cross-talk between commensals and their host should consider how luminal and
Conclusions and the future
The B. thetaiotaomicron-gnotobiotic mouse model provides an opportunity to gain a general understanding of the molecular events associated with colonization of the gut since both the microbe and host are genetically manipulatable. By introducing B. thetaiotaomicron or other commensals into developing and adult germ-free mice, it should also be possible to correlate changes in microbial gene expression with changes in host gene expression. Obtaining this type of comprehensive ‘moving picture’ of
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
• of special interest
•• of outstanding interest
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