Dysbiosis in the inflamed intestine: chance favors the prepared microbe

Abstract

The bacterial microbiota of the human large bowel is a complex ecosystem consisting of several hundred, mostly anaerobic, species. To maintain colonization of the gut lumen and maximize growth in the presence of nutritional competitors, highly diverse metabolic pathways have evolved, with each microbe utilizing a different "winning strategy" for nutrient acquisition and utilization. Conditions and diseases leading to intestinal inflammation are accompanied by a severe disruption the microbiota composition characterized by an expansion of facultative anaerobic Enterobacteriaceae. Here, we review evidence that the local inflammatory response creates a unique nutritional environment that is conducive to a bloom of bacterial species whose genomes encode the capability of utilizing inflammation-derived nutrients.

Keywords: Enterobacteriaceae; dysbiosis; enteric pathogens; inflammatory bowel disease; irritable bowel syndrome; necrotizing entercolitis.

Figure 1. Schematic representation of the prevalence of nitrate reductase-encoding genomes within major phyla. 2476 genome sequences deposited in the Kyoto Encyclopedia of Genes and Genomes (Release 67.1; http://www.kegg.jp/)^29,30 were searched for the predicted presence of respiratory nitrate reductase activity (E.C.1.7.99.4). Phyla comprising thermophilic organisms (representing a total of 61 genomes) were excluded from this analysis, as these bacteria are unlikely to be present in the mammalian gut. Phyla commonly present in the gut-associated microbial community (ubiquitous phyla) and phyla present occasionally (rare phyla) are indicated in the inner circle, but the size of each sector is not proportional to their relative abundances. The prevalence of putative nitrate reductase activity (coloring of the outer circle) was calculated as the fraction of nitrate reductase-encoding genomes per total number of genomes within a given phylogenetic group.