| The adult human gut is colonized by 10-100 trillion microbes, the vast majority of whom belong to just two of the 70 known divisions of Bacteria---the Bacteroidetes and the Firmicutes. Acquiring a gut microbial community is highly beneficial: its collective genome ('microbiome') specifies functions that are not encoded by our H. sapiens genome, including digestion of prominent components of our diet that we are ill-equipped to process on our own (e.g., plant polysaccharides). We acquire our microbiota from our mothers and the environment in which we live. This process, which begins at birth, has not yet been characterized in individuals or populations using 16S rRNA sequence-based enumeration methods, nor are the mechanisms known that are used by members of the adult microbiota to adapt to their gut habitats so that they can persist through the suckling/weaning transition to adulthood. I have addressed the latter issue in my thesis by using a simplified model of the human gut microbiota.; I focused on a prominent member of the adult, and a minor member of the neonatal, distal gut microbiota---Bacteroides thetaiotaomicron. To define the transcriptome and proteome of this saccharolytic Bacteroidetes, I helped sequence and annotate its 6,250,361 bp genome. Among its 4779 predicted ORFs, we found a markedly expanded collection of 241 glycosyl hydrolases and polysaccharide lyases (our human genome contains 99). There was also a highly evolved sensory apparatus that includes 50 ECF-sigma factors, 26 anti-sigma factors and 32 novel hybrid two-component systems.; To examine the properties of B. thetaiotaomicron in vivo, germ-free NMRI mice were colonized at birth with this bacterium. Whole genome transcriptional profiling was performed using cecal populations of B. thetaiotaomicron harvested from suckling (P17) and weaned (P30) littermates. By combining in silico reconstructions of bacterial metabolism, based on these GeneChip datasets, with GC-MS and biochemical assays, I found that this anaerobe exploits host glycans in addition to mono-, di- and oligosaccharides in mother's milk to support its rapid rates of division during the suckling period. After weaning, B. thetaiotaomicron adaptively expands its glycan-harvesting machinery: this includes expression of additional paralogs of two outer membrane proteins (SusC and SusD) involved in binding and import of dietary polysaccharides, plus glycoside hydrolases needed for degradation of dietary plant polysaccharides. The bacterium's responses to these developmental stage-specific changes in the gut's nutritional landscape involve coordinate changes in transcription of clusters of genomically linked polysaccharide utilization genes. These are clusters that include ECF-sigma and anti-sigma factors, SusC/D paralogs, and glycoside hydrolases. Phylogenetic analysis revealed unique expansions of these loci in B. thetaiotaomicron, compared with other Bacteroides---a feature that likely reflects its evolved niche (profession) and that may provide clues about its contribution to digestive health. |
