Functional Genomic and Metabolic Studies of the Adaptations of a Prominent Adult Human Gut Symbiont, Bacteroides thetaiotaomicron, to the Suckling Period

Abstract

The adult human gut microbiota is dominated by two divisions of Bacteria, the Bacteroidetes and the Firmicutes. Assembly of this community begins at birth through processes that remain largely undefined. In this report, we examine the adaptations of Bacteroides thetaiotaomicron, a prominent member of the adult distal intestinal microbiota, during the suckling and weaning periods. Germ-free NMRI mice were colonized at birth from their gnotobiotic mothers, who harbored this anaerobic Gram-negative saccharolytic bacterium. B. thetaiotaomicron was then harvested from the ceca of these hosts during the suckling period (postnatal day 17) and after weaning (postnatal day 30). Whole genome transcriptional profiles were obtained at these two time points using custom B. thetaiotaomicron GeneChips. Transcriptome-based in silico reconstructions of bacterial metabolism and gas chromatography-mass spectrometry and biochemical assays of carbohydrate utilization in vivo indicated that in the suckling gut B. thetaiotaomicron prefers hostderived polysaccharides, as well as mono-and oligosaccharides present in mother's milk. After weaning, B. thetaiotaomicron expands its metabolism to exploit abundant, plant-derived dietary polysaccharides. The bacterium's responses to postnatal alterations in its nutrient landscape involve expression of gene clusters encoding environmental sensors, outer membrane proteins involved in binding and import of glycans, and glycoside hydrolases. These expression changes are interpreted in light of a phylogenetic analysis that revealed unique expansions of related polysaccharide utilization loci in three human alimentary tract-associated Bacteroidetes, expansions that likely reflect the evolutionary adaptations of these species to different nutrient niches.Our adult gut is colonized with a community of 10 -100 trillion microbes. This microbiota, and its collective genome (microbiome), provide us with important physiological attributes that are not encoded in our own human genome, including the ability to break down otherwise indigestible nutrients that are delivered to the distal gut, such as dietary plant polysaccharides (1, 2). A recent comprehensive 16 S rRNA-based enumeration study of the distal intestinal microbiota of a small number of healthy adult humans demonstrated that Ͼ99% of detected phylogenetic types (phylotypes) belong to two of the 70 bacterial divisions (superkingdoms) currently known in nature: the Bacteroidetes and the Firmicutes (3, 4). Within each division there is great diversity at the species and subspecies levels. Moreover, these shallow lineages show considerable variation between individual humans (3, 4).The mechanisms controlling assembly of our microbiotas remain ill defined. This issue can be framed as follows. What is the effect of the microbial community that is available to colonize a host at the time of birth (the legacy effect)? What is the effect of the gut environment itself on shaping the available community, and is the gut selecting for properties that are common ...

Bacteroides: the Good, the Bad, and the Nitty-Gritty

“…Also, studies with mice indicate that B. thetaiotaomicron can redirect its carbohydrate-utilizing capability from dietary to host polysaccharides according to nutrient availability (265). In another study, the adaptation of B. thetaiotomicron to utilize different nutrients during the suckling and weaning periods was investigated (27). Transcriptome analysis indicated that B. thetaiotaomicron harvested from the ceca of suckling mice has increased expression of enzymes that can utilize host-derived polysaccharides (host glycans, hexoseamines, and sialic acids that are present in mucus and the underlying gut epithelium), as well as enzymes to aid in the catabolism of mono-and oligosaccharides present in mother's milk.…”

“…Transcriptome analysis indicated that B. thetaiotaomicron harvested from the ceca of suckling mice has increased expression of enzymes that can utilize host-derived polysaccharides (host glycans, hexoseamines, and sialic acids that are present in mucus and the underlying gut epithelium), as well as enzymes to aid in the catabolism of mono-and oligosaccharides present in mother's milk. After weaning, the repertoire of sugar-digesting metabolic enzymes was expanded so that plant-derived polysaccharides (which would now be present in the gut) could be utilized (27).…”

“…By analyzing whole-genome transcriptional profiles of the bacterium harvested from the intestines of mice at different time points, the authors demonstrated that in sucking animals, glucose/galactose transporters and other glycosidases (enzymes that would be important in using host glycans sources) were expressed at higher levels, whereas B. thetaiotaomicron harvested from mice in the weaned stage showed increased expression of genes for enzymes that can liberate sugars from plant polysaccharides. Thus, during the suckling period, B. thetaiotomicron preferentially used host-derived polysaccharides as well as mono-and oligosaccharides present in mother's milk, and after weaning, this organism expanded its metabolism to exploit abundant polysaccharides of plant origin (27).…”

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

“…These genes are assembled in similarly organized, selectively regulated polysaccharide utilization loci (PULs) that encode functions necessary to detect, bind, degrade and import carbohydrate species encountered in the gut habitateither from the diet or from host glycans associated with mucus and the surfaces of epithelial cells (5)(6)(7). Studies of gnotobiotic mice colonized only with human gut-derived Bacteroides thetaiotaomicron have demonstrated that this organism can vary its pattern of expression of PULs as a function of diet, e.g., during the transition from mother's milk to a polysaccharide-rich chow consumed when mice are weaned (5), or when adult mice are switched from a diet rich in plant polysaccharides to a diet devoid of these glycans and replete with simple sugars (under the latter conditions, the organism forages on host glycans) (6,7).…”

Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging

“…Apart from dietary components, host-derived glycans are believed to constitute a nutrient resource for (certain) members of the intestinal microbiota (3) and thus may influence the composition and activities of this complex microbial consortium. Indeed, in the absence of dietary nutrients colonization of the intestinal microorganism Bacteroides thetaiotaomicron is reliant on host-derived glycans, which it metabolizes by means of polysaccharide utilization loci (4), showing that under such circumstances endogenous carbohydrates influence the composition of the intestinal microbiota (3). Recently, another constituent of human gut microbiota, Akkermansia muciniphila, was identified as an important mucin degrader (5,6), but little is known regarding the genetic elements required for this property.…”