Complex metabolic networks of interacting microbes in the gastrointestinal tract of humans and other mammals yield a wide range of metabolites. The short chain fatty acids (SCFA’s), in particular butyrate, propionate and acetate are the most abundant products of carbohydrate fermentation.
So far metabolic networks were documented in in vitro models. In this project interactions between diet, microbiota and host will be quantitatively studied and subsequently modeled using a Systems Biology approach. In initial experiments the cecum and colon of conventionally raised mice on different fiber diets are analyzed. Determinations of the microbiota composition using phylogenetic microarray (MITChip) technology will be complemented with metatranscriptome and metabolome analyses to obtain microbiota metadata that can be modeled in relation to the dietary regimes.
Get insight in relationship between exogenous (diet, probiotic intervention) and endogenous (host response) factors in the population dynamics in the gut.
1. Microbiota composition dynamics in the gut will be analyzed by the application of phylogenetic microarray technology that has recently been developed at the Laboratory of Microbiology, Wageningen University. These DNA oligonucleotide microarrays, which target variable regions within the small subunit ribosomal RNA (SSU rRNA) sequences of intestinal microbiota, allow the comprehensive profiling of gut microbiota composition at high spatio-temporal resolution (Rajilić-Stojanović et al., 2009). In addition to the prototype, the HITChip (Human Intestinal Tract Chip), platforms have been recently developed and extensively validated that are specific for murine (MITChip; Derrien et al., in preparation) and porcine (PITChip; Perez et al., in preparation) intestinal microbiota.
2. To address not only microbiota composition, but rather focus on metabolic potential and actual activity of gut microbiota, we will apply emerging technologies that allow meta-transcriptomic and meta-proteomic analysis by next generation HTP sequencing (e.g. 454 pyrosequencing, Solexa, SOLiD, Pacific Biosciences) (MacLean et al., 2009). Non-gel based shot gun proteomics can be performed through a standing agreement with Biqualys, Wageningen.
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