The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

Increasing evidence suggests that a combination of host genetics and the composition of the gut microbiota are important for development of Crohn's disease (CD). Our aim was to study identical twins with CD to determine microbial factors independent of host genetics. Fecal samples were studied from 10 monozygotic twin pairs with CD (discordant n=6 and concordant n=4) and 8 healthy twin pairs. DNA was extracted, 16S rRNA genes were PCR amplified and T-RFLP fingerprints generated using general bacterial and Bacteroides group-specific primers. The microbial communities were also profiled based on their percentage G+C contents. Bacteroides 16S rRNA genes were cloned and sequenced from a subset of the samples. The bacterial diversity in each sample and similarity indices between samples were estimated based on the T-RFLP data using a combination of statistical approaches. Healthy individuals had a significantly higher bacterial diversity compared to individuals with CD. The fecal microbial communities were more similar between healthy twins than between twins with CD, especially when these were discordant for the disease. The microbial community profiles of individuals with ileal CD were significantly different from healthy individuals and those with colonic CD. Also, CD individuals had a lower relative abundance of B. uniformis and higher relative abundances of B. ovatus and B. vulgatus. Our results suggest that genetics and/or environmental exposure during childhood, in part, determine the gut microbial composition. However, CD is associated with dramatic changes in the gut microbiota and this was particularly evident for individuals with ileal CD.

SUMMARY. Microbiota in the intestine of an animal species has evolved together with the host. This coevolution has produced specific host-microbe combinations,

The different sections of the broiler chicken intestinal tract are inhabited by specialist microbiota adapted to the physicochemical conditions, host physiology and available nutrients of the specific habitat. The small intestine is dominated by lactic acid bacteria which have complex nutrient requirements resembling those of the chicken host itself. Lactobacilli are unable to synthesise amino acids for their anabolism and are therefore highly dependent on amino acid availability in the growth environment. Thus, in the small intestine there is competition for amino acids between the microbiota and the chicken host. According to rough estimates, lactobacilli in the small intestine may assimilate 3–6% of total dietary amino acids. If the protein is highly digestible and amino acids are largely absorbed in the upper small intestine, where bacterial growth is suppressed, the proportion captured by the host may be higher. Exogenous enzymes which promote protein digestion are also likely to provide a competitive advantage to the chicken, offering less growth potential for amino acid-dependent bacteria.Protein escaping the ileum comprises resistant protein of dietary origin, protein assimilated to intestinal bacteria and endogenous protein synthesised and secreted by the host, the latter synthesised in host tissues from dietary amino acids and thus representing true endogenous protein. Activities of small intestinal bacteria affect the size of the microbial protein fraction and also the production of endogenous proteins originating from mucin, epithelial cells and antibodies.Ileal bypass protein is subject to fermentation by putrefactive bacteria in the caecum. Putrefaction produces many harmful and toxic compounds, which in high concentrations may have adverse effects on chicken growth and performance. The protein fermentation products include amines, indoles, phenols, cresol and ammonia, which can all negatively affect host or cell health. All actions to reduce the amount of ileal bypass protein potentially also reduce production of toxic protein fermentation metabolites in the caecum. Enzymes which facilitate protein digestion in the upper intestine and soluble carbohydrates resistant to ileal digestion both reduce caecal putrefaction. In the distal intestine, saccharolytic fermentation is preferred and putrefaction accelerates only when utilisable carbohydrates are depleted. Soluble oligo- and polysaccharides are produced in situ by non-starch polysaccharide degrading enzymes and can also be added directly to the diet as health-promoting prebiotics