Characterization of the human predominant fecal microbiota. With special focus on the Clostridial clusters IV and XIVa. [Ihmisen vallitsevan ulostemikrobiston karakterisointi. Painopiste erityisesti klostridien fylogeneettisissä ryhmissä IV ja XIVa]

The human gut microbiota is considered to be a complex fermentor with a metabolic potential rivaling that of the liver. In addition to its primary function in digestion, it affects the human host in numerous ways: maturation and modulation of the immune system, production of short-chain fatty acids and gases, transformation of bile acids, formation of vitamins, and also potential formation of mutagenic, toxic, and carcinogenic substances. Commensal bacteria are able to modulate the expression of host genes that regulate diverse and fundamental physiological functions. Thus the indigenous microbial community has an important influence on host physiological, nutritional and immunological processes. The primary aim of this study was to characterize human predominant fecal microbiota with a special focus on Clostridial clusters XIV (Lachnospiraceae, Eubacterium rectale – Blautia coccoides group) and IV (Ruminococcaceae, Clostridium leptum group). The specific aims were: 1) To develop molecular methods for characterization of the human predominant fecal microbiota; 2) To assess the specificity, practicality, and usability of the developed methods for human fecal samples in healthy adults, elderly people, and people having IBS; 3) To assess possible confounding factors in the analysis of human fecal samples. Molecular tools were developed for rapid, sensitive, and highly specific characterization of the human predominant fecal and salivary microbiota. DNAand rRNAbased denaturing gradient gel electrophoresis methods (DGGE) were developed for Eubacterium rectale – Blautia coccoides group (Erec), rRNA-based DGGE method for predominant bacteria, and DNA-based DGGE methods for Clostridium leptum group (Clept) and Bacteroides spp. In addition, quantitative real-time PCR (qPCR) methods targeting predominant bacteria, Erec-group, Clept-group, Bacteroides spp., bifidobacteria, and Atopobium group were developed. Predominant bacterial, Erec-group, Clept-group, and Bacteroides spp. populations of healthy adults were temporally rather stable, showing intra-individual diversity and inter-individual variability. The rRNA-based profiles showed more temporal instability than DNA-based profiles. The enumerated clostridial groups (Erec, Clept, C. lituseburense, and C. histolyticum) represented the dominant fecal microbiota of most of the studied subjects, comprising altogether 29–87% of the total bacteria. Erec-group was the dominant group, accounting on average for 43% of total bacteria in control subjects, and 30% and 50% in irritable bowel syndrome (IBS) subjects affected by constipation and diarrhea, respectively. The proportion of Erec-group was significantly lower in the constipation type IBS subjects than in