Molecular epidemiology of intestinal microbiota reveals a dysbiotic state due to environmental factors: a comparative study of different lifestyles

Abstract

INTRODUCTION: Epidemiologic studies point to the critical role of environmental factors in the pathogenesis of the chronic inflammatory bowel diseases (IBD). Lifestyle factors, such as nutrition, hygiene habits and improved medical services, were accounted for the raising incidence of these disorders over the last decades in the industrialized countries (hygiene hypothesis). The intestinal microbiota as an integral part of the enteric mucosal barrier reflects the evolution of lifestyle factors. Novel metagenomic techniques have enriched the repertoire of molecular microbiology in the description of complex ecosystems. AIMS & METHODS: To compare the composition of the intestinal microbiota of individuals living in rural areas of a region with low incidence of civilization diseases with that of a region in an industrialized region with high incidence rates using 16S rDNA clone libraries. Colonic mucosal biopsy samples (n=10) from the sigma of healthy individuals from a rural area in Lithuania were compared to those of a German city (n=10). Large-scale, pooled clone libraries with a total of more than 1.500 sequenced 16 S rDNA clones were generated using broad-range universal primers. Modern statistical algorithms were employed to analyse richness and diversity as well as markers of the quality and appropriateness of clone libraries. RESULTS: The libraries showed significant qualitative differences in the composition of bacterial species and groups. The overall richness of bacterial operational taxonomic units (OTUs) was significantly higher in the Lithuanian population in contrast to German individuals (n=193 vs. 133). Bacterial phyla showed significant increase in the Lithuanian group of Firmicutes (50.5 vs. 40.6%) and Proteobacteria (16.5 vs. 11.9%), in the German population of Bacteriodetes (25.7 vs. 41.4%, all p<0.05). [...].