| This present work examines the current knowledge of the diversity of microbial communities inhabiting the human colon. Specifically, this research focuses on the analysis of the diversity of hydrogenotrophic microbes in the human colon.;Chapter 1 reviews a series of studies describing the structure of the human intestinal microbiota. This chapter presents and discusses published reports indicating that the human intestine is inhabited by hundreds of different microbial phylogenetic species. These studies have shown that microorganisms of the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla are the most predominant in the intestinal ecosystem. Also presented are recent studies revealing new insights into the comprehensive inventory of microbial genes and genomes (microbiome). Metagenomic analyses derived from intestinal samples have revealed that the intestinal microbiome is rich in gene sets associated with carbohydrate transport and metabolism.;Chapter 2 is dedicated to the review and examination of different statistical methods for the analysis of data generated by molecular techniques designed to study the diversity of microbial communities in the human colon. It is demonstrated that data ordination by means of principal component analysis (PCA) is not a robust and reproducible technique and is inadequate for the analysis of microbial profiles. In contrast, principal coordinate analysis (PCoA) and non-metric multidimensional scaling analysis (NMDS) are more robust and highly reproducible ordination methods for multivariate microbial analyses. More importantly, this study introduces a comprehensive statistical schema for the use of multivariate methods for the quantitative analysis of microbial profiles.;Chapter 3 describes studies analyzing the diversity of hydrogenotrophic microbes, both sulfate reducing bacteria (SRB) and methanogens, in the colon of healthy humans. The work described in this chapter examines the diversity of mucosa-associated SRB and methanogens. The design and use of robust PCR-based methods and multivariate analyses are described in Chapter 2 for the analysis of these hydrogenotrophic microbes in colonic biopsies. This study revealed that SRB populations are ubiquitous in the human colon of healthy subjects. Sulfate reducing bacteria populations are similar across the right colon, left colon and rectum, and these communities are highly variable among human subjects and colonic regions. In contrast, the study also revealed that only 40% percent of subjects harbored mucosa-associated Archaea populations in at least one region of the colon. Analyses of functional genes recovered from these microbial populations revealed that SRB were phylogenetically related to Desulfovibrio piger, D. desulfuricans, Bilophila wadsworthia (sulfite reducer) and some uncharacterized SRB; whereas, methanogenic Archaea were related to Methanobrevibacter sp., M. smithii, Methanoculleus chikugoensis and some uncharacterized methanogens.;Chapter 4 describes the diversity of colonic SRB and methanogens in native African (NA), African American (AA) and Caucasian American (CA) healthy subjects. In this study, stool samples from NA, who were consuming a diet low in animal protein, versus AA and CA, with both cohorts consuming a typical Western diet, were used to examine the diversity of SRB and methanogenic microbes using PCR-based methods. Inferential and multivariate statistical analyses revealed that SRB populations in NA are more homogenous than in AA and that SRB communities in NA are distinguishable from those in AA and CA. Also, it was revealed that the African groups, NA and AA, harbor different Archaea populations than CA and that the microbial communities in NA and AA are distinguishable from those in CA. This observation is consistent with the hypothesis that interactions among ethnic background, diet and microbial mechanisms of H2 disposal may influence susceptibility to sporadic colorectal cancer. (Abstract shortened by UMI.)... |
