Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes

Abstract

Bacterial diversity of the mucosal biopsies from human jejunum, distal ileum, ascending colon and rectum were compared by analysis of PCR-amplified 16S rDNA clone libraries. A total of 347 clones from the mucosal biopsies were partially sequenced and assigned to six phylogenetic phyla of the domain Bacteria: Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Verrucomicrobia, and Actinobacteria. The jejunum sample had least microbial diversity compared to the other samples and a trend towards highest diversity in ascending colon was observed. The clone libraries of distal ileum, ascending colon and rectum were not significantly different from each other (P>0.0043), but they differed significantly from the jejunum library (P=0.001). The population of sequences retrieved from jejunal biopsies was dominated by sequences closely related to Streptococcus (67%), while the population of sequences derived from distal ileum, ascending colon and rectum were dominated by sequences affiliated with Bacteroidetes (27-49%), and Clostridium clusters XIVa (20-34%) and IV (7-13%). The results indicate that the microbial community in jejunum is different from those in distal ileum, ascending colon and rectum, and that the major phylogenetic groups are similar from distal ileum to rectum.

Characterization of the complex bacterial communities colonizing biliary stents reveals a host-dependent diversity

“…By contrast, Bacteroides sp. are among the most predominant genera of intestinal microbiota (Hold et al, 2002) and have been found to be dominant among bacteria on the ileal mucosal surface (Wang et al, 2005) and in accordance with the hypothesis of invasion of microorganisms through an ascending infection by duodenal biliary reflux (Sung et al, 1992) were observed in a high number (approximately 20%) of stent communities. This also explains the high prevalence in stent communities of acid-tolerant Streptococcus spp.…”

“…This also explains the high prevalence in stent communities of acid-tolerant Streptococcus spp. and Lactobacillus spp., which were reported to be highly abundant in the ileum (Hayashi et al, 2005;Wang et al, 2005) and probably are major colonizers of the duodenum (Wilson, 2005). The immense prevalence of Veillonella sp.…”

“…Bifidobacteria are autochthonous bacteria in the gastrointestinal tract (Klijn et al, 2005), but so far they have not been characterized as abundant in biliary stents. Culture-independent studies on the small intestine found them to be in low abundance (Hayashi et al, 2005;Wang et al, 2005), whereas they are more abundant in the colon and have been reported to comprise 3.3% in faeces (Vaughan et al, 2002). However, the sequences obtained were related to B. animalis, which has been extensively used in functional dairy products (Masco et al, 2005), rather than to B. longum, B. bifidum, B. adolescentis and B. angulatum, which are assumed to be the predominant species in the human gastrointestinal tract (Gueimonde et al, 2004;Mangin et al, 2006).…”

Microbiomic analysis of the bifidobacterial population in the human distal gut

“…Earlier investigations have not rigorously addressed possible differences in the intestinal bifidobacteria between individuals (Eckburg et al, 2005;Wang et al, 2005). We applied techniques that are based on the relative abundance of sequences within communities and the extent of genetic divergence between sequences.…”

“…Advances in microbial ecology including metagenomic studies of environmental samples have allowed microbial ecologists to access earlier unimaginable genetic diversity. Recently, metagenomic and microbiomic studies based on the analysis of genomic DNA-and rRNA gene libraries have highlighted the diversity of the GIT microbiota and have shown that it consists of many novel and, as yet, unculturable bacterial components (Eckburg et al, 2005;Wang et al, 2005;Gill et al, 2006;Kurokawa et al, 2007;Palmer et al, 2007). However, relatively few bifidobacterial rRNA gene sequences have so far been identified in these metagenomic studies, which are in striking contrast to what was described earlier in several bifidobacterial surveys, which had adopted culture-dependent approaches (Poxton et al, 1997;Harmsen et al, 2000;Fanaro et al, 2003).…”