Bacterial biogeography of the human digestive tract

Abstract

We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated >32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing >95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with >99% Good's coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highly similar within individuals and largely distinct from those in stool. Within an individual, OTU overlap among broad site definitions (mouth, stomach/duodenum, colon and stool) ranged from 32–110 OTUs, 25 of which were common to all individuals and included OTUs affiliated with Faecalibacterium prasnitzii and the TM7 phylum. This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease.

The gastric microbial community,Helicobacter pyloricolonization, and disease

“…11,14 These caveats aside, cultivationindependent methods suggest that the gastric community is in fact distinct, even when H. pylori is not present. 11,[14][15][16] This conclusion is supported by both sequence abundance weighted and unweighted phylogeny-based community analyses, irrespective of H. pylori infection status or gastric anatomical site. While communities sampled from oral (dental plaque, tongue, pharynx) and gastric habitats (antrum, corpus) frequently segregate by site, there is some degree of overlap among samples, which is perhaps to be expected given the continual flow of food and saliva from the mouth to the stomach.…”

“…Based on 16S rDNA sequence signatures, the human gastric microbiota is comprised of several hundred operational taxonomic units (OTUs), 11,12,15,17 which span 44 bacterial phyla.…”

Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity

“…This results in an aggregation of species composition variations within the bands and may contribute to the low turnover rate observed 4 . In addition, DNA fingerprinting precludes consideration of the accumulation of new minor species ARTICLE with increasing distance, which may represent a large proportion of the total soil microbial species richness 33 and determine the slope of TAR 14,31 . The low z bacteria might also be related to the grain size of our sampling design (16 km  16 km: 256 km 2 ), which did not consider scales less than landscape, and smoothed significant local variations in soil microbial community composition that might potentially affect TAR 34 .…”

The role of the human gut microbiome in ankylosing spondylitits

“…The dominant phyla previously reported to inhabit the gut are Bacteroidetes and Firmicutes with lower abundance of Actinobacteria, Proteobacteria, Fusobacteria and Verrucomicrobia (152,178). The purpose of this experiment was to demonstrate that the primer pairs covered the range of expected phyla as well as the capacity to discriminate other phyla.…”

“…This demonstrates that either primer set would adequately profile the intestinal microbiome. However, 517F 803R identified seven more phyla, including some phyla that have been reported as being low in abundance such as Verrucomicrobia and Lentisphaerae (178). Based on the in silico simulation, the primer set 517F 803R would be better suited to interrogate human gut biopsies moving forward.…”