Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

ISME J. 2014 Apr;8(4):881-93. doi: 10.1038/ismej.2013.185. Epub 2013 Oct 17.


Human gut microbiota shows high inter-subject variations, but the actual spatial distribution and co-occurrence patterns of gut mucosa microbiota that occur within a healthy human instestinal tract remain poorly understood. In this study, we illustrated a model of this mucosa bacterial communities' biogeography, based on the largest data set so far, obtained via 454-pyrosequencing of bacterial 16S rDNAs associated with 77 matched biopsy tissue samples taken from terminal ileum, ileocecal valve, ascending colon, transverse colon, descending colon, sigmoid colon and rectum of 11 healthy adult subjects. Borrowing from macro-ecology, we used both Taylor's power law analysis and phylogeny-based beta-diversity metrics to uncover a highly heterogeneous distribution pattern of mucosa microbial inhabitants along the length of the intestinal tract. We then developed a spatial dispersion model with an R-squared value greater than 0.950 to map out the gut mucosa-associated flora's non-linear spatial distribution pattern for 51.60% of the 188 most abundant gut bacterial species. Furthermore, spatial co-occurring network analysis of mucosa microbial inhabitants together with occupancy (that is habitat generalists, specialists and opportunist) analyses implies that ecological relationships (both oppositional and symbiotic) between mucosa microbial inhabitants may be important contributors to the observed spatial heterogeneity of mucosa microbiota along the human intestine and may even potentially be associated with mutual cooperation within and functional stability of the gut ecosystem.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Biodiversity
  • Ecosystem*
  • Female
  • Humans
  • Intestinal Mucosa / microbiology*
  • Male
  • Microbiota / genetics
  • Microbiota / physiology*
  • Middle Aged
  • Models, Biological*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Young Adult


  • RNA, Ribosomal, 16S