High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

Gut Microbes. 2015;6(3):173-81. doi: 10.1080/19490976.2015.1044711.


Background: The intestinal microbiota is associated with human health and diseases. The luminal microbiota (LM) and the mucosal-associated microbiota (MAM) are 2 distinct ecosystems with different metabolic and immunological functions.

Aim: To characterize the intestinal LM and MAM in humans using high throughput sequencing of the 16S rRNA gene.

Methods: Fresh fecal samples and distal colonic mucosal biopsies collected from 24 healthy subjects before (fecal) and during (mucosa) a flexible sigmoidoscopy of an un-prepared bowel. High throughput sequencing of the 16S rRNA gene was used to characterize bacterial communities. Sequences were processed using the QIIME pipeline.

Results: LM and MAM populations were significantly different (ANOSIM: R = 0.49, P = 0.001). The LM displayed tighter clustering compared to the MAM (average weighted UniFrac distances 0.27 ± 0.05 vs. 0.43 ± 0.09, P < 0.001, respectively), and showed higher diversity (Shannon diversity index: 4.96 ± 0.37 vs 4.14 ± 0.56, respectively, P < 0.001). The dominant phyla in the LM and MAM were significantly different: Firmicutes (41.4% vs. 29.1%, FDR < 0.0001, respectively), Bacteroidetes (20.2% vs. 26.3%, FDR < 0.05, respectively), Actinobacteria (22% vs. 12.6%, FDR < 0.0001, respectively) and Proteobacteria (9.3% vs. 19.3%, FDR < 0.0001, respectively). The abundance of 56 genera differed significantly (FDR < 0.1) between the 2 niches. All of the genera in the fecal microbiota were present in the MAM while 10 genera were found to be unique to the MAM.

Conclusion: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease.

Keywords: 16S rRNA gene; IBD, Inflammatory bowel diseases; IBS, Irritable bowel syndrome; IRB, Internal Review Board; LM, Luminal microbiota; MAM, Mucosal-associated microbiota; UNC, University of North Carolina; high throughput sequencing; human microbiota; intestinal microbiota; mucosal microbiota.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Colon / microbiology
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / chemistry
  • DNA, Ribosomal / genetics
  • Female
  • Gastrointestinal Contents / microbiology*
  • Gastrointestinal Microbiome*
  • Healthy Volunteers
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Intestinal Mucosa / microbiology*
  • Male
  • Microbiota*
  • Middle Aged
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Young Adult


  • DNA, Bacterial
  • DNA, Ribosomal
  • RNA, Ribosomal, 16S