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

Yehuda Ringel*, Nitsan Maharshak, Tamar Ringel-Kulka, Elizabeth Ashley Wolber, R. Balfour Sartor, Ian M. Carroll

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

142 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)173-181
Number of pages9
JournalGut Microbes
Volume6
Issue number3
DOIs
StatePublished - 1 Jan 2015

Funding

FundersFunder number
National Institutes of HealthR03DK084294
National Institutes of Health
National Institute of Diabetes and Digestive and Kidney DiseasesP30DK034987
National Institute of Diabetes and Digestive and Kidney Diseases
National Center for Research ResourcesUL1RR025747
National Center for Research Resources

    Keywords

    • 16S rRNA gene
    • High throughput sequencing
    • Human microbiota
    • Intestinal microbiota
    • Mucosal microbiota

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