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Cell Host Microbe. 2015 Mar 11;17(3):385-391. doi: 10.1016/j.chom.2015.01.015. Epub 2015 Feb 26.

Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque.

Author information

1
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA.
2
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
3
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
4
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Division of Comparative Medicine, Massachusetts Institute of Technology, Boston, MA 02139, USA.
5
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Biomedical Sciences, Section of Anatomic Pathology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA.
6
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA.
7
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA.
8
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA.
9
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Pharmaceutical Sciences, Bouvé College of Health Science, Northeastern University, Boston, MA 02115, USA.
10
Broad Institute, Cambridge, MA 02142, USA.
11
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address: xmorgan@hsph.harvard.edu.

Abstract

The gut microbiome is widely studied by fecal sampling, but the extent to which stool reflects the commensal composition at intestinal sites is poorly understood. We investigated this relationship in rhesus macaques by 16S sequencing feces and paired lumenal and mucosal samples from ten sites distal to the jejunum. Stool composition correlated highly with the colonic lumen and mucosa and moderately with the distal small intestine. The mucosal microbiota varied most based on location and was enriched in oxygen-tolerant taxa (e.g., Helicobacter and Treponema), while the lumenal microbiota showed inter-individual variation and obligate anaerobe enrichment (e.g., Firmicutes). This mucosal and lumenal community variability corresponded to functional differences, such as nutrient availability. Additionally, Helicobacter, Faecalibacterium, and Lactobacillus levels in stool were highly predictive of their abundance at most other gut sites. These results quantify the composition and biogeographic relationships between gut microbial communities in macaques and support fecal sampling for translational studies.

PMID:
25732063
PMCID:
PMC4369771
DOI:
10.1016/j.chom.2015.01.015
[Indexed for MEDLINE]
Free PMC Article

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