Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque.
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.
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.
Koji
K
Yasuda
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
Keunyoung
K
Oh
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
Boyu
B
Ren
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
Timothy L
TL
Tickle
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
Eric A
EA
Franzosa
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Division of Comparative Medicine, Massachusetts Institute of Technology, Boston, MA 02139, USA.
Lynn M
LM
Wachtman
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.
Andrew D
AD
Miller
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA.
Susan V
SV
Westmoreland
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA.
Keith G
KG
Mansfield
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Eric J
EJ
Vallender
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.
Gregory M
GM
Miller
New England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA.
James K
JK
Rowlett
Broad Institute, Cambridge, MA 02142, USA.
Dirk
D
Gevers
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
Curtis
C
Huttenhower
Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address: xmorgan@hsph.harvard.edu.
Xochitl C
XC
Morgan
D000818:Animals; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D007413:Intestinal Mucosa / Q000382:microbiology; D008253:Macaca mulatta; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S