Evidence map›Paper›PMID 25732063›Full record

ArticleCell host & microbe2015

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

Koji Yasuda, Keunyoung Oh, Boyu Ren, Timothy L Tickle, Eric A Franzosa, Lynn M Wachtman, Andrew D Miller, Susan V Westmoreland, Keith G Mansfield, Eric J Vallender and 5 more

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell host & microbe, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 188 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
188citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

188 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
  2. Pooled it
  3. Trial
  4. Review
  5. Article
  6. The Microbiota in the Diagnosis and Treatment of Autism Spectrum Disorder.International journal of molecular sciences · 2026
    Review
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128 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Koji YasudaDepartment 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.
Keunyoung OhDepartment of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
Boyu RenDepartment of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
Timothy L TickleDepartment of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
Eric A FranzosaDepartment of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
Lynn M WachtmanNew England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Division of Comparative Medicine, Massachusetts Institute of Technology, Boston, MA 02139, USA.
Andrew D MillerNew 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.
Susan V WestmorelandNew England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA.
Keith G MansfieldNew England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Novartis Institute for Biomedical Research, Cambridge, MA 02139, USA.
Eric J VallenderNew England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Gregory M MillerNew 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.
James K RowlettNew England Primate Research Center, Harvard Medical School, Southborough, MA 01772, USA; Department of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA.
Dirk GeversBroad Institute, Cambridge, MA 02142, USA.
Curtis HuttenhowerDepartment of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
Xochitl C MorganDepartment of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address: xmorgan@hsph.harvard.edu.

Funding

ZETA CHAIN OF T CELL RECEPTOR INTERACTS W/ NEF OF SIV &HIV2P51RR000168 · NCRR · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI ROWLETT, JAMES K · 1985 to 2011
$139.3M
New England Primate Research Center Base GrantP51OD011103 · OD · HARVARD MEDICAL SCHOOL · PI FLIER, JEFFREY S · 2012 to 2013
$24.7M
Functional activity and inter-organismal interactions in the human microbiomeR01HG005969 · NHGRI · HARVARD SCHOOL OF PUBLIC HEALTH · PI HUTTENHOWER, CURTIS · 2010 to 2012
$1.3M
MOUSE MODELS OF CANCER, BONE DISEASE, AND LACTATIONK26RR000168 · NCRR · OHIO STATE UNIVERSITY · PI ROSOL, THOMAS J · 2000 to 2004
$547k
NCRR NIH HHS K26 RR000168NCRR NIH HHS P51 RR000168NCRR NIH HHS P51 RR000168-48NHGRI NIH HHS NIHR01HG005969NHGRI NIH HHS R01 HG005969NIH HHS P51 OD011103
6 · The paper itself

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.

Indexed as

Gastrointestinal MicrobiomeAnimalsCluster AnalysisDNA, BacterialDNA, RibosomalFecesIntestinal MucosaMacaca mulattaMolecular Sequence DataPhylogenyRNA, Ribosomal, 16SSequence Analysis, DNADNA, BacterialDNA, RibosomalRNA, Ribosomal, 16S

Identifiers

PMID25732063
PMCPMC4369771

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.