Evidence map›Paper›PMID 31028005›Full record

ArticleCell host & microbe2019

Adaptive Evolution within Gut Microbiomes of Healthy People.

Shijie Zhao, Tami D Lieberman, Mathilde Poyet, Kathryn M Kauffman, Sean M Gibbons, Mathieu Groussin, Ramnik J Xavier, Eric J Alm

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell host & microbe, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 278 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
278citing papers in PubMed, 1 pooled it
21.1field-weighted citation impact, top 1% of its field
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

278 citing papers in PubMed, 1 synthesis or guideline pooled it, 449 citations in OpenAlex.

  1. Pooled it
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  12. Comparative genomic analysis ofMicrobiology spectrum · 2026
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  18. Remodelling of the gut virome after long-term fasting.NPJ biofilms and microbiomes · 2026
    Article
  19. Article
  20. Article

218 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors at 2 institutions in 1 country.

Shijie ZhaoDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
Tami D LiebermanCenter for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: tami@mit.edu.
Mathilde PoyetDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Kathryn M KauffmanDepartment of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Sean M GibbonsDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Institute for Systems Biology, Seattle, WA 98109, USA; eScience Institute, University of Washington, Seattle, WA 98195, USA.
Mathieu GroussinDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ramnik J XavierCenter for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
Eric J AlmDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: ejalm@mit.edu.
Massachusetts Institute of Technology · USBroad Institute · US

Funding

Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI RAYMOND T CHUNG · 1991 to 2026
$35.3M
NIDDK NIH HHS P30 DK043351
6 · The paper itself

Abstract

Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.

Indexed as

Adaptation, BiologicalGastrointestinal MicrobiomeMicrobiotaAdultBacteroides fragilisFemaleGenetics, PopulationHealthy VolunteersHumansMaleMetagenomicsMutationSelection, GeneticYoung Adultadaptive evolutionBacteroidesde novo mutationhorizontal gene transferhuman microbiomemetagenomicsmicrobial evolutionmicrobial genomicswhole-genome sequencing

Identifiers

PMID31028005
PMCPMC6749991
OpenAlexW2941703063

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.