Evidence map›Paper›PMID 31477907›Full record

ArticleNature medicine2019

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research.

M Poyet, M Groussin, S M Gibbons, J Avila-Pacheco, X Jiang, S M Kearney, A R Perrotta, B Berdy, S Zhao, T D Lieberman and 14 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 240 papers, 6 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
240citing papers in PubMed, 6 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

240 citing papers in PubMed, 6 syntheses or guidelines pooled it.

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180 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

24 authors.

M Poyet *Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
M Groussin *Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
S M Gibbons *Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8724-7916
J Avila-PachecoThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
X JiangDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
S M KearneyDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
A R PerrottaDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
B BerdyDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8593-0762
S ZhaoDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
T D LiebermanDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
P K SwansonDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
M SmithFinch Therapeutics, Somerville, MA, USA.
S RoesemannThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-9466-0733
J E AlexanderThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
S A RichThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
J LivnyThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
H VlamakisThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
C ClishThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-8259-9245
K BullockThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
A DeikThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
J ScottThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
K A PierceThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
R J XavierCenter for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA. xavier@molbio.mgh.harvard.edu.
E J AlmDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. ejalm@mit.edu.ORCID http://orcid.org/0000-0001-8294-9364

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Our understanding of how the gut microbiome interacts with its human host has been restrained by limited access to longitudinal datasets to examine stability and dynamics, and by having only a few isolates to test mechanistic hypotheses. Here, we present the Broad Institute-OpenBiome Microbiome Library (BIO-ML), a comprehensive collection of 7,758 gut bacterial isolates paired with 3,632 genome sequences and longitudinal multi-omics data. We show that microbial species maintain stable population sizes within and across humans and that commonly used 'omics' survey methods are more reliable when using averages over multiple days of sampling. Variation of gut metabolites within people over time is associated with amino acid levels, and differences across people are associated with differences in bile acids. Finally, we show that genomic diversification can be used to infer eco-evolutionary dynamics and in vivo selection pressures for strains within individuals. The BIO-ML is a unique resource designed to enable hypothesis-driven microbiome research.

Indexed as

PhylogenyBacteriaBile Acids and SaltsBiological Specimen BanksFecesGastrointestinal MicrobiomeGenetic VariationGenome, BacterialHumansMetabolomeSelection, GeneticBile Acids and Salts

Identifiers

PMID31477907

What OpenQuestion holds

Textmetadata
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.