Evidence map›Paper›PMID 36070752›Full record

ArticleCell2022

Design, construction, and in vivo augmentation of a complex gut microbiome.

Alice G Cheng, Po-Yi Ho, Andrés Aranda-Díaz, Sunit Jain, Feiqiao B Yu, Xiandong Meng, Min Wang, Mikhail Iakiviak, Kazuki Nagashima, Aishan Zhao and 14 more

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

Article in Cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
168citing 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

168 citing papers in PubMed, 1 synthesis or guideline pooled it, 252 citations in OpenAlex.

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108 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 at 4 institutions in 1 country.

Alice G ChengDepartment of Gastroenterology & Hepatology, Stanford School of Medicine, Stanford, CA 94305, USA. Electronic address: alicec2@stanford.edu.
Po-Yi HoDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Andrés Aranda-DíazDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Sunit JainChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Feiqiao B YuChan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
Xiandong MengChan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
Min WangDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Mikhail IakiviakDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Kazuki NagashimaDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Aishan ZhaoDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Pallavi MurugkarChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
Advait PatilDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Katayoon AtabakhshDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Allison WeakleyChan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
Jia YanChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Ariel R BrumbaughDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Steven HigginbottomDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Alejandra DimasDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Anthony L ShiverDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Adam DeutschbauerEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Norma NeffChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Justin L SonnenburgChan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Kerwyn Casey HuangDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA. Electronic address: kchuang@stanford.edu.
Michael A FischbachDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA. Electronic address: fischbach@fischbachgroup.org.
Stanford University · USChan Zuckerberg Initiative (United States) · USLawrence Berkeley National Laboratory · USStanford Medicine · US

Funding

Project 3: Microbiota generated aryl sulfates and secondary bile acids in cardiometabolic diseaseP01HL147823 · NHLBI · CLEVELAND CLINIC LERNER COM-CWRU · PI Stanley L Hazen · 2019 to 2026
$17.0M
A universal pipeline for functional characterization of the human microbiota at a massive scaleRM1GM135102 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BUIE, CULLEN RICHARD, DEUTSCHBAUER, ADAM M · 2020 to 2024
$7.6M
Dietary and Microbial Reprogramming of Intestinal Microbiota-Produced MetabolitesR01DK101674 · NIDDK · STANFORD UNIVERSITY · PI FISCHBACH, MICHAEL ANDREW, MEYER, TIMOTHY W · 2014 to 2024
$6.5M
A complete map of the top 100 molecules from the gut microbiomeDP1DK113598 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FISCHBACH, MICHAEL ANDREW · 2016 to 2020
$5.5M
Antimicrobial Resistance and Horizontal Gene Transfer in the Human Gut Microbiome in Response to an AntibioticR01AI147023 · NIAID · PALO ALTO VETERANS INSTIT FOR RESEARCH · PI RELMAN, DAVID A. · 2020 to 2024
$3.5M
Mechanistic models for predicting the dynamics of microbial communitiesF32GM143859 · NIGMS · STANFORD UNIVERSITY · PI HO, PO-YI · 2021 to 2023
$95k
Howard Hughes Medical InstituteNHLBI NIH HHS P01 HL147823NIAID NIH HHS R01 AI147023NIDDK NIH HHS DP1 DK113598NIDDK NIH HHS R01 DK101674NIGMS NIH HHS F32 GM143859NIGMS NIH HHS RM1 GM135102
6 · The paper itself

Abstract

Efforts to model the human gut microbiome in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or complex, but not both, limiting their utility. Here, we construct and characterize in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota (hCom1). We then used an iterative experimental process to fill open niches: germ-free mice were colonized with hCom1 and then challenged with a human fecal sample. We identified new species that engrafted following fecal challenge and added them to hCom1, yielding hCom2. In gnotobiotic mice, hCom2 exhibited increased stability to fecal challenge and robust colonization resistance against pathogenic Escherichia coli. Mice colonized by either hCom2 or a human fecal community are phenotypically similar, suggesting that this consortium will enable a mechanistic interrogation of species and genes on microbiome-associated phenotypes.

Indexed as

Gastrointestinal MicrobiomeMicrobiotaAnimalsBacteriaEscherichia coliFecesGerm-Free LifeHumansMice

Identifiers

PMID36070752
PMCPMC9691261
OpenAlexW4294782938

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.