Evidence map›Paper›PMID 40068681›Full record

ArticleCell2025

Genome-scale resources in the infant gut symbiont Bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions.

Anthony L Shiver, Jiawei Sun, Rebecca Culver, Arvie Violette, Char Wynter, Marta Nieckarz, Samara Paula Mattiello, Prabhjot Kaur Sekhon, Francesca Bottacini, Lisa Friess and 19 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–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

15 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Aromatic lactic acid production byApplied and environmental microbiology · 2026
    Article
  6. Article
  7. Article
  8. Effects and mechanism ofWorld journal of gastroenterology · 2026
    Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Review
  14. Article
  15. Article
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

29 authors.

Anthony L ShiverDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Jiawei SunDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Rebecca CulverDepartment of Genetics, Stanford University, Stanford, CA 94305, USA.
Arvie VioletteDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Char WynterDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Marta NieckarzDepartment of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Umeå University, Umeå 90187, Sweden.
Samara Paula MattielloDepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; College of Mathematics and Science, The University of Tennessee Southern, Pulaski, TN 38478, USA.
Prabhjot Kaur SekhonDepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74074, USA; Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
Francesca BottaciniSchool of Microbiology, University College Cork, Cork, Ireland; Department of Biological Sciences, Munster Technological University, Cork, Ireland.
Lisa FriessSchool of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
Hans K CarlsonEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Daniel P G H WongDepartment of Applied Physics, Stanford University, Stanford, CA 94305, USA.
Steven HigginbottomDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Meredith WeglarzStanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA 94305, USA.
Weigao WangDepartment of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
Benjamin D KnappBiophysics Program, Stanford University, Stanford, CA 94305, USA.
Emma GuibersonDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT 05753, USA.
Juan SanchezChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Po-Hsun HuangDepartment of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Paulo A GarciaDepartment of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Cullen R BuieDepartment of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Benjamin H GoodDepartment of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Brian DeFeliceChan Zuckerberg Biohub, San Francisco, CA 94158, USA.
Felipe CavaDepartment of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Umeå University, Umeå 90187, Sweden.
Joy ScariaDepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74074, USA.
Justin L SonnenburgDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Douwe Van SinderenSchool of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
Adam M 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.
Kerwyn Casey HuangDepartment of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address: kchuang@stanford.edu.

Funding

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
Impact of Diet on Intestinal Microbiota-Host DynamicsR01DK085025 · NIDDK · STANFORD UNIVERSITY · PI JUSTIN L SONNENBURG · 2010 to 2026
$6.4M
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
Quantitative approaches for mapping the real-time evolution of the gut microbiotaR35GM146949 · NIGMS · STANFORD UNIVERSITY · PI Benjamin H Good · 2022 to 2026
$2.0M
NIAID NIH HHS R01 AI147023NIDDK NIH HHS R01 DK085025NIGMS NIH HHS R35 GM146949NIGMS NIH HHS RM1 GM135102
6 · The paper itself

Abstract

Bifidobacteria represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest in bifidobacteria as a live biotic therapy, our understanding of colonization, host-microbe interactions, and the health-promoting effects of bifidobacteria is limited. To address these major knowledge gaps, we used a large-scale genetic approach to create a mutant fitness compendium in Bifidobacterium breve. First, we generated a high-density randomly barcoded transposon insertion pool and used it to determine fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. Second, to enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1,462 genes. We leveraged these tools to reveal community- and diet-specific requirements for colonization and to connect the production of immunomodulatory molecules to growth benefits. These resources will catalyze future investigations of this important beneficial microbe.

Indexed as

Bifidobacterium breveGastrointestinal MicrobiomeGenome, BacterialHost Microbial InteractionsAnimalsChickensDNA Transposable ElementsFemaleGerm-Free LifeHumansInfantMiceMice, Inbred C57BLSymbiosisDNA Transposable Elementsbifidobacteriafunctional genomicsgenome-scale metabolic reconstructiongenome-scale ordered mutant collectionglucose-phosphate stressindole-3-lactic acidinfant microbiomemetabolomicsmicrobiome assemblyRB-TnSeq

Identifiers

PMID40068681
PMCPMC13403077

What OpenQuestion holds

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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.