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; Hans K Carlson; Daniel P G H Wong; Steven Higginbottom; Meredith Weglarz; Weigao Wang; Benjamin D Knapp; Emma Guiberson; Juan Sanchez; Po-Hsun Huang; Paulo A Garcia; Cullen R Buie; Benjamin H Good; Brian DeFelice; Felipe Cava; Joy Scaria; Justin L Sonnenburg; Douwe Van Sinderen; Adam M Deutschbauer; Kerwyn Casey Huang

doi:10.1016/j.cell.2025.02.010

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

Cell. 2025 Mar 7:S0092-8674(25)00195-3. doi: 10.1016/j.cell.2025.02.010. Online ahead of print.

Authors

Anthony L Shiver¹, Jiawei Sun¹, Rebecca Culver², Arvie Violette¹, Char Wynter¹, Marta Nieckarz³, Samara Paula Mattiello⁴, Prabhjot Kaur Sekhon⁵, Francesca Bottacini⁶, Lisa Friess⁷, Hans K Carlson⁸, Daniel P G H Wong⁹, Steven Higginbottom¹⁰, Meredith Weglarz¹¹, Weigao Wang¹², Benjamin D Knapp¹³, Emma Guiberson¹⁴, Juan Sanchez¹⁵, Po-Hsun Huang¹⁶, Paulo A Garcia¹⁶, Cullen R Buie¹⁶, Benjamin H Good¹⁷, Brian DeFelice¹⁵, Felipe Cava³, Joy Scaria¹⁸, Justin L Sonnenburg¹⁰, Douwe Van Sinderen⁷, Adam M Deutschbauer¹⁹, Kerwyn Casey Huang²⁰

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
² Department of Genetics, Stanford University, Stanford, CA 94305, USA.
³ Department 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.
⁴ Department 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.
⁵ Department 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.
⁶ School of Microbiology, University College Cork, Cork, Ireland; Department of Biological Sciences, Munster Technological University, Cork, Ireland.
⁷ School of Microbiology, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
⁸ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
⁹ Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
¹⁰ Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
¹¹ Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA 94305, USA.
¹² Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
¹³ Biophysics Program, Stanford University, Stanford, CA 94305, USA.
¹⁴ Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT 05753, USA.
¹⁵ Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
¹⁶ Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
¹⁷ Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
¹⁸ Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA; Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74074, USA.
¹⁹ Environmental 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.
²⁰ Department 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.

PMID: 40068681
DOI: 10.1016/j.cell.2025.02.010

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.

Keywords: RB-TnSeq; bifidobacteria; functional genomics; genome-scale metabolic reconstruction; genome-scale ordered mutant collection; glucose-phosphate stress; indole-3-lactic acid; infant microbiome; metabolomics; microbiome assembly.