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Design, construction, and in vivo augmentation of a complex gut microbiome.
Cheng, Alice G; Ho, Po-Yi; Aranda-Díaz, Andrés; Jain, Sunit; Yu, Feiqiao B; Meng, Xiandong; Wang, Min; Iakiviak, Mikhail; Nagashima, Kazuki; Zhao, Aishan; Murugkar, Pallavi; Patil, Advait; Atabakhsh, Katayoon; Weakley, Allison; Yan, Jia; Brumbaugh, Ariel R; Higginbottom, Steven; Dimas, Alejandra; Shiver, Anthony L; Deutschbauer, Adam; Neff, Norma; Sonnenburg, Justin L; Huang, Kerwyn Casey; Fischbach, Michael A.
Afiliación
  • Cheng AG; Department of Gastroenterology & Hepatology, Stanford School of Medicine, Stanford, CA 94305, USA. Electronic address: alicec2@stanford.edu.
  • Ho PY; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
  • Aranda-Díaz A; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
  • Jain S; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
  • Yu FB; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
  • Meng X; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
  • Wang M; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
  • Iakiviak M; Department 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.
  • Nagashima K; Department 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.
  • Zhao A; Department 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.
  • Murugkar P; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
  • Patil A; Department 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.
  • Atabakhsh K; Department 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.
  • Weakley A; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
  • Yan J; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
  • Brumbaugh AR; Department 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.
  • Higginbottom S; Department 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.
  • Dimas A; Department 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.
  • Shiver AL; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
  • Deutschbauer A; 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.
  • Neff N; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
  • Sonnenburg JL; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
  • Huang KC; Department 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, St
  • Fischbach MA; Department 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, St
Cell ; 185(19): 3617-3636.e19, 2022 09 15.
Article en En | MEDLINE | ID: mdl-36070752
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Microbiota / Microbioma Gastrointestinal Límite: Animals / Humans Idioma: En Revista: Cell Año: 2022 Tipo del documento: Article Pais de publicación: Estados Unidos
Texto completo
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PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Microbiota / Microbioma Gastrointestinal Límite: Animals / Humans Idioma: En Revista: Cell Año: 2022 Tipo del documento: Article Pais de publicación: Estados Unidos