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

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Gut microbiome Microbiome In vivo Computational biology Biology Bioinformatics Genetics

Alice G. Cheng , Po-Yi Ho , Andrés Aranda-Díaz , Sunit Jain , Feiqiao Brian Yu , Xiandong Meng , M Wang , Mikhail Iakiviak , Kazuki Nagashima , Aishan Zhao , Pallavi P. Murugkar , Advait Patil , Katayoon Atabakhsh , Allison M. Weakley , Yan Jun , Brumbaugh AR , Steven K. Higginbottom , Antigone S. Dimas , Shiver AL , Adam M. Deutschbauer , Norma Neff , Sonnenburg JL , Huang KC , Fischbach MA ·

YOU? · · 2022 · Open Access · · DOI: https://doi.org/10.5281/zenodo.7734778 · OA: W4393682104

Please cite: 10.1016/j.cell.2022.08.003 Cheng AG, Ho PY, Aranda-Díaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA. Design, construction, and in vivo augmentation of a complex gut microbiome. Cell. 2022 Sep 15;185(19):3617-3636.e19. doi: 10.1016/j.cell.2022.08.003. Epub 2022 Sep 6. PMID: 36070752; PMCID: PMC9691261. Original raw sequencing data is available in the BioProject: PRJNA746600 Article summary: 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. File Descriptions: hCom2.tar.gz: This dataset contains genomic sequences and bakta annotations of members of the hCom2 community. Please note that these may not be identical to the ones used in the publication. For the exact versions used in the publication, please reach out to the authors. hCom2_20221117.ninjaIndex.tar.gz: This tarball contains the ninjamap index and the source files used to create this index. Please use this tarball if you wish to run NinjaMap against the hCom2 community.