ArticleCell2022
Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome.
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Article in Cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
0numbers the graph read from it
0cells of the map it votes in
98citing papers in PubMed
12.9field-weighted citation impact, top 1% of its field
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Who cites it
98 citing papers in PubMed, 162 citations in OpenAlex.
- The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome.eLife · 2026Article
- Transferable genetic toolsets for nonmodel gut Clostridia enable in vivo reversible control of metabolite production.Nature biotechnology · 2026Article
- Commensal bacteria inhibit viral infections via a tryptophan metabolite.Nature communications · 2026Article
- Maternal and infant gut microbiome.iMeta · 2026Review
- Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer.Gut · 2026Article
- AI-empowered human microbiome research.Gut · 2026Review
- Ecology and engineering to modify the bile acid output of a defined microbial community.bioRxiv : the preprint server for biology · 2026Article
- Engineering the Gut Microbiome: Emerging Genome-Editing Strategies and Therapeutic Applications.Microorganisms · 2026Review
- Keystone concept revisited: insights into microbial community dynamics and control.Nature reviews. Microbiology · 2026Review
- How the gut microbiome affects the immunotherapy response in hepatocellular carcinoma.Cancer biology & medicine · 2026Review
- Capecitabine combined with fecal microbiota transplantation prevents colorectal cancer progression through correction of microbial dysbiosis and immune regulation.Scientific reports · 2026Article
- A genetic toolkit for the human gut bacterium Mediterraneibacter gnavus identifies capsular polysaccharides as a competitive colonization factor.Nature communications · 2026Article
- Mobile-CRISPRi as a tool for genetic manipulation in the intracellular pathogenApplied and environmental microbiology · 2026Article
- Occurrence and applications of CRISPR-Cas systems in bifidobacteria.Applied and environmental microbiology · 2026Review
- In situ visualization of Clostridioides difficile phenotypic heterogeneity and single-cell morphology during gut infection.Nature communications · 2026Article
- Microbiota utilization of intestinal amino acids modulates cancer progression and anticancer immunity.Cell host & microbe · 2026Article
- Microbial transformation of secondary bile acids: roles in gut ecology and autoimmune diseases.Frontiers in immunology · 2026Review
- Tuft Cells in the Gut Limit Cognitive Disorders by Regulating Gut Homeostasis.Cellular and molecular gastroenterology and hepatology · 2026Article
- Engineered Clostridium butyricum: a promising application of synthetic biology in comprehensive health.Microbial cell factories · 2025Review
- Precision microbiota therapy for IBD: premise and promise.Gut microbes · 2025Review
38 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors at 1 institution in 1 country.
Wen-Bing JinJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Ting-Ting LiJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Da HuoJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Sophia QuJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Xin V LiJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Mohammad ArifuzzamanJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Svetlana F LimaJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Hui-Qing ShiJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Aolin WangJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Gregory G PutzelJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
Randy S LongmanJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
David ArtisJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
Chun-Jun GuoJill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA. Electronic address: cj@guo-group.org.
Cornell University · US
Funding
Regulation of protective immunity following enteric viral infectionU01AI095608 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI ARTIS, DAVID, SONNENBERG, GREGORY F · 2011 to 2025
$11.0MRegulation and function of innate lymphoid cells in the gutR01AI095466 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI ARTIS, DAVID · 2011 to 2022
$3.7MNeuropeptide-mediated regulation of antihelminth immunityR01AI151599 · NIAID · RUTGERS BIOMEDICAL AND HEALTH SCIENCES · PI ARTIS, DAVID, SIRACUSA, MARK CHRISTOPHER · 2020 to 2024
$3.2MNeuro-immune regulation of intestinal inflammationR01DK126871 · NIDDK · WEILL MEDICAL COLL OF CORNELL UNIV · PI ARTIS, DAVID · 2020 to 2024
$3.2MAn integrative and generalizable approach to modulate microbiota small molecules in the hostDP2HD101401 · NICHD · WEILL MEDICAL COLL OF CORNELL UNIV · PI GUO, CHUN-JUN · 2019 to 2019
$2.5MHost-Microbiota Interactions in Crohn's Disease-associated SpondyloarthritisR01DK114252 · NIDDK · WEILL MEDICAL COLL OF CORNELL UNIV · PI LONGMAN, RANDY S · 2018 to 2022
$1.9MA randomized, placebo-controlled clinical trial examining the efficacy of Fecal Microbiota Transplantation (FMT) and subsequent dietary fiber in patients with moderate ulcerative colitis (MINDFUL)R01DK128257 · NIDDK · WEILL MEDICAL COLL OF CORNELL UNIV · PI LONGMAN, RANDY S · 2021 to 2023
$1.0MMicrobiota-dependent regulation of the gut-brain axisR21AI142213 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI ARTIS, DAVID · 2019 to 2020
$466kNIAID NIH HHS R01 AI095466NIAID NIH HHS R01 AI151599NIAID NIH HHS R21 AI142213NIAID NIH HHS U01 AI095608NICHD NIH HHS DP2 HD101401NIDDK NIH HHS R01 DK114252NIDDK NIH HHS R01 DK126871NIDDK NIH HHS R01 DK128257
Abstract
Hundreds of microbiota genes are associated with host biology/disease. Unraveling the causal contribution of a microbiota gene to host biology remains difficult because many are encoded by nonmodel gut commensals and not genetically targetable. A general approach to identify their gene transfer methodology and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. We developed a pipeline that identifies the gene transfer methods for multiple nonmodel microbes spanning five phyla, and we demonstrated the utility of their genetic tools by modulating microbiome-derived short-chain fatty acids and bile acids in vitro and in the host. In a proof-of-principle study, by deleting a commensal gene for bile acid synthesis in a complex microbiome, we discovered an intriguing role of this gene in regulating colon inflammation. This technology will enable genetically engineering the nonmodel gut microbiome and facilitate mechanistic dissection of microbiota-host interactions.
Indexed as
Genes, BacterialAnimalsBile Acids and SaltsClostridiumColitisCRISPR-Cas SystemsDextran SulfateDrug Resistance, MicrobialFemaleGastrointestinal MicrobiomeGene Expression Regulation, BacterialGene Transfer TechniquesGerm-Free LifeInflammationIntestinesMaleBile Acids and SaltsDextran SulfateRNA, Ribosomal, 16Sbile acid metabolismcolitiscomplex gut microbiomeFirmicutes/Clostridiagenetic manipulation toolshost-microbe interactionsnonmodel gut microbes
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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.