ArticleCell reports2023
Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression.
Open access · goldAbstract read
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Article in Cell reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56citing papers in PubMed
10.6field-weighted citation impact, top 1% of its field
What it found
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Who cites it
56 citing papers in PubMed, 69 citations in OpenAlex.
- A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial.Nature communications · 2025Trial
- Host diets drive microbiome evolution and functional divergence.Genes & diseases · 2027Review
- The gut microbiome-bile acid-FXR interplay: a pivotal axis in metabolic and gastrointestinal diseases.Gut microbes · 2026Review
- Pleiotropic roles of microbial bile acid metabolism in intestinal health and diseases.Cell host & microbe · 2026Review
- Bacteroides fragilis toxin promotes gall bladder cancer in mice.Nature microbiology · 2026Article
- Effects of High-Fat Diet on Intestinal Microbiota in Largemouth Bass (Animals : an open access journal from MDPI · 2026Article
- Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice.Nature microbiology · 2026Article
- Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.Journal of animal science and biotechnology · 2026Article
- Multi Omics Integration in Colorectal Cancer: From Molecular Insights to Precision Oncology.Cancers · 2026Review
- Anti-Cancer Effects of Quercetin: What Role Does the Gut Microbiota Play?Molecules (Basel, Switzerland) · 2026Review
- Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal.bioRxiv : the preprint server for biology · 2026Article
- Glucuronolactone Alleviates Metabolic Stress Induced by High-Fat Diet in Turbot (Antioxidants (Basel, Switzerland) · 2026Article
- Microbial regulation of intestinal stem cell function: implications for alleviating intestinal injury of weaned piglets.NPJ biofilms and microbiomes · 2026Review
- MS/MS Mass Spectrometry Filtering Tree for Bile Acid Regio- and Stereoisomer Annotation.Analytical chemistry · 2026Article
- The functions of gut microbiota-mediated bile acid metabolism in intestinal immunity.Journal of advanced research · 2026Review
- Gut microbiome-driven colorectal cancer via immune, metabolic, neural, and endocrine axes reprogramming.NPJ biofilms and microbiomes · 2026Review
- Nutritional Modulation of the Gut-Kidney Axis.Nutrients · 2026Review
- Microbial transformation of secondary bile acids: roles in gut ecology and autoimmune diseases.Frontiers in immunology · 2026Review
- Gut Microbial Metabolism in Colorectal Cancer.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Gut metabolites: key factors in the cross-talk between the gut microbiota and tumor immunotherapy.Frontiers in immunology · 2026Review
Corrections and comments
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Authors and funding
26 authors at 4 institutions in 3 countries.
Ting FuGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Tao HuanDepartment of Chemistry, UBC Faculty of Science, Vancouver Campus, Vancouver, BC V6T 1Z4, Canada.
Gibraan RahmanDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
Hui ZhiDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Zhenjiang XuUCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
Tae Gyu OhGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Jian GuoDepartment of Chemistry, UBC Faculty of Science, Vancouver Campus, Vancouver, BC V6T 1Z4, Canada.
Sally CoulterStorr Liver Centre, Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Westmead, NSW 2145, Australia.
Anupriya TripathiUCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
Cameron MartinoDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
Justin L McCarvilleMolecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Qiyun ZhuUCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
Fritz CayabyabGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Brian LowDepartment of Chemistry, UBC Faculty of Science, Vancouver Campus, Vancouver, BC V6T 1Z4, Canada.
Mingxiao HeGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Shipei XingDepartment of Chemistry, UBC Faculty of Science, Vancouver Campus, Vancouver, BC V6T 1Z4, Canada.
Fernando VargasUCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
Ruth T YuGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Annette AtkinsGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Christopher LiddleStorr Liver Centre, Westmead Institute for Medical Research and Sydney Medical School, University of Sydney, Westmead, NSW 2145, Australia.
Janelle AyresMolecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Manuela RaffatelluDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunity, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA 92093, USA.
Pieter C DorresteinUCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
Michael DownesGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Rob KnightDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Engineering, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: robknight@eng.ucsd.edu.
Ronald M EvansGene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address: evans@salk.edu.
Salk Institute for Biological Studies · USUniversity of California San Diego · USUniversity of British Columbia Hospital · CAThe University of Sydney · AU
Funding
Viral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Ye Zheng · 1985 to 2026
$82.8MProject 3: The AMPK Autophagy Pathway as a Metabolic Liability in Pancratic Ductal AdenocarcinomaP01CA265762 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Dannielle Engle · 2023 to 2026
$14.6MTissue-specific roles of FXR in CVD and NASHP01HL147835 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LOOMBA, ROHIT · 2020 to 2024
$12.2MMapping host-microbe-metabolite interactions in 3D to find diet-derived enhancers of immunityDP1AT010885 · NCCIH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KNIGHT, ROB · 2019 to 2023
$5.5MC3-Dependent Intracellular Killing in Innate Immunity and Bacterial PathogenesisR01AI145325 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NIZET, VICTOR, RAFFATELLU, MANUELA · 2019 to 2023
$3.1MCollaborative Microbial Metabolite CenterU24DK133658 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PIETER C DORRESTEIN · 2022 to 2026
$2.9MHormonal Regulation of Mammalian Gene ExpressionR01DK057978 · NIDDK · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI EVANS, RONALD M · 2021 to 2024
$2.6MNutritional immunity during Salmonella infectionR01AI126277 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI RAFFATELLU, MANUELA · 2016 to 2020
$1.9MDevelopment of siderophore-based vaccines against non-typhoidal Salmonella infectionR01AI114625 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NOLAN, ELIZABETH M, RAFFATELLU, MANUELA · 2015 to 2019
$1.9MNutritional immunity during Salmonella infectionR37AI126277 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Manuela Raffatellu · 2023 to 2026
$1.8MAntimicrobial activity of Escherichia coli Nissle 1917 microcin MR21AI154644 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NOLAN, ELIZABETH M, RAFFATELLU, MANUELA · 2020 to 2021
$440kHarnessing iron acquisition to hinder enterobacterial pathogenesisR56AI114625 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI NOLAN, ELIZABETH M, RAFFATELLU, MANUELA · 2022 to 2022
$400kNCCIH NIH HHS DP1 AT010885NCI NIH HHS P01 CA265762NCI NIH HHS P30 CA014195NHLBI NIH HHS P01 HL147835NIAID NIH HHS R01 AI114625NIAID NIH HHS R01 AI126277NIAID NIH HHS R01 AI145325NIAID NIH HHS R21 AI154644NIAID NIH HHS R37 AI126277NIAID NIH HHS R56 AI114625NIDDK NIH HHS R01 DK057978NIDDK NIH HHS U24 DK133658
Abstract
Colorectal cancer (CRC) is driven by genomic alterations in concert with dietary influences, with the gut microbiome implicated as an effector in disease development and progression. While meta-analyses have provided mechanistic insight into patients with CRC, study heterogeneity has limited causal associations. Using multi-omics studies on genetically controlled cohorts of mice, we identify diet as the major driver of microbial and metabolomic differences, with reductions in α diversity and widespread changes in cecal metabolites seen in high-fat diet (HFD)-fed mice. In addition, non-classic amino acid conjugation of the bile acid cholic acid (AA-CA) increased with HFD. We show that AA-CAs impact intestinal stem cell growth and demonstrate that Ileibacterium valens and Ruminococcus gnavus are able to synthesize these AA-CAs. This multi-omics dataset implicates diet-induced shifts in the microbiome and the metabolome in disease progression and has potential utility in future diagnostic and therapeutic developments.
Indexed as
Colorectal NeoplasmsGastrointestinal MicrobiomeMicrobiotaAnimalsBile Acids and SaltsMetabolomeMiceBile Acids and Saltsbile acidscolorectal cancerconjugated bile acidsCP: CancerCP: Microbiologyhigh-fat dietmetabolomemicrobiome
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