{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T18:41:28Z","timestamp":1793040088541,"version":"4.5.0"},"reference-count":77,"publisher":"Elsevier BV","issue":"12","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T00:00:00Z","timestamp":1763078400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM124724"],"award-info":[{"award-number":["GM124724"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM158026"],"award-info":[{"award-number":["GM158026"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI157106"],"award-info":[{"award-number":["AI157106"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI181381"],"award-info":[{"award-number":["AI181381"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI178908"],"award-info":[{"award-number":["AI178908"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI181382"],"award-info":[{"award-number":["AI181382"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Host &amp; Microbe"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1016\/j.chom.2025.11.004","type":"journal-article","created":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T16:14:00Z","timestamp":1764605640000},"page":"2085-2099.e5","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"title":["Diet modulates Vibrio cholerae colonization and competitive outcomes with the gut microbiota"],"prefix":"10.1016","volume":"33","author":[{"given":"Rui","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyi","family":"Ge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer Y.","family":"Cho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaniel C.","family":"Esteves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0258-6960","authenticated-orcid":false,"given":"Ansel","family":"Hsiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2025.11.004_bib1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0003832","article-title":"Updated global burden of cholera in endemic countries","volume":"9","author":"Ali","year":"2015","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.chom.2025.11.004_bib2","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1084\/jem.168.4.1487","article-title":"Toxin, toxin-coregulated pili, and the toxR regulon are essential for Vibrio cholerae pathogenesis in humans","volume":"168","author":"Herrington","year":"1988","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.chom.2025.11.004_bib3","doi-asserted-by":"crossref","first-page":"5542","DOI":"10.1128\/IAI.01094-07","article-title":"Regulatory networks controlling Vibrio cholerae virulence gene expression","volume":"75","author":"Matson","year":"2007","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2025.11.004_bib4","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/ni.2608","article-title":"Control of pathogens and pathobionts by the gut microbiota","volume":"14","author":"Kamada","year":"2013","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.chom.2025.11.004_bib5","doi-asserted-by":"crossref","DOI":"10.1128\/IAI.00746-18","article-title":"CitAB two-component system-regulated citrate utilization contributes to Vibrio cholerae competitiveness with the gut microbiota","volume":"87","author":"Liu","year":"2019","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2025.11.004_bib6","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1016\/j.cell.2020.05.036","article-title":"Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection","volume":"181","author":"Alavi","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.chom.2025.11.004_bib7","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/nri.2016.42","article-title":"Gut microbiota, metabolites and host immunity","volume":"16","author":"Rooks","year":"2016","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.chom.2025.11.004_bib8","article-title":"A commensal-encoded genotoxin drives restriction of Vibrio cholerae colonization and host gut microbiome remodeling","volume":"119","author":"Chen","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.11.004_bib9","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1126\/science.1206025","article-title":"Predicting a human gut microbiota's response to diet in gnotobiotic mice","volume":"333","author":"Faith","year":"2011","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.11.004_bib10","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1126\/science.1198719","article-title":"Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans","volume":"332","author":"Muegge","year":"2011","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.11.004_bib11","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1016\/j.chom.2020.06.018","article-title":"An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut","volume":"28","author":"Caballero-Flores","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2025.11.004_bib12","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-18928-1","article-title":"Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization","volume":"11","author":"Pereira","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2025.11.004_bib13","doi-asserted-by":"crossref","first-page":"282","DOI":"10.4049\/jimmunol.1801068","article-title":"Microbiota metabolite short-chain fatty acids facilitate mucosal adjuvant activity of cholera toxin through GPR43","volume":"203","author":"Yang","year":"2019","journal-title":"J. Immunol."},{"key":"10.1016\/j.chom.2025.11.004_bib14","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/nature12726","article-title":"Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation","volume":"504","author":"Arpaia","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.chom.2025.11.004_bib15","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.immuni.2019.06.002","article-title":"Microbiota-Derived Short-Chain Fatty Acids Promote the Memory Potential of Antigen-Activated CD8+ T Cells","volume":"51","author":"Bachem","year":"2019","journal-title":"Immunity"},{"key":"10.1016\/j.chom.2025.11.004_bib16","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-18262-6","article-title":"Intestinal microbiota-derived short-chain fatty acids regulation of immune cell IL-22 production and gut immunity","volume":"11","author":"Yang","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2025.11.004_bib17","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1038\/nature12820","article-title":"Diet rapidly and reproducibly alters the human gut microbiome","volume":"505","author":"David","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.chom.2025.11.004_bib18","doi-asserted-by":"crossref","first-page":"3028","DOI":"10.1073\/pnas.0409559102","article-title":"Bile acids induce cholera toxin expression in Vibrio cholerae in a ToxT-independent manner","volume":"102","author":"Hung","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.11.004_bib19","doi-asserted-by":"crossref","DOI":"10.1128\/IAI.00707-16","article-title":"Calcium Enhances Bile Salt-Dependent Virulence Activation in Vibrio cholerae","volume":"85","author":"Hay","year":"2017","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2025.11.004_bib20","doi-asserted-by":"crossref","first-page":"2860","DOI":"10.1073\/pnas.0915021107","article-title":"Structure of Vibrio cholerae ToxT reveals a mechanism for fatty acid regulation of virulence genes","volume":"107","author":"Lowden","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.11.004_bib21","doi-asserted-by":"crossref","DOI":"10.1080\/19490976.2021.1937015","article-title":"The Interface of Vibrio cholerae and the Gut Microbiome","volume":"13","author":"Cho","year":"2021","journal-title":"Gut Microbes"},{"key":"10.1016\/j.chom.2025.11.004_bib22","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.bbapap.2018.11.004","article-title":"Mechanistic basis of vitamin B12 and cobinamide salvaging by the Vibrio species","volume":"1867","author":"Agarwal","year":"2019","journal-title":"Biochim. Biophys. Acta Proteins Proteom."},{"key":"10.1016\/j.chom.2025.11.004_bib23","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1093\/infdis\/134.1.8","article-title":"Nutritional status: a determinant of severity of diarrhea in patients with cholera","volume":"134","author":"Palmer","year":"1976","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.chom.2025.11.004_bib24","doi-asserted-by":"crossref","first-page":"28","DOI":"10.4269\/ajtmh.1992.47.28","article-title":"Diarrhea as a cause and an effect of malnutrition: diarrhea prevents catch-up growth and malnutrition increases diarrhea frequency and duration","volume":"47","author":"Guerrant","year":"1992","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"10.1016\/j.chom.2025.11.004_bib25","doi-asserted-by":"crossref","first-page":"19520","DOI":"10.1073\/pnas.1012931107","article-title":"The Vibrio cholerae type VI secretion system displays antimicrobial properties","volume":"107","author":"MacIntyre","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.11.004_bib26","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1084\/jem.104.3.411","article-title":"Experimental enteric Shigella and Vibrio infections in mice and guinea pigs","volume":"104","author":"Freter","year":"1956","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.chom.2025.11.004_bib27","doi-asserted-by":"crossref","first-page":"3733","DOI":"10.1128\/IAI.67.8.3733-3739.1999","article-title":"Vibrio cholerae intestinal population dynamics in the suckling mouse model of infection","volume":"67","author":"Angelichio","year":"1999","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2025.11.004_bib28","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1271\/bbb.56.195","article-title":"Inhibition by lactoferrin and \u03ba-casein glycomacropeptide of binding of cholera toxin to its receptor","volume":"56","author":"Kawasaki","year":"1992","journal-title":"Biosci. Biotechnol. Biochem."},{"key":"10.1016\/j.chom.2025.11.004_bib29","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2025.11.004_bib30","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1046\/j.1365-2958.2003.03546.x","article-title":"Secretion of a soluble colonization factor by the TCP type 4 pilus biogenesis pathway in Vibrio cholerae","volume":"49","author":"Kirn","year":"2003","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib31","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2212664120","article-title":"Mechanism of secretion of TcpF by the Vibrio cholerae toxin-coregulated pilus","volume":"120","author":"Nguyen","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.11.004_bib32","doi-asserted-by":"crossref","first-page":"6555","DOI":"10.1128\/JB.00949-09","article-title":"The Vibrio cholerae flagellar regulatory hierarchy controls expression of virulence factors","volume":"191","author":"Syed","year":"2009","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2025.11.004_bib33","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/978-1-4939-2398-4_3","article-title":"Defining essential genes and identifying virulence factors of Porphyromonas gingivalis by massively parallel sequencing of transposon libraries (Tn-seq)","volume":"1279","author":"Klein","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.chom.2025.11.004_bib34","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/j.celrep.2015.12.038","article-title":"Differential Thiol-Based Switches Jump-Start Vibrio cholerae Pathogenesis","volume":"14","author":"Liu","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2025.11.004_bib35","doi-asserted-by":"crossref","DOI":"10.1128\/JB.00029-18","article-title":"A Critical Region in the FlaA Flagellin Facilitates Filament Formation of the Vibrio cholerae Flagellum","volume":"200","author":"Echazarreta","year":"2018","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2025.11.004_bib36","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1099\/mic.0.064865-0","article-title":"Central metabolism controls transcription of a virulence gene regulator in Vibrio cholerae","volume":"159","author":"Minato","year":"2013","journal-title":"Microbiology (Reading)"},{"key":"10.1016\/j.chom.2025.11.004_bib37","doi-asserted-by":"crossref","DOI":"10.1128\/aem.01095-23","article-title":"Increased iron utilization and oxidative stress tolerance in a Vibrio cholerae flrA mutant confers resistance to amoeba predation","volume":"89","author":"Hoque","year":"2023","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib38","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1099\/mic.0.000656","article-title":"Chitin-induced T6SS in Vibrio cholerae is dependent on ChiS activation","volume":"164","author":"Chourashi","year":"2018","journal-title":"Microbiology (Reading)"},{"key":"10.1016\/j.chom.2025.11.004_bib39","doi-asserted-by":"crossref","first-page":"8937","DOI":"10.1073\/pnas.1406478111","article-title":"Multiplex genome editing by natural transformation","volume":"111","author":"Dalia","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.11.004_bib40","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1038\/nature13738","article-title":"Members of the human gut microbiota involved in recovery from Vibrio cholerae infection","volume":"515","author":"Hsiao","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.chom.2025.11.004_bib41","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2011.00228","article-title":"Gut microbiota of healthy and malnourished children in bangladesh","volume":"2","author":"Monira","year":"2011","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib42","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1111\/mmi.12432","article-title":"Cyclic di-GMP inhibits Vibrio cholerae motility by repressing induction of transcription and inducing extracellular polysaccharide production","volume":"90","author":"Srivastava","year":"2013","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib43","doi-asserted-by":"crossref","first-page":"21128","DOI":"10.1073\/pnas.1014998107","article-title":"Quorum sensing and a global regulator TsrA control expression of type VI secretion and virulence in Vibrio cholerae","volume":"107","author":"Zheng","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.11.004_bib44","doi-asserted-by":"crossref","first-page":"42","DOI":"10.4161\/cib.1.1.6662","article-title":"Coordinated regulation of virulence by quorum sensing and motility pathways during the initial stages of Vibrio cholerae infection","volume":"1","author":"Tsou","year":"2008","journal-title":"Commun. Integr. Biol."},{"key":"10.1016\/j.chom.2025.11.004_bib45","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1046\/j.1365-2958.1998.00809.x","article-title":"Distinct roles of an alternative sigma factor during both free-swimming and colonizing phases of the Vibrio cholerae pathogenic cycle","volume":"28","author":"Klose","year":"1998","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib46","doi-asserted-by":"crossref","first-page":"5043","DOI":"10.1128\/IAI.00508-07","article-title":"Prolonged colonization of mice by Vibrio cholerae El Tor O1 depends on accessory toxins","volume":"75","author":"Olivier","year":"2007","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2025.11.004_bib47","doi-asserted-by":"crossref","first-page":"14542","DOI":"10.1073\/pnas.0604650103","article-title":"Vibrio cholerae virulence regulator-coordinated evasion of host immunity","volume":"103","author":"Hsiao","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2025.11.004_bib48","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1128\/iai.33.1.136-141.1981","article-title":"Nonimmunoglobulin fraction of human milk inhibits bacterial adhesion (hemagglutination) and enterotoxin binding of Escherichia coli and Vibrio cholerae","volume":"33","author":"Holmgren","year":"1981","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2025.11.004_bib49","doi-asserted-by":"crossref","first-page":"2309","DOI":"10.1128\/AAC.45.8.2309-2315.2001","article-title":"Kappacin, a novel antibacterial peptide from bovine milk","volume":"45","author":"Malkoski","year":"2001","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.chom.2025.11.004_bib50","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1051\/rnd:19940602","article-title":"Effects of caseinomacropeptide (CMP) on digestion regulation","volume":"34","author":"Yvon","year":"1994","journal-title":"Reprod. Nutr. Dev."},{"key":"10.1016\/j.chom.2025.11.004_bib51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/1471-0307.12421","article-title":"Immunomodulation by hydrolysates and peptides derived from milk proteins","volume":"71","author":"Reyes-D\u00edaz","year":"2018","journal-title":"Int. J. Dairy Technol."},{"key":"10.1016\/j.chom.2025.11.004_bib52","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1038\/s41586-019-1453-3","article-title":"Cholera toxin promotes pathogen acquisition of host-derived nutrients","volume":"572","author":"Rivera-Ch\u00e1vez","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.chom.2025.11.004_bib53","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2019.00793","article-title":"Structural and Proteomic Changes in Viable but Non-culturable Vibrio cholerae","volume":"10","author":"Brenzinger","year":"2019","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib54","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.111368","article-title":"Vibrio cholerae high cell density quorum sensing activates the host intestinal innate immune response","volume":"40","author":"Jugder","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2025.11.004_bib55","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1046\/j.1365-2958.2000.01745.x","article-title":"Phosphorylation of the flagellar regulatory protein FlrC is necessary for Vibrio cholerae motility and enhanced colonization","volume":"35","author":"Correa","year":"2000","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib56","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1128\/JB.180.2.303-316.1998","article-title":"Differential regulation of multiple flagellins in Vibrio cholerae","volume":"180","author":"Klose","year":"1998","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2025.11.004_bib57","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1011250","article-title":"Dps-dependent in vivo mutation enhances long-term host adaptation in Vibrio cholerae","volume":"19","author":"Luo","year":"2023","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2025.11.004_bib58","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1038\/s41396-021-01134-2","article-title":"Adaptation to an amoeba host drives selection of virulence-associated traits in Vibrio cholerae","volume":"16","author":"Hoque","year":"2022","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2025.11.004_bib59","doi-asserted-by":"crossref","first-page":"3315","DOI":"10.1128\/IAI.00052-07","article-title":"Role of motility and the flhDC Operon in Escherichia coli MG1655 colonization of the mouse intestine","volume":"75","author":"Gauger","year":"2007","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2025.11.004_bib60","doi-asserted-by":"crossref","DOI":"10.1038\/emi.2016.82","article-title":"flrA, flrB and flrC regulate adhesion by controlling the expression of critical virulence genes in Vibrio alginolyticus","volume":"5","author":"Luo","year":"2016","journal-title":"Emerg. Microbes Infect."},{"key":"10.1016\/j.chom.2025.11.004_bib61","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0006734","article-title":"Quorum sensing regulation of the two hcp alleles in Vibrio cholerae O1 strains","volume":"4","author":"Ishikawa","year":"2009","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2025.11.004_bib62","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1016\/j.celrep.2016.03.092","article-title":"Independent Regulation of Type VI Secretion in Vibrio cholerae by TfoX and TfoY","volume":"15","author":"Metzger","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2025.11.004_bib63","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1111\/j.1365-2958.2004.04155.x","article-title":"Cyclic diguanylate (c-di-GMP) regulates Vibrio cholerae biofilm formation","volume":"53","author":"Tischler","year":"2004","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib64","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.mib.2006.12.006","article-title":"c-di-GMP-mediated regulation of virulence and biofilm formation","volume":"10","author":"Cotter","year":"2007","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.chom.2025.11.004_bib65","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1101\/gad.502409","article-title":"Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression","volume":"23","author":"Duerig","year":"2009","journal-title":"Genes Dev."},{"key":"10.1016\/j.chom.2025.11.004_bib66","doi-asserted-by":"crossref","DOI":"10.1038\/srep10052","article-title":"C-di-GMP regulates Pseudomonas aeruginosa stress response to tellurite during both planktonic and biofilm modes of growth","volume":"5","author":"Chua","year":"2015","journal-title":"Sci. Rep."},{"key":"10.1016\/j.chom.2025.11.004_bib67","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1126\/science.aap8775","article-title":"Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence","volume":"359","author":"Zhao","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.chom.2025.11.004_bib68","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2025.11.004_bib69","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.11.004_bib70","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.chom.2025.11.004_bib71","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq--a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.11.004_bib72","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2025.11.004_bib73","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"Omics"},{"key":"10.1016\/j.chom.2025.11.004_bib74","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation (Camb.)"},{"key":"10.1016\/j.chom.2025.11.004_bib75","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1128\/jb.171.3.1288-1293.1989","article-title":"Identification of toxS, a regulatory gene whose product enhances toxR-mediated activation of the cholera toxin promoter","volume":"171","author":"Miller","year":"1989","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2025.11.004_bib76","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2021.103443","article-title":"A dysbiotic gut microbiome suppresses antibody mediated-protection against Vibrio cholerae","volume":"24","author":"Macbeth","year":"2021","journal-title":"iScience"},{"key":"10.1016\/j.chom.2025.11.004_bib77","doi-asserted-by":"crossref","first-page":"8736","DOI":"10.1073\/pnas.0803281105","article-title":"A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae","volume":"105","author":"Cameron","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Cell Host &amp; Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312825004640?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312825004640?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T15:10:05Z","timestamp":1766157005000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312825004640"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12]]},"references-count":77,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["S1931312825004640"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2025.11.004","relation":{},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2025,12]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Diet modulates Vibrio cholerae colonization and competitive outcomes with the gut microbiota","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2025.11.004","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}