Publications

For the latest publications, see PubMed.

Selected Publications:

  1. Carrillo Terrazas M, Oles RE, Loomis LR, Hsu C-Y, Vasquez Ayala A, Lee MH, Paulchakrabarti M, Pride D, Choudhury B, Nizet V, Raffatellu M, Knight R, Chu H. Antimicrobial resistance is widespread among intestinal and extra-intestinal Bacteroides fragilis strains. Infect Immun. 2025 Dec 16;93(12):e0052925. doi: 10.1128/iai.00529-25. Epub 2025 Nov 24. PubMed PMID: 41277826; PubMed Central PMCID: PMC12707147.
  2. Weng Y, Guccione C, McDonald D, Oles R, Devkota S, Kopylova E, Sepich-Poore GD, Salido RA, Din MO, Song SJ, Curtius K, Chu H, Bartko A, Hasty J, Knight R. Calculating fast differential genome coverages among metagenomic sources using micov. Commun Biol. 2025 Nov 20;8(1):1624. doi: 10.1038/s42003-025-09007-6. PubMed PMID: 41266796; PubMed Central PMCID: PMC12635244.
  3. Mannochio-Russo H, Charron-Lamoureux V, van Faassen M, Lamichhane S, Gonçalves Nunes WD, Deleray V, Ayala AV, Tanaka Y, Patan A, Vittali K, Rajkumar P, El Abiead Y, Zhao HN, Gomes PWP, Mohanty I, Lee C, Sund A, Sharma M, Liu Y, Pattynama D, Walker GT, Norton GJ, Khatib L, Andalibi MS, Wang CX, Ellis RJ, Moore DJ, Iudicello JE, Franklin D Jr, Letendre S, Chin L, Walker C, Renwick S, Zemlin J, Meehan MJ, Song X, Kasper D, Burcham Z, Kim JJ, Kadakia S, Raffatellu M, Bode L, Chu H, Zengler K, Wang M, Siegel D, Knight R, Dorrestein PC. The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids. Cell. 2025 Jul 24;188(15):4154-4169.e19. doi: 10.1016/j.cell.2025.05.015. Epub 2025 Jun 10. PubMed PMID: 40499541; PubMed Central PMCID: PMC12428309.
  4. Gilbert JA, Azad MB, Bäckhed F, Blaser MJ, Byndloss M, Chiu CY, Chu H, Dugas LR, Elinav E, Gibbons SM, Gilbert KE, Henn MR, Ishaq SL, Ley RE, Lynch SV, Segal E, Spector TD, Strandwitz P, Suez J, Tropini C, Whiteson K, Knight R. Clinical translation of microbiome research. Nat Med. 2025 Apr;31(4):1099-1113. doi: 10.1038/s41591-025-03615-9. Epub 2025 Apr 11. Review. PubMed PMID: 40217076.
  5. Salido RA, Zhao HN, McDonald D, Mannochio-Russo H, Zuffa S, Oles RE, Aron AT, El Abiead Y, Farmer S, González A, Martino C, Mohanty I, Parker CW, Patel L, Portal Gomes PW, Schmid R, Schwartz T, Zhu J, Barratt MR, Rubins KH, Chu H, Karouia F, Venkateswaran K, Dorrestein PC, Knight R. The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns. Cell. 2025 Apr 3;188(7):2022-2041.e23. doi: 10.1016/j.cell.2025.01.039. Epub 2025 Feb 27. PubMed PMID: 40020666; PubMed Central PMCID: PMC12068931.
  6. Oles RE, Carrillo Terrazas M, Loomis LR, Hsu C-Y, Tribelhorn C, Belda-Ferre P, Ea AC, Bryant M, Young JA, Carrow HC, Sandborn WJ, Dulai PS, Sivagnanam M, Pride D, Knight R, Chu H. Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems. 2024 Jul 23;9(7):e0051624. doi: 10.1128/msystems.00516-24. Epub 2024 Jun 27. PubMed PMID: 38934546; PubMed Central PMCID: PMC11265264.
  7. Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe. 2024 Feb 14;32(2):181-190.e9. doi: 10.1016/j.chom.2023.12.014. Epub 2024 Jan 15. PubMed PMID: 38228143; PubMed Central PMCID: PMC10922750.
  8. Vasquez Ayala A, Hsu CY, Oles RE, Matsuo K, Loomis LR, Buzun E, Carrillo Terrazas M, Gerner RR, Lu HH, Kim S, Zhang Z, Park JH, Rivaud P, Thomson M, Lu LF, Min B, Chu H. Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice. J Exp Med. 2024 Jan 1;221(1). doi: 10.1084/jem.20230063. Epub 2023 Dec 12. PubMed PMID: 38085267; PubMed Central PMCID: PMC10716256.
  9. Gentry EC, Collins SL, Panitchpakdi M, Belda-Ferre P, Stewart AK, Carrillo Terrazas M, Lu HH, Zuffa S, Yan T, Avila-Pacheco J, Plichta DR, Aron AT, Wang M, Jarmusch AK, Hao F, Syrkin-Nikolau M, Vlamakis H, Ananthakrishnan AN, Boland BS, Hemperly A, Vande Casteele N, Gonzalez FJ, Clish CB, Xavier RJ, Chu H, Baker ES, Patterson AD, Knight R, Siegel D, Dorrestein PC. Reverse metabolomics for the discovery of chemical structures from humans. Nature. 2024 Feb;626(7998):419-426. doi: 10.1038/s41586-023-06906-8. Epub 2023 Dec 5. PubMed PMID: 38052229; PubMed Central PMCID: PMC10849969.
  10. Lin CH, Wu CJ, Cho S, Patkar R, Huth WJ, Lin LL, Chen MC, Israelsson E, Betts J, Niedzielska M, Patel SA, Duong HG, Gerner RR, Hsu CY, Catley M, Maciewicz RA, Chu H, Raffatellu M, Chang JT, Lu LF. Selective IL-27 production by intestinal regulatory T cells permits gut-specific regulation of T(H)17 cell immunity. Nat Immunol. 2023 Dec;24(12):2108-2120. doi: 10.1038/s41590-023-01667-y. Epub 2023 Nov 6. PubMed PMID: 37932457; PubMed Central PMCID: PMC11058069.
  11. Carrow HC, Batachari LE, Chu H. Strain diversity in the microbiome: Lessons from Bacteroides fragilis. PLoS Pathog. 2020 Dec;16(12):e1009056. doi: 10.1371/journal.ppat.1009056. eCollection 2020 Dec. Review. PubMed PMID: 33301530; PubMed Central PMCID: PMC7728264.
  12. Donaldson GP, Chou WC, Manson AL, Rogov P, Abeel T, Bochicchio J, Ciulla D, Melnikov A, Ernst PB, Chu H, Giannoukos G, Earl AM, Mazmanian SK. Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice. Nat Microbiol. 2020 May;5(5):746-756. doi: 10.1038/s41564-020-0683-3. Epub 2020 Mar 9. PubMed PMID: 32152589; PubMed Central PMCID: PMC7426998.
  13. Ramakrishna C, Kujawski M, Chu H, Li L, Mazmanian SK, Cantin EM. Bacteroides fragilis polysaccharide A induces IL-10 secreting B and T cells that prevent viral encephalitis. Nat Commun. 2019 May 14;10(1):2153. doi: 10.1038/s41467-019-09884-6. PubMed PMID: 31089128; PubMed Central PMCID: PMC6517419.
  14. Cohen LJ, Cho JH, Gevers D, Chu H. Genetic Factors and the Intestinal Microbiome Guide Development of Microbe-Based Therapies for Inflammatory Bowel Diseases. Gastroenterology. 2019 Jun;156(8):2174-2189. doi: 10.1053/j.gastro.2019.03.017. Epub 2019 Mar 14. Review. PubMed PMID: 30880022; PubMed Central PMCID: PMC6568267.
  15. Chu H. Host gene-microbiome interactions: molecular mechanisms in inflammatory bowel disease. Genome Med. 2017 Jul 24;9(1):69. doi: 10.1186/s13073-017-0459-4. Review. PubMed PMID: 28738853; PubMed Central PMCID: PMC5525272.
  16. Chu H, Khosravi A, Kusumawardhani IP, Kwon AH, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu WL, Kambal A, Targan SR, Xavier RJ, Ernst PB, Green DR, McGovern DP, Virgin HW, Mazmanian SK. Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science. 2016 May 27;352(6289):1116-20. doi: 10.1126/science.aad9948. Epub 2016 May 5. PubMed PMID: 27230380; PubMed Central PMCID: PMC4996125.
  17. Chairatana P, Chu H, Castillo PA, Shen B, Bevins CL, Nolan EM. Proteolysis Triggers Self-Assembly and Unmasks Innate Immune Function of a Human α-Defensin Peptide. Chem Sci. 2016 Mar 1;7(3):1738-1752. doi: 10.1039/C5SC04194E. Epub 2015 Dec 10. PubMed PMID: 27076903; PubMed Central PMCID: PMC4827351.
  18. Chu H, Mazmanian SK. Winning the Microbial Battle, but Not the War. Cell. 2015 Oct 8;163(2):271-2. doi: 10.1016/j.cell.2015.09.050. PubMed PMID: 26451475.
  19. Yang Y, Wang C, Yang Q, Kantor AB, Chu H, Ghosn EE, Qin G, Mazmanian SK, Han J, Herzenberg LA. Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires. Elife. 2015 Sep 30;4:e09083. doi: 10.7554/eLife.09083. PubMed PMID: 26422511; PubMed Central PMCID: PMC4714975.
  20. Chu H, Mazmanian SK. Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat Immunol. 2013 Jul;14(7):668-75. doi: 10.1038/ni.2635. Review. PubMed PMID: 23778794; PubMed Central PMCID: PMC4109969.
  21. Chu H, Pazgier M, Jung G, Nuccio SP, Castillo PA, de Jong MF, Winter MG, Winter SE, Wehkamp J, Shen B, Salzman NH, Underwood MA, Tsolis RM, Young GM, Lu W, Lehrer RI, Bäumler AJ, Bevins CL. Human α-defensin 6 promotes mucosal innate immunity through self-assembled peptide nanonets. Science. 2012 Jul 27;337(6093):477-81. doi: 10.1126/science.1218831. Epub 2012 Jun 21. PubMed PMID: 22722251; PubMed Central PMCID: PMC4332406.
  22. Underwood MA, Kananurak A, Coursodon CF, Adkins-Reick CK, Chu H, Bennett SH, Wehkamp J, Castillo PA, Leonard BC, Tancredi DJ, Sherman MP, Dvorak B, Bevins CL. Bifidobacterium bifidum in a rat model of necrotizing enterocolitis: antimicrobial peptide and protein responses. Pediatr Res. 2012 May;71(5):546-51. doi: 10.1038/pr.2012.11. Epub 2012 Feb 9. PubMed PMID: 22322385; PubMed Central PMCID: PMC3619207.
  23. Salzman NH, Hung K, Haribhai D, Chu H, Karlsson-Sjöberg J, Amir E, Teggatz P, Barman M, Hayward M, Eastwood D, Stoel M, Zhou Y, Sodergren E, Weinstock GM, Bevins CL, Williams CB, Bos NA. Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol. 2010 Jan;11(1):76-83. doi: 10.1038/ni.1825. Epub 2009 Oct 22. PubMed PMID: 19855381; PubMed Central PMCID: PMC2795796.
  24. Raffatellu M, George MD, Akiyama Y, Hornsby MJ, Nuccio SP, Paixao TA, Butler BP, Chu H, Santos RL, Berger T, Mak TW, Tsolis RM, Bevins CL, Solnick JV, Dandekar S, Bäumler AJ. Lipocalin-2 resistance confers an advantage to Salmonella enterica serotype Typhimurium for growth and survival in the inflamed intestine. Cell Host Microbe. 2009 May 8;5(5):476-86. doi: 10.1016/j.chom.2009.03.011. PubMed PMID: 19454351; PubMed Central PMCID: PMC2768556.
  25. Mukherjee S, Partch CL, Lehotzky RE, Whitham CV, Chu H, Bevins CL, Gardner KH, Hooper LV. Regulation of C-type lectin antimicrobial activity by a flexible N-terminal prosegment. J Biol Chem. 2009 Feb 20;284(8):4881-8. doi: 10.1074/jbc.M808077200. Epub 2008 Dec 18. PubMed PMID: 19095652; PubMed Central PMCID: PMC2643518.
  26. Wehkamp J, Chu H, Shen B, Feathers RW, Kays RJ, Lee SK, Bevins CL. Paneth cell antimicrobial peptides: topographical distribution and quantification in human gastrointestinal tissues. FEBS Lett. 2006 Oct 2;580(22):5344-50. doi: 10.1016/j.febslet.2006.08.083. Epub 2006 Sep 12. PubMed PMID: 16989824.
  27. Wehkamp J, Salzman NH, Porter E, Nuding S, Weichenthal M, Petras RE, Shen B, Schaeffeler E, Schwab M, Linzmeier R, Feathers RW, Chu H, Lima H Jr, Fellermann K, Ganz T, Stange EF, Bevins CL. Reduced Paneth cell alpha-defensins in ileal Crohn’s disease. Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18129-34. doi: 10.1073/pnas.0505256102. Epub 2005 Dec 5. PubMed PMID: 16330776; PubMed Central PMCID: PMC1306791.