Faculty Appointments
Assistant Professor of Pathology, Microbiology and Immunology
Education
Ph.D., Biological Sciences, Purdue University, West Lafayette, IndianaB.Sc., Biotechnology, Sun Yat-Sen University, Guangzhou, China
Office Address
1161 21st Ave
Nashville, TN 37232
Nashville, TN 37232
Research Description
Our laboratory studies how microbes survive, compete, and cause disease in the metabolically dynamic environment of the intestine. We are particularly interested in a fundamental question in host–microbe biology: how do changes in host physiology reshape microbial metabolism, and how do microbes exploit these changes to establish disease-promoting niches? By combining bacterial genetics, microbial physiology, animal models, metabolomics, and systems-level approaches, we seek to define the metabolic mechanisms that govern microbial behavior during inflammation and translate these discoveries into new strategies for preventing and treating intestinal disease.
A major focus of our research is understanding how intestinal inflammation alters the chemical environment of the gut. The healthy colon is dominated by obligate anaerobic bacteria that thrive under extremely low oxygen conditions. During inflammation, however, epithelial metabolism and immune responses change dramatically, increasing the availability of oxygen, reactive oxygen and nitrogen species, metals, and alternative nutrients. These changes create powerful selective pressures that can favor particular members of the microbiota. Our laboratory investigates how commensal and pathogenic bacteria sense these environmental changes, reprogram their metabolism, and compete for resources within the intestinal ecosystem.
We are especially interested in the relationship between microbial metabolism and colorectal cancer. Our work has shown that carcinogenic microbes do not simply colonize the gut passively; they actively remodel their environment and cooperate metabolically with other organisms. We study how microbial toxins, inflammation, diet-derived nutrients, and host metabolism interact to create ecological niches that support cancer-associated bacterial communities. Current projects investigate how Bacteroides fragilis toxin alters both host and bacterial physiology, how inflammatory electron acceptors promote microbial expansion, and how dietary nutrients such as fructose can support interactions between cancer-promoting bacterial species. Ultimately, we aim to identify metabolic vulnerabilities that can be targeted to collapse these disease-associated microbial ecosystems before cancer develops.
A second major area of our program examines how beneficial obligate anaerobes survive oxidative and inflammatory stress. Despite their importance to human health, we still know remarkably little about how these organisms tolerate transient exposure to oxygen, reactive metabolites, metal limitation, and other stresses encountered in the inflamed intestine. We use genetic screens, experimental evolution, proteomics, transcriptomics, structural approaches, and metabolic modeling to uncover previously unknown stress-response pathways. These studies may ultimately allow us to engineer inflammation-resistant commensal bacteria capable of maintaining microbiome function during disease.
Across these projects, our laboratory moves freely between fundamental microbiology and translational questions. Trainees learn approaches ranging from anaerobic bacterial genetics and biochemistry to gnotobiotic and conventional mouse models, intestinal organoids, metabolomics, sequencing, computational biology, and protein engineering. We encourage students to pursue mechanistic questions deeply while thinking broadly about how microbial metabolism can be manipulated therapeutically.
Our long-term goal is to understand the intestine as an ecosystem governed by metabolism and to use that knowledge to develop new approaches for microbiome-based disease prevention and precision intervention.
A major focus of our research is understanding how intestinal inflammation alters the chemical environment of the gut. The healthy colon is dominated by obligate anaerobic bacteria that thrive under extremely low oxygen conditions. During inflammation, however, epithelial metabolism and immune responses change dramatically, increasing the availability of oxygen, reactive oxygen and nitrogen species, metals, and alternative nutrients. These changes create powerful selective pressures that can favor particular members of the microbiota. Our laboratory investigates how commensal and pathogenic bacteria sense these environmental changes, reprogram their metabolism, and compete for resources within the intestinal ecosystem.
We are especially interested in the relationship between microbial metabolism and colorectal cancer. Our work has shown that carcinogenic microbes do not simply colonize the gut passively; they actively remodel their environment and cooperate metabolically with other organisms. We study how microbial toxins, inflammation, diet-derived nutrients, and host metabolism interact to create ecological niches that support cancer-associated bacterial communities. Current projects investigate how Bacteroides fragilis toxin alters both host and bacterial physiology, how inflammatory electron acceptors promote microbial expansion, and how dietary nutrients such as fructose can support interactions between cancer-promoting bacterial species. Ultimately, we aim to identify metabolic vulnerabilities that can be targeted to collapse these disease-associated microbial ecosystems before cancer develops.
A second major area of our program examines how beneficial obligate anaerobes survive oxidative and inflammatory stress. Despite their importance to human health, we still know remarkably little about how these organisms tolerate transient exposure to oxygen, reactive metabolites, metal limitation, and other stresses encountered in the inflamed intestine. We use genetic screens, experimental evolution, proteomics, transcriptomics, structural approaches, and metabolic modeling to uncover previously unknown stress-response pathways. These studies may ultimately allow us to engineer inflammation-resistant commensal bacteria capable of maintaining microbiome function during disease.
Across these projects, our laboratory moves freely between fundamental microbiology and translational questions. Trainees learn approaches ranging from anaerobic bacterial genetics and biochemistry to gnotobiotic and conventional mouse models, intestinal organoids, metabolomics, sequencing, computational biology, and protein engineering. We encourage students to pursue mechanistic questions deeply while thinking broadly about how microbial metabolism can be manipulated therapeutically.
Our long-term goal is to understand the intestine as an ecosystem governed by metabolism and to use that knowledge to develop new approaches for microbiome-based disease prevention and precision intervention.
Research Keywords
Microbiota, resilience, commensal bacteria, microbiota, inflammation, precision editing, rational engineering, cancer, carcinogenic bacteria, nutritional immunity, anaerobic bacteria, colon cancer, precision interception.
Publications
Fansler RT, Bak DW, Langford-Butler M, Chen L, Singla D, Spiga L, Livny J, Karijolich J, Meers C, Zhou Q, Weerapana E, Zhu W. A nitrite-responsive regulatory RNA locus sustains commensal resilience against nitrosative stress. BioRxiv. 2026 Jul 7/10/2026; PMID: 42465283, PMCID: PMC13370916, PII: 2026.07.09.736866, DOI: 10.64898/2026.07.09.736866, ISSN: 2692-8205.
Spiga L, Fansler RT, Wu Y, Grote A, Langford-Butler M, Miller AK, Neal M, Hale OF, Singla D, Calcutt MW, Rose AE, Bresson MM, Schrimpe-Rutledge AC, Berdy B, Codreanu SG, Washington MK, Bratton BP, Sherrod SD, McLean JA, Zengler K, Sears CL, Behringer MG, Gnirke A, Tao L, Livny J, Olivares-Villagómez D, Earl AM, Zhu W. An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut. Cell [print-electronic]. 2026 Jun 6/25/2026; 189(13): 3968-3990.e38-3990.e38. PMID: 42066751, PMCID: PMC13185528, PII: S0092-8674(26)00401-0, DOI: 10.1016/j.cell.2026.04.012, ISSN: 1097-4172.
Rose AE, Langford-Butler M, Spiga L, Bak DW, Neal M, Shen M, Calcutt MW, Fansler RT, Rohaun SK, Feron M, Schrimpe-Rutledge AC, Berdy B, Codreanu SG, Sherrod SD, Hale OF, Livny J, McLean JA, Zengler K, Behringer MG, Weerapana E, Imlay JA, Zhu W. Rational engineering of facultative anaerobiosis enables commensal survival in the oxygenated gut. BioRxiv. 2026 Jun 6/6/2026; PMID: 42282681, PMCID: PMC13252398, PII: 2026.06.05.730451, DOI: 10.64898/2026.06.05.730451, ISSN: 2692-8205.
Koo E, Quinn G, Behrendt CL, Hassell B, Kang KN, Ruhn KA, Vale G, McDonald JG, Zhu W, Winter SE, Hooper LV. Salmonella lipopolysaccharide stimulates uptake of long-chain fatty acids in the small intestine. BioRxiv. 2026 May 5/20/2026; PMID: 42239099, PMCID: PMC13228628, PII: 2026.05.19.726283, DOI: 10.64898/2026.05.19.726283, ISSN: 2692-8205.
Spencer PN, Brown ME, Smith EP, Wang J, Kim W, Spiga L, Tasneem N, Simmons AJ, Kim T, Yang Y, Xu Y, Zheng L, Ro J, Kaur H, Kang SW, Helou MD, Lee MA, Arceneaux D, Mueller KD, Kuddar OS, Harned MH, Li J, Banerjee A, Markham NO, Wilson KT, Coburn LA, Goettel JA, Liu Q, Washington MK, Valdivia RH, Zhu W, Lau KS. Pathobiont-triggered induction of goblet cell response drives regional susceptibility to inflammatory bowel disease. J Clin Invest. 2026 Apr 4/1/2026; 136(7): PMID: 41701533, PMCID: PMC13038202, PII: 201729, DOI: 10.1172/JCI201729, ISSN: 1558-8238.
Fansler RT, Wu Y, Zhu W. Friend or foe? Contextualizing Bacteroides through the lens of niche remodeling. Trends Microbiol [print-electronic]. 2026 Mar; 34(3): 318-29. PMID: 41318265, PII: S0966-842X(25)00331-2, DOI: 10.1016/j.tim.2025.11.005, ISSN: 1878-4380.
Rose AE, Fansler RT, Zhu W. Commensal resilience: ancient ecological lessons for the modern microbiota. Infect Immun [print-electronic]. 2025 Jun 6/10/2025; 93(6): e0050224. PMID: 40387449, PMCID: PMC12150765, DOI: 10.1128/iai.00502-24, ISSN: 1098-5522.
Singla D, Rose AE, Zhu W. Small intestine changes, large intestine problems. Trends Microbiol [print-electronic]. 2025 Mar; 33(3): 255-7. PMID: 39890504, PMCID: PMC11885040, PII: S0966-842X(25)00010-1, DOI: 10.1016/j.tim.2025.01.010, ISSN: 1878-4380.
Spencer PN, Wang J, Smith EP, Spiga L, Simmons AJ, Kim T, Kim W, Brown ME, Yang Y, Kaur H, Xu Y, Kang SW, Helou MD, Lee MA, Zheng L, Arceneaux D, Tasneem N, Mueller KD, Kuddar OS, Harned MH, Ro J, Li J, Banerjee A, Markham NO, Wilson KT, Coburn LA, Goettel JA, Liu Q, Kay Washington M, Valdivia RH, Zhu W, Lau KS. Pathobiont-triggered induction of epithelial IDO1 drives regional susceptibility to Inflammatory Bowel Disease. BioRxiv. 2025 Jan 1/4/2025; PMID: 39803424, PMCID: PMC11722351, PII: 2025.01.04.630951, DOI: 10.1101/2025.01.04.630951, ISSN: 2692-8205.
Rüttiger AS, Ryan D, Spiga L, Lamm-Schmidt V, Prezza G, Reichardt S, Langford M, Barquist L, Faber F, Zhu W, Westermann AJ. The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron. Nat Commun. 2025 Jan 1/2/2025; 16(1): 208. PMID: 39747016, PMCID: PMC11697453, PII: 10.1038/s41467-024-55383-8, DOI: 10.1038/s41467-024-55383-8, ISSN: 2041-1723.
Spiga L, Fansler RT, Perera YR, Shealy NG, Munneke MJ, David HE, Torres TP, Lemoff A, Ran X, Richardson KL, Pudlo N, Martens EC, Folta-Stogniew E, Yang ZJ, Skaar EP, Byndloss MX, Chazin WJ, Zhu W. Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection. Cell Host Microbe [print-electronic]. 2023 Oct 10/11/2023; 31(10): 1639-1654.e10-1654.e10. PMID: 37776864, PMCID: PMC10599249, PII: S1931-3128(23)00343-8, DOI: 10.1016/j.chom.2023.08.018, ISSN: 1934-6069.
Spiga L, Fansler RT, Perera YR, Shealy NG, Munneke MJ, Torres TP, David HE, Lemoff A, Ran X, Richardson KL, Pudlo N, Martens EC, Yang ZJ, Skaar EP, Byndloss MX, Chazin WJ, Zhu W. Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection. BioRxiv. 2023 Jun 6/26/2023; PMID: 37425782, PMCID: PMC10326984, PII: 2023.06.25.546471, DOI: 10.1101/2023.06.25.546471.
Fansler RT, Spiga L, Langford M, Zhu W. Respire or expire-precision killing of Helicobacter pylori by targeting complex I respiration. Cell Chem Biol. 2023 May 5/18/2023; 30(5): 417-9. PMID: 37207630, PII: S2451-9456(23)00122-8, DOI: 10.1016/j.chembiol.2023.04.015, ISSN: 2451-9448.
Bessho S, Grando KCM, Kyrylchuk K, Miller A, Klein-Szanto AJ, Zhu W, Gallucci S, Tam V, Tükel Ç. Systemic exposure to bacterial amyloid curli alters the gut mucosal immune response and the microbiome, exacerbating Salmonella-induced arthritis. Gut Microbes. 2023; 15(1): 2221813. PMID: 37317012, PMCID: PMC10269392, DOI: 10.1080/19490976.2023.2221813, ISSN: 1949-0984.
Taylor SJ, Winter MG, Gillis CC, Silva LAD, Dobbins AL, Muramatsu MK, Jimenez AG, Chanin RB, Spiga L, Llano EM, Rojas VK, Kim J, Santos RL, Zhu W, Winter SE. Colonocyte-derived lactate promotes E. coli fitness in the context of inflammation-associated gut microbiota dysbiosis. Microbiome. 2022 Nov 11/26/2022; 10(1): 200. PMID: 36434690, PMCID: PMC9701030, PII: 10.1186/s40168-022-01389-7, DOI: 10.1186/s40168-022-01389-7, ISSN: 2049-2618.
Fansler RT, Zhu W. Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota. MSystems [print-electronic]. 2022 Jun 6/28/2022; 7(3): e0020722. PMID: 35695430, PMCID: PMC9239041, DOI: 10.1128/msystems.00207-22, ISSN: 2379-5077.
Hughes ER, Winter MG, Alves da Silva L, Muramatsu MK, Jimenez AG, Gillis CC, Spiga L, Chanin RB, Santos RL, Zhu W, Winter SE. Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation. Elife. 2021 Jun 6/4/2021; 10: PMID: 34085924, PMCID: PMC8177889, PII: 58609, DOI: 10.7554/eLife.58609, ISSN: 2050-084X.
Chanin RB, Winter MG, Spiga L, Hughes ER, Zhu W, Taylor SJ, Arenales A, Gillis CC, Büttner L, Jimenez AG, Smoot MP, Santos RL, Winter SE. Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation. Cell Host Microbe [print-electronic]. 2020 Dec 12/9/2020; 28(6): 780-788.e5. PMID: 33053375, PMCID: PMC7736183, PII: S1931-3128(20)30506-0, DOI: 10.1016/j.chom.2020.09.005, ISSN: 1934-6069.
Ellermann M, Pacheco AR, Jimenez AG, Russell RM, Cuesta S, Kumar A, Zhu W, Vale G, Martin SA, Raj P, McDonald JG, Winter SE, Sperandio V. Endocannabinoids Inhibit the Induction of Virulence in Enteric Pathogens. Cell [print-electronic]. 2020 Oct 10/29/2020; 183(3): 650-665.e15. PMID: 33031742, PMCID: PMC7606741, PII: S0092-8674(20)31163-6, DOI: 10.1016/j.cell.2020.09.022, ISSN: 1097-4172.
Menezes-Garcia Z, Kumar A, Zhu W, Winter SE, Sperandio V. L-Arginine sensing regulates virulence gene expression and disease progression in enteric pathogens. Proc Natl Acad Sci U S A [print-electronic]. 2020 Jun 6/2/2020; 117(22): 12387-93. PMID: 32409599, PMCID: PMC7275701, PII: 1919683117, DOI: 10.1073/pnas.1919683117, ISSN: 1091-6490.
Zhu W, Winter MG, Spiga L, Hughes ER, Chanin R, Mulgaonkar A, Pennington J, Maas M, Behrendt CL, Kim J, Sun X, Beiting DP, Hooper LV, Winter SE. Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis. Cell Host Microbe [print-electronic]. 2020 Mar 3/11/2020; 27(3): 376-388.e8. PMID: 32075741, PMCID: PMC7439322, PII: S1931-3128(20)30049-4, DOI: 10.1016/j.chom.2020.01.010, ISSN: 1934-6069.
Zhu W, Miyata N, Winter MG, Arenales A, Hughes ER, Spiga L, Kim J, Sifuentes-Dominguez L, Starokadomskyy P, Gopal P, Byndloss MX, Santos RL, Burstein E, Winter SE. Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer. J Exp Med [print-electronic]. 2019 Oct 10/7/2019; 216(10): 2378-93. PMID: 31358565, PMCID: PMC6781011, PII: jem.20181939, DOI: 10.1084/jem.20181939, ISSN: 1540-9538.
Wilson RP, Tursi SA, Rapsinski GJ, Medeiros NJ, Le LS, Kotredes KP, Patel S, Liverani E, Sun S, Zhu W, Kilpatrick L, Winter SE, Gamero AM, Tükel Ç. STAT2 dependent Type I Interferon response promotes dysbiosis and luminal expansion of the enteric pathogen Salmonella Typhimurium. PLoS Pathog. 2019 Apr; 15(4): e1007745. PMID: 31009517, PMCID: PMC6513112, PII: PPATHOGENS-D-18-01529, DOI: 10.1371/journal.ppat.1007745, ISSN: 1553-7374.
Gillis CC, Winter MG, Chanin RB, Zhu W, Spiga L, Winter SE. Host-Derived Metabolites Modulate Transcription of Salmonella Genes Involved in l-Lactate Utilization during Gut Colonization. Infect Immun [electronic-print]. 2019 Apr; 87(4): PMID: 30617205, PMCID: PMC6434127, PII: IAI.00773-18, DOI: 10.1128/IAI.00773-18, ISSN: 1098-5522.
Duerkop BA, Kleiner M, Paez-Espino D, Zhu W, Bushnell B, Hassell B, Winter SE, Kyrpides NC, Hooper LV. Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol [print-electronic]. 2018 Sep; 3(9): 1023-31. PMID: 30038310, PMCID: PMC6112176, PII: 10.1038/s41564-018-0210-y, DOI: 10.1038/s41564-018-0210-y, ISSN: 2058-5276.
Miyata N, Morris LL, Chen Q, Thorne C, Singla A, Zhu W, Winter M, Melton SD, Li H, Sifuentes-Dominguez L, Llano E, Huff-Hardy K, Starokadomskyy P, Lopez A, Reese TA, Turer E, Billadeau DD, Winter SE, Burstein E. Microbial Sensing by Intestinal Myeloid Cells Controls Carcinogenesis and Epithelial Differentiation. Cell Rep. 2018 Aug 8/28/2018; 24(9): 2342-55. PMID: 30157428, PMCID: PMC6177233, PII: S2211-1247(18)31184-7, DOI: 10.1016/j.celrep.2018.07.066, ISSN: 2211-1247.
Gillis CC, Hughes ER, Spiga L, Winter MG, Zhu W, Furtado de Carvalho T, Chanin RB, Behrendt CL, Hooper LV, Santos RL, Winter SE. Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth. Cell Host Microbe. 2018 Apr 4/11/2018; 23(4): 570. PMID: 29649446, PMCID: PMC5907491, PII: S1931-3128(18)30142-2, DOI: 10.1016/j.chom.2018.03.013, ISSN: 1934-6069.
Zhu W, Winter MG, Byndloss MX, Spiga L, Duerkop BA, Hughes ER, Büttner L, de Lima Romão E, Behrendt CL, Lopez CA, Sifuentes-Dominguez L, Huff-Hardy K, Wilson RP, Gillis CC, Tükel Ç, Koh AY, Burstein E, Hooper LV, Bäumler AJ, Winter SE. Precision editing of the gut microbiota ameliorates colitis. Nature [print-electronic]. 2018 Jan 1/11/2018; 553(7687): 208-11. PMID: 29323293, PMCID: PMC5804340, PII: nature25172, DOI: 10.1038/nature25172, ISSN: 1476-4687.
Gillis CC, Hughes ER, Spiga L, Winter MG, Zhu W, Furtado de Carvalho T, Chanin RB, Behrendt CL, Hooper LV, Santos RL, Winter SE. Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth. Cell Host Microbe [print-electronic]. 2018 Jan 1/10/2018; 23(1): 54-64.e6. PMID: 29276172, PMCID: PMC5764812, PII: S1931-3128(17)30500-0, DOI: 10.1016/j.chom.2017.11.006, ISSN: 1934-6069.
Spiga L, Winter MG, Furtado de Carvalho T, Zhu W, Hughes ER, Gillis CC, Behrendt CL, Kim J, Chessa D, Andrews-Polymenis HL, Beiting DP, Santos RL, Hooper LV, Winter SE. An Oxidative Central Metabolism Enables Salmonella to Utilize Microbiota-Derived Succinate. Cell Host Microbe [print-electronic]. 2017 Sep 9/13/2017; 22(3): 291-301.e6. PMID: 28844888, PMCID: PMC5599368, PII: S1931-3128(17)30301-3, DOI: 10.1016/j.chom.2017.07.018, ISSN: 1934-6069.
Hughes ER, Winter MG, Duerkop BA, Spiga L, Furtado de Carvalho T, Zhu W, Gillis CC, Büttner L, Smoot MP, Behrendt CL, Cherry S, Santos RL, Hooper LV, Winter SE. Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis. Cell Host Microbe. 2017 Feb 2/8/2017; 21(2): 208-19. PMID: 28182951, PMCID: PMC5313043, PII: S1931-3128(17)30027-6, DOI: 10.1016/j.chom.2017.01.005, ISSN: 1934-6069.
Liu Y, Zhu W, Tan Y, Nakayasu ES, Staiger CJ, Luo ZQ. A Legionella Effector Disrupts Host Cytoskeletal Structure by Cleaving Actin. PLoS Pathog. 2017 Jan; 13(1): e1006186. PMID: 28129393, PMCID: PMC5298343, PII: PPATHOGENS-D-16-00655, DOI: 10.1371/journal.ppat.1006186, ISSN: 1553-7374.
Zhu W, Luo ZQ. Cell biology and immunology lessons taught by Legionella pneumophila. Sci China Life Sci [print-electronic]. 2016 Jan; 59(1): 3-10. PMID: 26596966, PII: 10.1007/s11427-015-4945-x, DOI: 10.1007/s11427-015-4945-x, ISSN: 1869-1889.
Wang T, Si M, Song Y, Zhu W, Gao F, Wang Y, Zhang L, Zhang W, Wei G, Luo ZQ, Shen X. Type VI Secretion System Transports Zn2+ to Combat Multiple Stresses and Host Immunity. PLoS Pathog. 2015 Jul; 11(7): e1005020. PMID: 26134274, PMCID: PMC4489752, PII: PPATHOGENS-D-14-02456, DOI: 10.1371/journal.ppat.1005020, ISSN: 1553-7374.
Zhu W, Luo ZQ. A new way to detect the danger: Lysosomal cell death induced by a bacterial ribosomal protein. J Nat Sci. 2015 Jun; 1(6): PMID: 26052550, PMCID: PMC4457467, ISSN: 2377-2700.
Zhu W, Tao L, Quick ML, Joyce JA, Qu JM, Luo ZQ. Sensing cytosolic RpsL by macrophages induces lysosomal cell death and termination of bacterial infection. PLoS Pathog. 2015 Mar; 11(3): e1004704. PMID: 25738962, PMCID: PMC4349785, PII: PPATHOGENS-D-14-02610, DOI: 10.1371/journal.ppat.1004704, ISSN: 1553-7374.
Zhu W, Hammad LA, Hsu F, Mao Y, Luo ZQ. Induction of caspase 3 activation by multiple Legionella pneumophila Dot/Icm substrates. Cell Microbiol [print-electronic]. 2013 Nov; 15(11): 1783-95. PMID: 23773455, PMCID: PMC3797225, DOI: 10.1111/cmi.12157, ISSN: 1462-5822.
Tao L, Zhu W, Hu BJ, Qu JM, Luo ZQ. Induction of rapid cell death by an environmental isolate of Legionella pneumophila in mouse macrophages. Infect Immun [print-electronic]. 2013 Sep; 81(9): 3077-88. PMID: 23753633, PMCID: PMC3754228, PII: IAI.00252-13, DOI: 10.1128/IAI.00252-13, ISSN: 1098-5522.
Zhu W, Luo ZQ. Methods for determining protein translocation by the Legionella pneumophila Dot/Icm type IV secretion system. Methods Mol Biol. 2013; 954: 323-32. PMID: 23150405, DOI: 10.1007/978-1-62703-161-5_19, ISSN: 1940-6029.
Hsu F, Zhu W, Brennan L, Tao L, Luo ZQ, Mao Y. Structural basis for substrate recognition by a unique Legionella phosphoinositide phosphatase. Proc Natl Acad Sci U S A [print-electronic]. 2012 Aug 8/21/2012; 109(34): 13567-72. PMID: 22872863, PMCID: PMC3427105, PII: 1207903109, DOI: 10.1073/pnas.1207903109, ISSN: 1091-6490.
Zhu W, Banga S, Tan Y, Zheng C, Stephenson R, Gately J, Luo ZQ. Comprehensive identification of protein substrates of the Dot/Icm type IV transporter of Legionella pneumophila. PLoS One. 2011 Mar 3/9/2011; 6(3): e17638. PMID: 21408005, PMCID: PMC3052360, DOI: 10.1371/journal.pone.0017638, ISSN: 1932-6203.
Du L, Su Y, Sun D, Zhu W, Wang J, Zhuang X, Zhou S, Lu Y. Formic acid induces Yca1p-independent apoptosis-like cell death in the yeast Saccharomyces cerevisiae. FEMS Yeast Res [print-electronic]. 2008 Jun; 8(4): 531-9. PMID: 18452540, PII: FYR375, DOI: 10.1111/j.1567-1364.2008.00375.x, ISSN: 1567-1356.
Spiga L, Fansler RT, Wu Y, Grote A, Langford-Butler M, Miller AK, Neal M, Hale OF, Singla D, Calcutt MW, Rose AE, Bresson MM, Schrimpe-Rutledge AC, Berdy B, Codreanu SG, Washington MK, Bratton BP, Sherrod SD, McLean JA, Zengler K, Sears CL, Behringer MG, Gnirke A, Tao L, Livny J, Olivares-Villagómez D, Earl AM, Zhu W. An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut. Cell [print-electronic]. 2026 Jun 6/25/2026; 189(13): 3968-3990.e38-3990.e38. PMID: 42066751, PMCID: PMC13185528, PII: S0092-8674(26)00401-0, DOI: 10.1016/j.cell.2026.04.012, ISSN: 1097-4172.
Rose AE, Langford-Butler M, Spiga L, Bak DW, Neal M, Shen M, Calcutt MW, Fansler RT, Rohaun SK, Feron M, Schrimpe-Rutledge AC, Berdy B, Codreanu SG, Sherrod SD, Hale OF, Livny J, McLean JA, Zengler K, Behringer MG, Weerapana E, Imlay JA, Zhu W. Rational engineering of facultative anaerobiosis enables commensal survival in the oxygenated gut. BioRxiv. 2026 Jun 6/6/2026; PMID: 42282681, PMCID: PMC13252398, PII: 2026.06.05.730451, DOI: 10.64898/2026.06.05.730451, ISSN: 2692-8205.
Koo E, Quinn G, Behrendt CL, Hassell B, Kang KN, Ruhn KA, Vale G, McDonald JG, Zhu W, Winter SE, Hooper LV. Salmonella lipopolysaccharide stimulates uptake of long-chain fatty acids in the small intestine. BioRxiv. 2026 May 5/20/2026; PMID: 42239099, PMCID: PMC13228628, PII: 2026.05.19.726283, DOI: 10.64898/2026.05.19.726283, ISSN: 2692-8205.
Spencer PN, Brown ME, Smith EP, Wang J, Kim W, Spiga L, Tasneem N, Simmons AJ, Kim T, Yang Y, Xu Y, Zheng L, Ro J, Kaur H, Kang SW, Helou MD, Lee MA, Arceneaux D, Mueller KD, Kuddar OS, Harned MH, Li J, Banerjee A, Markham NO, Wilson KT, Coburn LA, Goettel JA, Liu Q, Washington MK, Valdivia RH, Zhu W, Lau KS. Pathobiont-triggered induction of goblet cell response drives regional susceptibility to inflammatory bowel disease. J Clin Invest. 2026 Apr 4/1/2026; 136(7): PMID: 41701533, PMCID: PMC13038202, PII: 201729, DOI: 10.1172/JCI201729, ISSN: 1558-8238.
Fansler RT, Wu Y, Zhu W. Friend or foe? Contextualizing Bacteroides through the lens of niche remodeling. Trends Microbiol [print-electronic]. 2026 Mar; 34(3): 318-29. PMID: 41318265, PII: S0966-842X(25)00331-2, DOI: 10.1016/j.tim.2025.11.005, ISSN: 1878-4380.
Rose AE, Fansler RT, Zhu W. Commensal resilience: ancient ecological lessons for the modern microbiota. Infect Immun [print-electronic]. 2025 Jun 6/10/2025; 93(6): e0050224. PMID: 40387449, PMCID: PMC12150765, DOI: 10.1128/iai.00502-24, ISSN: 1098-5522.
Singla D, Rose AE, Zhu W. Small intestine changes, large intestine problems. Trends Microbiol [print-electronic]. 2025 Mar; 33(3): 255-7. PMID: 39890504, PMCID: PMC11885040, PII: S0966-842X(25)00010-1, DOI: 10.1016/j.tim.2025.01.010, ISSN: 1878-4380.
Spencer PN, Wang J, Smith EP, Spiga L, Simmons AJ, Kim T, Kim W, Brown ME, Yang Y, Kaur H, Xu Y, Kang SW, Helou MD, Lee MA, Zheng L, Arceneaux D, Tasneem N, Mueller KD, Kuddar OS, Harned MH, Ro J, Li J, Banerjee A, Markham NO, Wilson KT, Coburn LA, Goettel JA, Liu Q, Kay Washington M, Valdivia RH, Zhu W, Lau KS. Pathobiont-triggered induction of epithelial IDO1 drives regional susceptibility to Inflammatory Bowel Disease. BioRxiv. 2025 Jan 1/4/2025; PMID: 39803424, PMCID: PMC11722351, PII: 2025.01.04.630951, DOI: 10.1101/2025.01.04.630951, ISSN: 2692-8205.
Rüttiger AS, Ryan D, Spiga L, Lamm-Schmidt V, Prezza G, Reichardt S, Langford M, Barquist L, Faber F, Zhu W, Westermann AJ. The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron. Nat Commun. 2025 Jan 1/2/2025; 16(1): 208. PMID: 39747016, PMCID: PMC11697453, PII: 10.1038/s41467-024-55383-8, DOI: 10.1038/s41467-024-55383-8, ISSN: 2041-1723.
Spiga L, Fansler RT, Perera YR, Shealy NG, Munneke MJ, David HE, Torres TP, Lemoff A, Ran X, Richardson KL, Pudlo N, Martens EC, Folta-Stogniew E, Yang ZJ, Skaar EP, Byndloss MX, Chazin WJ, Zhu W. Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection. Cell Host Microbe [print-electronic]. 2023 Oct 10/11/2023; 31(10): 1639-1654.e10-1654.e10. PMID: 37776864, PMCID: PMC10599249, PII: S1931-3128(23)00343-8, DOI: 10.1016/j.chom.2023.08.018, ISSN: 1934-6069.
Spiga L, Fansler RT, Perera YR, Shealy NG, Munneke MJ, Torres TP, David HE, Lemoff A, Ran X, Richardson KL, Pudlo N, Martens EC, Yang ZJ, Skaar EP, Byndloss MX, Chazin WJ, Zhu W. Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection. BioRxiv. 2023 Jun 6/26/2023; PMID: 37425782, PMCID: PMC10326984, PII: 2023.06.25.546471, DOI: 10.1101/2023.06.25.546471.
Fansler RT, Spiga L, Langford M, Zhu W. Respire or expire-precision killing of Helicobacter pylori by targeting complex I respiration. Cell Chem Biol. 2023 May 5/18/2023; 30(5): 417-9. PMID: 37207630, PII: S2451-9456(23)00122-8, DOI: 10.1016/j.chembiol.2023.04.015, ISSN: 2451-9448.
Bessho S, Grando KCM, Kyrylchuk K, Miller A, Klein-Szanto AJ, Zhu W, Gallucci S, Tam V, Tükel Ç. Systemic exposure to bacterial amyloid curli alters the gut mucosal immune response and the microbiome, exacerbating Salmonella-induced arthritis. Gut Microbes. 2023; 15(1): 2221813. PMID: 37317012, PMCID: PMC10269392, DOI: 10.1080/19490976.2023.2221813, ISSN: 1949-0984.
Taylor SJ, Winter MG, Gillis CC, Silva LAD, Dobbins AL, Muramatsu MK, Jimenez AG, Chanin RB, Spiga L, Llano EM, Rojas VK, Kim J, Santos RL, Zhu W, Winter SE. Colonocyte-derived lactate promotes E. coli fitness in the context of inflammation-associated gut microbiota dysbiosis. Microbiome. 2022 Nov 11/26/2022; 10(1): 200. PMID: 36434690, PMCID: PMC9701030, PII: 10.1186/s40168-022-01389-7, DOI: 10.1186/s40168-022-01389-7, ISSN: 2049-2618.
Fansler RT, Zhu W. Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota. MSystems [print-electronic]. 2022 Jun 6/28/2022; 7(3): e0020722. PMID: 35695430, PMCID: PMC9239041, DOI: 10.1128/msystems.00207-22, ISSN: 2379-5077.
Hughes ER, Winter MG, Alves da Silva L, Muramatsu MK, Jimenez AG, Gillis CC, Spiga L, Chanin RB, Santos RL, Zhu W, Winter SE. Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation. Elife. 2021 Jun 6/4/2021; 10: PMID: 34085924, PMCID: PMC8177889, PII: 58609, DOI: 10.7554/eLife.58609, ISSN: 2050-084X.
Chanin RB, Winter MG, Spiga L, Hughes ER, Zhu W, Taylor SJ, Arenales A, Gillis CC, Büttner L, Jimenez AG, Smoot MP, Santos RL, Winter SE. Epithelial-Derived Reactive Oxygen Species Enable AppBCX-Mediated Aerobic Respiration of Escherichia coli during Intestinal Inflammation. Cell Host Microbe [print-electronic]. 2020 Dec 12/9/2020; 28(6): 780-788.e5. PMID: 33053375, PMCID: PMC7736183, PII: S1931-3128(20)30506-0, DOI: 10.1016/j.chom.2020.09.005, ISSN: 1934-6069.
Ellermann M, Pacheco AR, Jimenez AG, Russell RM, Cuesta S, Kumar A, Zhu W, Vale G, Martin SA, Raj P, McDonald JG, Winter SE, Sperandio V. Endocannabinoids Inhibit the Induction of Virulence in Enteric Pathogens. Cell [print-electronic]. 2020 Oct 10/29/2020; 183(3): 650-665.e15. PMID: 33031742, PMCID: PMC7606741, PII: S0092-8674(20)31163-6, DOI: 10.1016/j.cell.2020.09.022, ISSN: 1097-4172.
Menezes-Garcia Z, Kumar A, Zhu W, Winter SE, Sperandio V. L-Arginine sensing regulates virulence gene expression and disease progression in enteric pathogens. Proc Natl Acad Sci U S A [print-electronic]. 2020 Jun 6/2/2020; 117(22): 12387-93. PMID: 32409599, PMCID: PMC7275701, PII: 1919683117, DOI: 10.1073/pnas.1919683117, ISSN: 1091-6490.
Zhu W, Winter MG, Spiga L, Hughes ER, Chanin R, Mulgaonkar A, Pennington J, Maas M, Behrendt CL, Kim J, Sun X, Beiting DP, Hooper LV, Winter SE. Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis. Cell Host Microbe [print-electronic]. 2020 Mar 3/11/2020; 27(3): 376-388.e8. PMID: 32075741, PMCID: PMC7439322, PII: S1931-3128(20)30049-4, DOI: 10.1016/j.chom.2020.01.010, ISSN: 1934-6069.
Zhu W, Miyata N, Winter MG, Arenales A, Hughes ER, Spiga L, Kim J, Sifuentes-Dominguez L, Starokadomskyy P, Gopal P, Byndloss MX, Santos RL, Burstein E, Winter SE. Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer. J Exp Med [print-electronic]. 2019 Oct 10/7/2019; 216(10): 2378-93. PMID: 31358565, PMCID: PMC6781011, PII: jem.20181939, DOI: 10.1084/jem.20181939, ISSN: 1540-9538.
Wilson RP, Tursi SA, Rapsinski GJ, Medeiros NJ, Le LS, Kotredes KP, Patel S, Liverani E, Sun S, Zhu W, Kilpatrick L, Winter SE, Gamero AM, Tükel Ç. STAT2 dependent Type I Interferon response promotes dysbiosis and luminal expansion of the enteric pathogen Salmonella Typhimurium. PLoS Pathog. 2019 Apr; 15(4): e1007745. PMID: 31009517, PMCID: PMC6513112, PII: PPATHOGENS-D-18-01529, DOI: 10.1371/journal.ppat.1007745, ISSN: 1553-7374.
Gillis CC, Winter MG, Chanin RB, Zhu W, Spiga L, Winter SE. Host-Derived Metabolites Modulate Transcription of Salmonella Genes Involved in l-Lactate Utilization during Gut Colonization. Infect Immun [electronic-print]. 2019 Apr; 87(4): PMID: 30617205, PMCID: PMC6434127, PII: IAI.00773-18, DOI: 10.1128/IAI.00773-18, ISSN: 1098-5522.
Duerkop BA, Kleiner M, Paez-Espino D, Zhu W, Bushnell B, Hassell B, Winter SE, Kyrpides NC, Hooper LV. Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol [print-electronic]. 2018 Sep; 3(9): 1023-31. PMID: 30038310, PMCID: PMC6112176, PII: 10.1038/s41564-018-0210-y, DOI: 10.1038/s41564-018-0210-y, ISSN: 2058-5276.
Miyata N, Morris LL, Chen Q, Thorne C, Singla A, Zhu W, Winter M, Melton SD, Li H, Sifuentes-Dominguez L, Llano E, Huff-Hardy K, Starokadomskyy P, Lopez A, Reese TA, Turer E, Billadeau DD, Winter SE, Burstein E. Microbial Sensing by Intestinal Myeloid Cells Controls Carcinogenesis and Epithelial Differentiation. Cell Rep. 2018 Aug 8/28/2018; 24(9): 2342-55. PMID: 30157428, PMCID: PMC6177233, PII: S2211-1247(18)31184-7, DOI: 10.1016/j.celrep.2018.07.066, ISSN: 2211-1247.
Gillis CC, Hughes ER, Spiga L, Winter MG, Zhu W, Furtado de Carvalho T, Chanin RB, Behrendt CL, Hooper LV, Santos RL, Winter SE. Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth. Cell Host Microbe. 2018 Apr 4/11/2018; 23(4): 570. PMID: 29649446, PMCID: PMC5907491, PII: S1931-3128(18)30142-2, DOI: 10.1016/j.chom.2018.03.013, ISSN: 1934-6069.
Zhu W, Winter MG, Byndloss MX, Spiga L, Duerkop BA, Hughes ER, Büttner L, de Lima Romão E, Behrendt CL, Lopez CA, Sifuentes-Dominguez L, Huff-Hardy K, Wilson RP, Gillis CC, Tükel Ç, Koh AY, Burstein E, Hooper LV, Bäumler AJ, Winter SE. Precision editing of the gut microbiota ameliorates colitis. Nature [print-electronic]. 2018 Jan 1/11/2018; 553(7687): 208-11. PMID: 29323293, PMCID: PMC5804340, PII: nature25172, DOI: 10.1038/nature25172, ISSN: 1476-4687.
Gillis CC, Hughes ER, Spiga L, Winter MG, Zhu W, Furtado de Carvalho T, Chanin RB, Behrendt CL, Hooper LV, Santos RL, Winter SE. Dysbiosis-Associated Change in Host Metabolism Generates Lactate to Support Salmonella Growth. Cell Host Microbe [print-electronic]. 2018 Jan 1/10/2018; 23(1): 54-64.e6. PMID: 29276172, PMCID: PMC5764812, PII: S1931-3128(17)30500-0, DOI: 10.1016/j.chom.2017.11.006, ISSN: 1934-6069.
Spiga L, Winter MG, Furtado de Carvalho T, Zhu W, Hughes ER, Gillis CC, Behrendt CL, Kim J, Chessa D, Andrews-Polymenis HL, Beiting DP, Santos RL, Hooper LV, Winter SE. An Oxidative Central Metabolism Enables Salmonella to Utilize Microbiota-Derived Succinate. Cell Host Microbe [print-electronic]. 2017 Sep 9/13/2017; 22(3): 291-301.e6. PMID: 28844888, PMCID: PMC5599368, PII: S1931-3128(17)30301-3, DOI: 10.1016/j.chom.2017.07.018, ISSN: 1934-6069.
Hughes ER, Winter MG, Duerkop BA, Spiga L, Furtado de Carvalho T, Zhu W, Gillis CC, Büttner L, Smoot MP, Behrendt CL, Cherry S, Santos RL, Hooper LV, Winter SE. Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis. Cell Host Microbe. 2017 Feb 2/8/2017; 21(2): 208-19. PMID: 28182951, PMCID: PMC5313043, PII: S1931-3128(17)30027-6, DOI: 10.1016/j.chom.2017.01.005, ISSN: 1934-6069.
Liu Y, Zhu W, Tan Y, Nakayasu ES, Staiger CJ, Luo ZQ. A Legionella Effector Disrupts Host Cytoskeletal Structure by Cleaving Actin. PLoS Pathog. 2017 Jan; 13(1): e1006186. PMID: 28129393, PMCID: PMC5298343, PII: PPATHOGENS-D-16-00655, DOI: 10.1371/journal.ppat.1006186, ISSN: 1553-7374.
Zhu W, Luo ZQ. Cell biology and immunology lessons taught by Legionella pneumophila. Sci China Life Sci [print-electronic]. 2016 Jan; 59(1): 3-10. PMID: 26596966, PII: 10.1007/s11427-015-4945-x, DOI: 10.1007/s11427-015-4945-x, ISSN: 1869-1889.
Wang T, Si M, Song Y, Zhu W, Gao F, Wang Y, Zhang L, Zhang W, Wei G, Luo ZQ, Shen X. Type VI Secretion System Transports Zn2+ to Combat Multiple Stresses and Host Immunity. PLoS Pathog. 2015 Jul; 11(7): e1005020. PMID: 26134274, PMCID: PMC4489752, PII: PPATHOGENS-D-14-02456, DOI: 10.1371/journal.ppat.1005020, ISSN: 1553-7374.
Zhu W, Luo ZQ. A new way to detect the danger: Lysosomal cell death induced by a bacterial ribosomal protein. J Nat Sci. 2015 Jun; 1(6): PMID: 26052550, PMCID: PMC4457467, ISSN: 2377-2700.
Zhu W, Tao L, Quick ML, Joyce JA, Qu JM, Luo ZQ. Sensing cytosolic RpsL by macrophages induces lysosomal cell death and termination of bacterial infection. PLoS Pathog. 2015 Mar; 11(3): e1004704. PMID: 25738962, PMCID: PMC4349785, PII: PPATHOGENS-D-14-02610, DOI: 10.1371/journal.ppat.1004704, ISSN: 1553-7374.
Zhu W, Hammad LA, Hsu F, Mao Y, Luo ZQ. Induction of caspase 3 activation by multiple Legionella pneumophila Dot/Icm substrates. Cell Microbiol [print-electronic]. 2013 Nov; 15(11): 1783-95. PMID: 23773455, PMCID: PMC3797225, DOI: 10.1111/cmi.12157, ISSN: 1462-5822.
Tao L, Zhu W, Hu BJ, Qu JM, Luo ZQ. Induction of rapid cell death by an environmental isolate of Legionella pneumophila in mouse macrophages. Infect Immun [print-electronic]. 2013 Sep; 81(9): 3077-88. PMID: 23753633, PMCID: PMC3754228, PII: IAI.00252-13, DOI: 10.1128/IAI.00252-13, ISSN: 1098-5522.
Zhu W, Luo ZQ. Methods for determining protein translocation by the Legionella pneumophila Dot/Icm type IV secretion system. Methods Mol Biol. 2013; 954: 323-32. PMID: 23150405, DOI: 10.1007/978-1-62703-161-5_19, ISSN: 1940-6029.
Hsu F, Zhu W, Brennan L, Tao L, Luo ZQ, Mao Y. Structural basis for substrate recognition by a unique Legionella phosphoinositide phosphatase. Proc Natl Acad Sci U S A [print-electronic]. 2012 Aug 8/21/2012; 109(34): 13567-72. PMID: 22872863, PMCID: PMC3427105, PII: 1207903109, DOI: 10.1073/pnas.1207903109, ISSN: 1091-6490.
Zhu W, Banga S, Tan Y, Zheng C, Stephenson R, Gately J, Luo ZQ. Comprehensive identification of protein substrates of the Dot/Icm type IV transporter of Legionella pneumophila. PLoS One. 2011 Mar 3/9/2011; 6(3): e17638. PMID: 21408005, PMCID: PMC3052360, DOI: 10.1371/journal.pone.0017638, ISSN: 1932-6203.
Du L, Su Y, Sun D, Zhu W, Wang J, Zhuang X, Zhou S, Lu Y. Formic acid induces Yca1p-independent apoptosis-like cell death in the yeast Saccharomyces cerevisiae. FEMS Yeast Res [print-electronic]. 2008 Jun; 8(4): 531-9. PMID: 18452540, PII: FYR375, DOI: 10.1111/j.1567-1364.2008.00375.x, ISSN: 1567-1356.