Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance. Cole CG, Zhang ZJ, Dommaraju SR, Dong Q, Pope RL, Son SS, McSpadden EJ, Woodson CK, Lin H, Dylla NP, Sidebottom AM, Sundararajan A, Mitchell DA, Pamer EG. bioRxiv [Preprint]. 2025 May 9
Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples. Ju CW, Lyu R, Li H, Wei J, Parra Vitela AJ, Dougherty U, Kwesi A, Luna A, Zhu X, Shen S, Liu Y, Wang L, Cui X, Xu Y, Jiang B, Ji Y, Xia P, West-Szymanski DC, Sun C, Zhong Y, Ye C, Moran A, Lehmann C, Pamer E, Zhang W, Bissonnette M, Zhang LS, He C. Nat Biotechnol. 2025 Jul 8
Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease. Odenwald MA, Ramaswamy R, Lin H, Lehmann C, Moran A, Mullowney MW, Sidebottom AM, Hernandez A, McMillin M, Rose A, Moran D, Little J, Sulakhe D, D'Souza M, Woodson C, Tanveer T, de Porto A, Dylla N, Sundararajan A, Burgo V, Cantoral J, Jadczak C, Adler E, Aronsohn A, Pamer EG, Rinella ME. Gastro Hep Adv. 2025 May 9
Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models. Roichman A, Reyes-Castellanos G, Chen Z, Chen Z, Mitchell SJ, MacArthur MR, Sawant A, Levett L, Powers JR, Burgo V, Gomez-Jenkins M, Ibrahim M, Xu X, Tomlinson B, Hang X, Pamer EG, Wei Y, Kang Y, White EP, Rabinowitz JD. Cancer Res. 2025 Jun 20
Flagellar switch inverted repeats impact heterogeneity in flagellar gene expression and thus C. difficile RT027/MLST1 virulence. Nhu NTQ, Lin H, Pigli Y, Sia JK, Kuhn P, Ruppel H, Snitkin ES, Young VB, Kamboj M, Pamer EG, Rice PA, Shen A, Dong Q. Cell Rep. 2025 Jun 24
Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality. de Porto AP, Dylla NP, Stutz M, Lin H, Khalid M, Mullowney MW, Little J, Rose A, Moran D, McMillin M, Burgo V, Smith R, Woodson C, Metcalfe C, Ramaswamy R, Lehmann C, Odenwald M, Bandealy N, Zhao J, Kim M, Adler E, Sundararajan A, Sidebottom A, Kress JP, Wolfe KS, Pamer EG, Patel BK. Sci Adv. 2025 Jun 6
Author Correction: Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Little AS, Younker IT, Schechter MS, Bernardino PN, Méheust R, Stemczynski J, Scorza K, Mullowney MW, Sharan D, Waligurski E, Smith R, Ramaswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH. Nat Microbiol. 2025 Jun;
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom. Doran BA, Chen RY, Giba H, Behera V, Barat B, Sundararajan A, Lin H, Sidebottom A, Pamer EG, Raman AS. Cell Syst. 2025 Feb 19
Protection against Clostridioides difficile disease by a naturally avirulent strain. Dong Q, Harper S, McSpadden E, Son SS, Allen MM, Lin H, Smith RC, Metcalfe C, Burgo V, Woodson C, Sundararajan A, Rose A, McMillin M, Moran D, Little J, Mullowney MW, Sidebottom AM, Fortier LC, Shen A, Pamer EG. Cell Host Microbe. 2025 Jan 8
Quantitative insights into the efficacy of genome-resolved surveys of microbial communities through ribosomal protein phylogeography and EcoPhylo. Schechter MS, Trigodet F, Veseli IA, Miller SE, Klein ML, Sever M, Maignien L, Delmont TO, Light SH, Eren AM. bioRxiv [Preprint]. 2025 Apr 23
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom. Doran BA, Chen RY, Giba H, Behera V, Barat B, Sundararajan A, Lin H, Sidebottom A, Pamer EG, Raman AS. Cell Syst. 2025 Feb 19
Designing live bacterial therapeutics for cancer. Lee J, McClure S, Weichselbaum RR, Mimee M. Adv Drug Deliv Rev. 2025 Jun
Swarm-seq Reveals Functional Divergence in CsrA Homologs Across Bacteria. Winkelman JT, Yarberry E, Winkelman JD, Mukherjee S. bioRxiv [Preprint]. 2025 May 6
Gut microbes fend off harmful bacteria by depriving them of nutrients. Pamer EG. Nature. 2024 Sep
Flagellar switch inverted repeat impacts flagellar invertibility and varies Clostridioides difficile RT027/MLST1 virulence. Nhu NTQ, Lin H, Pigli Y, Sia JK, Kuhn P, Snitkin ES, Young V, Kamboj M, Pamer EG, Rice PA, Shen A, Dong Q. bioRxiv [Preprint]. 2024 Sep 24
A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont. Sheahan ML, Flores K, Coyne MJ, García-Bayona L, Chatzidaki-Livanis M, Holst AQ, Smith RC, Sundararajan A, Barquera B, Comstock LE. Science. 2024 Oct 25
Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome. Yuan Y, DeMott MS, Byrne SR, Flores K, Poyet M, Groussin M, Microbiome Conservancy G, Berdy B, Comstock L, Alm EJ, Dedon PC.bioRxiv [Preprint]. 2024 Jun 3
Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution. Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Pappas TE, Townson SA, Laliwala N, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE. Cell Host Microbe. 2024 Oct 9
Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway. Jacoby C, Scorza K, Ecker L, McMillin M, Ramaswamy R, Sundararajan A, Sidebottom AM, Lin H, Dufault-Thompson K, Hall B, Jiang X, Light SH. bioRxiv [Preprint]. 2024 Oct 9
Regulation of immune responses to food by commensal microbes. Light SH, Nagler CR. Immunol Rev. 2024 Sep
Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer. Huang S, Méheust R, Barquera B, Light SH. mSystems. 2024 Aug 20
Combatting superbugs using the evolutionary record of microbial warfare. Raman AS. Cell Host Microbe. 2024 Jul 10
Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae. Rotman E, McClure S, Glazier J, Fuerte-Stone J, Foldi J, Erani A, McGann R, Arnold J, Lin H, Valaitis S, Mimee M. Cell Host Microbe. 2024 Nov 13
A synbiotic of Anaerostipes caccae and lactulose prevents and treats food allergy in mice. Hesser LA, Puente AA, Arnold J, Ionescu E, Mirmira A, Talasani N, Lopez J, Maccio-Maretto L, Mimee M, Nagler CR. Cell Host Microbe. 2024 Jul 10
Combinatorial control of Pseudomonas aeruginosa biofilm development by quorum-sensing and nutrient-sensing regulators Gong Chen, Georgia Fanouraki, Aathmaja Anandhi Rangarajan, Bradford T Winkelman, Jared T Winkelman, Christopher M Waters, Sampriti Mukherjee. mSystems. 2024 Sep 17
Fidaxomicin versus oral vancomycin for Clostridioides difficile infection among patients at high risk for recurrence based on real-world experience. Pettit NN, Lew AK, Nguyen CT, Bell E, Lehmann CJ, Pisano J.Infect Control Hosp Epidemiol. 2024 Oct 4
Distant relatives of a eukaryotic cell-specific toxin family evolved a complement-like mechanism to kill bacteria. Abrahamsen HL, Sanford TC, Collamore CE, Johnstone BA, Coyne MJ, García-Bayona L, Christie MP, Evans JC, Farrand AJ, Flores K, Morton CJ, Parker MW, Comstock LE, Tweten RK.Nat Commun. 2024 Jun 12
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Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. Carasso S, Zaatry R, Hajjo H, Kadosh-Kariti D, Ben-Assa N, Naddaf R, Mandelbaum N, Pressman S, Chowers Y, Gefen T, Jeffrey KL, Jofre J, Coyne MJ, Comstock LE, Sharon I, Geva-Zatorsky N.Cell Host Microbe. 2024 Mar 13
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Protection against Clostridioides difficile disease by a naturally avirulent C. difficile strain. Dong Q, Harper S, McSpadden E, Son SS, Allen MM, Lin H, Smith RC, Metcalfe C, Burgo V, Woodson C, Sundararajan A, Rose A, McMillin M, Moran D, Little J, Mullowney M, Sidebottom AM, Shen A, Fortier LC, Pamer EG. bioRxiv [Preprint]. 2024 May
Intestinal carbapenem-resistant Klebsiella pneumoniae undergoes complex transcriptional reprogramming following immune activation. David C, Czauderna A, Cheng L, Lagune M, Jung HJ, Kim SG, Pamer EG, Prados J, Chen L, Becattini S. Gut Microbes. 2024 Jan-Dec
Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution. Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE. bioRxiv [Preprint]. 2024 Mar 9
Activity of Gut-Derived Nisin-like Lantibiotics against Human Gut Pathogens and Commensals. Zhang ZJ, Wu C, Moreira R, Dorantes D, Pappas T, Sundararajan A, Lin H, Pamer EG, van der Donk WA. ACS Chem Biol. 2024 Feb 16
Exposure and resistance to lantibiotics impact microbiota composition and function. Zhang ZJ, Cole C, Lin H, Wu C, Haro F, McSpadden E, van der Donk WA, Pamer EG. bioRxiv [Preprint]. 2023 Dec 30
Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection. Lehmann CJ, Dylla NP, Odenwald M, Nayak R, Khalid M, Boissiere J, Cantoral J, Adler E, Stutz MR, Dela Cruz M, Moran A, Lin H, Ramaswamy R, Sundararajan A, Sidebottom AM, Little J, Pamer EG, Aronsohn A, Fung J, Baker TB, Kacha A. Cell Host Microbe. 2024 Jan 10
A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. bioRxiv [Preprint]. 2024 Apr 29
A cryptic plasmid is among the most numerous genetic elements in the human gut. Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM. Cell. 2024 Feb 29
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Bacteria on the foundational kelp in kelp forest ecosystems: Insights from culturing, whole genome sequencing and metabolic assays. Younker IT, Molnar N, Scorza K, Weed R, Light SH, Pfister CA. Environ Microbiol Rep. 2024 Jun
Successful Treatment of Refractory Chylous Ascites With Octreotide in a Patient With Decompensated Cirrhosis. DiBattista JV, Odenwald MA, Te H. ACG Case Rep J. 2024 Mar 28
Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements. Hayashi N, Lai Y, Fuerte-Stone J, Mimee M, Lu TK. Nat Commun. 2024 Mar 7
An evolution-based framework for describing human gut bacteria. Doran BA, Chen RY, Giba H, Behera V, Barat B, Sundararajan A, Lin H, Sidebottom A, Pamer EG, Raman AS. bioRxiv. 2023 Dec 5
Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease. Odenwald MA, Lin H, Lehmann C, Dylla NP, Cole CG, Mostad JD, Pappas TE, Ramaswamy R, Moran A, Hutchison AL, Stutz MR, Dela Cruz M, Adler E, Boissiere J, Khalid M, Cantoral J, Haro F, Oliveira RA, Waligurski E, Cotter TG, Light SH, Beavis KG, Sundararajan A, Sidebottom AM, Reddy KG, Paul S, Pillai A, Te HS, Rinella ME, Charlton MR, Pamer EG, Aronsohn AI. Nat Microbiol. 2023 Nov
Purine-ifying uric acid by gut microbes. Grelska A, Sharan D, Light SH. Cell Chem Biol. 2023 Jul 20
Genetic Engineering of Resident Bacteria in the Gut Microbiome. Arnold J, Glazier J, Mimee M.J Bacteriol. 2023 Jul 25
Commensal bacteria signal through TLR5 and AhR to improve barrier integrity and prevent allergic responses to food. Kemter AM, Patry RT, Arnold J, Hesser LA, Campbell E, Ionescu E, Mimee M, Wang S, Nagler CR. Cell Rep. 2023 Sep 22
Statistically learning the functional landscape of microbial communities. Skwara A, Gowda K, Yousef M, Diaz-Colunga J, Raman AS, Sanchez A, Tikhonov M, Kuehn S. Nat Ecol Evol. 2023 Oct 2.
Recurrent NAFLD post-LT: Sisyphus' boulder or Proteus' parable? Odenwald MA, Rinella ME. Liver Transpl. 2023 Sep 1
Evolving challenges with long-term care of liver transplant recipients. Odenwald MA, Roth HF, Reticker A, Segovia M, Pillai A. Clin Transplant. 2023 Oct;
Artificial intelligence for natural product drug discovery. Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kautsar SA, Kim H, Leao TF, Masschelein J, Rees ER, Reher R, Reker D, Schwaller P, Segler M, Skinnider MA, Walker AS, Willighagen EL, Zdrazil B, Ziemert N, Goss RJM, Guyomard P, Volkamer A, Gerwick WH, Kim HU, Müller R, van Wezel GP, van Westen GJP, Hirsch AKH, Linington RG, Robinson SL, Medema MH. Nat Rev Drug Discov. 2023 Sep 11
Distinct Energy-Coupling Factor Transporter Subunits Enable Flavin Acquisition and Extracytosolic Trafficking for Extracellular Electron Transfer in Listeria monocytogenes. Rivera-Lugo R, Huang S, Lee F, Méheust R, Iavarone AT, Sidebottom AM, Oldfield E, Portnoy DA, Light SH. mBio. 2023 Feb 28
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J. Nature. 2023 Jan
Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions. Oliveira RA, Pamer EG. Cell Host Microbe. 2023 Apr 12
Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile. Dong Q, Lin H, Allen MM, Garneau JR, Sia JK, Smith RC, Haro F, McMillen T, Pope RL, Metcalfe C, Burgo V, Woodson C, Dylla N, Kohout C, Sundararajan A, Snitkin ES, Young VB, Fortier LC, Kamboj M, Pamer EG. Cell Rep. 2023 Jul 30
The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia. Schluter J, Djukovic A, Taylor BP, Yan J, Duan C, Hussey GA, Liao C, Sharma S, Fontana E, Amoretti LA, Wright RJ, Dai A, Peled JU, Taur Y, Perales MA, Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Xavier JB. Cell Host Microbe. 2023 Jul 12
Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile. Dong Q, Lin H, Allen MM, Garneau JR, Sia JK, Smith RC, Haro F, McMillen T, Pope RL, Metcalfe C, Burgo V, Woodson C, Dylla N, Kohout C, Sundararajan A, Snitkin ES, Young VB, Fortier LC, Kamboj M, Pamer EG. Cell Rep. 2023 Aug 29
Plasma metabolites with mechanistic and clinical links to the neurovascular disease cavernous angioma. Srinath A, Xie B, Li Y, Sone JY, Romanos S, Chen C, Sharma A, Polster S, Dorrestein PC, Weldon KC, DeBiasse D, Moore T, Lightle R, Koskimäki J, Zhang D, Stadnik A, Piedad K, Hagan M, Shkoukani A, Carrión-Penagos J, Bi D, Shen L, Shenkar R, Ji Y, Sidebottom A, Pamer E, Gilbert JA, Kahn ML, D'Souza M, Sulakhe D, Awad IA, Girard R. Commun Med (Lond). 2023 Mar 3
Bacteroides fragilis Maintains Concurrent Capability for Anaerobic and Nanaerobic Respiration. Butler NL, Ito T, Foreman S, Morgan JE, Zagorevsky D, Malamy MH, Comstock LE, Barquera B.J Bacteriol. 2023 Jan 26
High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients. Nguyen CL, Markey KA, Miltiadous O, Dai A, Waters N, Sadeghi K, Fei T, Shouval R, Taylor BP, Liao C, Slingerland JB, Slingerland AE, Clurman AG, Maloy MA, Bohannon L, Giardina PA, Brereton DG, Armijo GK, Fontana E, Gradissimo A, Gyurkocza B, Sung AD, Chao NJ, Devlin SM, Taur Y, Giralt SA, Perales MA, Xavier JB, Pamer EG, Peled JU, Gomes ALC, van den Brink MRM. Cell. 2023 Jun 8
Corrigendum: A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia. Asare PT, Lee CH, Hürlimann V, Teo Y, Cuénod A, Akduman N, Gekeler C, Afrizal A, Corthesy M, Kohout C, Thomas V, de Wouters T, Greub G, Clavel T, Pamer EG, Egli A, Maier L, Vonaesch P.Front Microbiol. 2023 May 22