Publications

Distinct trajectories of urbanization shape the human gut microbiome across South Asia.  Ramachandran SL, Pasupuleti N, Abdill RJ, Adikari G, Ahlawat B, Blekhman R, Burgo V, Davenport ER, Dwivedi A, Gupta S, Ijinu TP, Jamir T, Karu R, Kaushik A, Komarabathini JM, Laithangpuii, Lalzarliana J, Norbu T, Pautu T, Pawar K, Raman AS, Ramaswamy R, Ranasinghe R, Rashmi, Sasidharan SP, Satheesh T, Shaji S, Shapiro JW, Singh E, Singson V, Sundararajan A, Kamani H T, Tetso D, Urban Aragon JA, Welikala AHJ, Yhome RR, Rai N, Raghavan M. Gut Microbes. 2026 Dec 31;  Epub 2026 Jul 14

Intracellular acidification by microbiota-derived valeric acid facilitates trans-kingdom ecology limiting Candida parapsilosis colonization.  Yasuma-Mitobe K, Liao C, Németh T, Byrne K, Billips A, Faustino Ramos RJJ, Salinas CN, Chan E, Perissinoto M, Adami-Sampson S, Salman A, Sidebottom AM, Plitas G, Butler G, Cross JR, Pamer EG, Gácser A, Xavier JB, Hohl TM. Cell Host Microbe. 2026 Jul 8

Host metabolism can produce many indoles and phenols independently of the microbiome.  AbuSalim JE, Olszewski K, Youssef S, Mitchell SJ, Hunter CJ, Little J, Sidebottom A, Boyer JA, Knutson SD, Samarah LZ, MacArthur MR, Henneberg AL, Ryseck RP, Opitz CA, MacMillan DWC, Donia MS, Pamer EG, Imam S, Lehmann CJ, Odenike O, Rabinowitz JD.  Nat Metab. 2026 Jun 23

Microbiome histidine competition mediates dietary control of systemic imidazole propionate.  Bernardino PN, Jacoby C, Younker IT, Stemczynski J, Little AS, Mullowney MW, Brunner TH, Ghali J, Fardin M, Rose K, Ramaswamy R, Sidebottom AM, Tersey SA, Pamer EG, Mirmira RG, Mimee M, Light SH.  bioRxiv [Preprint]. 2026 Jun 23

Practical Considerations for the Use of Semaglutide in MASH.  Odenwald MA, Rinella ME.  Am J Gastroenterol. 2026 Jun 1

Gut Microbiota-derived Acetate Safeguards the Colonic Epithelial Acetyl-CoA Reserve to Avert Colonic Senescence.  Du J, Sarkar R, Wang L, Tabrizi RA, Gao L, Li Y, Sidebottom A, Shah H, Chen M, Odenwald M, Li YC. bioRxiv [Preprint]. 2026 May 19

The intestinal microbiota impacts nutritional immunity and resistance to Acinetobacter baumannii pneumonia. Green ER, Negretti NM, Brunner TH, Shealy NG, Moser FA, Drury SL, Traina KA, Reyes Ruiz VM, Yang TS, Lehmann CJ, Byndloss MX, van de Plas R, Zackular JP, Light SH, Sucre JMS, Skaar EP.  Proc Natl Acad Sci U S A. 2026 Apr 28

High-throughput analyses of Phocaeicola vulgatus reveal fitness determinants for gut colonization and during colitis.  Elmekki NM, Coyne MJ, Flores K, García-Bayona L, Comstock LE.  Gut Microbes. 2026 Dec 31; Epub 2026 Apr 23.

Antagonism by the type VI secretion system of Bacteroides fragilis is controlled by a TetR family regulator and released small molecule.  Tuzlak L, Pappas TE, Coyne MJ, Sheahan ML, Burgo V, Rice PA, Comstock LE. Proc Natl Acad Sci U S A. 2026 Apr 14 

Physiological architecture and evolutionary origins of cellular adaptability.  Dea A, Lan Y, Doran BA, Ali A, Igarashi MG, Dyer L, Aksianiuk V, Pincus D, Raman AS. bioRxiv [Preprint]. 2026 Apr 11

Uncovering bacterial pseudaminylation with pan-specific antibody tools.  Tang AH, Soler NM, Karlic KI, Corcilius L, Clarke-Shepperson CE, Lehmann C, Debowski AW, Dale AL, Zavan L, Cielesh M, Adewale AP, Moulton KD, Li L, Guan C, McCrory C, Kaparakis-Liaskos M, Howden BP, Sherry NL, Wei R, Li X, Hall RM, Kenyon JJ, Wakim LM, Short FL, Dube DH, Cordwell SJ, Larance M, Stubbs KA, Carter GP, Scott NE, Goddard-Borger ED, Payne RJ.  Nat Chem Biol. 2026 Apr

Discovery of a secreted Bacteroides fragilis mucinase that cleaves mucins with bis-T O-glycans through a carbohydrate binding module-dependent mechanism.  Narimatsu Y, Pleguezuelos-Manzano C, Hornikx D, Goerdeler F, Jaroentomeechai T, Flores K, Narimatsu S, Boot C, Hansen L, Durbesson F, Vincentelli R, Comstock L, Clevers H, Taleb V, Corzana F, Henrissat B, Clausen H, Hurtado-Guerrero R, Büll C.  Gut Microbes. 2026 Dec 31; Epub 2026 Mar 19

Ribosomal Translation and Display Selection of Cyclic Glycopeptides through Genetic Reprogramming.  Johansen-Leete J, Zhong Y, Cui B, Sebold BC, Kambanis L, Clarke-Shepperson CE, Lehmann C, Toby Mak KH, Tang AH, Burchfield J, Becker W, Perdomo J, McDonald DM, Corcilius L, Passioura T, Passam FH, Ford DJ, Payne RJ.  J Am Chem Soc. 2026 Mar 18

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, Berdy B, Bahunde JR, Girard C, Lehtimäki J, Mabulla AZP, Mwikarago IE, Nartey YA, Nguyen LTT, Onyekwere CA, Roberts LR, Shapiro BJ, Vatanen T, Comstock LE, Alm EJ, Dedon PC.  Nat Commun. 2026 Jan 22

Fecal butyrate and deoxycholic acid quantitation for rapid assessment of the gut microbiome.  Mullowney MW, Moran A, Hernandez A, McMillin M, Rose AR, Moran D, Little J, Nguyen AB, Patel BK, Lehmann CJ, Odenwald MA, Pamer EG, Yeo KJ, Sidebottom AM. PLoS One. 2026 Jan 9

Post-COVID impairment of memory T cell responses to community-acquired pathogens can be rectified by activating cellular metabolism.  Carroll DD, Cira K, Archer J, Shapiro J, Pen UY, Tieri D, Leonor L, Roofchayee ND, Yee SS, Wahab M, Koralnik IJ, Alverdy JC, Raman AS, Visvabharathy L.  bioRxiv [Preprint]. 2026 Jan 2

Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.  Oliveira RA, McSpadden E, Pandey B, Lee K, Yousef M, Chen RY, Triebold C, Haro F, Aksianiuk V, Patel R, Shriram K, Ramanujam R, Kuehn S, Raman AS. bioRxiv [Preprint]. 2025 Dec 31

Lessons from the model gut Bacteroidales Bacteroides fragilis and Bacteroides thetaiotaomicron and future opportunities.  Comstock LE.  J Bacteriol. 2025 Nov 20

Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway.  Jacoby C, Scorza K, Ecker L, Nol Bernardino P, Little AS, McMillin M, Ramaswamy R, Sundararajan A, Sidebottom AM, Lin H, Dufault-Thompson K, Hall B, Jiang X, Light SH. Cell Host Microbe. 2025 Nov 12

DNA-utilization loci enable exogenous DNA metabolism in gut Bacteroidales.  Sharan D, Nurek A, Stemczynski J, Turan K, Little AS, Coyne MJ, McMillin M, Sidebottom AM, Comstock LE, Light SH.  Proc Natl Acad Sci U S A. 2025 Sep 23

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

ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images.Wu E, Bieniosek M, Wu Z, Thakkar N, Charville GW, Makky A, Schürch CM, Huyghe JR, Peters U, Li CI, Li L, Giba H, Behera V, Raman A, Trevino AE, Mayer AT, Zou J.  Nat Commun. 2025 Aug 16

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

Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare.  Kennedy NW, Comstock LE.Cell Host Microbe. 2024 Jun 12

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

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, Ramanswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH.  Nat Microbiol. 2024 Jan

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

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

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

Stickland metabolism in the gut.  Little AS, Light SH.  Nat Microbiol. 2022 May

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. 2022 Dec 7

A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response.  Evans JC, McEneany VL, Coyne MJ, Caldwell EP, Sheahan ML, Von SS, Coyne EM, Tweten RK, Comstock LE.  Nat Commun. 2022 Jul 23

Analysis of Effector and Immunity Proteins of the GA2 Type VI Secretion Systems of Gut Bacteroidales.  Bao H, Coyne MJ, García-Bayona L, Comstock LE.J Bacteriol. 2022 Jul 19

Listeria monocytogenes two component system PieRS regulates secretion chaperones PrsA1 and PrsA2 and enhances bacterial translocation across the intestine  Cahoon LA, Alejandro-Navarreto X, Gururaja AN, Light SH, Alonzo F, Anderson WF, Freitag NE. Mol Microbiol. 2022 Sep

A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes.  Bousbaine D, Fisch LI, London M, Bhagchandani P, Rezende de Castro TB, Mimee M, Olesen S, Reis BS, VanInsberghe D, Bortolatto J, Poyet M, Cheloha RW, Sidney J, Ling J, Gupta A, Lu TK, Sette A, Alm EJ, Moon JJ, Victora GD, Mucida D, Ploegh HL, Bilate AM.  Science. 2022 Aug 5

Host happy hour: Phage cocktail targets IBD-associated microbes.  Fuerte-Stone J, Mimee M.Cell Host Microbe. 2022 Oct 12

Proceedings from the 3rd International Conference on Microbiome Engineering.  McClure S, Enam F, Arnold J, Mimee M.  Biotechnol Prog. 2022 May

Viral hepatitis: Past, present, and future.  Odenwald MA, Paul S.World J Gastroenterol. 2022 Apr 14

Tight junction proteins occludin and ZO-1 as regulators of epithelial proliferation and survival.  Kuo WT, Odenwald MA, Turner JR, Zuo L.Ann N Y Acad Sci. 2022 Aug

Vedolizumab for perianal fistulizing Crohn's disease: systematic review and meta-analysis.  Ayoub F, Odenwald M, Micic D, Dalal SR, Pekow J, Cohen RD, Rubin DT, Sakuraba A.  Intest Res. 2022 Apr

PRO: Coronavirus disease 2019 vaccination should be mandatory for liver transplant candidates.  Gampa A, Odenwald MA, Pillai A.  Clin Liver Dis (Hoboken). 2022 Nov 25

Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure. Stutz MR, Dylla NP, Pearson SD, Lecompte-Osorio P, Nayak R, Khalid M, Adler E, Boissiere J, Lin H, Leiter W, Little J, Rose A, Moran D, Mullowney MW, Wolfe KS, Lehmann C, Odenwald M, De La Cruz M, Giurcanu M, Pohlman AS, Hall JB, Chaubard JL, Sundararajan A, Sidebottom A, Kress JP, Pamer EG, Patel BK.  Nat Commun. 2022 Nov 3

The Practice of Retransplantation for Recurrent Alcohol-associated Liver Disease in the United States Is Uncommon With Acceptable Outcomes.  Cotter TG, Odenwald MA, Lieber SR, Rich NE, Im G, Charlton M, Singal AG, Mitchell MC.Transplant Direct. 2022 Feb 11

Listeria monocytogenes requires cellular respiration for NAD+ regeneration and pathogenesis.  Rivera-Lugo R, Deng D, Anaya-Sanchez A, Tejedor-Sanz S, Tang E, Reyes Ruiz VM, Smith HB, Titov DV, Sauer JD, Skaar EP, Ajo-Franklin CM, Portnoy DA, Light SH.  Elife. 2022 Apr 5

Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes.  Pfister CA, Light SH, Bohannan B, Schmidt T, Martiny A, Hynson NA, Devkota S, David L, Whiteson K.  mSystems. 2022 Feb 22

RibU is an essential determinant of Listeria pathogenesis that mediates acquisition of FMN and FAD during intracellular growth.  Rivera-Lugo R, Light SH, Garelis NE, Portnoy DA.  Proc Natl Acad Sci U S A. 2022 Mar 29

Preservation solutions for static cold storage in donation after circulatory death and donation after brain death liver transplantation in the United States.  Cotter TG, Odenwald MA, Perez-Gutierrez A, Jayant K, DiSabato D, Charlton M, Fung J.  Liver Transpl. 2022 Sep

Microbiome-based therapeutics.  Sorbara MT, Pamer EG. Nat Rev Microbiol. 2022 Jun

A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response.  Evans JC, McEneany VL, Coyne MJ, Caldwell EP, Sheahan ML, Von SS, Coyne EM, Tweten RK, Comstock LE.Nat Commun. 2022 Jul 23

Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy.  Smith M, Dai A, Ghilardi G, Amelsberg KV, Devlin SM, Pajarillo R, Slingerland JB, Beghi S, Herrera PS, Giardina P, Clurman A, Dwomoh E, Armijo G, Gomes ALC, Littmann ER, Schluter J, Fontana E, Taur Y, Park JH, Palomba ML, Halton E, Ruiz J, Jain T, Pennisi M, Afuye AO, Perales MA, Freyer CW, Garfall A, Gier S, Nasta S, Landsburg D, Gerson J, Svoboda J, Cross J, Chong EA, Giralt S, Gill SI, Riviere I, Porter DL, Schuster SJ, Sadelain M, Frey N, Brentjens RJ, June CH, Pamer EG, Peled JU, Facciabene A, van den Brink MRM, Ruella M. Nat Med. 2022 Apr

Translating Microbiome Research From and To the Clinic.  Zhang ZJ, Lehmann CJ, Cole CG, Pamer EG. Annu Rev Microbiol. 2022 Sep 8

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.  Yan J, Liao C, Taylor BP, Fontana E, Amoretti LA, Wright RJ, Littmann ER, Dai A, Waters N, Peled JU, Taur Y, Perales MA, Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Schluter J, Xavier JB.Sci Data. 2022 May 18

Author Correction: Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy.  Smith M, Dai A, Ghilardi G, Amelsberg KV, Devlin SM, Pajarillo R, Slingerland JB, Beghi S, Herrera PS, Giardina P, Clurman A, Dwomoh E, Armijo G, Gomes ALC, Littmann ER, Schluter J, Fontana E, Taur Y, Park JH, Palomba ML, Halton E, Ruiz J, Jain T, Pennisi M, Afuye AO, Perales MA, Freyer CW, Garfall A, Gier S, Nasta S, Landsburg D, Gerson J, Svoboda J, Cross J, Chong EA, Giralt S, Gill SI, Riviere I, Porter DL, Schuster SJ, Sadelain M, Frey N, Brentjens RJ, June CH, Pamer EG, Peled JU, Facciabene A, van den Brink MRM, Ruella M. Nat Med. 2022 Oct 17

Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes  Zaydman MA, Little AS, Haro F, Aksianiuk V, Buchser WJ, DiAntonio A, Gordon JI, Milbrandt J, Raman AS. Elife. 2022 Aug 17

Immediate Effect of Mechanical Ventilation Mode and Sedative Infusion on Measured Diaphragm Thickness.  Pearson SD, Lin J, Stutz MR, Lecompte-Osorio P, Pohlman AS, Wolfe KS, Hall JB, Kress JP, Patel BK.Ann Am Thorac Soc. 2022 Sep

Identification of a Novel EIF2AK Variant and Genetics-Assisted Approach to Diagnosis of Pulmonary Capillary Hemangiomatosis.  Kimmig LM, Stutz MR, Husain AN, Bag R.Lung. 2022 Apr

Bacteroidetocins Target the Essential Outer Membrane Protein BamA of Bacteroidales Symbionts and Pathogens.  Matano LM, Coyne MJ, García-Bayona L, Comstock LE. mBio. 2021 Oct 26

Mobile Type VI secretion system loci of the gut Bacteroidales display extensive intra-ecosystem transfer, multi-species spread and geographical clustering.  García-Bayona L, Coyne MJ, Comstock LE. PLoS Genet. 2021 Apr 26

A Combination of Structural, Genetic, Phenotypic and Enzymatic Analyses Reveals the Importance of a Predicted Fucosyltransferase to Protein O-Glycosylation in the Bacteroidetes.  Tomek MB, Janesch B, Braun ML, Taschner M, Figl R, Grünwald-Gruber C, Coyne MJ, Blaukopf M, Altmann F, Kosma P, Kählig H, Comstock LE, Schäffer C .Biomolecules. 2021 Nov 30

Engineered yeast tune down gut inflammation  Mimee M, Nagler C. Nat Med. 2021 Jul

Searching for the Secret of Stickiness: How Biofilms Adhere to Surfaces.  Jiang Z, Nero T, Mukherjee S, Olson R, Yan J. Front Microbiol. 2021 Jul 8

Another battle won in the phage-host arms race: Pseudomonas phage blocks quorum sensing regulator LasR.  van Kessel JC, Mukherjee S. Mol Cell. 2021 Feb 4

The Tight Junction Protein ZO-1 Is Dispensable for Barrier Function but Critical for Effective Mucosal Repair.  Kuo WT, Zuo L, Odenwald MA, Madha S, Singh G, Gurniak CB, Abraham C, Turner JR.Gastroenterology. 2021 Dec

A Rare Case of an Aggressive Liver Tumor.  Odenwald MA, Aronsohn A, Peeraphatidit TB.Clin Gastroenterol Hepatol. 2021 Jul

Small Bowel Giant Polypoid Gastric Heterotopia Causing Refractory Iron Deficiency Anemia.  Ihionkhan EO, Odenwald MA, Ayoub F, Kumar SD, McDonald EK 4th.ACG Case Rep J. 2021 Jun 30

"Raising HOPE": Improved Outcomes for HIV/HCV-coinfected Liver Transplant Recipients in the Direct-acting Antiviral Era.  Cotter TG, Wang J, Lieber SR, Odenwald MA, Rich NE, Marrero JA, Singal AG, Mitchell MC, Aronsohn A, Charlton M, Fung J.Transplant Direct. 2021 Jun 8

Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation.  Becattini S, Sorbara MT, Kim SG, Littmann EL, Dong Q, Walsh G, Wright R, Amoretti L, Fontana E, Hohl TM, Pamer EG.Cell Host Microbe. 2021 Mar 10

Fecal microbiota diversity disruption and clinical outcomes after auto-HCT: a multicenter observational study.  Khan N, Lindner S, Gomes ALC, Devlin SM, Shah GL, Sung AD, Sauter CS, Landau HJ, Dahi PB, Perales MA, Chung DJ, Lesokhin AM, Dai A, Clurman A, Slingerland JB, Slingerland AE, Brereton DG, Giardina PA, Maloy M, Armijo GK, Rondon-Clavo C, Fontana E, Bohannon L, Ramalingam S, Bush AT, Lew MV, Messina JA, Littmann E, Taur Y, Jenq RR, Chao NJ, Giralt S, Markey KA, Pamer EG, van den Brink MRM, Peled JU. Blood. 2021 Mar 18

Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients.  Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG, Schluter J, Xavier JB. Sci Data. 2021 Mar 2

TAM mediates adaptation of carbapenem-resistant Klebsiella pneumoniae to antimicrobial stress during host colonization and infection.  Jung HJ, Sorbara MT, Pamer EG. PLoS Pathog. 2021 Feb 8

Author Correction: Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients.  Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG, Schluter J, Xavier JB.Sci Data. 2021 Apr 23

Compositional Flux Within the Intestinal Microbiota and Risk for Bloodstream Infection With Gram-negative Bacteria.  Stoma I, Littmann ER, Peled JU, Giralt S, van den Brink MRM, Pamer EG, Taur Y.Clin Infect Dis. 2021 Dec 6

Cervicovaginal bacterial communities in reproductive-aged Tanzanian women with Schistosoma mansoni, Schistosoma haematobium, or without schistosome infection.  Bullington BW, Lee MH, Mlingi J, Paul N, Aristide C, Fontana E, Littmann ER, Mukerebe C, Shigella P, Kashangaki P, Kalluvya SE, de Dood CJ, van Dam GJ, Corstjens PLAM, Fitzgerald DW, Pamer EG, Downs JA. ISME J. 2021 May

A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains.  Miles-Jay A, Young VB, Pamer EG, Savidge TC, Kamboj M, Garey KW, Snitkin ES. Microb Genom. 2021 Jun

A Microbiota-Directed Food Intervention for Undernourished Children.  Chen RY, Mostafa I, Hibberd MC, Das S, Mahfuz M, Naila NN, Islam MM, Huq S, Alam MA, Zaman MU, Raman AS, Webber D, Zhou C, Sundaresan V, Ahsan K, Meier MF, Barratt MJ, Ahmed T, Gordon JI. N Engl J Med. 2021 Apr 22

Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans.  Delannoy-Bruno O, Desai C, Raman AS, Chen RY, Hibberd MC, Cheng J, Han N, Castillo JJ, Couture G, Lebrilla CB, Barve RA, Lombard V, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Kirbach K, Wilmot T, Heath AC, Klein S, Barratt MJ, Gordon JI. Nature. 2021 Jul

Early Rehabilitation Feasibility in a COVID-19 ICU.  Stutz MR, Leonhard AG, Ward CM, Pearson SD, Osorio PL, Herbst PR, Wolfe KS, Pohlman AS, Hall JB, Kress JP, Patel BK. Chest. 2021 Dec

ICU mobility and improved outcomes: still searching for the Holy Grail.  Stutz MR, Kress JP, Wolfe KS. Thorax. 2021 Jul 

Bedside estimates of dead space using end-tidal CO2 are independently associated with mortality in ARDS.  Lecompte-Osorio P, Pearson SD, Pieroni CH, Stutz MR, Pohlman AS, Lin J, Hall JB, Htwe YM, Belvitch PG, Dudek SM, Wolfe K, Patel BK, Kress JP.Crit Care. 2021 Sep 15

Utilizing Ribose Compounds: How Bacteroides PUL It Off.  García-Bayona L, Comstock LE. Cell Host Microbe. 2020 Jan 8

The evolution of tit-for-tat in bacteria via the type VI secretion system.  Smith WPJ, Brodmann M, Unterweger D, Davit Y, Comstock LE, Basler M, Foster KR. Nat Commun. 2020 Oct 26

The evolution of the type VI secretion system as a disintegration weapon.  Smith WPJ, Vettiger A, Winter J, Ryser T, Comstock LE, Basler M, Foster KR. PLoS Biol. 2020 May 26

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis.  Ben-Assa N, Coyne MJ, Fomenkov A, Livny J, Robins WP, Muniesa M, Carey V, Carasso S, Gefen T, Jofre J, Roberts RJ, Comstock LE, Geva-Zatorsky N. Nucleic Acids Res. 2020 Nov 4

Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts.  García-Bayona L, Coyne MJ, Hantman N, Montero-Llopis P, Von SS, Ito T, Malamy MH, Basler M, Barquera B, Comstock LE. Proc Natl Acad Sci U S A. 2020 Sep 29

Genetic and Biochemical Analysis of Anaerobic Respiration in Bacteroides fragilis and Its Importance In Vivo.  Ito T, Gallegos R, Matano LM, Butler NL, Hantman N, Kaili M, Coyne MJ, Comstock LE, Malamy MH, Barquera B. mBio. 2020 Feb 4

Hepatotoxicity From Immune Checkpoint Inhibitors: A Systematic Review and Management Recommendation.  Peeraphatdit TB, Wang J, Odenwald MA, Hu S, Hart J, Charlton MR. Hepatology. 2020 Jul

A Rare Case of an Aggressive Liver Tumor.  Odenwald MA, Aronsohn A, Peeraphatidit TB. Clin Gastroenterol Hepatol. 2021 Jul

Quantification of Proliferative and Dead Cells in Enteroids.  Li HS, Xu SF, Sheng JY, Jiang ZH, Wang J, Ding N, Wang T, Odenwald MA, Turner JR, He WQ, Xu H, Zha JM. J Vis Exp. 2020 Jan 31

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation.  Peled JU, Gomes ALC, Devlin SM, Littmann ER, Taur Y, Sung AD, Weber D, Hashimoto D, Slingerland AE, Slingerland JB, Maloy M, Clurman AG, Stein-Thoeringer CK, Markey KA, Docampo MD, Burgos da Silva M, Khan N, Gessner A, Messina JA, Romero K, Lew MV, Bush A, Bohannon L, Brereton DG, Fontana E, Amoretti LA, Wright RJ, Armijo GK, Shono Y, Sanchez-Escamilla M, Castillo Flores N, Alarcon Tomas A, Lin RJ, Yáñez San Segundo L, Shah GL, Cho C, Scordo M, Politikos I, Hayasaka K, Hasegawa Y, Gyurkocza B, Ponce DM, Barker JN, Perales MA, Giralt SA, Jenq RR, Teshima T, Chao NJ, Holler E, Xavier JB, Pamer EG, van den Brink MRM. N Engl J Med. 2020 Feb 27

Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity.  Sorbara MT, Littmann ER, Fontana E, Moody TU, Kohout CE, Gjonbalaj M, Eaton V, Seok R, Leiner IM, Pamer EG. Cell Host Microbe. 2020 Jul 8

The microbe-derived short-chain fatty acids butyrate and propionate are associated with protection from chronic GVHD.  Markey KA, Schluter J, Gomes ALC, Littmann ER, Pickard AJ, Taylor BP, Giardina PA, Weber D, Dai A, Docampo MD, Armijo GK, Slingerland AE, Slingerland JB, Nichols KB, Brereton DG, Clurman AG, Ramos RJ, Rao A, Bush A, Bohannon L, Covington M, Lew MV, Rizzieri DA, Chao N, Maloy M, Cho C, Politikos I, Giralt S, Taur Y, Pamer EG, Holler E, Perales MA, Ponce DM, Devlin SM, Xavier J, Sung AD, Peled JU, Cross JR, van den Brink MRM. Blood. 2020 Jul 2

Enhancing mucosal immunity by transient microbiota depletion.  Becattini S, Littmann ER, Seok R, Amoretti L, Fontana E, Wright R, Gjonbalaj M, Leiner IM, Plitas G, Hohl TM, Pamer EG. Nat Commun. 2020 Sep 8

Antibiotic Degradation by Commensal Microbes Shields Pathogens.  Gjonbalaj M, Keith JW, Do MH, Hohl TM, Pamer EG, Becattini S. Infect Immun. 2020 Mar 23

Impact of TCR Diversity on the Development of Transplanted or Chemically Induced Tumors.  Schreiber K, Karrison TG, Wolf SP, Kiyotani K, Steiner M, Littmann ER, Pamer EG, Kammertoens T, Schreiber H, Leisegang M. Cancer Immunol Res. 2020 Feb

Monocyte Reconstitution and Gut Microbiota Composition after Hematopoietic Stem Cell Transplantation.  Morjaria S, Zhang AW, Kim S, Peled JU, Becattini S, Littmann ER, Pamer EG, Abt MC, Perales MA. Clin Hematol Int. 2020 Nov 23

Impact of Antibiotic-Resistant Bacteria on Immune Activation and Clostridioides difficile Infection in the Mouse Intestine.  Keith JW, Dong Q, Sorbara MT, Becattini S, Sia JK, Gjonbalaj M, Seok R, Leiner IM, Littmann ER, Pamer EG. Infect Immun. 2020 Mar 23

Intestinal Dysbiosis and Markers of Systemic Inflammation in Viscerally and Generally Obese Persons Living With HIV.  Gogokhia L, Taur Y, Juluru K, Yagan N, Zhu YS, Pamer E, Glesby MJ. J Acquir Immune Defic Syndr. 2020 Jan 1

Outbreaks of Typhlocolitis Caused by Hypervirulent Group ST1 Clostridioides difficile in Highly Immunocompromised Strains of Mice.  Ma KGL, Lertpiriyapong K, Piersigilli A, Dobtsis I, Wipf JRK, Littmann ER, Leiner I, Pamer EG, Ricart Arbona RJ, Lipman NS. Comp Med. 2020 Jun 1

Understanding the mother-breastmilk-infant "triad".  Bode L, Raman AS, Murch SH, Rollins NC, Gordon JI. Science. 2020 Mar 6

Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum.  López García de Lomana A, Kusebauch U, Raman AV, Pan M, Turkarslan S, Lorenzetti APR, Moritz RL, Baliga NS. mSystems. 2020 Jul 28

Identifying determinants of bacterial fitness in a model of human gut microbial succession.  Feng L, Raman AS, Hibberd MC, Cheng J, Griffin NW, Peng Y, Leyn SA, Rodionov DA, Osterman AL, Gordon JI. Proc Natl Acad Sci U S A. 2020 Feb 4

Type VI Secretion Systems and the Gut Microbiota.  Coyne MJ, Comstock LE. Microbiol Spectr. 2019 Mar

A family of anti-Bacteroidales peptide toxins wide-spread in the human gut microbiota.  Coyne MJ, Béchon N, Matano LM, McEneany VL, Chatzidaki-Livanis M, Comstock LE. Nat Commun. 2019 Aug 1

Identification of a Fifth Antibacterial Toxin Produced by a Single Bacteroides fragilis Strain.  Shumaker AM, Laclare McEneany V, Coyne MJ, Silver PA, Comstock LE. J Bacteriol. 2019 Mar 26

Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota.  García-Bayona L, Comstock LE. mBio. 2019 Aug 13

Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis.  Yehl K, Lemire S, Yang AC, Ando H, Mimee M, Torres MT, de la Fuente-Nunez C, Lu TK. Cell. 2019 Oct 3

Cell-based biosensors for immunology, inflammation, and allergy.  Inda ME, Mimee M, Lu TK. J Allergy Clin Immunol. 2019 Sep

Bacterial quorum sensing in complex and dynamically changing environments.  Mukherjee S, Bassler BL. Nat Rev Microbiol. 2019 Jun

Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling.  Yan J, Moreau A, Khodaparast S, Perazzo A, Feng J, Fei C, Mao S, Mukherjee S, Košmrlj A, Wingreen NS, Bassler BL, Stone HA. Adv Mater. 2019 Jan

Photosensing and quorum sensing are integrated to control Pseudomonas aeruginosa collective behaviors.  Mukherjee S, Jemielita M, Stergioula V, Tikhonov M, Bassler BL. PLoS Biol. 2019 Dec 12

Interleukin 22 Expands Transit-Amplifying Cells While Depleting Lgr5+ Stem Cells via Inhibition of Wnt and Notch Signaling.  Zha JM, Li HS, Lin Q, Kuo WT, Jiang ZH, Tsai PY, Ding N, Wu J, Xu SF, Wang YT, Pan J, Zhou XM, Chen K, Tao M, Odenwald MA, Tamura A, Tsukita S, Turner JR, He WQ. Cell Mol Gastroenterol Hepatol. 2019

Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus.  Kim SG, Becattini S, Moody TU, Shliaha PV, Littmann ER, Seok R, Gjonbalaj M, Eaton V, Fontana E, Amoretti L, Wright R, Caballero S, Wang ZX, Jung HJ, Morjaria SM, Leiner IM, Qin W, Ramos RJJF, Cross JR, Narushima S, Honda K, Peled JU, Hendrickson RC, Taur Y, van den Brink MRM, Pamer EG. Nature. 2019 Aug

Enlisting commensal microbes to resist antibiotic-resistant pathogens.  Keith JW, Pamer EG. J Exp Med. 2019 Jan 7

Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them.  Sorbara MT, Pamer EG. Mucosal Immunol. 2019 Jan

Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification.  Sorbara MT, Dubin K, Littmann ER, Moody TU, Fontana E, Seok R, Leiner IM, Taur Y, Peled JU, van den Brink MRM, Litvak Y, Bäumler AJ, Chaubard JL, Pickard AJ, Cross JR, Pamer EG. J Exp Med. 2019 Jan 7

Gut microbiota dysbiosis and diarrhea in kidney transplant recipients.  Lee JR, Magruder M, Zhang L, Westblade LF, Satlin MJ, Robertson A, Edusei E, Crawford C, Ling L, Taur Y, Schluter J, Lubetzky M, Dadhania D, Pamer E, Suthanthiran M. Am J Transplant. 2019 Feb

Diversification and Evolution of Vancomycin-Resistant Enterococcus faecium during Intestinal Domination.  Dubin KA, Mathur D, McKenney PT, Taylor BP, Littmann ER, Peled JU, van den Brink MRM, Taur Y, Pamer EG, Xavier JB. Infect Immun. 2019 Jun 20

Intestinal Bile Acids Induce a Morphotype Switch in Vancomycin-Resistant Enterococcus that Facilitates Intestinal Colonization.  McKenney PT, Yan J, Vaubourgeix J, Becattini S, Lampen N, Motzer A, Larson PJ, Dannaoui D, Fujisawa S, Xavier JB, Pamer EG. Cell Host Microbe. 2019 May 8

Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection.  Magruder M, Sholi AN, Gong C, Zhang L, Edusei E, Huang J, Albakry S, Satlin MJ, Westblade LF, Crawford C, Dadhania DM, Lubetzky M, Taur Y, Littman E, Ling L, Burnham P, De Vlaminck I, Pamer E, Suthanthiran M, Lee JR. Nat Commun. 2019 Dec 4

Minimal residual disease negativity in multiple myeloma is associated with intestinal microbiota composition.  Pianko MJ, Devlin SM, Littmann ER, Chansakul A, Mastey D, Salcedo M, Fontana E, Ling L, Tavitian E, Slingerland JB, Slingerland AE, Clurman A, Gomes ALC, Taur Y, Pamer EG, Peled JU, van den Brink MRM, Landgren O, Lesokhin AM. Blood Adv. 2019 Jul 9

Correction: Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them.  Sorbara MT, Pamer EG. Mucosal Immunol. 2019 May

A sparse covarying unit that describes healthy and impaired human gut microbiota development.  Raman AS, Gehrig JL, Venkatesh S, Chang HW, Hibberd MC, Subramanian S, Kang G, Bessong PO, Lima AAM, Kosek MN, Petri WA Jr, Rodionov DA, Arzamasov AA, Leyn SA, Osterman AL, Huq S, Mostafa I, Islam M, Mahfuz M, Haque R, Ahmed T, Barratt MJ, Gordon JI. Science, 2019 Jul 12