Publications

Author Correction: Evolution of immune genes is associated with the Black Death. Klunk J, Vilgalys TP, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB.Nature. 2025 Jan 15

β-Glucan reprograms neutrophils to promote disease tolerance against influenza A virus. Khan N, Tran KA, Chevre R, Locher V, Richter M, Sun S, Sadeghi M, Pernet E, Herrero-Cervera A, Grant A, Saif A, Downey J, Kaufmann E, Khader SA, Joubert P, Barreiro LB, Yipp BG, Soehnlein O, Divangahi M.Nat Immunol. 2025 Jan 8

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

Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity. Saba J, Flores K, Marshall B, Engstrom MD, Peng Y, Garje AS, Comstock LE, Landick R.Nat Commun. 2024 Dec 30

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. 2024 Nov 13

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. 2024 Oct 24

PcdA promotes orthogonal division plane selection in Staphylococcus aureus. Ramos-León F, Anjuwon-Foster BR, Anantharaman V, Updegrove TB, Ferreira CN, Ibrahim AM, Tai CH, Kruhlak MJ, Missiakas DM, Camberg JL, Aravind L, Ramamurthi KS. 2024 Oct 28

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. 2024 Oct 9

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. 2024 Sep 24

Gut microbes fend off harmful bacteria by depriving them of nutrients. Pamer EG. Nature. 2024 Sep

Mast cells promote pathology and susceptibility in tuberculosis. Gupta A, Taneja V, Moreno JR, Abhimanyu, Ahmed M, Naqvi N, Chauhan KS, de León DT, Ramírez-Martínez G, Jiménez-Alvarez L, Luna-Rivero C, Zuniga J, Kaushal D, Khader SA. 2024 Sep 9

Novel antibody language model accelerates IgG screening and design for broad-spectrum antiviral therapy. Almubarak HF, Tan W, Hoffmann AD, Sun Y, Wei J, El-Shennawy L, Squires JR, Dashzeveg NK, Simonton B, Jia Y, Iyer R, Xu Y, Nicolaescu V, Elli D, Randall GC, Schipma MJ, Swaminathan S, Ison MG, Liu H, Fang D, Shen Y. 2024 Aug 20

Restriction of arginine induces antibiotic tolerance in Staphylococcus aureus. Freiberg JA, Reyes Ruiz VM, Gimza BD, Murdoch CC, Green ER, Curry JM, Cassat JE, Skaar EP. 2024 Aug 7

Novel Antibody-Based Protection/Therapeutics in Staphylococcus aureus. Chen X, Missiakas D.Annu Rev Microbiol. 2024 Aug 15

Restriction of arginine induces antibiotic tolerance in Staphylococcus aureus. Freiberg JA, Reyes Ruiz VM, Gimza BD, Murdoch CC, Green ER, Curry JM, Cassat JE, Skaar EP. 2024 Aug 7

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

Development of Luminescent Biosensors for Calprotectin. Lan T, Slezak T, Pu J, Zinkus-Boltz J, Adhikari S, Pekow JR, Taneja V, Zuniga J, Gómez-García IA, Regino-Zamarripa N, Ahmed M, Khader SA, Rubin DT, Kossiakoff AA, Dickinson BC.ACS Chem Biol. 2024 Jun 21

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

Vaccination with Mincle agonist UM-1098 and mycobacterial antigens induces protective Th1 and Th17 responses Rungelrath V, Ahmed M, Hicks L, Miller SM, Ryter KT, Montgomery K, Ettenger G, Riffey A, Abdelwahab WM, Khader SA, Evans JT.NPJ Vaccines. 2024 Jun 6

Deficiency in non-classical major histocompatibility class II-like molecule, H2-O confers protection against Staphylococcus aureus in mice. Cullum E, Perez-Betancourt Y, Shi M, Gkika  E, Schneewind O, Missiakas D, Golovkina T.PLoS Pathog. 2024 Jun 6

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

SARS-CoV-2 ORF3a drives dynamic dense body formation for optimal viral infectivity. Hartmann S, Radochonski L, Ye C, Martinez-Sobrido L, Chen J.Res Sq. 2024 May 17

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. 2024 May 7

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. 2024 Apr 29

A protective role for type I interferon signaling following infection with Mycobacterium tuberculosis carrying the rifampicin drug resistance-conferring RpoB mutation H445Y.Bobba S, Chauhan KS, Akter S, Das S, Mittal E, Mathema B, Philips JA, Khader SA. 2024 Apr 11

Lung type 3 innate lymphoid cells respond early following Mycobacterium tuberculosis infection. Das S, Chauhan KS, Ahmed M, Akter S, Lu L, Colonna M, Khader SA. 2024 Apr 10

Phospholipase C epsilon-1 (PLCƐ1) mediates macrophage activation and protection against tuberculosis. Gupta A, Thirunavukkarasu S, Rangel-Moreno J, Ahmed M, Swanson RV, Mbandi SK, Smrcka AV, Kaushal D, Scriba TJ, Khader SA.Infect Immun. 2024 Apr 9

Versatile roles of protein flavinylation in bacterial extracyotosolic electron transfer. Huang S, Méheust R, Barquera B, Light SH. 2024 Mar 14

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

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. 2024 Mar 9

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

The endogenous Mtv8 locus and the immunoglobulin repertoire. Beilinson HA, Erickson SA, Golovkina T. Front Immunol. 2024 Mar 5

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

 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

Processing of LtaS restricts LTA assembly and YSIRK preprotein trafficking into Staphylococcus aureus cross-walls.Ibrahim AM, Azam MS, Schneewind O, Missiakas D.mBio. 2024 Feb 14

NF-κB signaling deficiency in CD11c-expressing phagocytes mediates early inflammatory responses and enhances Mycobacterium tuberculosis control. Chauhan KS, Dunlap MD, Akter S, Gupta A, Ahmed M, Rosa BA, Dela Peña NB, Mitreva M, Khader SA.J Infect Dis. 2024 Feb 7

Soluble Angiotensin-Converting Enzyme 2 Protein Improves Survival and Lowers Viral Titers in Lethal Mouse Model of Severe Acute Respiratory Syndrome Coronavirus Type 2 Infection with the Delta Variant. Cianfarini C, Hassler L, Wysocki J, Hassan A, Nicolaescu V, Elli D, Gula H, Ibrahim AM, Randall G, Henkin J, Batlle D.Cells. 2024 Jan 23

Saponin TQL1055 adjuvant-containing vaccine confers protection upon Mycobacterium tuberculosis challenge in mice. Ahmed M, Farris E, Swanson RV, Das S, Yang Y, Martin T, Khader SA. Epub 2024 Jan 8.

Processing of LtaS restricts LTA assembly and YSIRK preprotein trafficking into Staphylococcus aureus cross-walls. Ibrahim AM, Azam MS, Schneewind O, Missiakas D. Jan 4

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. Jan 4.

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

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. Dec 30

Roles of epidermal growth factor receptor, claudin-1 and occludin in multi-step entry of hepatitis C virus into polarized hepatoma spheroids. So CW, Sourisseau M, Sarwar S, Evans MJ, Randall G. Dec 29

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

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. 2023 Oct 31

Mycobacterium tuberculosis infection drives differential responses in the bone marrow hematopoietic stem and progenitor cells. Bobba S, Howard NC, Das S, Ahmed M, Khan N, Marchante I, Barreiro LB, Sanz J, Divangahi M, Khader SA. 2023 Oct 17

Elevated Level of Circulating but Not Urine S100A8/A9 Identifies Poor COVID-19 Outcomes. Mellett L, Amarasinghe G, Farnsworth CW, Khader SA. 2023 Oct 13

Restriction of Arginine Induces Antibiotic Tolerance in Staphylococcus aureus. Freiberg JA, Ruiz VMR, Green ER, Skaar EP. 2023 Oct 12.

Microbiota may affect the tumor type but not overall tumor development in two models of heritable cancer. Spring J, Gurbuxani S, Golovkina T. 2023 Oct 12

Mycobacterium tuberculosis carrying the rifampicin drug-resistance-conferring rpoB mutation H445Y is associated with suppressed immunity through type I interferons. Bobba S, Howard NC, Das S, Ahmed M, Tang L, Thirunavukkarasu S, Larsen MH, Mathema B, Divangahi M, Khader SA.mBio. 2023 Sep 8

Protein coopted from a phage restriction system dictates orthogonal cell division plane selection in Staphylococcus aureus. Ramos-León F, Anjuwon-Foster BR, Anantharaman V, Ferreira CN, Ibrahim AM, Tai CH, Missiakas DM, Camberg JL, Aravind L, Ramamurthi KS. 2023 Sep 3

Rifampicin drug resistance and host immunity in tuberculosis: more than meets the eye Bobba S, Khader SA. 2023 Sep

A protocol to analyze single-cell RNA-seq data from Mycobacterium tuberculosis-infected mice lung. Akter S, Khader SA. 2023 Aug 31

A single dominant locus restricts retrovirus replication in YBR/Ei mice. Beilinson HA, Sevilleja A, Spring J, Benavides F, Beilinson V, Neokosmidis N, Golovkina T. 2023 Aug 31

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. 2023 Aug 29

A ubiquitous mobile genetic element disarms a bacterial antagonist of the gut microbiota. Sheahan ML, Coyne MJ, Flores K, Garcia-Bayona L, Chatzidaki-Livanis M, Sundararajan A, Holst AQ, Barquera B, Comstock LE. 2023 Aug 26.

A humanized monoclonal antibody targeting protein a promotes opsonophagocytosis of Staphylococcus aureus in human umbilical cord blood. Bernardino PN, Bhattacharya M, Chen X, Jenkins J, Missiakas D, Thammavongsa V. 2023 Aug 7

Genetic Engineering of Resident Bacteria in the Gut Microbiome. Arnold J, Glazier J, Mimee M. 2023 Jul 25

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. 2023 Jul 12

Bdellovibrio predation cycle characterized at nanometre-scale resolution with cryo-electron tomography. Kaplan M, Chang YW, Oikonomou CM, Nicolas WJ, Jewett AI, Kreida S, Dutka P, Rettberg LA, Maggi S, Jensen GJ.Nat Microbiol. 2023 Jul

Morphological remodeling of Coxiella burnetii during its biphasic developmental cycle revealed by cryo-electron tomography Shepherd DC, Kaplan M, Vankadari N, Kim KW, Larson CL, Dutka P, Beare PA, Krzymowski E, Heinzen RA, Jensen GJ, Ghosal D. 2023 Jun 24

Poly(ADP-ribose) polymerase 9 mediates early protection against Mycobacterium tuberculosis infection by regulating type I IFN production. Thirunavukkarasu S, Ahmed M, Rosa BA, Boothby M, Cho SH, Rangel-Moreno J, Mbandi SK, Schreiber V, Gupta A, Zuniga J, Mitreva M, Kaushal D, Scriba TJ, Khader SA. 2023 Jun 15

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. 2023 Jun 8

CAPRIN1 Is Required for Control of Viral Replication Complexes by Interferon Gamma. Kurhade C, Kang S, Biering SB, Hwang S, Randall G. 2023 Jun 2

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. 2023 May 22

Structure and Assembly of the Proteus mirabilis Flagellar Motor by Cryo-Electron Tomography. Kaplan M, Yao Q, Jensen GJ. 2023 May 5

Antigen-specific B cells direct T follicular-like helper cells into lymphoid follicles to mediate Mycobacterium tuberculosis control. Swanson RV, Gupta A, Foreman TW, Lu L, Choreno-Parra JA, Mbandi SK, Rosa BA, Akter S, Das S, Ahmed M, Garcia-Hernandez ML, Singh DK, Esaulova E, Artyomov MN, Gommerman J, Mehra S, Zuniga J, Mitreva M, Scriba TJ, Rangel-Moreno J, Kaushal D, Khader SA.Nat Immunol. 2023 May

Hyperglycemia Increases Severity of Staphylococcus aureus Osteomyelitis and Influences Bacterial Genes Required for Survival in Bone. Butrico CE, Klopfenstein N, Green ER, Johnson JR, Peck SH, Ibberson CB, Serezani CH, Cassat JE. 2023 Apr 18.

Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions. Oliveira RA, Pamer EG. 2023 Apr 12

Intranasal soluble ACE2 improves survival and prevents brain SARS-CoV-2 infection. Hassler L, Wysocki J, Ahrendsen JT, Ye M, Gelarden I, Nicolaescu V, Tomatsidou A, Gula H, Cianfarini C, Forster P, Khurram N, Singer BD, Randall G, Missiakas D, Henkin J, Batlle D. 2023 Apr 11

Reply to Barton et al: signatures of natural selection during the Black Death. Vilgalys TP, Klunk J, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB. 2023 Apr 7

Immunoglobulin G subclasses confer protection against Staphylococcus aureus bloodstream dissemination through distinct mechanisms in mouse models. Chen X, Gula H, Pius T, Ou C, Gomozkova M, Wang LX, Schneewind O, Missiakas D. Proc Natl Acad Sci U S A. 2023 Apr 4

Antigen-specific B cells direct T follicular-like helper cells into lymphoid follicles to mediate Mycobacterium tuberculosis control. Swanson RV, Gupta A, Foreman TW, Lu L, Choreno-Parra JA, Mbandi SK, Rosa BA, Akter S, Das S, Ahmed M, Garcia-Hernandez ML, Singh DK, Esaulova E, Artyomov MN, Gommerman J, Mehra S, Zuniga J, Mitreva M, Scriba TJ, Rangel-Moreno J, Kaushal D, Khader SA. Nat Immunol. 2023 Apr 3.

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut. Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore R, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Mclellan SL, Willis AD, Comstock LE, Eren AM. bioRxiv. 2023 Mar 25

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

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

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 Feb 21

Neutrophils Protect Against Staphylococcus aureus Endocarditis Progression Independent of Extracellular Trap Release. Meyers S, Lox M, Kraisin S, Liesenborghs L, Martens CP, Frederix L, Van Bruggen S, Crescente M, Missiakas D, Baatsen P, Vanassche T, Verhamme P, Martinod K. Arterioscler Thromb Vasc Biol. 2023 Feb

Retroviral Infection and Commensal Bacteria Dependently Alter the Metabolomic Profile in a Sterile Organ.  Spring J, Beilinson V, DeFelice BC, Sanchez JM, Fischbach M, Chervonsky A, Golovkina T. Viruses. 2023 Jan 29

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

Modeling gastrointestinal anthrax disease. Oh SY, Chateau A, Tomatsidou A, Elli D, Gula H, Schneewind O, Missiakas D. Res Microbiol. 2023 Jan 13

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. bioRxiv. 2023 Jan 12

Retroviral infection and commensal bacteria dependently alter the metabolomic profile in a sterile organ.  Spring J, Beilinson V, DeFelice BC, Sanchez JM, Fischbach M, Chervonsky A, Golovkina T. bioRxiv. 2023 Jan 11

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

A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Wang P, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H. Nat Biotechnol. 2023 Jan

Transcriptional Inhibition of MicroRNA miR-122 by Small Molecules Reduces Hepatitis C Virus Replication in Liver Cells.  Emanuelson C, Ankenbruck N, Kumbhare R, Thomas M, Connelly C, Baktash Y, Randall G, Deiters A. Med Chem. 2022 Dec 22

Superiority of intranasal over systemic administration of bioengineered soluble ACE2 for survival and brain protection against SARS-CoV-2 infection.  Hassler L, Wysocki J, Ahrendsen JT, Ye M, Gelarden I, Nicolaescu V, Tomatsidou A, Gula H, Cianfarini C, Khurram N, Kanwar Y, Singer BD, Randall G, Missiakas D, Henkin J, Batlle D. bioRxiv. 2022 Dec 6

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

Evolution of immune genes is associated with the Black Death.  Klunk J, Vilgalys TP, Demeure CE, Cheng X, Shiratori M, Madej J, Beau R, Elli D, Patino MI, Redfern R, DeWitte SN, Gamble JA, Boldsen JL, Carmichael A, Varlik N, Eaton K, Grenier JC, Golding GB, Devault A, Rouillard JM, Yotova V, Sindeaux R, Ye CJ, Bikaran M, Dumaine A, Brinkworth JF, Missiakas D, Rouleau GA, Steinrücken M, Pizarro-Cerdá J, Poinar HN, Barreiro LB. Nature. 2022 Nov

Metagenomic and bile acid metabolomic analysis of fecal microbiota transplantation for recurrent Clostridiodes difficile and/or inflammatory bowel diseases.  Ramos RJ, Zhu C, Joseph DF, Thaker S, Lacomb JF, Markarian K, Lee HJ, Petrov JC, Monzur F, Buscaglia JM, Chawla A, Small-Harary L, Gathungu G, Morganstern JA, Yang J, Li J, Pamer EG, Robertson CE, Frank DN, Cross JR, Li E. Med Res Arch. 2022 Oct 31

SARS-CoV-2 Diverges from Other Betacoronaviruses in Only Partially Activating the IRE1α/XBP1 Endoplasmic Reticulum Stress Pathway in Human Lung-Derived Cells.  Nguyen LC, Renner DM, Silva D, Yang D, Parenti NA, Medina KM, Nicolaescu V, Gula H, Drayman N, Valdespino A, Mohamed A, Dann C, Wannemo K, Robinson-Mailman L, Gonzalez A, Stock L, Cao M, Qiao Z, Moellering RE, Tay S, Randall G, Beers MF, Rosner MR, Oakes SA, Weiss SR. mBio. 2022 Oct 26

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

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

One vaccine to counter many diseases? Modeling the economics of oral polio vaccine against child mortality and COVID-19.  Chang AY, Aaby P, Avidan MS, Benn CS, Bertozzi SM, Blatt L, Chumakov K, Khader SA, Kottilil S, Nekkar M, Netea MG, Sparrow A, Jamison DT. Front Public Health. 2022 Oct 5

Contribution of TagA-Like Glycosyltransferases to the Assembly of the Secondary Cell Wall Polysaccharide in Bacillus anthracis.  Tomatsidou A, Krunic M, Missiakas D. J Bacteriol. 2022 Sep 20

Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus. Spring J, Khan AA, Lara S, O'Grady K, Wilks J, Gurbuxani S, Erickson S, Fischbach M, Jacobson A, Chervonsky A, Golovkina T. Cell Rep. 2022 Sep 13

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

Contribution of the EssC ATPase to the assembly of the type 7b secretion system in Staphylococcus aureus.  Bobrovskyy M, Oh SY, Missiakas D. J Biol Chem. 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

CWHM-12, an Antagonist of Integrin-Mediated Transforming Growth Factor-Beta Activation Confers Protection During Early Mycobacterium tuberculosis Infection in Mice.  Scott NR, Thirunavukkarasu S, Rangel-Moreno J, Griggs DW, Khader SA. J Interferon Cytokine Res. 2022 Aug

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

Response to Hypoxia and the Ensuing Dysregulation of Inflammation Impacts Mycobacterium tuberculosis Pathogenicity. Bucşan AN, Veatch A, Singh DK, Akter S, Golden NA, Kirkpatrick M, Threeton B, Moodley C, Ahmed M, Doyle LA, Russell-Lodrigue K, Norton EB, Didier PJ, Roy CJ, Abramovitch RB, Mehra S, Khader SA, Kaushal D. Am J Respir Crit Care Med. 2022 Jul 1

A Novel Soluble ACE2 Protein Provides Lung and Kidney Protection in Mice Susceptible to Lethal SARS-CoV-2 Infection.  Hassler L, Wysocki J, Gelarden I, Sharma I, Tomatsidou A, Ye M, Gula H, Nicoleascu V, Randall G, Pshenychnyi S, Khurram N, Kanwar Y, Missiakas D, Henkin J, Yeldandi A, Batlle D. J Am Soc Nephrol. 2022 Jul

Advancing Lung Immunology Research: An Official American Thoracic Society Workshop Report.  Rahimi RA, Cho JL, Jakubzick CV, Khader SA, Lambrecht BN, Lloyd CM, Molofsky AB, Talbot S, Bonham CA, Drake WP, Sperling AI, Singer BD. Am J Respir Cell Mol Biol. 2022 Jul

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

Mitochondrial cyclophilin D promotes disease tolerance by licensing NK cell development and IL-22 production against influenza virus.  Downey J, Randolph HE, Pernet E, Tran KA, Khader SA, King IL, Barreiro LB, Divangahi M. Cell Rep. 2022 Jun 21

A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19.  Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H. Res Sq. 2022 Jun 7

SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells.  Nguyen LC, Renner DM, Silva D, Yang D, Parenti N, Medina KM, Nicolaescu V, Gula H, Drayman N, Valdespino A, Mohamed A, Dann C, Wannemo K, Robinson-Mailman L, Gonzalez A, Stock L, Cao M, Qiao Z, Moellering RE, Tay S, Randall G, Beers MF, Rosner MR, Oakes SA, Weiss SR. bioRxiv. 2022 Jun 13

The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection.  Schor S, Pu S, Nicolaescu V, Azari S, Kõivomägi M, Karim M, Cassonnet P, Saul S, Neveu G, Yueh A, Demeret C, Skotheim JM, Jacob Y, Randall G, Einav S. J Biol Chem. 2022 Jun

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

Inflammatory comorbidities: to train or not to train?  Bobba S, Khader SA. Trends Immunol. 2022 Jun

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

Solution structure and dynamics of the mitochondrial-targeted GTPase-activating protein (GAP) VopE by an integrated NMR/SAXS approach.   Smith KP, Lee W, Tonelli M, Lee Y, Light SH, Cornilescu G, Chakravarthy S. Protein Sci. 2022 May

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

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

Author Correction: The immunoregulatory landscape of human tuberculosis granulomas. McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF, Baranski A, Graf W, Kumar R, Bosse M, Fullaway CC, Ramdial PK, Forgó E, Jojic V, Van Valen D, Mehra S, Khader SA, Bendall SC, van de Rijn M, Kalman D, Kaushal D, Hunter RL, Banaei N, Steyn AJC, Khatri P, Angelo M. Nat Immunol. 2022 May

Toward Optimization of a Rabbit Model of Staphylococcus aureus (USA300) Skin and Soft Tissue Infection.  Malachowa N, McGuinness W, Kobayashi SD, Porter AR, Shaia C, Lovaglio J, Smith B, Rungelrath V, Saturday G, Scott DP, Falugi F, Missiakas D, Schneewind O, DeLeo FR. Microbiol Spectr. 2022 Apr 27

Differential effects of macrophage subtypes on SARS-CoV-2 infection in a human pluripotent stem cell-derived model.  Lian Q, Zhang K, Zhang Z, Duan F, Guo L, Luo W, Mok BW, Thakur A, Ke X, Motallebnejad P, Nicolaescu V, Chen J, Ma CY, Zhou X, Han S, Han T, Zhang W, Tan AY, Zhang T, Wang X, Xu D, Xiang J, Xu A, Liao C, Huang FP, Chen YW, Na J, Randall G, Tse HF, Chen Z, Chen Y, Chen HJ. Nat Commun. 2022 Apr 19

Spherical nucleic acids as an infectious disease vaccine platform.  Teplensky MH, Distler ME, Kusmierz CD, Evangelopoulos M, Gula H, Elli D, Tomatsidou A, Nicolaescu V, Gelarden I, Yeldandi A, Batlle D, Missiakas D, Mirkin CA. Proc Natl Acad Sci U S A. 2022 Apr 5

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

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

Corrigendum to "Rifampicin resistance mutations in the rpoB gene of Enterococcus faecalis affect the production of cytokines by host macrophages" Cytokine 151 (2022) 155788. Urusova DV, Merriman JA, Gupta A, Chen L, Mathema B, Caparon MG, Khader SA. Cytokine. 2022 Apr

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

Rifampin resistance mutations in the rpoB gene of Enterococcus faecalis impact host macrophage cytokine production. Urusova DV, Merriman JA, Gupta A, Chen L, Mathema B, Caparon MG, Khader SA. Cytokine. 2022 Mar

Cannabidiol inhibits SARS-CoV-2 replication through induction of the host ER stress and innate immune responses.  Nguyen LC, Yang D, Nicolaescu V, Best TJ, Gula H, Saxena D, Gabbard JD, Chen SN, Ohtsuki T, Friesen JB, Drayman N, Mohamed A, Dann C, Silva D, Robinson-Mailman L, Valdespino A, Stock L, Suárez E, Jones KA, Azizi SA, Demarco JK, Severson WE, Anderson CD, Millis JM, Dickinson BC, Tay S, Oakes SA, Pauli GF, Palmer KE; National COVID Cohort Collaborative Consortium; Meltzer DO, Randall G, Rosner MR. Sci Adv. 2022 Feb 25

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

Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism.  Tejedor-Sanz S, Stevens ET, Li S, Finnegan P, Nelson J, Knoesen A, Light SH, Ajo-Franklin CM, Marco ML. Elife. 2022 Feb 11

Myeloid cell interferon responses correlate with clearance of SARS-CoV-2. Singh DK, Aladyeva E, Das S, Singh B, Esaulova E, Swain A, Ahmed M, Cole J, Moodley C, Mehra S, Schlesinger LS, Artyomov MN, Khader SA, Kaushal D. Nat Commun. 2022 Feb 3

Antiretroviral therapy timing impacts latent tuberculosis infection reactivation in a Mycobacterium tuberculosis/SIV coinfection model.  Sharan R, Ganatra SR, Bucsan AN, Cole J, Singh DK, Alvarez X, Gough M, Alvarez C, Blakley A, Ferdin J, Thippeshappa R, Singh B, Escobedo R, Shivanna V, Dick EJ Jr, Hall-Ursone S, Khader SA, Mehra S, Rengarajan J, Kaushal D. J Clin Invest. 2022 Feb 1

The immunoregulatory landscape of human tuberculosis granulomas. McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF, Baranski A, Graf W, Kumar R, Bosse M, Fullaway CC, Ramdial PK, Forgó E, Jojic V, Van Valen D, Mehra S, Khader SA, Bendall SC, van de Rijn M, Kalman D, Kaushal D, Hunter RL, Banaei N, Steyn AJC, Khatri P, Angelo M. Nat Immunol. 2022 Feb

S100A8/A9 in COVID-19 pathogenesis: Impact on clinical outcomes.  Mellett L, Khader SA. Cytokine Growth Factor Rev. 2022 Feb

Engineered human antibodies for the opsonization and killing of Staphylococcus aureus.  Chen X, Schneewind O, Missiakas D. Proc Natl Acad Sci U S A. 2022 Jan 25

Development and Testing of a Spray-Dried Tuberculosis Vaccine Candidate in a Mouse Model.  Gomez M, Ahmed M, Das S, McCollum J, Mellett L, Swanson R, Gupta A, Carrigy NB, Wang H, Barona D, Bachchhav S, Gerhardt A, Press C, Archer MC, Liang H, Seydoux E, Kramer RM, Kuehl PJ, Vehring R, Khader SA, Fox CB. Front Pharmacol. 2022 Jan 21

Circulating ACE2-expressing extracellular vesicles block broad strains of SARS-CoV-2.  El-Shennawy L, Hoffmann AD, Dashzeveg NK, McAndrews KM, Mehl PJ, Cornish D, Yu Z, Tokars VL, Nicolaescu V, Tomatsidou A, Mao C, Felicelli CJ, Tsai CF, Ostiguin C, Jia Y, Li L, Furlong K, Wysocki J, Luo X, Ruivo CF, Batlle D, Hope TJ, Shen Y, Chae YK, Zhang H, LeBleu VS, Shi T, Swaminathan S, Luo Y, Missiakas D, Randall GC, Demonbreun AR, Ison MG, Kalluri R, Fang D, Liu H. Nat Commun. 2022 Jan 20

Corrigendum to: Staphylococcus aureus Decolonization of Mice With Monoclonal Antibody Neutralizing Protein A.  Chen X, Sun Y, Missiakas D, Schneewind O. J Infect Dis. 2022 Jan 18

A Multifunctional Neutralizing Antibody-Conjugated Nanoparticle Inhibits and Inactivates SARS-CoV-2.  Cai X, Chen M, Prominski A, Lin Y, Ankenbruck N, Rosenberg J, Nguyen M, Shi J, Tomatsidou A, Randall G, Missiakas D, Fung J, Chang EB, Penaloza-MacMaster P, Tian B, Huang J. Adv Sci (Weinh). 2022 Jan

A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets.  Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Wang P, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H. Nat Biotechnol. 2023 Jan

Myeloid-Derived Suppressor Cells Mediate T Cell Dysfunction in Nonhuman Primate TB Granulomas.  Singh B, Singh DK, Ganatra SR, Escobedo RA, Khader S, Schlesinger LS, Kaushal D, Mehra S. mBio. 2021 Dec 21

Mouse Homologue of Human HLA-DO Does Not Preempt Autoimmunity but Controls Murine Gammaherpesvirus MHV68.  Lee J, Cullum E, Stoltz K, Bachmann N, Strong Z, Millick DD, Denzin LK, Chang A, Tarakanova V, Chervonsky AV, Golovkina T. J Immunol. 2021 Dec 15

Longitudinal Dynamics of a Blood Transcriptomic Signature of Tuberculosis.  Mulenga H, Musvosvi M, Mendelsohn SC, Penn-Nicholson A, Kimbung Mbandi S, Fiore-Gartland A, Tameris M, Mabwe S, Africa H, Bilek N, Kafaar F, Khader SA, Carstens B, Hadley K, Hikuam C, Erasmus M, Jaxa L, Raphela R, Nombida O, Kaskar M, Nicol MP, Mbhele S, Van Heerden J, Innes C, Brumskine W, Hiemstra A, Malherbe ST, Hassan-Moosa R, Walzl G, Naidoo K, Churchyard G, Hatherill M, Scriba TJ; CORTIS Study Team.  Am J Respir Crit Care Med. 2021 Dec 15

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

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

Generation of potent cellular and humoral immunity against SARS-CoV-2 antigens via conjugation to a polymeric glyco-adjuvant.  Gray LT, Raczy MM, Briquez PS, Marchell TM, Alpar AT, Wallace RP, Volpatti LR, Sasso MS, Cao S, Nguyen M, Mansurov A, Budina E, Watkins EA, Solanki A, Mitrousis N, Reda JW, Yu SS, Tremain AC, Wang R, Nicolaescu V, Furlong K, Dvorkin S, Manicassamy B, Randall G, Wilson DS, Kwissa M, Swartz MA, Hubbell JA. Biomaterials. 2021 Nov

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

CXCL17 Is Dispensable during Hypervirulent Mycobacterium tuberculosis HN878 Infection in Mice.  Choreño-Parra JA, Dunlap MD, Swanson R, Jiménez-Álvarez LA, Muñoz-Torrico M, Guzmán-Beltrán S, Zúñiga J, Khader SA. Immunohorizons. 2021 Sep 24

Lung Epithelial Signaling Mediates Early Vaccine-Induced CD4+ T Cell Activation and Mycobacterium tuberculosis Control.  Das S, Marin ND, Esaulova E, Ahmed M, Swain A, Rosa BA, Mitreva M, Rangel-Moreno J, Netea MG, Barreiro LB, Divangahi M, Artyomov MN, Kaushal D, Khader SA. mBio. 2021 Aug 31

Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2.  Drayman N, DeMarco JK, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, Furlong K, Kathayat RS, Firpo MR, Mastrodomenico V, Bruce EA, Schmidt MM, Jedrzejczak R, Muñoz-Alía MÁ, Schuster B, Nair V, Han KY, O'Brien A, Tomatsidou A, Meyer B, Vignuzzi M, Missiakas D, Botten JW, Brooke CB, Lee H, Baker SC, Mounce BC, Heaton NS, Severson WE, Palmer KE, Dickinson BC, Joachimiak A, Randall G, Tay S. Science. 2021 Aug 20

Myeloid cell interferon responses correlate with clearance of SARS-CoV-2.  Singh D, Aladyeva E, Das S, Singh B, Esaulova E, Swain A, Ahmed M, Cole J, Moodley C, Mehra S, Schlesinger L, Artyomov M, Khader S, Kaushal D. Res Sq. 2021 Jul 15

Expression of Surfactant Protein D Distinguishes Severe Pandemic Influenza A(H1N1) from Coronavirus Disease 2019.  Choreño-Parra JA, Jiménez-Álvarez LA, Ramírez-Martínez G, Cruz-Lagunas A, Thapa M, Fernández-López LA, Carnalla-Cortés M, Choreño-Parra EM, Mena-Hernández L, Sandoval-Vega M, Hernández-Montiel EM, Hernández-García DL, Ramírez-Noyola JA, Reyes-López CE, Domínguez-Faure A, Zamudio-López GY, Márquez-García E, Moncada-Morales A, Mendoza-Milla C, Cervántes-Rosete D, Muñoz-Torrico M, Luna-Rivero C, García-Latorre EA, Guadarrama-Ortíz P, Ávila-Moreno F, Domínguez-Cherit G, Rodríguez-Reyna TS, Mudd PA, Hernández-Cárdenas CM, Khader SA, Zúñiga J. J Infect Dis. 2021 Jul 2

MHC Class II Presentation Is Affected by Polymorphism in the H2-Ob Gene and Additional Loci. Cullum E, Graves AM, Tarakanova VL, Denzin LK, Golovkina T. J Immunol. 2021 Jul 1

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

Author Correction: Trained immunity, tolerance, priming and differentiation: distinct immunological processes.  Divangahi M, Aaby P, Khader SA, Barreiro LB, Bekkering S, Chavakis T, van Crevel R, Curtis N, DiNardo AR, Dominguez-Andres J, Duivenvoorden R, Fanucchi S, Fayad Z, Fuchs E, Hamon M, Jeffrey KL, Khan N, Joosten LAB, Kaufmann E, Latz E, Matarese G, van der Meer JWM, Mhlanga M, Moorlag SJCFM, Mulder WJM, Naik S, Novakovic B, O'Neill L, Ochando J, Ozato K, Riksen NP, Sauerwein R, Sherwood ER, Schlitzer A, Schultze JL, Sieweke MH, Benn CS, Stunnenberg H, Sun J, van de Veerdonk FL, Weis S, Williams DL, Xavier R, Netea MG. Nat Immunol. 2021 Jul

A protein A based Staphylococcus aureus vaccine with improved safety.  Shi M, Chen X, Sun Y, Kim HK, Schneewind O, Missiakas D. Vaccine. 2021 Jun 29

Nanotraps for the containment and clearance of SARS-CoV-2.  Chen M, Rosenberg J, Cai X, Lee ACH, Shi J, Nguyen M, Wignakumar T, Mirle V, Edobor AJ, Fung J, Donington JS, Shanmugarajah K, Lin Y, Chang E, Randall G, Penaloza-MacMaster P, Tian B, Madariaga ML, Huang J. Matter. 2021 Jun 2

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

Old vaccines for new infections: Exploiting innate immunity to control COVID-19 and prevent future pandemics.  Chumakov K, Avidan MS, Benn CS, Bertozzi SM, Blatt L, Chang AY, Jamison DT, Khader SA, Kottilil S, Netea MG, Sparrow A, Gallo RC. Proc Natl Acad Sci U S A. 2021 May 25

Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life.  Méheust R, Huang S, Rivera-Lugo R, Banfield JF, Light SH. Elife. 2021 May 25

Corrigendum: CXCL17 Is a Specific Diagnostic Biomarker for Severe Pandemic Influenza A(H1N1) That Predicts Poor Clinical Outcome.  Choreño-Parra JA, Jiménez-Álvarez LA, Ramírez-Martínez G, Sandoval-Vega M, Salinas-Lara C, Sánchez-Garibay C, Luna-Rivero C, Hernández-Montiel EM, Fernández-López LA, Cabrera-Cornejo MF, Choreño-Parra EM, Cruz-Lagunas A, Domínguez A, Márquez-García E, Cabello-Gutiérrez C, Bolaños-Morales FV, Mena-Hernández L, Delgado-Zaldivar D, Rebolledo-García D, Guadarrama-Ortiz P, Regino-Zamarripa NE, Mendoza-Milla C, García-Latorre EA, Rodríguez-Reyna TS, Cervántes-Rosete D, Hernández-Cárdenas CM, Khader SA, Zlotnik A, Zúñiga J. Front Immunol. 2021 May 13

Regulated cleavage of glycan strands by the murein hydrolase SagB in S. aureus involves a direct interaction with LyrA (SpdC). Willing S, Schneewind O, Missiakas D. J Bacteriol. 2021 May 1

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

Phenotype of Peripheral NK Cells in Latent, Active, and Meningeal Tuberculosis.  Choreño-Parra JA, Jiménez-Álvarez LA, Maldonado-Díaz ED, Cárdenas G, Fernández-Lopez LA, Soto-Hernandez JL, Muñoz-Torrico M, Ramírez-Martínez G, Cruz-Lagunas A, Vega-López A, Domínguez-López ML, Sánchez-Garibay C, Guadarrama-Ortíz P, Giono S, Jiménez-Zamudio LA, Khader SA, García-Latorre EA, Salinas-Lara C, Zúñiga J. J Immunol Res. 2021 Apr 27

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

Polymersomes Decorated with the SARS-CoV-2 Spike Protein Receptor-Binding Domain Elicit Robust Humoral and Cellular Immunity.  Volpatti LR, Wallace RP, Cao S, Raczy MM, Wang R, Gray LT, Alpar AT, Briquez PS, Mitrousis N, Marchell TM, Sasso MS, Nguyen M, Mansurov A, Budina E, Solanki A, Watkins EA, Schnorenberg MR, Tremain AC, Reda JW, Nicolaescu V, Furlong K, Dvorkin S, Yu SS, Manicassamy B, LaBelle JL, Tirrell MV, Randall G, Kwissa M, Swartz MA, Hubbell JA.  ACS Cent Sci. 2021 Aug 25

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

Clinical and Immunological Factors That Distinguish COVID-19 From Pandemic Influenza A(H1N1).  Choreño-Parra JA, Jiménez-Álvarez LA, Cruz-Lagunas A, Rodríguez-Reyna TS, Ramírez-Martínez G, Sandoval-Vega M, Hernández-García DL, Choreño-Parra EM, Balderas-Martínez YI, Martinez-Sánchez ME, Márquez-García E, Sciutto E, Moreno-Rodríguez J, Barreto-Rodríguez JO, Vázquez-Rojas H, Centeno-Sáenz GI, Alvarado-Peña N, Salinas-Lara C, Sánchez-Garibay C, Galeana-Cadena D, Hernández G, Mendoza-Milla C, Domínguez A, Granados J, Mena-Hernández L, Pérez-Buenfil LÁ, Domínguez-Cheritt G, Cabello-Gutiérrez C, Luna-Rivero C, Salas-Hernández J, Santillán-Doherty P, Regalado J, Hernández-Martínez A, Orozco L, Ávila-Moreno F, García-Latorre EA, Hernández-Cárdenas CM, Khader SA, Zlotnik A, Zúñiga J. Front Immunol. 2021 Apr 21

Peptidoglycan Contribution to the B Cell Superantigen Activity of Staphylococcal Protein A.  Shi M, Willing SE, Kim HK, Schneewind O, Missiakas D. mBio. 2021 Apr 20

Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes.  Zeng Z, Boeren S, Bhandula V, Light SH, Smid EJ, Notebaart RA, Abee T.  mSystems. 2021 Apr 13

Staphylococcus aureus vWF-binding protein triggers a strong interaction between clumping factor A and host vWF.  Viljoen A, Viela F, Mathelié-Guinlet M, Missiakas D, Pietrocola G, Speziale P, Dufrêne YF. Commun Biol. 2021 Apr 12

Polymersomes decorated with SARS-CoV-2 spike protein receptor binding domain elicit robust humoral and cellular immunity.  Volpatti LR, Wallace RP, Cao S, Raczy MM, Wang R, Gray LT, Alpar AT, Briquez PS, Mitrousis N, Marchell TM, Sasso MS, Nguyen M, Mansurov A, Budina E, Solanki A, Watkins EA, Schnorenberg MR, Tremain AC, Reda JW, Nicolaescu V, Furlong K, Dvorkin S, Yu SS, Manicassamy B, LaBelle JL, Tirrell MV, Randall G, Kwissa M, Swartz MA, Hubbell JA. bioRxiv. 2021 Apr 8

Monocyte progenitors give rise to multinucleated giant cells.  Lösslein AK, Lohrmann F, Scheuermann L, Gharun K, Neuber J, Kolter J, Forde AJ, Kleimeyer C, Poh YY, Mack M, Triantafyllopoulou A, Dunlap MD, Khader SA, Seidl M, Hölscher A, Hölscher C, Guan XL, Dorhoi A, Henneke P. Nat Commun. 2021 Apr 1

A Novel Soluble ACE2 Variant with Prolonged Duration of Action Neutralizes SARS-CoV-2 Infection in Human Kidney Organoids.  Wysocki J, Ye M, Hassler L, Gupta AK, Wang Y, Nicoleascu V, Randall G, Wertheim JA, Batlle D. J Am Soc Nephrol. 2021 Apr

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

A novel soluble ACE2 protein totally protects from lethal disease caused by SARS-CoV-2 infection.  Hassler L, Wysocki J, Gelarden I, Tomatsidou A, Gula H, Nicoleascu V, Randall G, Henkin J, Yeldandi A, Batlle D. bioRxiv. 2021 Mar 15

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

Cannabidiol Inhibits SARS-CoV-2 Replication and Promotes the Host Innate Immune Response. Nguyen LC, Yang D, Nicolaescu V, Best TJ, Ohtsuki T, Chen SN, Friesen JB, Drayman N, Mohamed A, Dann C, Silva D, Gula H, Jones KA, Millis JM, Dickinson BC, Tay S, Oakes SA, Pauli GF, Meltzer DO, Randall G, Rosner MR. bioRxiv. 2021 Mar 10

IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection.  Rosa BA, Ahmed M, Singh DK, Choreño-Parra JA, Cole J, Jiménez-Álvarez LA, Rodríguez-Reyna TS, Singh B, Gonzalez O, Carrion R Jr, Schlesinger LS, Martin J, Zúñiga J, Mitreva M, Kaushal D, Khader SA. Commun Biol. 2021 Mar 5

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

NLRP9 in innate immunity and inflammation.  Mullins B, Chen J. Immunology. 2021 Mar

Author Correction: Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets.  Singh DK, Singh B, Ganatra SR, Gazi M, Cole J, Thippeshappa R, Alfson KJ, Clemmons E, Gonzalez O, Escobedo R, Lee TH, Chatterjee A, Goez-Gazi Y, Sharan R, Gough M, Alvarez C, Blakley A, Ferdin J, Bartley C, Staples H, Parodi L, Callery J, Mannino A, Klaffke B, Escareno P, Platt RN 2nd, Hodara V, Scordo J, Gautam S, Vilanova AG, Olmo-Fontanez A, Schami A, Oyejide A, Ajithdoss DK, Copin R, Baum A, Kyratsous C, Alvarez X, Ahmed M, Rosa B, Goodroe A, Dutton J, Hall-Ursone S, Frost PA, Voges AK, Ross CN, Sayers K, Chen C, Hallam C, Khader SA, Mitreva M, Anderson TJC, Martinez-Sobrido L, Patterson JL, Turner J, Torrelles JB, Dick EJ Jr, Brasky K, Schlesinger LS, Giavedoni LD, Carrion R Jr, Kaushal D. Nat Microbiol. 2021 Mar

CXCL17 Is a Specific Diagnostic Biomarker for Severe Pandemic Influenza A(H1N1) That Predicts Poor Clinical Outcome.  Choreño-Parra JA, Jiménez-Álvarez LA, Ramírez-Martínez G, Sandoval-Vega M, Salinas-Lara C, Sánchez-Garibay C, Luna-Rivero C, Hernández-Montiel EM, Fernández-López LA, Cabrera-Cornejo MF, Choreño-Parra EM, Cruz-Lagunas A, Domínguez A, Márquez-García E, Cabello-Gutiérrez C, Bolaños-Morales FV, Mena-Hernández L, Delgado-Zaldivar D, Rebolledo-García D, Guadarrama-Ortiz P, Regino-Zamarripa NE, Mendoza-Milla C, García-Latorre EA, Rodiguez-Reyna TS, Cervántes-Rosete D, Hernández-Cárdenas CM, Khader SA, Zlotnik A, Zúñiga J. Front Immunol. 2021 Feb 26

The immune landscape in tuberculosis reveals populations linked to disease and latency.  Esaulova E, Das S, Singh DK, Choreño-Parra JA, Swain A, Arthur L, Rangel-Moreno J, Ahmed M, Singh B, Gupta A, Fernández-López LA, de la Luz Garcia-Hernandez M, Bucsan A, Moodley C, Mehra S, García-Latorre E, Zuniga J, Atkinson J, Kaushal D, Artyomov MN, Khader SA. Cell Host Microbe. 2021 Feb 10

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.  Kim Y, Wower J, Maltseva N, Chang C, Jedrzejczak R, Wilamowski M, Kang S, Nicolaescu V, Randall G, Michalska K, Joachimiak A. Commun Biol. 2021 Feb 9

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

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.  Osipiuk J, Azizi SA, Dvorkin S, Endres M, Jedrzejczak R, Jones KA, Kang S, Kathayat RS, Kim Y, Lisnyak VG, Maki SL, Nicolaescu V, Taylor CA, Tesar C, Zhang YA, Zhou Z, Randall G, Michalska K, Snyder SA, Dickinson BC, Joachimiak A. Nat Commun. 2021 Feb 2

S100A8/A9 in COVID-19 pathogenesis: Impact on clinical outcomes.  Mellett L, Khader SA. Cytokine Growth Factor Rev. 2022 Feb

Three-Dimensional Cell Culture Systems for Studying Hepatitis C Virus.  So CW, Randall G. Viruses. 2021 Jan 30

Development and Testing of a Spray-Dried Tuberculosis Vaccine Candidate in a Mouse Model.  Gomez M, Ahmed M, Das S, McCollum J, Mellett L, Swanson R, Gupta A, Carrigy NB, Wang H, Barona D, Bachchhav S, Gerhardt A, Press C, Archer MC, Liang H, Seydoux E, Kramer RM, Kuehl PJ, Vehring R, Khader SA, Fox CB. Front Pharmacol. 2022 Jan 21

Selective Host Cell Death by Staphylococcus aureus: A Strategy for Bacterial Persistence.  Missiakas D, Winstel V. Front Immunol. 2021 Jan 21

Trained immunity, tolerance, priming and differentiation: distinct immunological processes.  Divangahi M, Aaby P, Khader SA, Barreiro LB, Bekkering S, Chavakis T, van Crevel R, Curtis N, DiNardo AR, Dominguez-Andres J, Duivenvoorden R, Fanucchi S, Fayad Z, Fuchs E, Hamon M, Jeffrey KL, Khan N, Joosten LAB, Kaufmann E, Latz E, Matarese G, van der Meer JWM, Mhlanga M, Moorlag SJCFM, Mulder WJM, Naik S, Novakovic B, O'Neill L, Ochando J, Ozato K, Riksen NP, Sauerwein R, Sherwood ER, Schlitzer A, Schultze JL, Sieweke MH, Benn CS, Stunnenberg H, Sun J, van de Veerdonk FL, Weis S, Williams DL, Xavier R, Netea MG. Nat Immunol. 2021 Jan

A Multifunctional Neutralizing Antibody-Conjugated Nanoparticle Inhibits and Inactivates SARS-CoV-2.  Cai X, Chen M, Prominski A, Lin Y, Ankenbruck N, Rosenberg J, Nguyen M, Shi J, Tomatsidou A, Randall G, Missiakas D, Fung J, Chang EB, Penaloza-MacMaster P, Tian B, Huang J.  Adv Sci (Weinh). 2022 Jan

Responses to acute infection with SARS-CoV-2 in the lungs of rhesus macaques, baboons and marmosets.  Singh DK, Singh B, Ganatra SR, Gazi M, Cole J, Thippeshappa R, Alfson KJ, Clemmons E, Gonzalez O, Escobedo R, Lee TH, Chatterjee A, Goez-Gazi Y, Sharan R, Gough M, Alvarez C, Blakley A, Ferdin J, Bartley C, Staples H, Parodi L, Callery J, Mannino A, Klaffke B, Escareno P, Platt RN 2nd, Hodara V, Scordo J, Gautam S, Vilanova AG, Olmo-Fontanez A, Schami A, Oyejide A, Ajithdoss DK, Copin R, Baum A, Kyratsous C, Alvarez X, Ahmed M, Rosa B, Goodroe A, Dutton J, Hall-Ursone S, Frost PA, Voges AK, Ross CN, Sayers K, Chen C, Hallam C, Khader SA, Mitreva M, Anderson TJC, Martinez-Sobrido L, Patterson JL, Turner J, Torrelles JB, Dick EJ Jr, Brasky K, Schlesinger LS, Giavedoni LD, Carrion R Jr, Kaushal D. Nat Microbiol. 2021 Jan