The Microbiome Center is home to some of the world's experts in fields from microbiology to engineering, medicine to ecology. Below is a small sampling of published work from our affiliated faculty and scientists. Please visit the directory for more complete collections of publications.


Natural polyreactive IgA antibodies coat the intestinal microbiota. Bunker, JJ, Erickson, SA, Flynn, TM, Henry, C, Koval, JC, Meisel, M, Jabri, B, Antonopoulos, DA, Wilson, PC, Bendelac, A. Science. Sept, 2017.

Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APPSWE/PS1ΔE9 murine model of Alzheimer’s disease. Minter, MR, Hinterleitner, R, Meisel, M, Zhang, C, Leone, V, Zhang, X, Oyler-Castrillo, P, Zhang, X, Musch, MW, Shen, X, Jabri, B, Chang, EB, Tanzi, RE & Sisodia, SS. Scientific Reports. Sept, 2017. 

Influence of the intestinal microbiome on anastomotic healing in the colon and rectum. Shao, C, Gaines, S, Alverdy, JC. Seminars in Colon and Rectal Surgery. 2017.

Microbial diversity in an intensively managed landscape is structured by landscape connectivity. Griffin, JS, Lu, N, Sangwan, N, Li, A, Dsouza, M, Stumpf, AJ, Sevilla, T, Culotti, A, Keefer, LL, Kelly, JJ, Gilbert, JA, Wells, GF, Packman, AI. FEMS Microbiology Ecology. Sept, 2017.

The role of the intestinal microbiota in the pathogenesis and treatment of inflammatory bowel diseases. Miyoshi, J, Qiao, Y, Chang, EB. Seminars in Colon and Rectal Surgery. 2017. 

Metabolic Reconstruction and Modeling Microbial Electrosynthesis. Marshall, CW, Ross, DE, Handley, KM, Weisenhorn, PB, Edirisinghe, JN, Henry, CS, Gilbert, JA, May, HD, Norman, RS. Scientific Reports. Aug, 2017. 

Cell-targetable DNA nanocapsules for spatiotemporal release of caged bioactive small molecules. Veetil AT, Chakrabortty, K, Xiao, K, Minter, MR, Sisodia, SS, Krishnan, Y. Nat. Nanotechnology, 2017.

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping. Mackey, KRM, Hunter-Cevera, K, Britten, GL, Murphy, LG, Sogin, ML, Huber JA. Front. Microbiology. 2017.

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow's milk containing heat-killed Lactobacillus paracasei CBA L74. Canna, RB, De Filippis, F, Nocerino, R, Laiola, M, Paparo, L, Calignano, A, De Caro, C, Coretti, L, Chiariotti, L, Gilbert, JA, Ercolini, D. Appl Environ Microbiol, 2017.

Ecological Network Inference From Long-Term Presence-Absence Data. Sander, EL, Wootton, TJ, Allesina, S. Sci Reports, 2017.

Media from macrophages co-incubated with Enterococcus faecalis induces epithelial cell monolayer reassembly and altered cell morphology. Belogortseva, N, Krezalek, M, Guyton, K, Labno, C, Poroyko, V, Zaborina, O, Alverdy, JC. PLOS One, 2017.

Patients with Ulcerative Colitis and Primary Sclerosing Cholangitis Frequently Have Subclinical Inflammation in the Proximal Colon. Cleveland, NK, Rubin, DT, Hart, J, Weber, CR, Meckel, K, Tran, AL, Aelvoet, AS, Pan, I, Gonsalves, A, Gaetano, JN, Williams, K, Wroblewski, K, Jabri, B, Pekow, J. Clinical Gastroenterology and Hepatology, 2017.

Fecal Microbiota Transplantation to Treat Sepsis of Unclear Etiology. Gaines, S, Alverdy, JC. Critical care medicine, 2017.

Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease. Bouziat, R, Hinterleitner, R, Brown, JJ, Stencel-Baerenwald, JE...Jabri, B. Science, 2017.

GigA and GigB are Master Regulators of Antibiotic Resistance, Stress Responses and Virulence in Acinetobacter baumanni. Gebhardt, M, Shuman, HA. Journal of Bacteriology, 2017.

Visualizing Adsorption of Cyanophage P-SSP7 onto Marine Prochlorococcus. Zhang, Q, Galaz-Montoya, JG, Fu, C, Coleman, ML, Osburne, M, Schmid, MF, Sullivan, MB, Chisholm, SW, Chiu, W.Scientific Reports, 2017.

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem. Gibbons, SM, Lekberg, Y, Mummey, DL, Sangwan, N, Ramsey, P, Gilbert, JA, mSystems, 2017.

Genome-wide transcriptomics of aging in the rotifer Brachionus Manjavacas, an emerging model system. Gribble, KE, Welch, DBM. BMC Genomics, 2017.

Glutathionylation of Tersinia pestis LcrV and Its Effects on Plague Pathogenesis... Osei-Owusu, P, Fazlollahi, F, Faull, KF, Schneewind, O. mBio, 2017.

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics. Lee, S, Kahn, S, Delmont, T, Shaiber, A, Esen, OC, Hubert, NA, Morrison, HG, Antonopoulos, D, Rubin, D, Eren, M. Microbiome, 2017.

The Influence of Dietary Micronutrients Upon the Risk of 'Pouchitis'-like Inflammation in Genetically Susceptible Hosts. Pierre, JF, Hinterleitner, R, Bouziat, R, Hubert, N, Miyoshi, J, Jabri, B, Chang, EB. FASEB Journal, 2017. 

A human gut ecosystem protects against C. difficile disease by targeting TcdA...Weese, s, Allen-Vercoe, E, Sun, J, Claud, EC,..Journal of gastroenterology, 2017.

Transport Capabilities of Environmental Pseudomonads for Sulfur Compounds. Zerbs, S, Korajczyk, PJ, Noirot, PH, Collart, FR. Protein Science, 2017. 


Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions Kwon, M, O’Loughlin, E, Boyanov, M, Brulc, J, Johnston, E, Kemner, K, Antonopoulos, D. Plos One. Jan 2016.

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System. Gibbons, SM, Scholz, M, Hutchison, AL, Dinner, A, Gilbert, JA, Coleman, ML – mBio. 2016

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses…, Schwenck, SM, Goldsmith, DB, Coleman, ML, Breitbart, M, Sullivan, MB. PeerJ. 2016.

Influence of nutrition therapy on the intestinal microbiome.
Krezalek, MA, Yeh, A, Alverdy, JC, Morowitz, M. - Current Opinion in Clinical Nutrition & Metabolic Care. 2016.

The critical role of microbiota within cecal crypts on the regenerative capacity of the intestinal epithelium following surgical stress
…, Bindokas, VP, Guo, Q, Zaborina, O, Alverdy, JC. American Journal of Physiology. 2016.

Identifying the plant associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery. Jackrel, SL, Owens, SM, Gilbert, JA, Pfister, CA. Molecular Ecology Resources, 2016.

Diel plant water use and competitive soil cation exchange interact to enhance NH4+ and K+ availability in the rhizosphere. Espeleta, JF Cardon, ZG, Mayer, KU, Neumann, RB. Plant and Soil. 2016.

The microbiome as a source of new enterprises and job creation: Considering clinical faecal and synthetic microbiome transplants and therapeutic regulation. Leslie, D, Taghavi, S, Henry, C, Gilbert, JA - Microbial Biotechnology, 2016.

A microfluidic device for measuring cell migration towards substrate-bound and soluble chemokine gradients. Schwarz, J, Bierbaum, V, Merrin, J, Frank, T, Hauschild, R, Bollenbach, T, Tay, S, & Mehling, M. Scientific Reports. 2016.

Density of immunogenic antigens does not explain the presence or absence of the T-cell–inflamed tumor microenvironment in melanoma. Spranger, S, Luke, J, Bao, R, Zha, Y, Hernandez, K, Li, Y, Gajewski, AP, Andrade, J, Gajewski, TF. PNAS. 2016.

Towards a predictive understanding of Earth's microbiomes to address 21st Century challenges. Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL. mBio. 7:e00714-16. 2016.

Functional responses of salt marsh microbial communities to long-term nutrient enrichment. Graves CJ, Makrides EJ, Schmidt VT, Giblin AE, Cardon ZG, Rand DM. Applied and Environmental Microbiology. 82:2862-2871. 206.

Tools for the Microbiome: Nano and Beyond. Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GC, Wright AT, Young TD. ACS Nano. 2016 Jan 26;10(1):6-37

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic Ridge. Meyer JL, Jaekel U, Tully BJ, Glazer BT, Wheat GC, Lin HT, Hsieh CC, Cowen JP, Hulme SM, Girguis PR, Huber JA. Scientific Reports. 2016 March 3; 6; 22541

Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria. Angermeyer A, Crosby SC, Huber JA. Environ Microbiol. 2016 Jan;18(1):75-86

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, Morrison HGSogin ML, Li H, Moore JH, Karagas MR. JAMA Pediatr. 2016 Jan 11:1-8

The Developing Microbiome of the Preterm Infant. DiBartolomeo ME, Claud EC. Clin Ther. 2016 Mar 2. pii: S0149-2918(16)30054-6.

Tumor and Host Factors Controlling Antitumor Immunity and Efficacy of Cancer Immunotherapy. Spranger S, Sivan A, Corrales L, Gajewski TF. Adv Immunol. 2016 Jan 22; 130:75-93

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease. Kamdar K, Khakpour S, Chen J, Leone V, Brulc J, Mangatu T, Antonopoulos DA, Chang EB, Kahn SA, Kirschner BS, Young G, DePaolo RW. Cell Host & Microbe. 2016 19(1), 21–31.

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants. Canani BR, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA, Nagler CR. ISME J. 2016 Mar; 10(3):742-50

Genomic analysis of 38 Legionella species identifies large and diverse effector repertoires. Burstein D, Amaro F, Zusman T, Lifshitz Z, Cohen O, Gilbert JA, Pupko T, Shuman HA, Segal G. Nat Genet. 2016 Feb;48(2)

Differential and enhanced response to climate forcing in diarrheal disease due to rotavirus across a megacity of the developing world. Martinez PP, King AA, Yunus M, Faruque AS, Pascual M. Proc Natl Acad Sci USA. 2016 Mar 28. pii 201518977.


A unified initiative to harness Earth's microbiomes. Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donahue TJ, Dorrenstein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA, Unified Microbiome Initiative Consortium. Science. 30 Oct 2015. 

Subseafloor microbial communities in hydrogen-rich vent fluids from hydrothermal systems along the Mid-Cayman Rise. Reveillaud J, Reddington E, McDermott J, Algar C, Meyer JL, Sylva S, Seewald J, German CR, Huber JA. Environ Microbiol. 2015 Dec 10

Sponge symbionts and the marine P cycle. Colman AS. Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4191-2. doi: 10.1073/pnas.1502763112. Epub 2015 Mar 30. 

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, Follows MJ, Fuhrman JA, Jover LF, Lennon JT, Middelboe M, Sonderegger DL, Suttle CA, Taylor BP, Frede Thingstad T, Wilson WH, Eric Wommack K. ISME J. 2015 Jun;9(6):1352-64

Processes affecting extinction risk in the laboratory and in nature. Wootton JT, Pfister CA. Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E5903

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti–PD-L1 efficacy. Corrales SA, Hubert L, Williams N, Aquino-Michaels JB, Earley K, Benyamin ZM, Lei FW, Jabri B, Alegre ML, Chang EB, Gajewski TF. Science. 2015 Nov 15. 350(6264)

The influence of the microbiota on the immune response to transplantation.     Bartman C, Chong AS, Alegre ML.  Current Opinion in Organ Transplantation, 20:1-7, 2015.

Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak. Shogan BD, Belogortseva N, Luong PM, Zaborin A, Lax S, Bethel C, Ward M, Muldoon JP, Singer M, An G, Umanskiy K, Konda V, Shakhsheer B, Luo J, Klabbers R, Hancock LE, Gilbert J, Zaborina O, Alverdy JCSci Transl Med. 2015 May 6;7(286)

Effects of diurnal variation of gut microbes and high fat feeding on host circadian clock function and metabolism. Leone VA, Gibbons, SM, Martinez K, Hutchison AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpalli A, Hubert N, Zale E, Wang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA,. Prendergast BJ, Gilbert JA, and Chang EB. Cell Host & Microbe, 2015;17(5):681-9.

Genome-Wide association studies of the human gut microbiota. Davenport ER, Cusanovich DA, Michelini K, Barreiro LB, Ober C. & Gilad Y. 2015. PLoS One. 10(11)

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice. Howe A, Ringus DL, Williams RJ, Choo ZN, Greenwald SM, Owens SM, Coleman ML, Meyer F, Chang EB. ISME J. 2015 Oct 16.

The role of the commensal microbioa in the regulation of tolerance to dietary allergens. Berni Canani R, Gilbert JA, Nagler CR. Curr Opin Allergy Clin Immunol. 2015 Mar 30

Diverse protist grazers select for virulence-related traits in Legionella. Amaro F, Wang W, Gilbert JA, Anderson OR, Shuman HA. ISME J. 2015 Jul;9(7):1607-18

Evolving new protein-protein interaction specificity through promiscuous intermediates. Aakre CD, Herrou J, Phung TN, Perchuk BS, Crosson S, Laub MT. Cell. 2015 Oct 22;163(3):594-606

Staphylococcal manipulation of host immune responses. Thammavongsa V, Kim HK, Missiakas D, Schneewind O. Nat Rev Microbiol. 2015 Sep;13(9):529-43

Rotifers as experimental tools for investigating aging. Snell TW, Johnston RK, Gribble KE, Mark Welch DB. Invertebr Reprod Dev. 2015 Jan 1;59(1):5-10.

Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health. Perron GG, Inglis RF, Pennings PS, Cobey S. Evol Appl. 2015 Mar;8(3):211-22


Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments. Thomas F, Giblin AE, Cardon ZG, Sievert SM. Front Microbiol. 2014 Jun 24;5:309

Host-specificity among abundant and rare taxa in the sponge microbiome. Reveillaud J, Maignien L, Murat Eren A, Huber JA, Apprill A, Sogin ML, Vanreusel A. ISME J. 2014 Jun;8(6):1198-209

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity. Shade A, Jones SE, Caporaso G, Handelsman J, Knight R, Fierer N, Gilbert JA. mBio. 2014. 5(4).

The long-term maintenance of a resistance polymorphism through diffuse interactions. Karasov TL, Kniskern JM, Gao L, DeYoung BJ, Ding J, Dubiella U, Lastra RO, Nallu S, Roux F, Innes RW, Barrett LG, Hudson RR, Bergelson J. Nature. 2014 Aug 28;512(7515):436-40

The Soil Microbiome Influences Grapevine-Associated Microbiota. Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NB, Mills DA, Martin G, Taghavi S, van der Lelie D, Gilbert JA. mBio. 2015. 6(2)

Longitudinal analysis of microbial interactions between humans and the indoor environment. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vazquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA. Science. 2014 Aug 29; 345(6200):1048-52

Intestinal anastomotic injury alters spatially defined microbiome composition and function. Shogan BD, Smith DP, Christley S, Gilbert JA, Zaborina O, Alverdy JCMicrobiome. 2014 Sep 15;2:35

Human and environmental impacts on river sediment microbial communities. Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA. PLoS One. 2014 May 19;9(5):e97435

VAMPS: a website for visualization and analysis of microbial population structures. Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML. BMC Bioinformatics. 2014 Feb 5;15:41

Exercise Prevents Weight Gain and Alters the Gut Microbiota in a Mouse Model of High Fat Diet-Induced Obesity. Evans CC, LePard KJ, Kwak JW, Stancukas MC, Laskowski S, Doughert J, Moulton L, Glawe A, Wang Y, Leon V, Antonopoulos DA, Smith D, Chang EB, Ciancio MJ. PLoS ONE. 2014 Mar 26. 9(3)

Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. Zaborin A, Smith D, Garfield K, Quensen J, Shakhsheer B, Kade M, Tirrell M, Tiedje J, Gilbert JA, Zaborina O, Alverdy JCMBio. 2014 Sep 23;5(5)

Seasonal variation in human gut microbiome composition. Davenport ER, Mizrahi-Man O, Michelini K, Barreiro LB, Ober C, Gilad Y. 2014 PLoS One. 9(3)

Maternal caloric restriction partially rescues the deleterious effects of advanced maternal age on offspring. Gribble KE, Jarvis G, Bock M, Mark Welch DB. Aging Cell. 2014 Aug;13(4):623-30

Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping. Mark Welch JL, Utter DR, Rossetti BJ, Mark Welch DB, Eren AM, Borisy GG. Front Microbiol. 2014 Nov 7;5:568

Host-directed antimicrobial drugs with broad-spectrum efficacy against intracellular bacterial pathogens. Czyż DM, Potluri LP, Jain-Gupta N, Riley SP, Martinez JJ, Steck TL, Crosson S, Shuman HA, Gabay JE. MBio. 2014 Jul 29;5(4)

Phosphorylation of Bacillus subtilis gene regulator AbrB modulates its DNA-binding properties. Kobir A, Poncet S, Bidenko V, Delumeau O, Jers C, Zouhir S, Grenha R, Nessler S, Noirot P, Mijakovic. Molecular Biology. 2014 Apr 29. 92:1129-1141

Sulfur-mediated electron shuttling during bacterial iron reduction. Flynn TMO'Loughlin EJ, Mishra B, DiChristina TJ, Kemner KM. Science. 2014 May 30. 344(6187):1039-42


Better to light a candle than curse the darkness: illuminating spatial localization and temporal dynamics of rapid microbial growth in the rhizosphere. Herron PM, Gage DJ, Arango Pinedo C, Haider ZK, Cardon ZG. Front Plant Sci. 2013 Sep 2;4:323

Sewage reflects the distribution of human faecal Lachnospiraceae. McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML. Environ Microbiol. 2013 Aug;15(8):2213-27

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML. Microbiome. 2013. 1:9

The roles of competition and mutation in shaping antigenic and genetic diversity in influenza. Zinder D, Bedford T, Gupta S, Pascual M. 2013. PLoS Pathogens 9(1)

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. Claud EC, Keegan KP, Brulc JM, Lu L, Bartels D, Glass E, Chang EB, Meyer F, Antonopoulos DA. Microbiome. 2013 Jul 10. 1:20.


Carbon system measurements and potential climatic drivers at a site of rapidly declining ocean pH. Wootton JT, Pfister CA. PLoS One. 2012;7(12):e53396

Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle. Waldbauer JR, Rodrigue S, Coleman ML, Chisholm SW. PLoS One. 2012;7(8):e43432