Publications

The Microbiome Center is home to some of the world's experts in fields from microbiology to engineering, medicine to ecology. Below is a curated selection of published work from our affiliated faculty and scientists. Please visit our affiliate directory to find complete publication lists via member's research group websites.

Alverdy, J. C. (2023a). Commentary on: Role of Microbiome in the Outcomes Following Surgical Repair of Perianal Fistula: Prospective Cohort Study Design and Preliminary Results. World Journal of Surgeryhttps://doi.org/10.1007/s00268-023-07230-y

Alverdy, J. C. (2023b). The role of dietary prehabilitation on anastomotic healing. Current Opinion in Clinical Nutrition & Metabolic Care26(5), 470. https://doi.org/10.1097/MCO.0000000000000956

Baker, J. L., Mark Welch, J. L., Kauffman, K. M., McLean, J. S., & He, X. (2023). The oral microbiome: Diversity, biogeography and human health. Nature Reviews Microbiology, 1–16. https://doi.org/10.1038/s41579-023-00963-6

Bösche, J., Wipfler, R. L., Sharma, K., Worden, A. Z., Hinrichs, K., & Orphan, V. J. (2023). In-Situ Activity of the Heterotrophic Microbial Community in Seep Sediments from the Santa Monica Basin2023(1), 1–2. https://doi.org/10.3997/2214-4609.202333297

Bowen, J. L., Spivak, A. C., Bernhard, A. E., Fulweiler, R. W., & Giblin, A. E. (2023). Salt marsh nitrogen cycling: Where land meets sea. Trends in Microbiology0(0). https://doi.org/10.1016/j.tim.2023.09.010

Frazier, K., Manzoor, S., Carroll, K., DeLeon, O., Miyoshi, S., Miyoshi, J., St. George, M., Tan, A., Chrisler, E. A., Izumo, M., Takahashi, J. S., Rao, M. C., Leone, V. A., & Chang, E. B. (2023). Gut microbes and the liver circadian clock partition glucose and lipid metabolism. Journal of Clinical Investigation133(18), e162515. https://doi.org/10.1172/JCI162515

Grieneisen, L., Blekhman, R., & Archie, E. (2023). How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome. Gut Microbes15(1), 2178797. https://doi.org/10.1080/19490976.2023.2178797

Hehmeyer, J., Spitz, F., & Marlow, H. (2023). Shifting landscapes: The role of 3D genomic organizations in gene regulatory strategies. Current Opinion in Genetics & Development81, 102064. https://doi.org/10.1016/j.gde.2023.102064

Hyoju, S., Machutta, K., Krezalek, M. A., & Alverdy, J. C. (2023). What Is the Role of the Gut in Wound Infections? Advances in Surgery57(1), 31–46. https://doi.org/10.1016/j.yasu.2023.05.002

Lee, E. E. L., O’Malley-Krohn, I., Edsinger, E., Wu, S., & Malamy, J. (2023). Epithelial wound healing in Clytia hemisphaerica provides insights into extracellular ATP signaling mechanisms and P2XR evolution. Scientific Reports13(1), Article 1. https://doi.org/10.1038/s41598-023-45424-5

Lee, K. K., Park, Y., & Kuehn, S. (2023). Robustness of microbiome function. Current Opinion in Systems Biology36, 100479. https://doi.org/10.1016/j.coisb.2023.100479

Li, Z., Sinha, V., & Kuehn, S. (2023). Constraints on microbial metabolic complexity. Nature Microbiology8(10), Article 10. https://doi.org/10.1038/s41564-023-01466-z

Lyu, R., Pajdzik, K., Sun, H.-L., Zhang, L., Zhang, L.-S., Wu, T., Yang, L., Pan, T., He, C., & Dai, Q. (n.d.). A Quantitative Sequencing Method for 5-Formylcytosine in RNA. Israel Journal of Chemistryn/a(n/a), e202300111. https://doi.org/10.1002/ijch.202300111

Massoud, E. C., Hoffman, F., Shi, Z., Tang, J., Alhajjar, E., Barnes, M., Braghiere, R. K., Cardon, Z., Collier, N., Crompton, O., Dennedy-Frank, P. J., Gautam, S., Gonzalez-Meler, M. A., Green, J. K., Koven, C., Levine, P., MacBean, N., Mao, J., Mills, R. T., … Zarakas, C. (2023). Perspectives on Artificial Intelligence for Predictions in Ecohydrology. Artificial Intelligence for the Earth Systems2(4). https://doi.org/10.1175/AIES-D-23-0005.1

Mullowney, M. W., Fiebig, A., Schnizlein, M. K., McMillin, M., Koval, J., Rubin, D., Dalal, S., Sogin, M. L., Chang, E. B., Sidebottom, A. M., & Crosson, S. (2023). Microbially-catalyzed conjugation of GABA and tyramine to bile acids (p. 2023.09.25.559407). bioRxiv. https://doi.org/10.1101/2023.09.25.559407

Pérez Castro, S., Peredo, E. L., Mason, O. U., Vineis, J., Bowen, J. L., Mortazavi, B., Ganesh, A., Ruff, S. E., Paul, B. G., Giblin, A. E., & Cardon, Z. G. (2023). Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes. Applied and Environmental Microbiology0(0), e00988-23. https://doi.org/10.1128/aem.00988-23

Ruff, S. E., Hrabe de Angelis, I., Mullis, M., Payet, J., Kiel Reese, B., Lloyd, K., Steen, A., Morrison, H., Sogin, M., Ladau, J., & Colwell, F. (2023). A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide. ARPHA Conference Abstracts6, e108531. https://doi.org/10.3897/aca.6.e108531

Skwara, A., Gowda, K., Yousef, M., Diaz-Colunga, J., Raman, A. S., Sanchez, A., Tikhonov, M., & Kuehn, S. (2023). Statistically learning the functional landscape of microbial communities. Nature Ecology & Evolution7(11), Article 11. https://doi.org/10.1038/s41559-023-02197-4

Strauss, J., Deng, L., Gao, S., Toseland, A., Bachy, C., Zhang, C., Kirkham, A., Hopes, A., Utting, R., Joest, E. F., Tagliabue, A., Löw, C., Worden, A. Z., Nagel, G., & Mock, T. (2023). Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans. Nature Microbiology8(11), Article 11. https://doi.org/10.1038/s41564-023-01498-5

Subbakrishna Adishesha, A., Vanselow, D. J., La Riviere, P., Cheng, K. C., & Huang, S. X. (2023). Sinogram domain angular upsampling of sparse-view micro-CT with dense residual hierarchical transformer and attention-weighted loss. Computer Methods and Programs in Biomedicine242, 107802. https://doi.org/10.1016/j.cmpb.2023.107802

Chandra, S., Di Meco, A., Dodiya, H. B., Popovic, J., Cuddy, L. K., Weigle, I. Q., Zhang, X., Sadleir, K., Sisodia, S. S., & Vassar, R. (2023). The gut microbiome regulates astrocyte reaction to Aβ amyloidosis through microglial dependent and independent mechanisms. Molecular Neurodegeneration18(1), 45. https://doi.org/10.1186/s13024-023-00635-2

Cho, S., Yang, X., Won, K.-J., Leone, V. A., Chang, E. B., Guzman, G., Ko, Y., Bae, O.-N., Lee, H., & Jeong, H. (2023). Phenylpropionic acid produced by gut microbiota alleviates acetaminophen-induced hepatotoxicity. Gut Microbes15(1), 2231590. https://doi.org/10.1080/19490976.2023.2231590

Feng, H., Bavister, G., Gribble, K. E., & Welch, D. B. M. (2023). Highly efficient CRISPR-mediated gene editing in a rotifer. PLOS Biology21(7), e3001888. https://doi.org/10.1371/journal.pbio.3001888

Grelska, A., Sharan, D., & Light, S. H. (2023). Purine-ifying uric acid by gut microbes. Cell Chemical Biology30(7), 706–708. https://doi.org/10.1016/j.chembiol.2023.06.022

Kennedy, M. S., Zhang, M., DeLeon, O., Bissell, J., Trigodet, F., Lolans, K., Temelkova, S., Carroll, K. T., Fiebig, A., Deutschbauer, A., Sidebottom, A. M., Lake, J., Henry, C., Rice, P. A., Bergelson, J., & Chang, E. B. (2023). Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization. Cell Reports42(8), 113009. https://doi.org/10.1016/j.celrep.2023.113009

Pierre, J. F., Peters, B. M., La Torre, D., Sidebottom, A. M., Tao, Y., Zhu, X., Cham, C. M., Wang, L., Kambal, A., Harris, K. G., Silva, J. F., Zaborina, O., Alverdy, J. C., Herzog, H., Witchley, J., Noble, S. M., Leone, V. A., & Chang, E. B. (2023). Peptide YY: A Paneth cell antimicrobial peptide that maintains Candida gut commensalism. Science381(6657), 502–508. https://doi.org/10.1126/science.abq3178

Rand, D. M., Nunez, J. C. B., Williams, S., Rong, S., Burley, J. T., Neil, K. B., Spierer, A. N., McKerrow, W., Johnson, D. S., Raynes, Y., Fayton, T. J., Skvir, N., Ferranti, D. A., Zeff, M. G., Lyons, A., Okami, N., Morgan, D. M., Kinney, K., Brown, B. R. P., … Cardon, Z. G. (n.d.). Parasite manipulation of host phenotypes inferred from transcriptional analyses in a trematode-amphipod system. Molecular Ecologyn/a(n/a). https://doi.org/10.1111/mec.17093

Schön, I., Fontaneto, D., & Peredo, E. L. (2023). Microbiomes of aquatic animals. Hydrobiologiahttps://doi.org/10.1007/s10750-023-05328-x

Alverdy, J. C. (n.d.). The role of dietary prehabilitation on anastomotic healing. Current Opinion in Clinical Nutrition & Metabolic Care, 10.1097/MCO.0000000000000956. https://doi.org/10.1097/MCO.0000000000000956

Arnold, J., Glazier, J., & Mimee, M. (2023). Genetic Engineering of Resident Bacteria in the Gut Microbiome. Journal of Bacteriology, e0012723. https://doi.org/10.1128/jb.00127-23

Dewey, J. A., Delalande, C., Azizi, S.-A., Lu, V., Antonopoulos, D., & Babnigg, G. (2023). Molecular Glue Discovery: Current and Future Approaches. Journal of Medicinal Chemistryhttps://doi.org/10.1021/acs.jmedchem.3c00449

Garcia Arredondo, M., Fang, Y., Jones, M., Yabusaki, S., Cardon, Z., & Keiluweit, M. (2023). Resolving dynamic mineral-organic interactions in the rhizosphere by combining in-situ microsensors with plant-soil reactive transport modeling. Soil Biology and Biochemistry184, 109097. https://doi.org/10.1016/j.soilbio.2023.109097

Peredo, E. L., Thomas, S. M., & Cardon, Z. (2023). Confirmation of axenic seedlingshttps://protocols.io/view/confirmation-of-axenic-seedlings-cvmww47e

Torres-Morales, J., Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G. (2023). Site-specialization of human oral Gemella species. Journal of Oral Microbiology15(1), 2225261. https://doi.org/10.1080/20002297.2023.2225261

Zhang, J. Y., Xiao, J., Xie, B., Barba, H., Boachie-Mensah, M., Nadeem, U., Spedale, M., Dylla, N., Lin, H., D’Souza, M., Theriault, B., Sulakhe, D., Chang, E. B., & Skondra, D. (2023). Effects of Oral Metformin on Choroidal Neovascularization, RPE/Choroidal Transcriptome, and Gut Microbiota. Investigative Ophthalmology & Visual Science64(8), 2825.

Arvans, D., Chang, C., Alshaikh, A., Tesar, C., Babnigg, G., Wolfgeher, D., Kron, S., Antonopoulos, D. A., Bashir, M., Cham, C., Musch, M., Chang, E. B., Joachimiak, A., & Hassan, H. (2023). Sel1-like Proteins and Peptides are the Major Oxalobacter formigenes-derived Factors Stimulating Oxalate Transport by Human Intestinal Epithelial Cells. American Journal of Physiology-Cell Physiologyhttps://doi.org/10.1152/ajpcell.00466.2021

Castro, S. P., Peredo, E. L., Mason, O. U., Vineis, J., Bowen, J., Mortazavi, B., Ganesh, A., Ruff, S. E., Paul, B. G., Giblin, A. E., & Cardon, Z. G. (2023). Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes (p. 2023.06.08.544202). bioRxiv. https://doi.org/10.1101/2023.06.08.544202

Hanke, P., Parrello, B., Vasieva, O., Akins, C., Chlenski, P., Babnigg, G., Henry, C., Foflonker, F., Brettin, T., Antonopoulos, D., Stevens, R., & Fonstein, M. (2023). Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning. Metabolic Engineering Communications, e00225. https://doi.org/10.1016/j.mec.2023.e00225

Kaplan, D. I., Smith, R. J., Parker, C. J., Roberts, K. A., Hazenberg, P., Morales, J., O’Loughlin, E. J., Boyanov, M. I., Weisenhorn, P., Kemner, K. M., & Powell, B. A. (2023). Natural attenuation of uranium in a fluvial Wetland: Importance of hydrology and speciation. Applied Geochemistry155, 105718. https://doi.org/10.1016/j.apgeochem.2023.105718

Koop-Jakobsen, K., & Dolch, T. (2023). Future climate conditions alter biomass of salt marsh plants in the Wadden Sea. Marine Biodiversity53(3), 41. https://doi.org/10.1007/s12526-023-01347-y

Miller, S. E., Colman, A. S., & Waldbauer, J. R. (2023). Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities. MSystems0(0), e01238-22. https://doi.org/10.1128/msystems.01238-22

Nichols, R. S., Moynihan, M. A., & Martin, P. (2023). Alkaline phosphatase activity in an equatorial coral reef ecosystem unrelated to seasonal nutrient dynamics. Coral Reefshttps://doi.org/10.1007/s00338-023-02383-7

Prabhakara, K. H., & Kuehn, S. (2023). Algae drive convergent bacterial community assembly at low dilution frequency. IScience26(6), 106879. https://doi.org/10.1016/j.isci.2023.106879

Ruff, S. E., Humez, P., de Angelis, I. H., Diao, M., Nightingale, M., Cho, S., Connors, L., Kuloyo, O. O., Seltzer, A., Bowman, S., Wankel, S. D., McClain, C. N., Mayer, B., & Strous, M. (2023). Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems. Nature Communications14(1), Article 1. https://doi.org/10.1038/s41467-023-38523-4

Subramanian, T., Pocivavsek, L., & Alverdy, J. C. (2023). To Operate or Not? Balancing Advanced Imaging, Machine Learning, and the Doctor-Patient Relationship in Complex Clinical Decision Making. Academic Medicine: Journal of the Association of American Medical Colleges98(6S), S34–S36. https://doi.org/10.1097/ACM.0000000000005189

Alverdy, J. C. (2023). Rationale for Colonic Pre-Habilitation Prior to Restoration of Gastrointestinal Continuity. Surgical Infections24(3), 265–270. https://doi.org/10.1089/sur.2023.001

Brown, J., Pascual, M., Wimberly, M., Johnson, L., & Murdock, C. (2023). Humidity—The Overlooked Variable in Thermal Biology of Mosquito-Borne Disease [Preprint]. Preprints. https://doi.org/10.22541/au.168053633.38060615/v1

Fogarty, E. C., Schechter, M. S., Lolans, K., Sheahan, M. L., Veseli, I., Moore, R., Kiefl, E., Moody, T., Rice, P. A., Yu, M. K., Mimee, M., Chang, E. B., Mclellan, S. L., Willis, A. D., Comstock, L. E., & Eren, A. M. (2023). A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut (p. 2023.03.25.534219). bioRxiv. https://doi.org/10.1101/2023.03.25.534219

Gopalakrishnappa, C., Li, Z., & Kuehn, S. (2023). Environmental modulators of algae-bacteria interactions at scale (p. 2023.03.23.534036). bioRxiv. https://doi.org/10.1101/2023.03.23.534036

Khatoon, H., Raza, R. Z., Saleem, S., Batool, F., Arshad, S., Abrar, M., Ali, S., Hussain, I., Shubin, N. H., & Abbasi, A. A. (2023). Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions. BMC Molecular and Cell Biology24(1), 13. https://doi.org/10.1186/s12860-023-00474-5

Skeen, H. R., Willard, D. E., Jones, A. W., Winger, B. M., Gyllenhaal, E. F., Tsuru, B. R., Hackett, S. J., & Novembre, J. (n.d.). Intestinal microbiota of Nearctic-Neotropical migratory birds vary more over seasons and years than between host species. Molecular Ecologyn/a(n/a). https://doi.org/10.1111/mec.16915

Skwara, A., Gowda, K., Yousef, M., Diaz-Colunga, J., Raman, A. S., Sanchez, A., Tikhonov, M., & Kuehn, S. (2023). Learning the functional landscape of microbial communities (p. 2023.03.24.534159). bioRxiv. https://doi.org/10.1101/2023.03.24.534159

 

Funsten, M. C., Yurkovetskiy, L. A., Kuznetsov, A., Reiman, D., Hansen, C. H. F., Senter, K. I., Lee, J., Ratiu, J., Dahal-Koirala, S., Antonopoulos, D. A., Dunny, G. M., Sollid, L. M., Serreze, D., Khan, A. A., & Chervonsky, A. V. (2023). Microbiota-dependent proteolysis of gluten subverts diet-mediated protection against type 1 diabetes. Cell Host & Microbe31(2), 213-227.e9. https://doi.org/10.1016/j.chom.2022.12.009

Giacomini, J. J., Torres-Morales, J., Dewhirst, F. E., Borisy, G. G., & Mark Welch, J. L. (2023). Site Specialization of Human Oral Veillonella Species. Microbiology Spectrum11(1), e04042-22. https://doi.org/10.1128/spectrum.04042-22

Grieneisen, L., Blekhman, R., & Archie, E. (2023). How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome. Gut Microbes15(1), 2178797. https://doi.org/10.1080/19490976.2023.2178797

Hernandez-Alias, X., Katanski, C. D., Zhang, W., Assari, M., Watkins, C. P., Schaefer, M. H., Serrano, L., & Pan, T. (2023). Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation. Nucleic Acids Research51(3), e17. https://doi.org/10.1093/nar/gkac1185

Krezalek, M. A., & Alverdy, J. C. (2023). The Role of the Gut Microbiome on the Development of Surgical Site Infections. Clinics in Colon and Rectal Surgery, 133–137. https://doi.org/10.1055/s-0043-1760719

Rivera-Lugo, R., Huang, S., Lee, F., Méheust, R., Iavarone, A. T., Sidebottom, A. M., Oldfield, E., Portnoy, D. A., & Light, S. H. (2023). Distinct Energy-Coupling Factor Transporter Subunits Enable Flavin Acquisition and Extracytosolic Trafficking for Extracellular Electron Transfer in Listeria monocytogenes. MBio14(1), e03085-22. https://doi.org/10.1128/mbio.03085-22

Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-Habbena, W. (2023). Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. Science of The Total Environment858, 159865. https://doi.org/10.1016/j.scitotenv.2022.159865

Alverdy, J. C. (2023). Biologically inspired gastrointestinal stapler design: “Getting to Zero” complications. The American Journal of Surgeryhttps://doi.org/10.1016/j.amjsurg.2023.01.030

Chandra, S., Sisodia, S. S., & Vassar, R. J. (2023). The gut microbiome in Alzheimer’s disease: What we know and what remains to be explored. Molecular Neurodegeneration18(1), 9. https://doi.org/10.1186/s13024-023-00595-7

Grim, S. L., Stuart, D. G., Aron, P., Levin, N. E., Kinsman-Costello, L. E., Waldbauer, J. E., & Dick, G. J. (2023). Seasonal Shifts in Community Composition and Proteome Expression in a Sulfur-Cycling
Cyanobacterial Mat
 (p. 2023.01.30.526236). bioRxiv. https://doi.org/10.1101/2023.01.30.526236

Krezalek, M. A., & Alverdy, J. C. (2023). The Role of the Gut Microbiome on the Development of Surgical Site Infections. Clinics in Colon and Rectal Surgery, 133–137. https://doi.org/10.1055/s-0043-1760719

Long, D. R., Alverdy, J. C., & Vavilala, M. S. (2023). Updates in Prevention of Surgical Site Infection: Reply. Anesthesiology, 10.1097/ALN.0000000000004463. https://doi.org/10.1097/ALN.0000000000004463

Seo, D., O’Donnell, D., Jain, N., Ulrich, J. D., Herz, J., Li, Y., Lemieux, M., Cheng, J., Hu, H., Serrano, J. R., Bao, X., Franke, E., Karlsson, M., Meier, M., Deng, S., Desai, C., Dodiya, H., Lelwala-Guruge, J., Handley, S. A., … Holtzman, D. M. (2023). ApoE isoform– and microbiota-dependent progression of neurodegeneration in a mouse model of tauopathy. Science379(6628), eadd1236. https://doi.org/10.1126/science.add1236

Subramanian, T., Pocivavsek, L., & Alverdy, J. C. (2023). To Operate or Not? Balancing Advanced Imaging, Machine Learning, and the Doctor-Patient Relationship in Complex Clinical Decision Making. Academic Medicine, e005189. https://doi.org/10.1097/acm.0000000000005189

Wilkes, R. A., Waldbauer, J., Caroll, A., Nieto-Domínguez, M., Parker, D. J., Zhang, L., Guss, A. M., & Aristilde, L. (2023). Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism. Nature Chemical Biology, 1–12. https://doi.org/10.1038/s41589-022-01237-7

Yan, J., Flynn, E., Catalano, J., Brooks, S., Kemner, K., & Weisenhorn, P. (2023). Wetland Soil Characterization and Methane Production Impacted by Nickel Addition, Argonne and Tims Branch Wetlands, September and October 2020. Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE) (United States); Trace Metal Dynamics and Limitations on Biogeochemical Cycling in Wetland Soils and Hyporheic Zones. https://doi.org/10.15485/1908426

Chitale, P., Lemenze, A. D., Fogarty, E. C., Shah, A., Grady, C., Odom-Mabey, A. R., Johnson, W. E., Yang, J. H., Eren, A. M., Brosch, R., Kumar, P., & Alland, D. (2022). A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome. Nature Communications13(1), Article 1. https://doi.org/10.1038/s41467-022-34853-x

DeWolf, E., Brock, M. T., Calder, W. J., Kliebenstein, D. J., Katz, E., Li, B., Morrison, H. G., Maïgnien, L., & Weinig, C. (n.d.). The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa. Molecular Ecologyn/a(n/a). https://doi.org/10.1111/mec.16782

Fuerte-Stone, J., & Mimee, M. (2022). Host happy hour: Phage cocktail targets IBD-associated microbes. Cell Host & Microbe30(10), 1352–1353. https://doi.org/10.1016/j.chom.2022.09.010

He, Q., Pilosof, S., Tiedje, K. E., Day, K. P., & Pascual, M. (2021). Frequency-Dependent Competition Between Strains Imparts Persistence to Perturbations in a Model of Plasmodium falciparum Malaria Transmission. Frontiers in Ecology and Evolution9https://www.frontiersin.org/articles/10.3389/fevo.2021.633263

Kim, H., Jeon, J., Lee, K. K., & Lee, Y.-H. (2022). Longitudinal transmission of bacterial and fungal communities from seed to seed in rice. Communications Biology5(1), Article 1. https://doi.org/10.1038/s42003-022-03726-w

Lee, K. K., Kim, H., & Lee, Y.-H. (2022). Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations. Frontiers in Microbiology13https://www.frontiersin.org/articles/10.3389/fmicb.2022.953300

Lewis, R., de Peiza, P., Chang, E., Lax, I., Croke, J., & Langelier, D. (2022). Feasibility of a Hydrotherapy and Self-Management Education Program for Breast Cancer Patients with Shoulder Impairment. Archives of Physical Medicine and Rehabilitation103(12), e169. https://doi.org/10.1016/j.apmr.2022.08.890

Matute, J. D., Duan, J., Flak, M. B., Griebel, P., Tascon-Arcila, J. A., Doms, S., Hanley, T., Antanaviciute, A., Gundrum, J., Mark Welch, J. L., Sit, B., Abtahi, S., Fuhler, G. M., Grootjans, J., Tran, F., Stengel, S. T., White, J. R., Krupka, N., Haller, D., … Blumberg, R. S. (2022). Intelectin-1 binds and alters the localization of the mucus barrier–modifying bacterium Akkermansia muciniphila. The Journal of Experimental Medicine220(1), e20211938. https://doi.org/10.1084/jem.20211938

Niu, M., Deng, L., Su, L., Ruff, S. E., Yang, N., Luo, M., Qi, Q., Li, J., & Wang, F. (n.d.). Methane supply drives prokaryotic community assembly and networks at cold seeps of the South China Sea. Molecular Ecologyn/a(n/a). https://doi.org/10.1111/mec.16786

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Chang, E. (2022). Effects of Vitamin D Supplementation on Adipose Tissue Inflammation and NF-κB/AMPK Activation in Obese Mice Fed a High-Fat Diet. International Journal of Molecular Sciences, 23(18), Article 18. https://doi.org/10.3390/ijms231810915

Chang, E. H. Y., Lee, H. S., & Volpe, S. J. (2022). The role of viruses in the inception of sinusitis. Clinical and Experimental Otorhinolaryngology. https://doi.org/10.21053/ceo.2022.01004

Crognale, S., Venturi, S., Tassi, F., Rossetti, S., Cabassi, J., Capecchiacci, F., Bicocchi, G., Vaselli, O., Morrison, H. G., Sogin, M. L., & Fazi, S. (2022). Geochemical and microbiological profiles in hydrothermal extreme acidic environments (Pisciarelli Spring, Campi Flegrei, Italy). FEMS Microbiology Ecology, 98(10), fiac088. https://doi.org/10.1093/femsec/fiac088

Feng, H., Bavister, G., Gribble, K. E., & Welch, D. B. M. (2022). Development of Highly Efficient CRISPR-Mediated Gene Editing in the Rotifer Brachionus manjavacas (p. 2022.10.25.513809). bioRxiv. https://doi.org/10.1101/2022.10.25.513809

He, Q., Pilosof, S., Tiedje, K. E., Day, K. P., & Pascual, M. (2022). Corrigendum: Frequency-dependent competition between strains imparts persistence to perturbations in a model of Plasmodium falciparum malaria transmission. Frontiers in Ecology and Evolution, 10. https://www.frontiersin.org/articles/10.3389/fevo.2022.971161

Hyoju, S. K., Keskey, R., Castillo, G., Machutta, K., Zaborin, A., Zaborina, O., & Alverdy, J. C. (2022). A Novel Nonantibiotic Gut-directed Strategy to Prevent Surgical Site Infections. Annals of Surgery, 276(3), 472–481. https://doi.org/10.1097/SLA.0000000000005547

Kim, S. J., Chi, C., Pattanayak, G., Dinner, A. R., & Rust, M. J. (2022). KidA, a multi-PAS domain protein, tunes the period of the cyanobacterial circadian oscillator. Proceedings of the National Academy of Sciences, 119(37), e2202426119. https://doi.org/10.1073/pnas.2202426119

Leone, V. A., Onishi, K. G., Kennedy, M., Riggle, J. P., Pierre, J. F., Maneval, A. C., Spedale, M. N., Theriault, B. R., Chang, E. B., & Prendergast, B. J. (2022). Atypical behavioral and thermoregulatory circadian rhythms in mice lacking a microbiome. Scientific Reports, 12(1), Article 1. https://doi.org/10.1038/s41598-022-18291-9

Lim, H. G., Rychel, K., Sastry, A. V., Bentley, G. J., Mueller, J., Schindel, H. S., Larsen, P. E., Laible, P. D., Guss, A. M., Niu, W., Johnson, C. W., Beckham, G. T., Feist, A. M., & Palsson, B. O. (2022). Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network. Metabolic Engineering, 72, 297–310. https://doi.org/10.1016/j.ymben.2022.04.004

Long, D. R., Alverdy, J. C., & Vavilala, M. S. (2022). Emerging Paradigms in the Prevention of Surgical Site Infection: The Patient Microbiome and Antimicrobial Resistance. Anesthesiology, 137(2), 252–262. https://doi.org/10.1097/ALN.0000000000004267

Miranda, K., Weigel, B. L., Fogarty, E. C., Veseli, I. A., Giblin, A. E., Eren, A. M., & Pfister, C. A. (2022). The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes. MSystems, 7(5), e00592-22. https://doi.org/10.1128/msystems.00592-22

Pfister, C. A. (2022). The evolutionary past and the uncertain future of foundational species. Proceedings of the National Academy of Sciences, 119(33), e2211134119. https://doi.org/10.1073/pnas.2211134119

Tsakalakis, I., Follows, M. J., Dutkiewicz, S., Follett, C. L., & Vallino, J. J. (2022). Diel light cycles affect phytoplankton competition in the global ocean. Global Ecology and Biogeography, 31(9), 1838–1849. https://doi.org/10.1111/geb.13562

Zhang, J. Y., Xie, B., Barba, H., Nadeem, U., Movahedan, A., Deng, N., Spedale, M., D’Souza, M., Luo, W., Leone, V., Chang, E. B., Theriault, B., Sulakhe, D., & Skondra, D. (2022). Absence of Gut Microbiota Is Associated with RPE/Choroid Transcriptomic Changes Related to Age-Related Macular Degeneration Pathobiology and Decreased Choroidal Neovascularization. International Journal of Molecular Sciences, 23(17), Article 17. https://doi.org/10.3390/ijms23179676

Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-Habbena, W. (2022). Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. Science of The Total Environment, 159865. https://doi.org/10.1016/j.scitotenv.2022.159865

Chang, E. (2022). Effects of Vitamin D Supplementation on Adipose Tissue Inflammation and NF-κB/AMPK Activation in Obese Mice Fed a High-Fat Diet. International Journal of Molecular Sciences, 23(18), Article 18. https://doi.org/10.3390/ijms231810915

Chang, E. H. Y., Lee, H. S., & Volpe, S. J. (2022). The role of viruses in the inception of sinusitis. Clinical and Experimental Otorhinolaryngology. https://doi.org/10.21053/ceo.2022.01004

Crognale, S., Venturi, S., Tassi, F., Rossetti, S., Cabassi, J., Capecchiacci, F., Bicocchi, G., Vaselli, O., Morrison, H. G., Sogin, M. L., & Fazi, S. (2022). Geochemical and microbiological profiles in hydrothermal extreme acidic environments (Pisciarelli Spring, Campi Flegrei, Italy). FEMS Microbiology Ecology, 98(10), fiac088. https://doi.org/10.1093/femsec/fiac088

Feng, H., Bavister, G., Gribble, K. E., & Welch, D. B. M. (2022). Development of Highly Efficient CRISPR-Mediated Gene Editing in the Rotifer Brachionus manjavacas (p. 2022.10.25.513809). bioRxiv. https://doi.org/10.1101/2022.10.25.513809

He, Q., Pilosof, S., Tiedje, K. E., Day, K. P., & Pascual, M. (2022). Corrigendum: Frequency-dependent competition between strains imparts persistence to perturbations in a model of Plasmodium falciparum malaria transmission. Frontiers in Ecology and Evolution, 10. https://www.frontiersin.org/articles/10.3389/fevo.2022.971161

Hyoju, S. K., Keskey, R., Castillo, G., Machutta, K., Zaborin, A., Zaborina, O., & Alverdy, J. C. (2022). A Novel Nonantibiotic Gut-directed Strategy to Prevent Surgical Site Infections. Annals of Surgery, 276(3), 472–481. https://doi.org/10.1097/SLA.0000000000005547

Kim, S. J., Chi, C., Pattanayak, G., Dinner, A. R., & Rust, M. J. (2022). KidA, a multi-PAS domain protein, tunes the period of the cyanobacterial circadian oscillator. Proceedings of the National Academy of Sciences, 119(37), e2202426119. https://doi.org/10.1073/pnas.2202426119

Leone, V. A., Onishi, K. G., Kennedy, M., Riggle, J. P., Pierre, J. F., Maneval, A. C., Spedale, M. N., Theriault, B. R., Chang, E. B., & Prendergast, B. J. (2022). Atypical behavioral and thermoregulatory circadian rhythms in mice lacking a microbiome. Scientific Reports, 12(1), Article 1. https://doi.org/10.1038/s41598-022-18291-9

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Long, D. R., Alverdy, J. C., & Vavilala, M. S. (2022). Emerging Paradigms in the Prevention of Surgical Site Infection: The Patient Microbiome and Antimicrobial Resistance. Anesthesiology, 137(2), 252–262. https://doi.org/10.1097/ALN.0000000000004267

Miranda, K., Weigel, B. L., Fogarty, E. C., Veseli, I. A., Giblin, A. E., Eren, A. M., & Pfister, C. A. (2022). The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes. MSystems, 7(5), e00592-22. https://doi.org/10.1128/msystems.00592-22

Pfister, C. A. (2022). The evolutionary past and the uncertain future of foundational species. Proceedings of the National Academy of Sciences, 119(33), e2211134119. https://doi.org/10.1073/pnas.2211134119

Tsakalakis, I., Follows, M. J., Dutkiewicz, S., Follett, C. L., & Vallino, J. J. (2022). Diel light cycles affect phytoplankton competition in the global ocean. Global Ecology and Biogeography, 31(9), 1838–1849. https://doi.org/10.1111/geb.13562

Zhang, J. Y., Xie, B., Barba, H., Nadeem, U., Movahedan, A., Deng, N., Spedale, M., D’Souza, M., Luo, W., Leone, V., Chang, E. B., Theriault, B., Sulakhe, D., & Skondra, D. (2022). Absence of Gut Microbiota Is Associated with RPE/Choroid Transcriptomic Changes Related to Age-Related Macular Degeneration Pathobiology and Decreased Choroidal Neovascularization. International Journal of Molecular Sciences, 23(17), Article 17. https://doi.org/10.3390/ijms23179676

Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-Habbena, W. (2022). Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. Science of The Total Environment, 159865. https://doi.org/10.1016/j.scitotenv.2022.159865

Gallagher, G. E., & Waldbauer, J. R. (2022). Proteome Expression and Survival Strategies of a Proteorhodopsin-Containing Vibrio Strain under Carbon and Nitrogen Limitation. MSystems7(2), e01263-21. https://doi.org/10.1128/msystems.01263-21

Ramírez-Puebla, S. T., Weigel, B. L., Jack, L., Schlundt, C., Pfister, C. A., & Mark Welch, J. L. (2022). Spatial organization of the kelp microbiome at micron scales. Microbiome10(1), 52. https://doi.org/10.1186/s40168-022-01235-w

Sorbara, M. T., & Pamer, E. G. (2022). Microbiome-based therapeutics. Nature Reviews. Microbiologyhttps://doi.org/10.1038/s41579-021-00667-9

Dellaert, Z., Vargas, P. A., La Riviere, P. J., & Roberson, L. M. (2022). Uncovering the Effects of Symbiosis and Temperature on Coral Calcification. The Biological Bulletin, 000–000. https://doi.org/10.1086/716711

Hubrich, F., Bösch, N. M., Chepkirui, C., Morinaka, B. I., Rust, M., Gugger, M., Robinson, S. L., Vagstad, A. L., & Piel, J. (2022). Ribosomally derived lipopeptides containing distinct fatty acyl moieties. Proceedings of the National Academy of Sciences119(3). https://doi.org/10.1073/pnas.2113120119

Wilkes, R. A., Waldbauer, J., & Aristilde, L. (2021). Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth. MBiohttps://doi.org/10.1128/mbio.03259-21

Upreti, K., Rivera-Monroy, V. H., Maiti, K., Giblin, A. E., & Castañeda-Moya, E. (2022). Dissimilatory nitrate reduction to ammonium (DNRA) is marginal relative to denitrification in emerging-eroding wetlands in a subtropical oligohaline and eutrophic coastal delta. Science of The Total Environment819, 152942. https://doi.org/10.1016/j.scitotenv.2022.152942

Klein, S., Frazier, V., Readdean, T., Lucas, E., Diaz-Jimenez, E. P., Sogin, M., Ruff, E. S., & Echeverri, K. (2021). Common Environmental Pollutants Negatively Affect Development and Regeneration in the Sea Anemone Nematostella vectensis Holobiont. Frontiers in Ecology and Evolution, 9, 884. https://doi.org/10.3389/fevo.2021.786037

 

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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.
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The critical role of microbiota within cecal crypts on the regenerative capacity of the intestinal epithelium following surgical stress
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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