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.
Publications
Alverdy, J. C. (2024a). Invited Commentary: Scientific Rationale behind Intestinal Alkaline Phosphatase Administration to Enhance Recovery after Pancreaticoduodenectomy. Journal of the American College of Surgeons, 238(1), 80. https://doi.org/10.1097/XCS.0000000000000888
Alverdy, J. C. (2024b). Studies Involving Surgical Site Infections (SSIs) Without Culture Results, the Antibiotics Chosen for Prophylaxis and Antibiotic Sensitivity Data: “Are they Actionable?” Annals of Surgery, 279(1), 13. https://doi.org/10.1097/SLA.0000000000006033
Bulseco, A. N., Murphy, A. E., Giblin, A. E., Tucker, J., Sanderman, J., & Bowen, J. L. (2024). Marsh sediments chronically exposed to nitrogen enrichment contain degraded organic matter that is less vulnerable to decomposition via nitrate reduction. Science of The Total Environment, 915, 169681. https://doi.org/10.1016/j.scitotenv.2023.169681
Chetty, A., & Blekhman, R. (2024). Multi-omic approaches for host-microbiome data integration. Gut Microbes, 16(1), 2297860. https://doi.org/10.1080/19490976.2023.2297860
Hou, Y., & Pan, T. (2024). TRNA flux and consistency in differentiation. Nature Cell Biology, 26(1), Article 1. https://doi.org/10.1038/s41556-023-01323-5
Hou, Y., Zhang, W., McGilvray, P. T., Sobczyk, M., Wang, T., Weng, S. H. S., Huff, A., Huang, S., Pena, N., Katanski, C. D., & Pan, T. (2023). Engineered mischarged transfer RNAs for correcting pathogenic missense mutations. Molecular Therapy, 0(0). https://doi.org/10.1016/j.ymthe.2023.12.014
Johnson, C., Guo, M., Schneider, M. C., Su, Y., Khuon, S., Reiser, N., Wu, Y., Riviere, P. L., & Shroff, H. (2024). Phase diversity-based wavefront sensing for fluorescence microscopy (p. 2023.12.19.572369). bioRxiv. https://doi.org/10.1101/2023.12.19.572369
Lehmann, C. J., Dylla, N. P., Odenwald, M., Nayak, R., Khalid, M., Boissiere, J., Cantoral, J., Adler, E., Stutz, M. R., Cruz, M. D., Moran, A., Lin, H., Ramaswamy, R., Sundararajan, A., Sidebottom, A. M., Little, J., Pamer, E. G., Aronsohn, A., Fung, J., … Kacha, A. (2024). Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection. Cell Host & Microbe, 32(1), 117-130.e4. https://doi.org/10.1016/j.chom.2023.11.016
Li, Z., Selim, A., & Kuehn, S. (2023). Statistical prediction of microbial metabolic traits from genomes. PLOS Computational Biology, 19(12), e1011705. https://doi.org/10.1371/journal.pcbi.1011705
Little, A. S., Younker, I. T., Schechter, M. S., Bernardino, P. N., Méheust, R., Stemczynski, J., Scorza, K., Mullowney, M. W., Sharan, D., Waligurski, E., Smith, R., Ramanswamy, R., Leiter, W., Moran, D., McMillin, M., Odenwald, M. A., Iavarone, A. T., Sidebottom, A. M., Sundararajan, A., … Light, S. H. (2024). Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nature Microbiology, 9(1), 55–69. https://doi.org/10.1038/s41564-023-01560-2
Mandot, S., Zannoni, E. M., Cai, L., Nie, X., Rivière, P. J. L., Wilson, M. D., & Meng, L. J. (2024). A High-Sensitivity Benchtop X-ray Fluorescence Emission Tomography (XFET) System with a Full-Ring of X-ray Imaging-Spectrometers and a Compound-Eye Collimation Aperture. IEEE Transactions on Medical Imaging, 1–1. https://doi.org/10.1109/TMI.2023.3348791Allert, M., Ferretti, P., Johnson, K. E., Heisel, T., Gonia, S., Knights, D., Fields, D. A., Albert, F. W., Demerath, E. W., Gale, C. A., & Blekhman, R. (2024). Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk (p. 2024.01.28.577594). bioRxiv. https://doi.org/10.1101/2024.01.28.577594
Durkee, M. S., Ai, J., Casella, G., Cao, T., Chang, A., Halper-Stromberg, A., Jabri, B., Clark, M. R., & Giger, M. L. (2024). Pseudo-spectral angle mapping for automated pixel-level analysis of highly multiplexed tissue image data (p. 2024.01.09.574920). bioRxiv. https://doi.org/10.1101/2024.01.09.574920
Mullowney, M. W., Fiebig, A., Schnizlein, M. K., McMillin, M., Rose, A. R., Koval, J., Rubin, D., Dalal, S., Sogin, M. L., Chang, E. B., Sidebottom, A. M., & Crosson, S. (2024). Microbially catalyzed conjugation of GABA and tyramine to bile acids. Journal of Bacteriology, 206(1), e00426-23. https://doi.org/10.1128/jb.00426-23
Oliverio, A. M., Narrowe, A. B., Villa, J. A., Rinke, C., Hoyt, D. W., Liu, P., McGivern, B. B., Bechtold, E. K., Ellenbogen, J. B., Daly, R. A., Smith, G. J., Angle, J. C., Flynn, R. M., Freiburger, A. P., Louie, K. B., Stemple, B., Northen, T. R., Henry, C., Miller, C. S., … Wrighton, K. C. (2024). Rendering the metabolic wiring powering wetland soil methane production (p. 2024.02.06.579222). bioRxiv. https://doi.org/10.1101/2024.02.06.579222
Saha, P., Weigle, I. Q., Slimmon, N., Poli, P. B., Patel, P., Zhang, X., Cao, Y., Michalkiewicz, J., Gomm, A., Zhang, C., Tanzi, R. E., Dylla, N., Al-Hendy, A., & Sisodia, S. S. (2024). Early modulation of the gut microbiome by female sex hormones alters amyloid pathology and microglial function. Scientific Reports, 14(1), Article 1. https://doi.org/10.1038/s41598-024-52246-6
Vineis, J. H., Reznikoff, W. S., Antonopoulos, D. A., Koval, J., Chang, E., Fallon, B. R., Paul, B. G., Morrison, H. G., & Sogin, M. L. (2024). A novel conjugative transposon carrying an autonomously amplified plasmid. MBio, 15(2), e02787-23. https://doi.org/10.1128/mbio.02787-23
Zhang, Z. J., Wu, C., Moreira, R., Dorantes, D., Pappas, T., Sundararajan, A., Lin, H., Pamer, E. G., & van der Donk, W. A. (2024). Activity of Gut-Derived Nisin-like Lantibiotics against Human Gut Pathogens and Commensals. ACS Chemical Biology, 19(2), 357–369. https://doi.org/10.1021/acschembio.3c00577Baker, J. L., Mark Welch, J. L., Kauffman, K. M., McLean, J. S., & He, X. (2024). The oral microbiome: Diversity, biogeography and human health. Nature Reviews Microbiology, 22(2), 89–104. https://doi.org/10.1038/s41579-023-00963-6
Bosch, M. E., Dodiya, H. B., Michalkiewicz, J., Lee, C., Shaik, S. M., Weigle, I. Q., Zhang, C., Osborn, J., Nambiar, A., Patel, P., Parhizkar, S., Zhang, X., Laury, M. L., Mondal, P., Gomm, A., Schipma, M. J., Mallah, D., Butovsky, O., Chang, E. B., … Sisodia, S. S. (2024). Sodium oligomannate alters gut microbiota, reduces cerebral amyloidosis and reactive microglia in a sex-specific manner. Molecular Neurodegeneration, 19(1), 18. https://doi.org/10.1186/s13024-023-00700-w
Campbell, E., Hesser, L. A., Berni Canani, R., Carucci, L., Paparo, L., Patry, R. T., & Nagler, C. R. (2024). A Lipopolysaccharide-Enriched Cow’s Milk Allergy Microbiome Promotes a TLR4-Dependent Proinflammatory Intestinal Immune Response. The Journal of Immunology, 212(4), 702–714. https://doi.org/10.4049/jimmunol.2300518
Fogarty, E. C., Schechter, M. S., Lolans, K., Sheahan, M. L., Veseli, I., Moore, R. M., Kiefl, E., Moody, T., Rice, P. A., Yu, M. K., Mimee, M., Chang, E. B., Ruscheweyh, H.-J., Sunagawa, S., Mclellan, S. L., Willis, A. D., Comstock, L. E., & Eren, A. M. (2024). A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell, 187(5), 1206-1222.e16. https://doi.org/10.1016/j.cell.2024.01.039
Hayashi, N., Lai, Y., Fuerte-Stone, J., Mimee, M., & Lu, T. K. (2024). Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements. Nature Communications, 15(1), 2096. https://doi.org/10.1038/s41467-024-45893-w
Keiluweit, M., Arredondo, M. G., Castro, S., Tfaily, M., & Cardon, Z. (2024). Nutrient and Water Availability Modulate the Destabilization of Mineral-Associated Organic Matter in the Rhizosphere (EGU24-16663). EGU24. Copernicus Meetings. https://doi.org/10.5194/egusphere-egu24-16663
Oliveira, R. A., Pandey, B., Lee, K., Yousef, M., Chen, R. Y., Triebold, C., McSpadden, E., Haro, F., Aksianiuk, V., Ramanujam, R., Kuehn, S., & Raman, A. S. (2024). Statistical design of a synthetic microbiome that clears a multi-drug resistant gut pathogen (p. 2024.02.28.582635). bioRxiv. https://doi.org/10.1101/2024.02.28.582635
Pamer, E. G., Dylla, N., & Lehmann, C. (2024). Biomarkers of Risk for Infection (Patent 20240068007). https://www.freepatentsonline.com/y2024/0068007.html
Pereira, H., Silva, P. C., Davis, M. W., Abraham, L., Babnigg, G., Bengtsson, H., & Johansson, B. (2024). SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences (p. 2024.02.28.582384). bioRxiv. https://doi.org/10.1101/2024.02.28.582384
Podowski, J. C., Forrester, S., Antonopoulos, D. A., Steeb, J. L., Kent, A. D., Davis, J. J., & Schabacker, D. S. (2024). Response of soil bacteria to PUREX chemicals suggests biomarker utility and bioremediation potential. Journal of Radioanalytical and Nuclear Chemistry. https://doi.org/10.1007/s10967-024-09389-7
Saha, P., Weigle, I. Q., Slimmon, N., Poli, P. B., Patel, P., Zhang, X., Cao, Y., Michalkiewicz, J., Gomm, A., Zhang, C., Tanzi, R. E., Dylla, N., Al-Hendy, A., & Sisodia, S. S. (2024). Early modulation of the gut microbiome by female sex hormones alters amyloid pathology and microglial function. Scientific Reports, 14(1), 1827. https://doi.org/10.1038/s41598-024-52246-6
Vigneswaran, Y., Hussain, M., Varsanik, M. A., Corvin, C., Gottlieb, L. J., & Alverdy, J. C. (n.d.). IDEAL Phase 2a Results: Posterior Rectus Sheath Flap for Hiatal Augmentation in Complex Paraesophageal Hernias. Annals of Surgery, 10.1097/SLA.0000000000006247. https://doi.org/10.1097/SLA.0000000000006247
Zhang, W., Chen, H., Sobczyk, M., Krochmal, D., Katanski, C. D., Assari, M., Chen, A., Hou, Y., Dai, Q., & Pan, T. (2024). Quantification of tRNA m1A modification by templated-ligation qPCR. RNA, rna.079895.123. https://doi.org/10.1261/rna.079895.123
Zhang, Z. J., Wu, C., Moreira, R., Dorantes, D., Pappas, T., Sundararajan, A., Lin, H., Pamer, E. G., & van der Donk, W. A. (2024). Activity of Gut-Derived Nisin-like Lantibiotics against Human Gut Pathogens and Commensals. ACS Chemical Biology, 19(2), 357–369. https://doi.org/10.1021/acschembio.3c00577Alverdy, J. (2024). Comment on: Evaluation of a quality improvement intervention to reduce anastomotic leak following right colectomy (EAGLE): pragmatic, batched stepped-wedge, cluster-randomized trial in 64 countries. British Journal of Surgery, 111(3), znae066. https://doi.org/10.1093/bjs/znae066
Chang, E. (2024). Vitamin D Mitigates Hepatic Fat Accumulation and Inflammation and Increases SIRT1/AMPK Expression in AML-12 Hepatocytes. Molecules, 29(6), Article 6. https://doi.org/10.3390/molecules29061401
Harbeitner, R. C., Wittmers, F., Yung, C. C. M., Eckmann, C. A., Hehenberger, E., Blum, M., Needham, D. M., & Worden, A. Z. (2024). Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions. PLOS ONE, 19(4), e0298139. https://doi.org/10.1371/journal.pone.0298139
Hochroth, A., & Pfister, C. A. (2024). Ammonification by kelp associated microbes increases ammonium availability. PLOS ONE, 19(3), e0296622. https://doi.org/10.1371/journal.pone.0296622
Lee, K. K., Liu, S., Crocker, K., Huggins, D. R., Tikhonov, M., Mani, M., & Kuehn, S. (2024). Functional phases define the response of the soil microbiome to environmental change (p. 2024.03.15.584851). bioRxiv. https://doi.org/10.1101/2024.03.15.584851
Oliphant, K., Cruz Ayala, W., Ilyumzhinova, R., Mbayiwa, K., Sroka, A., Xie, B., Andrews, B., Keenan, K., & Claud, E. C. (2024). Microbiome function and neurodevelopment in Black infants: Vitamin B12 emerges as a key factor. Gut Microbes, 16(1), 2298697. https://doi.org/10.1080/19490976.2023.2298697Alverdy, 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 Surgery. https://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 Care, 26(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 Basin. 2023(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 Microbiology, 0(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 Investigation, 133(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 Microbes, 15(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 & Development, 81, 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 Surgery, 57(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 Reports, 13(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 Biology, 36, 100479. https://doi.org/10.1016/j.coisb.2023.100479
Li, Z., Sinha, V., & Kuehn, S. (2023). Constraints on microbial metabolic complexity. Nature Microbiology, 8(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 Chemistry, n/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 Systems, 2(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 Microbiology, 0(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 Abstracts, 6, 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 & Evolution, 7(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 Microbiology, 8(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 Biomedicine, 242, 107802. https://doi.org/10.1016/j.cmpb.2023.107802Chandra, 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 Neurodegeneration, 18(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 Microbes, 15(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 Biology, 21(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 Biology, 30(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 Reports, 42(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. Science, 381(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 Ecology, n/a(n/a). https://doi.org/10.1111/mec.17093
Schön, I., Fontaneto, D., & Peredo, E. L. (2023). Microbiomes of aquatic animals. Hydrobiologia. https://doi.org/10.1007/s10750-023-05328-xAlverdy, 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 Chemistry. https://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 Biochemistry, 184, 109097. https://doi.org/10.1016/j.soilbio.2023.109097
Peredo, E. L., Thomas, S. M., & Cardon, Z. (2023). Confirmation of axenic seedlings. https://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 Microbiology, 15(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 Science, 64(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 Physiology. https://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
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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 JC. Microbiome. 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 JC. MBio. 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 TM, O'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