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van Wijngaarden EW, Brunette MP, Goetsch AG, Brito IL, Hershey DM, Silberstein MN. Rheinheimera sp. T2C2 Bacterial Biofilm for Bioremediation of Cobalt (II). bioRxiv. doi: 10.64898/2026.01.21.700925.
Neubert BC, Choo-Kang C, Petrone BL, iang S, Osborne OW, Subramanian AM, Gedye MJ, Cohen D, Beghini F, Brito IL, Dalisay ALP, Labrador JPH, Madrid ML, Nacis JS, Ronquillo DGD, Santos NLC, de Torres CL, Bedu-Addo K, Bovet P, Forrester TE, Gilbert JA, Lambert EV, Layden BT, Luke A, Muhsen K, Christakis KA, Gubat MJ, Dugas LR, David LA. Increasing plant diversity of global diets. Submitted.
Post, SE, Ceisler HS, Lal RG, Singh A, Deen MA, Bonomo LE, Brito IL. Discovery of a novel cell-penetrating peptide from a human gut commensal-encoded glycosyl hydrolase. Submitted.
Lee YY, Balint D, Ficco K, Cunic L, Morningstar J, Yang J, Zhou H, Post SE, Brito IL. Structure-guided discovery of human-commensal protein-protein interactions expands the human-microbiome interactome. Submitted.
van Wijngaarden EW, Chenc T, Brito IL, Bouklas N, Giometto A, Silberstein MN. Mechanically driven bacteria-based crack detection. (2026) Materials Advances. doi:10.1039/D5MA01053E
Chivu AG, Basso BA, Abuhashem A, Leger MM, Barshad G, Rice EJ, Vill AC, Wong W, Chou SP, Chovatiya G, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis AK, Lis JT, Lewis JJ, Danko CG. Evolution of promoter-proximal pausing enabled a new layer of transcription control. (2025) Nature Structural and Molecular Biology. 2026 Feb;33(2):282-292. doi: 10.1038/s41594-025-01718-y.
Beghini F, Brito IL, Gerstein M, Christakis NA. Characterization of gut microbiomes in rural Honduras reveals novel species and associations with human genetic variation. (2025) Cell Reports. doi:10.1016/j.celrep.2025.116724.
Jaya LE, Brito IL. (2025) Antibiotic effects on the gut microbiome across diverse geographies Trends in Microbiology. doi:10.1016/j.tim.2025.07.003
García-Martínez K, Chen J, Jones J, Woo A, Aucapina A, Brito IL, Leifer CA. Stimulator of interferon genes is required for Toll-Like Receptor-8 induced interferon response. Preprint posted on bioXriv. doi:10.1101/2023.05.15.540812.
Ntekas I, Takayasu L, McKellar DW, Grodner BM, Holdener C, Schweitzer P, Sauthoff M, Shi Q, Brito IL, De Vlaminck I. High resolution spatial mapping of microbiome-host interactions via in situ polyadenylation and spatial RNA sequencing. Preprint posted on bioXriv. doi:10.1101/2024.11.18.624127.
Jones J, García-Martínez KY, Lee YY, Rhee M, Nath RR, Takahashi S, Grodner B, De Vlaminck I, Leifer CA, Brito IL. Gut commensal microbiota drive tailored macrophage responses. (2025) Cell Reports. doi: 10.1016/j.celrep.2025.116157.
Arias SL, van Wijngaarden EW, Balint D, Jones J, Crawford CC, Shukla PJ, Silberstein M, Brito IL. Environmental factors drive bacterial degradation of gastrointestinal mucus. npj Biofilms Microbiomes. 2025 Jul 16;11(1):133. doi: 10.1038/s41522-025-00741-7.
van Wijngaarden EW, Arias SL, Rhee M, Silberstein MN, Brito IL. The role of human intestinal mucus in the prevention of microplastic migration and cell damage. (2025) Biomaterials Science. doi: 10.1039/D4BM01574F.
Zhou H, Shi Q, Vartanian T, Kriegel MA, Brito IL. Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders. (2025) Annals of Rheumatic Disease. doi:10.1136/ard-2024-225829.
Beghini F, Pullman J, Alexander M, Shridhar SV, Prinster D, Singh A, Juárez RM, Airoldi EM, Brito IL, Christakis N. Gut microbiome strain-sharing within isolated village social networks. (2025) Nature. doi: 10.1038/s41586-024-08222-1.
Han L, Pendleton AR, Singh A, Xu R, Scott SA, Palma JA, Diebold P, Malarney KP, Brito IL, Chang PV. Chemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases. (2024) Cell Chemical Biology. doi:10.1016/j.chembiol.2024.05.009.
Zhou H, Shi Q, Vartanian T, Kriegel MA, Brito IL. Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders. (2024) Annals of Rheumatic Disease. doi:10.1136/ard-2024-225829.
Liu C, Cyphert EL, Stephn SJ, Wang B, Morales AL, Nixon JC, Natsoulas NR, Garcia M, Blazquez Carmona P, Vill AC, Donnelly EL, Brito IL, Vashishth D, Hernandez CJ. Microbiome-induced increases and decreases in bone tissue strength can be initiated after skeletal maturity. (2024) Journal of Bone and Mineral Research. doi:10.1093/jbmr/zjae157.
Vanden Brink H, Vandeputte DF, Brito IL, Burgert TS, Barral R, Ronnekleiv OK, Roberson MS, Lomniczi A. Changes in the bile acid pool and timing of female puberty: potential novel role of hypothalamic TGR5. (2024) Endocrinology. doi:10.1210/endocr/bqae098.
Shridhar SV, Beghini F, Alexander M, Singh A, Juarez RM, Brito IL*, Christakis NA*. Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in rural Honduras. (2024) Cell Reports. doi: 10.1016/j.celrep.2024.114442
Bowers RM, Gonzalez-Pena V, Wardhani K, Goudeau D, Blow M, Udwary DW, Klein D, Vill AC, Brito IL, Woyke T, Malmstrom RR, Gawad C. scMicrobePTA: Near complete genomes from single bacterial cells. (2024) ISME Communications. doi: 10.1093/ismeco/ycae085.
Cyphert EL, Liu C, Morales AL, Nixon JC, Blackford E, Garcia M, Cevallos N, Turnbaugh PJ, Donnelly E, Brito IL, Booth SL, Hernandez CJ. Effects of high dose aspartame-based sweetener on the gut microbiota and bone strength in young and aged mice. (2024) JBMR Plus. doi:10.1093/jbmrpl/ziae082..
Han L, Pendleton AR, Singh A, Xu R, Scott SA, Palma JA, Diebold P, Malarney KP, Brito IL, Chang PV. Chemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases. (2024) Cell Chemical Biology. doi:10.1016/j.chembiol.2024.05.009.
Grodner B, Shi H, Farchione O, Vill AC, Diebold P, Ntekas I, Zipfel W, Brito IL, De Vlaminck I. Spatial mapping of mobile DNA elements in complex microbiomes at single-cell resolution. (2024) Nature Microbiology. doi:10.1038/s41564-024-01735-5.
Xiao X, Singh A, Giometto A, Brito IL. Segatella copri clades adopt distinct roles within a single individual's gut. (2024) npj Biofilms and Microbiomes. doi:10.1038/s41522-024-00590-w.
Van Wijngaarden EW, Brito IL, Hershey D, Silberstein MN. Engineering bacterial biomanufacturing: characterization and manipulation of Sphingomonas sp. LM7 extracellular polymers (2024) RCS Soft Matter doi:10.1039/D4SM00712C
Zhao L*, Arias SL*, Brito IL**, Yeo J**. Coarse-grained modeling and experimental investigation of the viscoelasticity of human gut mucus and nanoparticle dynamics. (2024) (*contributed equally; **co-corresponding author) International Journal of Biological Macromolecules. doi:10.1016/j.ijbiomac.2024.131434
Reutera MA, Tuckera M, Marforia Z, Shishania R, Bustamantea JM, Morenoa R, Nikhil Joshic N, Brito IL, Durbin-Johnson B, Nandakumare R, Cummings BP. Dietary resistant starch supplementation upregulates deoxycholic acid production in mice. (2024) Gut Microbes. doi:10.1080/19490976.2024.2315632
Jones J, Shi Q, Nath RR, Brito IL. Keystone pathobionts associated with colorectal cancer promote an oncogenic reprograming. (2024) PLoS One. doi: 10.1371/journal.pone.0297897
Xiao X*, Le HH*, Lee MT, Lamm D, Johnson EL*, Brito IL*. (2023) Prevotella copri variants among a single host diverge in sphingolipid production. mBio. doi:10.1128/mbio.02409-23. (§contributed equally; *co-corresponding author)
Vill AC, Rice EJ, De Vlaminck I, Danko C, Brito IL. (2023) Run-on sequencing enables nascent metatranscriptomics of the human microbiome. Nature Microbiology. doi: 10.1038/s41564-023-01558-w
Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Vallès-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. The Role of Social Transmission of Microbes in Host Immunity, Disease, and Health. (2024) Cell. doi:10.1016/j.cell.2023.12.014.
Diebold P, Rhee M, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V,
Deshpande P, Alexander M, Hoa NT, Christakis N, Iqbal N, Ali A, Mathad J,
Brito IL. (2023) Clinically relevant antimicrobial genes are carried by a restricted
set of organisms in individuals’ gut microbiomes worldwide.
Nature Communications doi:10.1038/s41467-023-42998-6.
Balint D, Brito IL. Human-gut bacterial protein-protein interactions: Understudied
but impactful to human health. (2023)
Trends in Microbiology. doi:10.1016/j.tim.2023.09.009.
Loyola Irizarry HG, Brito IL. Characterizing conjugative plasmids from an antibiotic-
resistant dataset for use as broad-host delivery vectors. (2023) Frontiers of Microbiology.
doi:10.3389/fmicb.2023.1199640.
Grodner B, Shi H, Farchione O, Vill A, Diebold P, Ntekas I, Zipfel W, Brito IL, De Vlaminck I. Spatial mapping of mobile DNA elements in complex microbiomes at single-cell resolution. (2023) bioXriv. doi:10.1101/2023.06.09.544291v1
García-Martínez K, Chen J, Jones J, Woo A, Aucapina A, Brito IL, Leifer CA. Stimulator of interferon genes is required for Toll-Like Receptor-8 induced interferon response. (2023) bioXriv. doi:10.1101/2023.05.15.540812.
Jones J, Shi Q, Nath RR, Brito IL. Keystone pathobionts
associated with colorectal cancer promote an oncogenic
reprogramming. (2023) bioXriv. doi:10.1101/2023.04.03.535410
Pullman J, Beghini F, Alexander M, Shridhar SV, Prinster D, Brito IL,
Christakis N. Detailed social network interactions and gut
microbiome strain-sharing within isolated villages in Honduras.
(2023) bioXriv. doi: 10.1101/2023.04.06.535875.
Shridhar SV, Beghini F, Alexander M, Brito IL*, Christakis NA*.
Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in rural Honduras. (2023) medxriv. doi: 10.1101/2023.04.11.23288404.
Ma Y, Sannino D, Linden JR, Haigh S, Zhao B, Grigg JB, Zumbo P, Dündar F, Butler D, Profaci CP, Telesford KM, Winokur P, Rumah KR, Gauthier S, Fischetti VA, McClane B, Uzal FA, Zexter L, Mazzucco M, Rudick R, Danko D, Balmuth E, Nealon N, Perumal J, Kaunzner UW, Brito IL, Chen Z, Xiang J, Betel D, Daneman R, Sonnenberg GF, Mason C, Vartanian T. Epsilon toxin-producing Clostridium perfringens colonize the MS gut microbiome and epsilon toxin overcomes immune privilege. (2023) Journal of Clinical Investigation doi:10.1172/JCI163239.
Chivu AG, Abuhashem A, Barshad G, Rice EJ, Leger MM, Vill AC, Wong W, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis AK, Lis JT, Lewis JJ, Danko CG. Evolution of promoter-proximal pausing enabled a new layer of transcription control. (2023) Preprint posted to bioXriv. doi:10.1101/2023.02.19.529146
Porras AM, Zhou H, Shi Q, Xiao X, JRI Live Cell Bank, Longman R, Brito IL. Inflammatory bowel disease-associated gut commensals degrade components of the extracellular matrix. (2022) mBio. doi:10.1128/mbio.02201-22
Graney P, Zhong Z, Post S, Brito IL, Singh A. Engineering early memory B cell-like phenotype in hydrogel-based immune organoids. (2022) Journal of Biomedical Materials Research. doi: 10.1002/jbm.a.37388.
New FN, Baer BR, Clark AG, Wells MT, Brito IL. Collective effects of human genomic variation on microbiome function. (2022) Scientific Reports. doi: 10.1038/s41598-022-07632-3.
Post SE, Brito IL. Commensal protein structures and interactions provide mechanistic insight into microbiota-host crosstalk.(2022) Current Opinion in Structural Biology. doi:10.1016/j.sbi.2022.102354.
Zhou H*, Beltrán JF*, Brito IL. Host-microbiome protein-protein interactions capture mechanisms in human disease. (*contributed equally) (2022) Genome Biology. doi: 10.1186/s13059-022-02643-9
New FN, Baer BR, Clark AG, Wells MT, Brito IL. Collective effects of human genomic variation on microbiome function. (2022) Scientific Reports. doi: 10.1038/s41598-022-07632-3.
Zhou H, Beltran J, Brito IL. Functions predict horizontal gene transfer and the emergence of antibiotic resistance (2021) Science Advances. doi: 10.1126/sciadv.abj5056.
Porras AM, Shi Q, Zhou H, Callahan RL, Montenegro G, Solomons N, Brito IL. Geographic differences in gut microbiome composition affect susceptibility to enteric infection. (2021) Cell Reports. doi:10.1016/j.celrep.2021.109457.
Diebold P, New F, Hovan M, Satlin M, Brito IL. Detecting mobilized antibiotic resistant genes in natural bacterial communities using one-step isolation and lysis PCR. (2021) eLife. doi:10.7554/eLife.66834
Brito IL. The comings and goings of the healthy human gut microbiota. (2021) Cell Host & Microbe. doi:10.1016/j.chom.2021.06.011.
N’Guessan A, Brito IL, Serohijos AWR, Shapiro BJ. Mobile gene sequence evolution within individual human gut microbiomes is better explained by gene-specific than host-specific selective pressures.(2021) Genome Biology and Evolution. doi: 10.1093/gbe/evab142.
Brito IL. Systems-level methods to examine gene flow in the human microbiome. (2021) Nature Reviews Microbiology. doi: 10.1038/ s41579-021-00534-7
Arias SL, Brito IL. Biophysical determinants of biofilm formation in the gut. (2021) Current Opinion in Biomedical Engineering. doi.org/10.1016/j.cobme.2021.100275
Shi, H, Shi, Q, Grodner B, Zipfel W, Brito IL, De Vlaminck I. Highly multiplexed spatial mapping of microbial communities. (2020) Nature. doi: 10.1038/s41586-020-2983-4
Shin JH, Choe D, Ransegnola B, Hong HR, Onyekwere I, Cross T, Shi Q, Westblade LF, Brito IL, Dörr T. (2020) A multifaceted cellular damage repair and prevention pathway promotes high level tolerance to β-lactam antibiotics. EMBO Reports doi:10.15252.embr.202051790
Kent AG, Vill AC, Shi Q, Satlin M, Brito IL. Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C. Nature Communications. (2020) 11, 4379. doi: 10.1038/s41467-020-18164-7.
Graney P, Lai K, Post SE, Brito IL, Cyster J, Singh A. Organoid polymer functionality and mode of Klebsiella pneumoniae membrane antigen presentation regulates ex vivo germinal center epigenetics in young and aged B cells. (2020) Advanced Functional Materials. doi:10.1002/adfm.202001232
Beltrán JF, Brito IL. (2019) Host-microbiome protein-protein interactions capture mechanisms in human disease. bioRxiv. doi: 10.1101/821926.
Matus M, Duvallet C, Soule MK, Kearney SM, Endo N, Ghaeli N, Brito IL, Ratti C, Kujawinski EB, Alm EJ. (2019) 24-hour multi-omics analysis of residential sewage reflects human activity and informs public health. bioRxiv. doi:10.1101/728022
Porras AM, Brito IL. The internationalization of human microbiome research. (2019) Current Opinion in Microbiology. doi: 10.1016/j.mib.2019.09.012.
Hernandez CJ, Yang X, Ji G, Niu Y, Sethuraman AS, Koressel J, Shirley M, Fields MW, Chyou S, Li TM, Luna M, Callahan RL, Ross FP, Lu TT, Brito IL, Carli AV, Bostrom MPG. Disruption of the Gut Microbiome Increases the Risk of Periprosthetic Joint Infection in Mice. Clinical Orthopaedics and Related Research. (2019) 477(11):2588-2598. doi: 10.1097/CORR.0000000000000851.
Parasar, B, Zhou H, Xiao X, Shi Q, Brito IL, Chang P. Chemoproteomic profiling of gut microbiota-associated bile salt hydrolase activity. (2019) ACS Central Science. doi: 10.1021/acscentsci.9b00147.
Brito IL*, Gurry T, Zhao S, Huang K, Young S, Shea T, Naisilisili W, Jenkins AP, Jupiter SD, Gevers D, Alm EJ*. Transmission of human-associated microbiota along family and social networks. (2019) Nature Microbiology. doi: 10.1038/s41564-019-0409-6 *co-corresponding authors
Mosquera MJ, Kim S, Zhou H, Jing TT, Luna M, Guss JD, Reddy P, Lai K, Leifer CA, Brito IL, Hernandez C, Singh A. Immunomodulatory nanogels overcome restricted immunity in a murine model of gut microbiome-mediated metabolic syndrome. (2019) Science Advances. 5(3), eaav9788. doi: 10.1126/sciadv.aav9788
Guss JD, Ziemian SN, Luna M, Sandoval TN, Holyoak DT, Guisado GG, Roubert S, Callahan RL, Brito IL, van der Meulen MCH, Goldring SR, Hernandez CJ. The effects of metabolic syndrome, obesity, and the gut microbiome on load-induced osteoarthritis. (2018) Osteoarthritis and Cartilage. S1063-4584(18)31461-4. doi: 10.1016/j.joca.2018.07.020.
Singh A, Brito IL, Lammerding J. Beyond tissue stiffness: Advanced materials to model the tumor microenvironment and drug resistance. (2018) Trends in Cancer. doi: 10.1016/j.trecan.2018.01.008
Champer M, Wong AM, Champer J, Brito IL, Messer PW, Clark AG, Hou JY, Wright JD. (2017) The role of the vaginal microbiome in gynecological cancer. British Journal of Obstetrics and Gynecology. doi: 10.1111/1471-0528.14631.
Xu L, Brito IL, Alm EJ, Blainey PB. (2016) ‘Virtual Microfluidics’ for digital quantification and single-cell sequencing. Nature Methods. doi: 10.1038/nmeth.3955.
Brito IL, Yilmaz S, Huang K, Tamminen M, Smillie CS, Jupiter SD,
Naisilisili W, Jenkins AP, Wortman JR, Birren BW, Singh AK, Gevers D, Alm EJ. (2016) Mobile genes in the human microbiome are structured at global, regional, and individual scales. Nature. doi: 10.1038/nature18927
Brito IL, Alm EJ. (2016) Tracking Strains in the Microbiome: Insights from Metagenomics and Models. Frontiers in Microbiology. 7(109) doi:10.3389/fmicb.2016.00712.
Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, Weitz D, Pitkänen LK, Vigneault F, Virta MP, Alm EJ. (2016) Massively parallel sequencing of gene pairs within single cells by emulsion-fusion PCR. ISME J. 10(2):427-436.
Cleary B, Brito IL, Huang K, Gevers D, Alm EJ. (2015) Eigen-genome informed partitioning of metagenomic collections. Nature Biotechnology. 33(10):1053-60.
Preheim SP, Perrotta AR, Friedman J, Smilie C, Brito IL, Smith MB, Alm EJ. (2013) Computational methods for high-throughput comparative analyses of natural microbial communities. Methods in Enzymology. 2013. 531:353-70.
Papers unrelated to our current work:
Ferguson PFB, Breyta R, Brito IL, Kurath G, Ladeau SL. An epidemiological model of virus transmission in salmonid fishes of the Columbia River Basin. (2018) Ecological Modelling. 377, 1-15. doi: 10.1016/j.ecolmodel.2018.03.002.
Breyta R*, Brito IL*, Ferguson P, Kurath G, Naish K, Purcell M, Wargo A, LaDeau S. Transmission routes maintaining a viral pathogen of steelhead trout within a complex multi-host assemblage. (2017) Ecology and Evolution. *co-first authors. doi: 10.1002/ece3.3276, PMC5648648
Bogich TL, Olival KJ, Hosseini P, Zambrana-Torrelio C, Funk S, Brito IL, Epstein JH, Brownstein J, Joly D., Levy M, Jones KE, Morse SS, Karesh W, Mazet J, Daszak P. “Using mathematical models in a unified approach to predicting the next emerging infectious disease.” In Conservation Medicine: Applied Cases of Ecological Health. Ed. AA Aguirre, RS Ostfeld, and Daszak P. (2012) Oxford University. New York, USA.
Sheltzer JM, Blank HM, Pfau SJ, Tange Y, George BM, Humpton TJ, Brito IL, Takeda J, Hiraoka Y, Niwa O, Amon A. (2011) Aneuploidy Drives Genomic Instability. Science. 333(6045):1026-30.
Breyta R, Brito IL, Kurath G, LaDeau S. (2016) Infectious hematopoietic necrosis virus virological and genetic surveillance 2000-2012. Ecology. doi: 10.1002/ecy.1634.
Kennedy DA, Kurath G, Brito IL, Purcell MK, Read AF, Winton JR, Wargo AR. (2016) Potential drivers of virulence evolution in aquaculture. Evolutionary Applications. 9(2):344-54.
Hung AY, Sung CC, Brito IL, Sheng, M. (2010) Degradation of postsynaptic scaffold GKAP spine morphology by the TRIM3 ubiquitin ligase in rat hippocampal neurons. PLoS One. 24:5(3):e9842.
Brito IL, Yu HG, Amon A. (2010) Condensins promote co-orientation of sister chromatids in budding yeast. Genetics. 185(1):55-64.
Huang J, Brito IL, Villén J, Gygi SP, Amon A, Moazed D. (2006) Inhibition of homologous recombination by a cohesion-associated clamp complex recruited to the rDNA recombination enhancer. Genes and Development. 20(20):2887-901.
Brito IL, Monje-Casas F., Amon A. (2010) The Lrs4-Csm1 monopolin complex associates with kinetochores during anaphase and is required for accurate chromosome segregation. Cell Cycle. 9(17)