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

               Vill AC, De Vlaminck I Danko C, Brito IL. Run-on sequencing enables nascent metatranscriptomics of the human microbiome. Preprint posted to bioRxiv.


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. Current Opinion in Structural Biology. doi:10.1016/

              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.


          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.

          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.


          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.

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.

          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.

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         ​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 lab, ilana brito, microbiome, horizontal gene transfer

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)