* co-first author ** co-corresponding author *** student supported by lab

link to Google Scholar page:


38. Bobilev, D., Bhattarai, S.K., Menon, M., Klein, B., Reddy, S., Olle, B., Roberts, B., Bucci, V., Norman J. 2019. VE303, a rationally designed bacterial consortium for prevention of recurrent Clostridioides difficile infection stably restores the gut microbiota after vancomycin-induced dysbiosis in adult healthy volunteers. Open Forum Infectious Diseases, Volume 6, Issue Supplement_2, October 2019, Page S60,

37. Hellweger F., Vick C., Ruckbeil, F., Bucci, V. Fresh ideas bloom in gut healthcare to cross-fertilize lake management. Environmental Science & Technology, Impact Factor 7.149

36. Hamilton, R.A, Borcuch, T., Allen, S.J., Cioffi, W.R., Bucci, V., Krützen, M., Connor, R.C. 2019. Aggression varies with consortship rate and habitat in a dolphin social network Behavioral Ecology and Sociobiology. Behavioral Ecology and Sociobiology (In Press)

35. Palmer J.D., Mortzfeld B.***, Piattelli, E.***, Silby, M.W., McCormick B.A., Bucci, V. 2019. Microcin H47: A Class IIb Microcin with Potent Activity Against Multi-Drug Resistant Enterobacteriaceae. Preliminary accepted in ACS Infectious Diseases.

34. Simmons, M.***, Bond, M., Drescher, Bucci, V.**, K., Nadell, C. 2019. Evolutionary dynamics of phage resistance in bacterial biofilms. Under Review (also available on

33. Kelly, M.S., Ward, D.V., Severyn, C.J., Arshad, M., Heston, S.M., Jenkins, K., Martin, P.L., McGill, L., Stokhuyzen, A., Bhattarai, S.K.***, Bucci, V., Seed, P.C. 2019 . Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection in Pediatric Hematopoietic Stem Cell Transplant Recipients: a Strain-Level Analysis. Biology of Blood and Marrow Transplantation S1083-8791(19)30451-3 DOI:

32. Haran, J.P., Bhattarai, S.K.***, Foley, S.E., Dutta, P., Ward, D.V., Bucci, V., McCormick, B.A. 2019. Alzheimer’s Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway. mBio, Volume 10 Issue 3 e00632-19,

31. Stein, R.R., Tanoue, T., Bhattarai, S.K.***, Olle,B., Norman, J.M., Suda, W., Oshima, K., Hattori, M., Gerber, G.K., Sander, C., Honda., K, Bucci, V. 2019. Resident microbiota determines the efficacy of therapeutic microbial consortia. Under Review

30. Rommel***, T., Kurosawa, K., McCully, L., Silby, M.W., Bucci, V., Brigham, C.J. 2019. Draft Genome Sequence of Halomonas sp. SL1, a PHA-Producing Halophile. Microbiol. Resour. Announc. 8 (1), e00915-18

29. Tanoue, T., Morita, S., Plichta, D.R., Skelly, A.N., Suda, W., Sugiura, Y., Narushima, S., Vlamakis, H., Motoo, I., Sugita, K., Shiota, A., Takeshita, K., Yasuma-Mitobe, K., Riethmacher, D., Kaisho, T., Norman, J.M., Mucida, D., Suematsu, M., Yaguchi, T., Bucci, V., Inoue, T., Kawakami, Y., Olle, B., Roberts, B., Hattori, M., Xavier, R.J., Atarashi, K., Honda, K. 2019. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature, DOI:


28. Vorkas, C., Wipperman, M., Li, K., Bean., J., Bhattarai, S.K.***, Adamow, L., Wong, P., Aube, J,. Jean Juste, M., Bucci, V., Fitzgerald, D.W., Glickman, M.. 2018. Innate T cell responses to early Mycobacterium tuberculosis infection are defined by differential responses of MAIT and gamma delta T cell subsets. JCI Insight 3(19):e121899. insight.121899.

27. Stein, R.R, Tanoue, T., Szabady, R.L. Bhattarai***, S.K., Olle, B., Norman, J.M., Suda, W., Oshima, K., Hattori, M., Gerber, G.K., Sander, C., Honda., K, Bucci, V. 2018 Computational prediction of immune effectors from the microbiome to select for optimal immune-modulating consortia. eLife 2018;7:e30916 DOI: 10.7554/eLife.30916

26. Campbell, C., Dikiy, S., Bhattarai, S.K.***, Chinen, T., Matheis, F., Calafiore, M., Hoyos, B., Hanash, A., Mucida, D., Bucci, V., Rudensky, A.Y. 2018. Extrathymically generated regulatory T cells shape the metabolic function of the intestinal microbiota. Immunity.


25. Haran, J., Bucci, V., Protiva, D., Ward, D., McCormick, B.A. 2017. The Nursing Home Elder Microbiome Stability and Associations with Age, Frailty, Nutrition, and Physical Location. J. Med. Microbiol. doi: 10.1099/jmm.0.000640

24. Simmons, M.***, Drescher, K., Nadell, C., Bucci, V. 2017. Phage mobility is a core determinant of phage-bacteria coexistence in biofilms. ISME Jdoi:10.1038/ismej.2017.190

23. Palmer, J.D.***, Piattelli, E.***, McCormick, B.A., Silby, M.W., Brigham, C.J., Bucci, V. An engineered probiotic for the inhibition of Salmonella via tetrathionate-induced production of microcin H47. ACS Infectious Disease, 10.1021/acsinfecdis.7b00114

22. Wipperman, M.F., Fitzgerald, D., Taur, Y., Namasivayam, S., Sher, A., Bean, J.M., Bucci, V.**, Michael S. Glickman. 2017. Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after completion of therapy. Scientific Reports 7 (10767)


21. Bucci, V.**, Tzen, B., Li, N., Simmons, M.***, Tanoue, T., Bogart, E., Deng,L., Yeliseyev, V., Delaney, M.L., Liu, Q., Olle, B., Stein, R.R., Honda, K., Bry, L., Gerber, G,K. 2016. Dynamical systems analysis for microbiome time-series studies. Genome Biology, 17:121 doi:10.1186/s13059-016-0980-62015

20. Haran, J.P., Wu, G., Bucci, V., Fisher, A., Keang, L., Boyer E.W., Hibberd, P.L. 2016. Antibiotic-associated diarrhoea in emergency department observation unit patients. Epidemiology and Infection DOI:


19. Haran, J.P., Wu, G., Bucci, V., Fisher, A., Keang, L., Boyer E.W., Hibberd, P.L. 2015. Treatment of bacterial skin infections in ED observation units: factors influencing prescribing practice. Am J. Em. Med. doi:10.1016/j.ajem.2015.08.035.

18. Ly LK***, Underwood GE, McCully LM, Bitzer AS, Godino A, Bucci V, Brigham CJ, Príncipe A, Fischer SE, Silby MW. 2015. Draft genome sequences of Pseudomonas fluorescens strains SF39a and SF4c, potential plant growth promotion and biocontrol agents. Genome Announc 3(2):e00219-15. doi:10.1128/genomeA.00219-15


17. Buffie, C.G.. Bucci, V., Stein,R.R., McKenney, P., Ling, L., Lipuma, L., Gobourne, A., No, D., Kinnebrew, M., Viale, A., van den Brink, M.R.M, Jenq, R.R., Taur,Y., Toussaint, N.C., Xavier, J.B., Pamer E.G. 2014. Precision microbiome reconstitution ameliorates Clostridium dicile infection by increasing secondary bile salt synthesis. Nature doi:10.1038/nature13828

16. Bucci, V**., Xavier, J.B. Towards predictive models of the human gut microbiome. Journal of Molecular Biology, S0022-2836(14)00178-8. doi: 10.1016/j.jmb.2014.03.017


15. Stein*,R.R., Bucci,V.*/**, Toussaint, N.C.,  Buffie, C.G., Rätsch, G., Pamer, E.G., Sander, C.,  Xavier, J.B. Ecological modeling from time-series inference: insights into  dynamics and stability of intestinal microbiota.PLoS Computational Biology, doi/10.1371/journal.pcbi.1003388

14. Carmona-Fontaine, C., Bucci, V., Akkari, L., Deforet, M., Joyce, J.A., Xavier, J.B. Emergence of spatial structure in the tumor microenvironment due to Warburg effect. PNAS, 100(48):19402-19407

13. Nadell, C.*, Bucci, V.*, Drescher, K.*, Levin, S., Bassler, B., Xavier, J.B. Cutting through the complexity of cell collectives. Proceedings of the Royal Society B. DOI:10.1098/rsbp.2012.2770

12. Ubeda, C., Bucci, V., Caballero, S., Djukovic, A., Toussaint, N.C.,  Lipuma, L., Ling, L., Goburne, A., No, D., Taur, Y., Jenq, R., van den  Brink, M., Xavier, J., Pamer, E.G. 2013 Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infection and Immunity, 81(3):965 DOI:10.1128/IAI.01197-12


11. Bucci, V.**, Bradde, S., Biroli, G., Xavier, J.B. 2012. Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PloS Computational Biology 8(4):e1002497.

10. Bucci, V., Majed, N., Hellweger, F.L., Gu, A.Z. 2012. Predictions and observations of heterogeneity in intracellular polymer storage states in EBPR populations. Environmental Science & Technology, DOI:10.1021/es204052p.


9. Bucci, V., Nadell, C., Xavier, J.B. 2011. The evolution of bacteriocin production in bacterial biofilms. The American Naturalist, 178(6):E162-173.

8. Bucci, V., Nunez-Milland, D., Twining, B., Hellweger, F.L. 2011. Microscale patchiness leads to large and important intraspecific internal nutrient heterogeneity in phytoplankton. Aquatic Ecology, DOI: 10.1007/s10452-011-9384-6.

7. Bucci, V., Hoover, S., Hellweger, F.L. 2011. Modeling adaptive mutation of Enteric Bacteria in surface water using agent-based methods. Water, Air and Soil Pollution, DOI: 10.1007/s11270-011-1003-6.

6. Bucci, V., Vulic, M., Ruan, X., Hellweger, F.L. 2011. Population dynamics of Escherichia coli in surface water.Journal of the American Water Resources Association, 47:3-611-619.

5. Schuler, A., Majed, N., Bucci, V., Hellweger, F.L., Tu, Y., Gu,  A.Z. 2011. Is the whole the sum of its parts? Agent-based modeling of wastewater treatment systems. Water Science & Technology, 63:8-1590-1598.

4. Mathew, M., Yao, Y., Cao, Y., Jain, K., Ghosh, I., Bucci,V., Leitao, C., Njoka, D., Wei, I., Hellweger, F.L. 2011. Anatomy of an Urban Waterbody: A Case Study of Boston’s Muddy River. Environmental Pollution, 159(8-9):1996-2002


3. Schuler, A., Majed, N., Bucci, V., Hellweger, F.L., Tu, Y., Gu, A.Z. 2010. Is the whole the sum of its parts? Agent-based modeling of wastewater treatment systems. Proceedings of 2nd IWA/WEF Wastewater Treatment Modeling Seminar 2010.


2. Hellweger, F.L., Bucci, V., Litman, M.R., Gu, A.Z., Onnis-Hayden, A. 2009. Biphasic Decay Kinetics of Fecal Bacteria in Surface Water: Not a Density Effect. Journal of Environmental Engineering, 135(5):372-376.

1. Hellweger, F.L., Bucci, V. 2009. A bunch of tiny individuals – Individual-based modeling for microbes.Ecological Modelling, 220(1):8-22.