Campus alert status is yellow: For the latest campus alert status, news and resources, visit

Search Close Search
Page Menu


* equal contribution
** co-corresponding

Preprints and submitted manuscripts

Bradley E, Schell B, Ward DV, Zeamer A, Bucci V, Haran JP. 2021. The Urinary Microbiome of Older Adults Residing in a Nursing Home Varies with Duration of Residence and Shows Increases in Potential Pathogens. Under Review

Ward DV, Bhattarai SK, Rojas-Correa M, Purkayastha A, Holler D, Qu MD, Mitchell WG, Yang J, Fountain S, Zeamer AL, Forconi C, Fujimori G, Odwar B, Cawley C, McCormick BA, Moormann A, Wessolossky M, Bucci V, Maldonado-Contreras A. 2021. The intestinal and oral microbiomes are robust predictors of covid-19 severity the main predictor of covid-19-related fatality. Under Review. (pre-print doi: 10.1101/2021.01.05.20249061)

Maringanti VS, Bucci V, Gerber GK. 2020. Scalable learning of interpretable rules for the dynamic microbiome domain. Under Review. (pre-print doi:

Dsouza M,  Bhattarai SK, Menon R, Schneider J, Minot S, Greenfield N, Schopf L, Harrison P, Kuijper EJ, Kelly CP, Olle B, Bobilev D, Bucci V, Roberts B, Norman JM. 2019. Pharmacokinetics and Pharmacodynamics of the Live Biotherapeutic Product VE303 in Normal Healthy Volunteers. Under Review. 


Peer-reviewed publications 


44. Haran JPBradley EZeamer ALCincotta LSalive MC Dutta PMutaawe SAnya OMeza-Segura MMoormann AMWard DVMcCormick BABucci V. 2021. Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long-COVID. JCI Insight. doi: 10.1172/jci.insight.152346

43. Haran JP, Zeamer A, Ward DV, Dutta P, Bucci V, McCormick BA. 2021. The Nursing Home Older Adult Gut Microbiome Composition Shows Time-dependent Dysbiosis and is Influenced by Medication Exposures, Age, Environment, and Frailty. The Journals of Gerontology: Series A. doi: 10.1093/gerona/glab167

42. Neto CC*/**, Mortzfeld BM*, Turbitt JR, Bhattarai SK, Yeliseyev V, DiBenedetto N, Bry LM, Bucci V**. 2021. Proanthocyanidin-enriched cranberry extract induces resilient bacterial community dynamics in a gnotobiotic mouse model. Microbial Cell. doi: 10.15698/mic2021.06.752

41. Haran JP, Ward DV, Bhattarai SK, Loew E, Dutta P, Higgins A, McCormick BA, Bucci V. 2021. The High Prevalence of Clostridioides difficile toxins among Nursing Home Elders Associates with a Dysbiotic Microbiome. Gut Microbes. doi: 10.1080/19490976.2021.1897209

40. Wipperman MF*, Bhattarai SK*, Vorkas CK, Maringanti VS, Taur Y, Mathurin L, McAulay K, Vilbrun SC, Francois D, Bean J, Walsh KF, Nathan C, Fitzgerald DW, Glickman MS**, Bucci V**. 2021. Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis. Nature Communications. doi: 10.1038/s41467-021-21475-y 


39. Liu W, Haran JP, Ash AS, Allison JJ, Ye S, Tjia J, Bucci V**, Zhang B**. 2020. High-dimensional Causal Mediation Analysis with a Large Number of Mediators Clumping at Zero to Assess the Contribution of the Microbiome to the Risk of Bacterial Pathogen Colonization in Older Adults. Current Bioinformatics. doi: 10.2174/1574893614666191115123219

38. Heston SM, Young RR, Arshad M, Jenkins K, Martin PL, Ward DV, Bhattarai S, Bucci V, Seed PC, Kelly MS. 2020. Shotgun Metagenomics and Colonization by Antibiotic-resistant Bacteria in Pediatric Hematopoietic Stem Cell Transplant Recipients. Open Forum Infectious Diseases. doi: 10.1093/ofid/ofaa439.484

37. Tanaka JS, Young RR, Heston SM, Jenkins K, Spees LP, Sung AD, Corbet K, Thompson JC, Bohannon L, Martin PL, Stokhuyzen A, Vinesett R, Ward DV, Bhattarai SK, Bucci V, Arshad M, Seed PC, Kelly MS. 2020. Anaerobic Antibiotics and the Risk of Graft-Versus-Host Disease after Allogeneic Hematopoietic Stem Cell Transplantation. Biology of Blood and Marrow Transplantation. doi: 10.1016/j.bbmt.2020.07.011

36. Simmons EL, Bond MC, Koskella B, Drescher K, Bucci V**, Nadell C**. 2020. Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria. mSystems. doi: 10.1128/mSystems.00877-19

35. Palmer JD, Mortzfeld BM, Piattelli E, Silby MW, McCormick BA, Bucci V. 2020. Microcin H47: A Class IIb Microcin with Potent Activity Against Multidrug Resistant Enterobacteriaceae. ACS Infectious Diseases. doi: 10.1021/acsinfecdis.9b00302


34. Bobilev D, Bhattarai SK, 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 Clostridiodes difficile infection stably restores the gut microbiota after vancomycin-induced dysbiosis in adult healthy volunteersOpen Forum Infectious Diseases. doi: 10.1093/ofid/ofz359.130

33. Hellweger F, Vick C, Ruckbeil F, Bucci V. 2019Fresh ideas bloom in gut healthcare to cross-fertilize lake management. Environmental Science & Technology. doi: 10.1021/acs.est.9b04218

32. Hamilton RA, Borcuch T, Allen SJ, Cioffi WR, Bucci V, Krützen M, Connor RC. 2019. Aggression varies with consortship rate and habitat in a dolphin social network Behavioral Ecology and SociobiologyBehavioral Ecology and Sociobiology. doi: 10.1007/s00265-019-2753-1

31. Kelly MS, Ward DV, Severyn CJ, Arshad M, Heston SM, Jenkins K, Martin PL, McGill L, Stokhuyzen A, Bhattarai SK, Bucci V, Seed PC. 2019. Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection in Pediatric Hematopoietic Stem Cell Transplantation Recipients. Biology of Blood & Marrow Transplantation. doi: 10.1016/j.bbmt.2019.07.019

30. Haran JP*, Bhattarai SK*, Foley SE, Dutta P, Ward DV, Bucci V, McCormick BA. 2019. Alzheimer’s Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway. mBio. doi: 10.1128/mBio.00632-19

29. Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, Shiota A, Takeshita K, Yasuma-Mitobe K, Riethmacher D, Kaisho T, Norman JM,  Mucida D, Suematsu M, Yaguchi T, Bucci V, Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier RJ, Atarashi K, Honda K. 2019. A defined commensal consortium elicits CD8 T cells and anti-cancer immunity. Nature. doi: 10.1038/s41586-019-0878-z


28. Rommel T, Kurosawa K, McCully L, Silby MW, Bucci V, Brigham CJ. 2018. Draft Genome Sequence of Halomonas sp. SL1, a PHA-Producing Halophile. Microbiology Resource Announcements. doi: 10.1128/MRA.00915-18

27. Vorkas C, Wipperman M, Li K, Bean, J, Bhattarai SK, Adamow L, Wong P, Aube J, Jean Juste M, Bucci V, Fitzgerald DW, 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. 2018. Journal of Clinical Investigation Insights. doi: 10.1172/jci.insight.121899

26. Campbell C, Dikiy S, Bhattarai SK, Chinen T, Matheis F, Calafiore M, Hoyos B, Hanash A, Mucida D, Bucci V, Rudensky AY. 2018. Extrathymically generated regulatory T cells shape the metabolic function of the intestinal microbiota. Immunity. doi: 10.1016/j.immuni.2018.04.013

25. Stein RR, Tanoue T, Szabady R, Bhattarai SK, Olle B, Norman JM,  Suda W, Oshima K, Hattori M, Gerber GK, Sander C, Honda K, Bucci V. 2018. Computer-guided design of optimal microbial consortia for immune system modulation. eLife. doi: 10.7554/eLife.30916.001

24. Haran J, Bucci V, Dutta P, Ward D, McCormick BA. 2018. The Nursing Home Elder Microbiome Stability and Associations with Age, Frailty, Nutrition, and Physical Location. Journal of Medical Microbiology.


23. Simmons M, Drescher K, Nadell C, Bucci V. 2017. Spatial simulations predict that phage diffusion is a core determinant of phage-bacteria coexistence in biofilms. ISME Journal. doi: 10.1038/ismej.2017.190

22. Palmer JD, Piattelli E, McCormick BA, Silby MW, Brigham CJ, Bucci V. 2017. An engineered probiotic for the inhibition of Salmonella via tetrathionate-induced production of microcin H47. ACS Infectious Diseases. doi: 10.1021/acsinfecdis.7b00114

21. Wipperman MF, Fitzgerald D, Taur Y, Namasivayam S, Sher A, Bean JM, Bucci V**, Glickman MS** 2017. Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after completion of therapy. Scientific Reports. doi: 10.1038/s41598-017-10346-6


20. Bucci V**, Tzen B, Li N, Simmons M, Tanoue T, Bogart E, Deng L, Yeliseyev V, Delaney ML, Liu Q, Olle B, Stein RR, Honda K, Bry L, Gerber GK**. 2016. MDSINE: Dynamical systems analysis for microbiome time-series studies. 2016. Genome Biology. doi: 10.1186/s13059-016-0980-6


19. Haran JP, Wu G, Bucci V, Fischer A, Keang L, Boyer E, Hibberd P. 2015. Antibiotic-Associated Diarrhea in the Emergency Department Observation Unit PatientsEpidemiology & Infection. doi: 10.1017/S0950268816000200

18. Haran JP, Wu G, Bucci V, Fischer A, Boyer E, Hibberd P. 2015. Treatment of Bacterial Skin Infections in Emergency Department Observation Units: Factors Influencing Prescribing Practice. American Journal of Emergency Medicine. doi: 10.1016/j.ajem.2015.08.035

17. Ly L, Underwood G, McCully L, Bitzer A, Godino A, Bucci V, Brigham C, Príncipe A, Fischer S, Silby MW. 2015. Draft Genome Sequences of Pseudomonas fluorescens strains SF39a and SF4c, potential plant growth promotion and biocontrol agents. Genome Announcements--Prokaryotes. doi: 10.1128/genomeA.00219-15


16. bBuffie CG, Bucci V, Stein RR, McKenney P, Ling L, Lipuma L, Gobourne A, No D, Kinnebrew M, Viale A, van den Brink MRM, Jenq RR, Taur Y, Toussaint NC, Xavier JB, Pamer EG. 2014. Precision microbiome reconstitution restores bile acid-mediated resistance to Clostridium difficileNature. doi: 10.1038/nature13828 

15. Bucci V**, Xavier JB**. 2014. Towards predictive models of the human gut microbiome. Journal of Molecular Biology. doi: 10.1016/j.jmb.2014.03.017


14. Stein RR*Bucci V*/**, Toussaint NC, Buffie CG, Ratsch GR, Pamer EG, Sander C, Xavier JB**. 2013. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLOS Computational Biology. doi: 10.1371/journal.pcbi.1003388

13. Carmona-Fontaine C, Bucci V, Akkari L, Deforet M, Joyce JA, Xavier JB. 2013. Emergence of spatial structure in the tumor microenvironment due to Warburg effect. PNAS

12. Nadell C*, Bucci V*/**, Drescher K, Levin S, Bassler B, Xavier JB**. 2013. Cutting through the complexity of cell collectives. Proceedings of the Royal Society B. doi: 10.1098/rspb.2012.2770

11. Ubeda C, Bucci V, Caballero S, Djukovic A, Toussaint NC, Lipuma L, Ling L, Goburne A, No D, Taur Y, Jenq R, van den Brink M, Xavier J, Pamer EG. 2013. Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infection and Immunity. doi: 10.1128/IAI.01197-12


10. Bucci V**, Bradde S, Biroli G, Xavier JB**. 2012. Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. PloS Computational Biology.  

9. Bucci V, Majed N, Hellweger FL, Gu AZ. 2012. Heterogeneity of Intracellular Polymer Storage States in Enhanced Biological Phosphorus Removal (EBPR) – Observation and Modeling. Environmental Science & Technology. doi: 10.1021/es204052p


8. Bucci V, Nunez-Milland D, Twining B, Hellweger FL. 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 VNadell C, Xavier JB. 2011. The evolution of bacteriocin production in bacterial biofilms. The American Naturalist 

6. Bucci VHoover S, Hellweger FL. 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

5. Bucci V, Vulic M, Ruan X, Hellweger FL. 2011. Population dynamics of Escherichia coli in surface water Journal of the American Water Resources Association 

4. Schuler A, Majed N, Bucci V, Hellweger FL, Tu Y, Gu AZ. 2011. Is the whole the sum of its parts? Agent-based modeling of wastewater treatment systems. Water Science Technology 

3. Mathew M, Yao Y, Cao Y, Jain K, Ghosh I, Bucci V, Leitao C, Njoka D, Wei I, Hellweger FL. 2011. Anatomy of an Urban Waterbody: A Case Study of Boston's Muddy River. Environmental Pollution.


2. Hellweger FL, Bucci V, Litman MR, Gu AZ, Onnis-Hayden A. 2009. Biphasic decay kinetics of fecal bacteria in surface water: not a density effect. ASCE-Journal of Environmental Engineering 

1. Hellweger FL, Bucci V. 2009. A bunch of tiny individuals – Individual-based modeling for microbes. Ecological Modeling. 


Non-peer-reviewed publications 

Schuler A, Majed N, Bucci V, Hellweger FL, Tu Y, Gu AZ. 2011. Is the whole the sum of its parts? Agent-based modeling of wastewater treatment systemsProceedings of 2nd IWA/WEF Wastewater Treatment Modeling Seminar 2010. 

Bucci V. 2010. Population Dynamics of Enteric Bacteria in Surface Water: Role of Mutation and Growth. Laboratory Experiments and Agent Based Modeling. ISBN: 9781124500096