Publications
* equally contributing author(s)** corresponding author(s)Preprints and submitted manuscripts
Mortzfeld BM**, Bhattarai SK, Bucci V. 2023. Expanding the toolbox: Novel class IIb microcins show activity against gram-negative ESKAPE and plant pathogens. Under Review. (pre-print doi: 10.1101/2023.12.05.570296v1)
Kellogg TD, Ceglia S, Mortzfeld BM, Zeamer AL, Foley SE, Ward DV, Bhattarai SK, McCormick BA, Reboldi, A, Bucci V. 2024. Microbiota encoded fatty-acid metabolism expands tuft cells to protect tissues homeostasis during Clostridioides difficile infection in the large intestine. Under Review. (pre-print doi: 1)
Peer-reviewed publications
2024
59. Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta DR, Hasegawa N, Ohya T, Bhattarai SK, Sasajima S, Aoto Y, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridooshi Y, Sugita K, Stražar M, Avila-Pacheco J, Pierce K, Clish CB, Skelly AN, Hattori M, Nakamoto N, Caballero S, Norman JM, Olle B, Tanoue T, Suda W, Arita M, Bucci V, Atarashi K, Xavier RJ, Honda 2024. Commensal consortia decolonize Enterobacteriaceae via ecological control. Nature https://doi.org/10.1038/s41586-024-07960-6
57. Heston SM, Young RR, Jenkins K, Martin PL, Stokhuyzen A, Ward DV, Bhattarai SK***, Bucci V, Arshad M, Chao NJ, Seed PC, Kelly MS. 2024. The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children. Gut Microbes, 16:1, 2333748.
56. van Lingen E, Nooij S, Terveer EM, Crossette E, Prince AL, Bhattarai SK, Watson A, Galazzo G, Menon R, Szabady RL, Bucci V, Norman JM, van der Woude CJ, van der Marel S, Verspaget HW, van der Meulen-de Jong AE, Keller JJ. 2024. Fecal Microbiota Transplantation engraftment after budesonide or placebo in patients with active ulcerative colitis using pre-selected donors: a randomized pilot study. Journal of Crohn’s and Colitis, jjae0
55. Bhattarai SK, Du M, Zeamer AL, Mortzfeld BM, Kellogg TD, Firat K, Benjamin A, Bean JM, Zimmermann M, Mardi G, Vilbrun SC, Walsh KF, Fitzgerald DW, Glickman MS**, Bucci V**. Commensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption. Science Translational Medicine. doi: 10.1126/scitranslmed.adi9711
2023
54. Zeamer AL, Salive MC, An X, Beaudoin FL, House SL, Stevens JS, Zeng D, Neylan TC, Clifford GD, Linnstaedt SD, Rauch SL, Storrow AB, Lewandowski C, Musey PI, Hendry PL, Sheikh S, Jones CW, Punches BE, Swor RA, Hudak LA, Pascual JL, Seamon MJ, Harris E, Pearson P, Peak DA, Merchant RC, Domeier RM, Rathlev NK, O’Neil BJ, Sergot P, Sanchez LD, Bruce SE, Kessler RC, Koenen KC, McLean SA, Bucci V**, Haran JP**. Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure. Translational Psychiatry. doi: 10.1038/s41398-023-02643-8
53. Bucci V**, 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, Moormann A, Wessolossky M, Maldonado-Contreras A**. 2023. The intestinal microbiota predicts COVID-19 severity and fatality regardless of hospital feeding method. mSystems. doi: 10.1128/msystems.00310-23
52. Leftwich HK, Vargas-Robles D, Rojas-Correa M, Yap YR, Bhattarai S, Ward DV, Fujimori G, Forconi CS, Yeboah T, Carter A, Kastrinakis A, Asirwatham AM, Bucci V, Moormann AM, Maldonado-Contreras A. 2023. The microbiota of pregnant women with SARS-CoV-2 and their infants. Microbiome. doi: 10.1186/s40168-023-01577-z
51. Ceglia S, Berthelette A, Howley K, Li Y, Mortzfeld BM, Bhattarai SK, Yiew NK, Xu Y, Brink R, Cyster JG, Hooper LV, Randolph GJ, Bucci V, Reboldi A. 2023. An epithelial cell-derived metabolite tunes immunoglobulin A secretion by gut resident plasma cells. Nature Immunology. doi: 10.1038/s41590-022-01413-w
2022
50.
Bradley ES, Zeamer AL, Bucci V, Cincotta L, Salive MC, Dutta P, Mutawee S, Anya O, Tocci C, Moorman A, Ward DW, McCormick BA, Haran JP. 2022. Oropharyngeal microbiome profiled at admission is predictive of the need for respiratory support among COVID-19 patients. Frontiers in Microbiology. doi: 10.3389/fmicb.2022.1009440
48. MDITRE: scalable and interpretable machine learning for predicting host status from temporal microbiome dynamics. mSystems. doi: 10.1128/msystems.00132-22
47. Dsouza M, Menon R, Crossette E, Bhattarai SK, Schneider J, Kim Y, Redd S, Caballero S, Felix C, Cornacchione L, Hendrikson J, Watson AR, Minot SS, Greenfield N, Schopf L, Szabady R, Patarroyo J, Smith W, Harrison P, Kuijper EJ, Kelly CP, Olle B, Bobilev D, Bucci V, Roberts B, Faith J, Norman JM. 2022. Colonization of the Live Biotherapeutic Product VE303 and Modulation of the Microbiota and Metabolites in Healthy Volounteers. Cell Host and Microbes. doi: 10.1016/j.chom.2022.03.016
46. Olendzki B, Bucci V, Cawley C, Maserati R, McManus M, Olednzki E, Madziar C, Chiang D, Ward DV, Pellish R, Foley C, Bhattarai S, McCormick BA, Maldonado-Contreras A. 2022. Dietary manipulation of the gut microbiome in inflammatory bowel disease patients: Pilot study. Gut Microbes. doi: 10.1080/19490976.2022.2046244
2021
45. 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. The Journals of Gerontology: Series A. doi: 10.1093/gerona/glab345
44. 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
2020
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
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
2019
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 volunteers. Open Forum Infectious Diseases. doi: 10.1093/ofid/ofz359.130
33. Hellweger F, Vick C, Ruckbeil F, Bucci V. 2019. Fresh 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 Sociobiology. Behavioral 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
2018
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.
2017
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
2016
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
2015
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 Patients. Epidemiology & 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
2014
16. Buffie 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 difficile. Nature. 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
2013
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
2012
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
2011
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 V, Nadell C, Xavier JB. 2011. The evolution of bacteriocin production in bacterial biofilms. The American Naturalist.
6. Bucci V, Hoover 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.
2009
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
Maringanti VS, Bucci V, Gerber GK. 2020. Scalable learning of interpretable rules for the dynamic microbiome domain. Conference paper.
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, Proceedings 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