Vanni Bucci




Profile Picture - Vanni Bucci


Assistant Professor
Northeastern University, 2004
Civil and Environmental Engineering
Phone: 508-999-8219
Office: Science and Engineering, Room 321







Being trained as an engineer my long-term goal is to apply quantitative analyses to investigate problems in computational and systems biology, microbial ecology and environmental microbiology and engineering. Specifically I am interested in understanding how bacteria populations dynamics evolve as a function of interspecies interactions and environmental pressures.






 Recent Publications | Graduate Students |  Courses


Current Projects

Mathematical modeling from metagenomics - minimizing risk of enteric infections

Enteric infections represent a critical issue in today’s healthcare. Recent analysis of DNA sequencing data has demonstrated that such infections are associated with the prophylactic treatment with broad-spectrum antibiotics. This is due to their role in killing the native intestinal microbiota, which normally antagonizes pathogens. The main goal of this project is to combine recently developed and novel mathematical modeling tools with metabolic pathways inference and experimentation to predict the risk of enteric diseases and to prototype rationally designed fecal transplantation therapies to minimize it. This project is funded by a NIH R15 (AREA) Grant: NIH R15 AI112985-01A1

A new computational framework for the prediction of microbiome dynamics

Dynamics of microbial communities play a fundamental role in the functioning of many natural, engineered and host-associated systems. Even though the application of DNA sequencing technologies has allowed profiling the response of these communities to external perturbations, the resulting knowledge stems from descriptive and correlation-based analysis of these data. This strongly limits the understanding of the ecology (e.g. how the microbes interact) of these systems and more importantly hinders from making quantitative predictions. The studies within this project will deliver new theoretical methods and related computational algorithms that, for the first time, allow forecasting microbiomes’ dynamics that are constrained on sequencing surveys. This project is funded by NSF-ABI 1458347

Fitness trade-off and evolutionary dynamics of enterophatogenic bacteria populations

When discharged into the external environment (e.g. natural surface water) enteropathogenic bacteria populations such as enterohemorrhagic Escherichia coli (EHEC) can survive for extended period of times through adaptation. This survival is potentially dangerous to human health. Principles of evolutionary biology state that adaptation to a particular environment may results in the loss of traits that are needed to succeed in other environments. In this research project we develop experimental and computational work to test the hypothesis that enteropathogenic bacteria populations survive in the natural environment by adapting to it and that this adaptation comes at the cost of reduced fitness in subsequent host colonization and toxicity. We use E. coli O157:H7 and C. rodentium as our model for EHEC.


  1. Gao, C., Bucci, V., Gu, A. 2015. Applying tensor decomposition model for high-dimensional toxicogenomics data analysis and interpretation to identify and understand environmental pollutants-induced toxicity. [Under Review]
  2. Haran J., Wu, G., Bucci, V., Fischer, A., Keang, L., Boyer, E., Hibberd, P. 2015. Antibiotic-Associated Diarrhea in the Emergency Department Observation Unit Patients. [Under Review]
  3. Ly, L., Underwood, G., McCully, L., Bitzer, A., Godino, A., Bucci, V., Brigham, C., Príncipe, A., Fischer, S., Silby, M. 2015. Draft Genome Sequences of Pseudomonas fluorescens strains SF39a and SF4c, potential plant growth promotion and biocontrol agents. Genome Announcements–Prokaryotes, 3(2):e00219-15.
  4. 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. 2014/2015. Precision microbiome reconstitution restores bile acid-mediated resistance to Clostridium difficile. Nature 517, 205–208 (doi:doi:10.1038/nature13828). [IF: 42.351]
  5. Bucci, V., Xavier, J.B. 2014. Towards predictive models of the human gut microbiome. Journal of Molecular Biology, [IF: 3.905]
  6. Stein, R., Bucci, V., Toussaint, N.C., Buffie, C.G., Ratsch, G.R., Pamer, E.G., Sander, C., Xavier, J.B. 2013. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Computational Biology, 9(12): e1003388. [IF: 5.2]
  7. Carmona-Fontaine, C., Bucci, V., Akkari, L., Deforet, M., Joyce, J.A., Xavier, J.B. 2013. Emergence of spatial structure in the tumor microenvironment due to Warburg effect. PNAS, 100(48):19402-19407. [IF: 9.7]
  8. Nadell, C., Bucci, V., Drescher, K., Levin, S., Bassler, B., Xavier, J.B. 2013. Cutting through the complexity of cell collectives. Proceedings of the Royal Society B,
  9. doi:10.1098/rsbp.2012.2770. [IF: 5.4]
  10. 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. [IF: 4.1]
  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. [IF: 5.2]
  12. 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 and Technology, doi: 10.1021/es204052p. [IF: 5.2]
  13. 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, 46(1):101-118, doi: 10.1007/s10452-011-9384-6. [IF: 1.4]
  14. Bucci, V., Nadell, C., Xavier, J.B. 2011. The evolution of bacteriocin production in bacterial biofilms. The American Naturalist, 178(6):E162-173. [IF: 4.7]
  15. 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. [IF: 1.6]
  16. 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. [IF: 1.8]
  17. 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. [IF: 1.1]
  18. 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. [IF: 3.7]
  19. 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. ASCE-Journal of Environmental Engineering, 135(5):372-376. [IF: 1.1]
  20. Hellweger, F.L., Bucci, V. 2009. A bunch of tiny individuals - Individual-based modeling for microbes. Ecological Modeling, 220(1):8-22. [IF: 2.3]

Recent Graduate Students

Matt Simmons (Ph.D. Candidate BMEBT program)

Shatki Bhattarai (Ph.D. Candidate EAS program)

Cybele Collins (Ph.D. Candidate BMEBT program)


Courses Professor Bucci has taught include:

  • BIO411–511: Dynamical modeling of Biological Systems - Lecture and Lab Spring 2015
  • CAS–101: Introduction to College of Arts and Sciences Fall 2014
  • BIO430–530: Introduction to Biological Statistics - Lecture and Lab Fall 2014
  • BIO411–511: Dynamical modeling of Biological Systems - Lecture and Lab Spring 2014
  • BIO430–530: Introduction to Biological Statistics - Lab Fall 2013



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