Current Projects

Inference and prediction of multispecies microbial communities dynamics

Multispecies microbial communities have a fundamental role in the functioning of many natural, engineered and host-associated systems.

Thanks to recent advances in molecular microbiology and DNA sequencing we now have an enormous amount of data to be analyzed such that we can now envision a near future where the results of this analysis will assist in the design of bioremediation strategies, biofuels and even rational antibiotic therapies.

In this research project we apply computational models proper of engineering disciplines, statistical inference and wet-lab experimentation to infer microbial ecosystems' structure and response to environmental stimuli and to predict their spatial and temporal dynamics.

Examples of model systems under investigation are the human intestinal microbiota, competition and cooperation in biofilms, microbial dynamics in wastewater treatment applications and microbial dynamics in natural surface water.

Cost-benefit of adaptation to external environment in enterophatogenic bacteria populations

When discharged into the external environment (e.g. natural surface water) enteropathogenic bacteria populations such as enterohemorrhagic Escherichia coli are able to survive for long period of times trough 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 costly traits 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 enterophathogenic E. coli O157:H7 as our model system.

Publications

Bucci, V., Xavier, J.B. Mathematical modeling of microbial communities: from bioreactors to the microbiome. Under Review

Stein, R.R., Bucci, V. *, Toussaint, N.T., 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. Under Review

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. Under Review

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

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

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.

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.

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

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.

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.

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.

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

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

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.

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.

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

Recent Graduate Students

Courses

Courses Professor Bucci has taught include:

BIO430 Introdcution to Biological Statistics