Research Projects
Dynamics of microbial populations are critical for human health. Auto-inflammatory disease, colitis, sepsis and obesity are all dysbiotic conditions that depend on the interactions between microbes (pathogenic and beneficial), the host, and the surrounding environment. As the traditional drug-based treatment to cure these conditions is ineffective due to selection for resistance and disruption of the healthy balance in the resident intestinal flora, it is necessary to determine targeted therapies that effectively cure these diseases while minimizing side effects. The goal of my research program is to develop new therapies that, by exploiting the ecological and evolutionary processes underlying these microbes’ dynamics, cure or prevent intestinal diseases. We achieve this by combining our expertise at the interface between engineering, systems biology and microbiology, with that in immunology, medicine and infectious disease from our collaborators.
The list of current and past lab funded projects is below:
Current
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NIH-NIAID 1U01AI172987-01 (Vanni Bucci) Development of targeted microbiome therapeutics and dietary interventions for potent intestinal barrier promotion to minimize GI-ARS Generation of novel microbiome therapeutic agents and microbiome-promoting dietary interventions that, by specifically targeting intestinal barrier function, minimize GI-ARS and increase survival after total body irradiation. Total $2,947,626.00, direct $1,795,750.00, indirect $1,151,876.00 Role: PI (10% effort) |
02/01/2023 – 01/31/2028 |
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DOD CDMRP W81XWH-20-2-0013 (Vanni Bucci) Mathematical modeling and synthetic biology to discover new ESBL-PE eradicating microbiome-based therapeutics Discovery and testing of new wildtype and engineered bacteriotherapeutics to decolonize ESBL-producing E. coli Total $2,048,296, direct $1,494,540, indirect $553,756 Role: PI (20% effort) |
09/01/2020 – 08/31/2023 |
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Gates Foundation INV-046284 (Vanni Bucci) MBQ2/3: Analytical support for Experimental Medicine Platform Develop a suite of computational methods allowing for the systematic identification and optimization of microbiome intervention strategies to maximize EED resolution in pregnant mothers from Pakistan, Bangladesh, Zambia, and Senegal Total $682,233 Role: PI (20% effort) |
09/01/2022 – 08/31/2024 |
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NIH-NGMS R01-1042312909A1 (Georg Gerber) Bayesian Machine Learning Tools for Analyzing Microbiome Dynamics Development of Machine Learning Methods and Software to analyze longitudinal microbiome data Total $352,296, direct $215,943, indirect $136,353 Role: Co-PI (12% effort) |
09/01/2018 – 08/31/2023 |
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Sponsored Research Agreement Vedanta Biosciences Inc (Vanni Bucci) Machine learning of immune-modulating microbial communities Application of machine learning and statistical inference methods to host-microbiome data to identify and optimize microbial consortia with potent anti-inflammatory properties. Total $636,016 Role: PI (5% effort) |
09/01/2019 – 08/31/2023 |
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NIH-NIDDK 1R01DK125407-01 (Beth McCormick) Intestinal Homeostasis Induced by Commensals to determine what members of the microbiota community and their metabolites regulate the P-gp signaling in the colon and determine the mechanism(s) by which the microbiota influence the balance between the P-gp/MRP2 axes in the intestine. Total $496,016 Role: Co-I (5% effort) |
7/15/2020 – 4/30/2024 |
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U19 AI162568-01 (Sabine Ehrt) Determinants of TB control, relapse and reinfection We will test the hypothesis that individual differences in microbiome composition and function, either pretreatment or induced by antimycobacterials during treatment, are associated with, and predictive of, different rates of pathogen clearance, resolution of inflammatory markers of active TB, and ultimately treatment success (both early sterilization and lack of relapse). Total $829,832 Role: Project 3 PI (10% effort) |
7/1/2021 – 6/30/2026 |
Completed
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NSF-MCB (1817342) (Carey Nadell) Viral micro-epidemics and evolutionary dynamics in bacterial biofilms Development of mathematical models and microfluidics experiments to investigate ecological and evolutionary dynamics of bacteriophages and bacteria in spatially structured biofilms Total $247,521, direct $171,159, indirect $76,362 (to Bucci) (total cost for Bucci were reduced to $147,000 after NSF asked to reduce budget and effort to three years) Role: Co-PI (10% effort) |
09/01/2018 – 08/31/2021 |
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UMass President Science and Technology Award (Vanni Bucci) Pipeline for probiotics discovery, engineering and manufacturing Development of genetically engineered probiotics for the treating drug-resistant Salmonella infections Total $125,000, direct $125,000, indirect $0.0 Role: PI (0.1% effort – funds directed only to support postdoc & students and for buying consumables) |
07/01/2017 – 12/31/2019 |
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Massachusetts Department of Public Health (Catherine Neto & Vanni Bucci) Exploring the potential impacts of bioactive compounds from cranberries on colon and gut health (https://www.umassd.edu/feature-stories/2018/cranberry-research.html) Total $100,000, direct $100,000, indirect $0.0 Role: MPI (0.1% effort – funds directed only to students and for buying consumables) |
01/01/2019 – 12/31/2019 |
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UMass Dartmouth Multidisciplinary Seed Fund (Michael Sheriff & Vanni Bucci) The role of the gut microbiome in mediating individual responses to predation risk Studies aimed at identifying microbiome members and functions that protect from stress-induced behaviors such as those in response to predation or enemy fire Total $31,560 Role: MPI (funds directed only to students and for buying consumables) |
01/01/2019 – 12/31/2019 |
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NIH-NIAID (1R15AI112985) (Vanni Bucci) Mathematical modeling from metagenomics - minimizing enteric infections risk Development of biostatistical methods to predict combinations of gut bacteria protecting from C. difficile and VRE bacteremia. Total $464,739, direct $334,449, indirect $130,290 Role: PI (15% effort) |
02/01/2015 – 06/31/2018 |
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NSF-ABI (DBI-1458347) (Vanni Bucci) ABI Innovation: A new computational framework for the prediction of microbiome dynamics Development, testing and validation of mathematical modeling tools for inference and predictions of temporal dynamics of polymicrobial systems. Total $491,682, direct $356,291, indirect $135,391 Role: PI (15% effort) |
09/01/2015 – 08/31/2019 |
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Vedanta Biosciences Sponsored Award (Vanni Bucci) Sponsored work to the UMass Dartmouth Microbial Informatics Core Development, testing and validation of mathematical modeling tools for inference and predictions of temporal dynamics of polymicrobial systems Total revenue $112,000 Role: PI (10% effort) |
02/01/2018 – 07/31/2019 |
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Albert Charitable Trust Fund (Catherine Neto & Vanni Bucci) Impact of bioactive compounds from cranberries on colon and gut health Exploration of effect of cranberry polyphenols on gastrointestinal microbiota and host immunity Total $150,000 Role: MPI (0.1% effort – funds directed only to students and for buying consumables) |
01/01/2018 – 12/31/2018 |
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Massachusetts DPH (Catherine Neto & Vanni Bucci) Impact of bioactive compounds from cranberries on colon and gut health Exploration of effect of cranberry polyphenols on gastrointestinal microbiota and host immunity (DPH Match to Albert Charitable Award, see above) Total $100,000 Role: MPI (0.1% effort – funds directed only to students and for buying consumables) |
01/01/2018 – 12/31/2018 |
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UMCCTS Life Sciences Moment Fund Award (John Haran & Vanni Bucci) Gut microbiome modeling to predict Clostridium difficile colonization in hospitalized patients Development of mathematical models to predict microbiome and C. difficile dynamics in emergency medicine patients Total $50,000 Role: MPI (funds directed to fellow and for buying server) |
01/01/2017 – 06/30/2017 |
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UMass Dartmouth Multidisciplinary Seed Fund (Christopher Brigham) Propane synthesis by engineered microbial consortia Engineering communities of bacteria to produce prophane from different waste sources Total $21,000 Role: Co-PI (funds directed only to students and for buying consumables) |
01/01/2017 – 06/30/2017 |
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UMass Dartmouth Multidisciplinary Seed Fund (Vanni Bucci) Leveraging evolution to develop therapeutics against enteropathogenic E. coli Experimental evolution experiment to investigate trade-offs between environmental adaptation and survival in the host in enteropathogenic E. coli Total $33,000 Role: PI (funds directed only to students and for buying consumables) |
01/01/2016 – 06/30/2016 |
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UMass Dartmouth Multidisciplinary Seed Fund (Vanni Bucci) Model reduction techniques for patient-specific data inference for gut microbiota dynamics Development of new mathematical and numerical methods for fast approximation of inverse problem solution using radial basis methods Total $31,000 Role: PI (funds directed only to students and for buying consumables) |
01/01/2014 – 06/30/2014 |
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UMass Dartmouth Multidisciplinary Seed Fund (Mark Silby) Understanding microbial dynamics to improve biotechnological applications Development of microbial genetic engineering techniques to build synthetic systems of interacting communities of soil microbes Total $22,000 Role: Co-PI (funds directed only to students and for buying consumables) |
01/01/2014 – 06/30/2014 |
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Sponsored Research Agreement Vedanta Biosciences (Vanni Bucci) Mathematical modeling of the intestinal microbiome to determine anti-inflammatory microbial consortia Analysis of time-series microbiome data from gnotobiotic mice inoculated with anti-inflammation-inducing microbial consortia Total $15,000 Role: PI (funds directed to purchasing High-Performance Computing Server) |
01/01/2014 – 06/30/2014 |