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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

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

 

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

 

 

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

 

 

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

 

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

 

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

 

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

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

 

 

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

 

 

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

 

 

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

 

 

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

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

 

 

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

 

 

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

 

 

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

 

 

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

 

 

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

 

 

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

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

 

 

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

 

 

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