Lab News
Welcome Pharvendra
February 01, 2024
Bucci lab is happy to welcome the new Postdoctoral Associate Dr. Pharvendra Kumar, who recently finished his Ph.D. at the
Paper published in Science Translational Medicine
January 17, 2024
Our work on the describing the human microbiome's adaptation to long-term antibiotic exposure during multidrug-resistant tuberculosis treatment is out today in Science Translational Medicine. We are very happy about this fruitful collaboration with the Glickman lab at the Memorial Sloan Kettering Cancer Center. doi: 10.1126/scitranslmed.adi9711
Commensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption.
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**
Paper published in Translational Psychiatry
November 18, 2023
We are happy to announce that our work exploring the role of the microbiota-gut-brain axis in understanding and influencing components of adverse post-traumatic neuropsychiatric sequelae (APNS) got published today. By analyzing stool samples from trauma-exposed emergency department patients, we identified specific gut microbial species and metabolic pathways associated with worse APNS outcomes. Find the paper here: doi: 10.1038/s41398-023-02643-8
Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure.
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**
Welcome Cyrus and Ziyuan
May 12, 2023
With a lab gathering involving 90 degree weather, a big BBQ, international sweets, soccer, table tennis matches, and cold beverages, the Bucci lab welcomed the new Postdoctoral Associates Dr. Cyrus Alexander and Dr. Ziyuan Huang.
NIH U01 Grant Awarded
December 21, 2022
The Bucci and McCormick labs received a five-year award from the National Institute of Allergy and Infectious Diseases for a total of $2,947,626.00. The grant will lead to the 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
Bill & Melinda Gates Foundation Grant Awarded
November 20, 2022
The Bucci lab received a two-year award from the Bill & Melinda Gates Foundation for the MBQ2/3: Analytical support for Experimental Medicine Platform for a total of $682,233.00. The goal of the grant is to 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.
Paper published in Gut Microbes
September 30, 2022
Our work on the characterization of narrow-spectrum bacteriocin MccI47 and its in vivo applicability against carbapenem-resistant Klebsiella pneumoniae using an enginnered E. coli Nissle strain is out today! We are incredibly proud and grateful to everyone involved in the study. Find the paper here:
Microcin MccI47 selectively inhibits enteric bacteria and reduces carbapenem-resistant Klebsiella pneumoniae colonization in vivo when administered via an engineered live biotherapeutic
Postdoc Position available Comp Biol!
September 27, 2022
A postdoctoral associate position is available in the Bucci Lab for a highly motivated candidate with a PhD in applied mathematics, engineering, computer science, computational biology, or related discipline. The Bucci Lab is embedded in the vibrant research environment of the Program in Molecular Medicine at the University of Massachusetts Chan Medical School and is highly collaborative with other labs within and external to UMass Chan. The position is funded via Bill and Melissa Gates Foundation grant to the Bucci Lab.
The selected candidate will work on the development of novel dynamical systems modeling and deep learning methods to predict the dynamics of the microbiome and how they impact host immunity. Applications of these methods will include forecasting microbial population and metabolite dynamics that are constrained on longitudinal data from human clinical trials, predicting interactions with the host immune system, and using the models to perform combinatorial analysis to identify microbial combinations and functions maximizing host phenotypes of interest.
This project provides an excellent opportunity to learn and further develop a variety of computational modeling, bioinformatics, and deep learning techniques. The selected candidate will work independently to design and execute experiments. Results of this project will be presented at seminars and scientific meetings, which may involve travel. The post-doctoral fellow will also prepare and submit manuscripts and may assist with grant preparation.
Qualifications: Education, experience and skills required for consideration:
- Ph.D. in quantitative sciences including Math, Physics, Engineering
- Required experience with development and running of mathematical models
- Required experience with inferential statistics
- Required experience with solving Ordinary and Partial Differential Equations numerically
- Required experience with Python/R/MATLAB
- Preferred experience with Linear Algebra (e.g. Matrix operations)
- Preferred experience with Bayesian Statistics is not required but welcome
- Highly collegial; works well independently and as a team member
- Strong written and verbal communication skills; ability to communicate with precision and tact
- Meticulous recordkeeping
To Apply:
Applicants should submit the following materials by email to vanni.bucci2@umassmed.edu. A letter describing past and current research and your specific interest in this position, a CV (including publications), and contact information for three references, one of which should be your Ph.D. advisor.
Paper published in mSystems
September 7, 2022
Our new tool MDITRE is finally out. Find the paper here: doi: 10.1128/msystems.00132-22
MDITRE: Scalable and Interpretable Machine Learning for Predicting Host Status from Temporal Microbiome Dynamics
Maringanti VS, Bucci V**, Gerber GK**
Postdoc Position available Microb/Immuno!
September 01, 2022
A postdoctoral associate position is available in the Bucci Lab for a highly motivated candidate with a PhD in immunology, molecular biology, microbiology, synthetic biology, or a related discipline. The Bucci Lab is embedded in the vibrant research environment of the Program in Microbiome Dynamics at the University of Massachusetts Chan Medical School and is highly collaborative with other labs within and external to UMass Chan.
The selected candidate will work on the development of live bacteriotherapeutic product to induce intestinal immunity. The selected candidate will combine aerobic and anaerobic culturing techniques, bacterial engineering, to construct next generation probiotics aimed at modulating immune systems and resident gut microbiome dynamics under different conditions. The selected candidate will perform in vivo experiments and record related immunological measurements to be used for calibration and validation of machine learning methods (developed in the Lab) needed to link microbial taxa and functions to specific immune effectors.
This project provides an excellent opportunity to learn and further develop a variety of techniques. The selected candidate will work independently to design and execute experiments. Results of this project will be presented at seminars and scientific meetings, which may involve travel. The post-doctoral fellow will also prepare and submit manuscripts, and may assist with grant preparation.
Qualifications: Education, experience and skills required for consideration:
- PhD. in immunology, molecular biology, synthetic biology, or related disciplines
- Experience with working with animal models (e.g., mice)
- Experience with ELISA, immunohistochemistry, bead-based or flow cytometric cell separation techniques
- Experience with sequencing libraries preparation
- Experience with bacterial metabolism and metabolic engineering highly preferred
- Experience with bioinformatics and sequence analysis pipelines highly preferred
- Strong work ethic, highly motivated to apply skills towards solving biological problems
- Excellent analytical skills and independent judgement
- Highly collegial; works well independently and as a team member
- Strong written and verbal communication skills; ability to communicate with precision and tact
- Meticulous recordkeeping
To Apply:
Applicants should submit the following materials by email to vanni.bucci2@umassmed.edu. A letter describing past and current research and your specific interest in this position, a CV (including publications), and contact information for three references, one of which should be your Ph.D. advisor.
Happy Holidays!
December 19, 2021
The Bucci Lab came together to celebrate the Holiday Season with Lasagna, pork roast, cookies, and cake. The freezing temperatures asked for gloves, hats, a bonfire, and some mold cider in the cups.
Paper published in JCI Insight
August 17, 2021
Our work on associations between oral dysbiotic microbiome and Long COVID-19 disease has been published in JCI Insight. Find the paper here: doi: 10.1172/jci.insight.152346
Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long-COVID.
Haran JP, Bradley E*, Zeamer AL, Cincotta L, Salive MC, Dutta P, Mutaawe S, Anya O, Meza-Segura M, Moormann AM, Ward DV, McCormick BA, Bucci V**
Paper in press in Microbial Cell
April 26, 2021
Our work on bacterial community dynamics induced by a proanthocyanidin-enriched cranberry extract has been accepted for publication in Microbial Cell. Find the final version here: doi: 10.15698/mic2021.06.752
Proanthocyanidin-enriched cranberry extract induces resilient bacterial community
dynamics in a gnotobiotic mouse model.
Neto CC*/**, Mortzfeld BM*, Turbitt JR, Bhattarai SK, Yeliseyev V, DiBenedetto N, Bry LM, Bucci V**
Paper published in Gut Microbes
March 25, 2021
We are proud to announce that our latest work in collaboration with John Haran and Beth McCormick has been published in Gut Microbes. doi: 10.1080/19490976.2021.1897209
The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome
John P. Haran, Doyle V. Ward, Shakti K. Bhattarai, Ethan Loew, Protiva Dutta, Amanda Higgins, Beth A. McCormick, Vanni Bucci
Paper published in Nature Communications
January 10, 2021
We are proud to announce that our latest work has been accepted by Nature Communications. Great job from everyone involved! doi: 10.1038/s41467-021-21475-y
Gastrointestinal microbiota composition predicts peripheral inflammatory state
during treatment of human tuberculosis.
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**
Funding from the National Institutes of Health (NIH)
September 9, 2020Our lab just got awarded a new collaborative grant with John Haran (PI), Beth McCormick (Co-I), Doyle Ward (Co-I), Paul Greer (Co-I) and Vanni Bucci (Co-I) to determine association between microbiome an immune-senescence in Alzheimer’s Disease.
"Understanding the microbiome-gut-brain axis in Alzheimer's disease and its role in cognitive decline"
For more details check out our funding page!
Scalable learning of interpretable rules for the dynamic microbiome domain
July 17, 2020Our PhD student Suhas Maringanti on scalable rule learning for interpretation of microbiome data in collaboration with UMass Dartmouth and the Gerber lab at Harvard Medical School.
Recorded for the ICML 2020 Workshop on Human Interpretability in Machine Learning.
Find the manuscript pre-print on biorxiv! (doi:
Funding awarded by the Department of Defense (DoD)
July 7, 2020I'm excited to announce that the lab will get future support from the United States Department of Defense. The 3-year award is for our project 'Mathematical modeling and synthetic biology to discover new ESBL-PE eradicating microbiome-based therapeutics' and will start August 1st 2020. For more details check out our funding page!
Paper published in mSystems
June 23, 2020Our new paper discussing the influence of biofilm structure on the bacterial community dynamics and the interplay with bacteriophages is now online! Check it out! doi: 10.1128/mSystems.00877-19
Biofilm Structure Promotes Coexistence of Phage-Resistant and Phage-Susceptible Bacteria
Simmons EL, Bond MC, Koskella B, Drescher K, Bucci V**, Nadell C**
How simple mathematics help explaining epidemics
March 30, 2020In the light of the recent events, I used one of my online lectures to tackle the simple mathematics behind the spreading of infectious diseases. Stay home and stay safe!
Paper published in ACS Infectious Diseases
February 25, 2020The paper from our wetlab regarding the potency of the antimicrobial peptide MccH47 against drug-resistant Enterobacteriaceae has just been published in ACS Infectious Diseases. We also describe a new variant of the class IIb microcin, termed MccH47-MGE.
Microcin H47: A Class IIb Microcin with Potent Activity Against Multidrug Resistant Enterobacteriaceae
Palmer JD, Mortzfeld BM, Piattelli E, Silby MW, McCormick BA, Bucci V.
doi: 10.1021/acsinfecdis.9b00302
Move to UMass Chan Medical School
September 1, 2019I'm happy to announce that we have moved our lab to the UMass Chan Medical School in Worcester, MA.
We leave behind great memories at the UMass Dartmouth campus and are looking forward to exciting projects and new collaborations in the Department of Microbiology and Physiological Systems.
Summer 2019 at UMass Dartmouth
Paper published in BBMT
July 22, 2019Our paper collaborative paper with Matt Kelly (Duke University) and Patrick Seed (Northwestern University) “Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection in Pediatric Hematopoietic Stem Cell Transplant Recipients: a Strain-Level Analysis” has been published today in Biology of Blood and Marrow Transplantation.
Paper published in mBio
May 7, 2019Our collaborative work with the UMass Chan CMR on investigating the axis Alzheimer’s – Immune System – Microbiome has been published today in mBio
https://mbio.asm.org/content/10/3/e00632-19
“Alzheimer’s Disease Microbiome Is Associated with Dysregulation of the Anti-Inflammatory P-Glycoprotein Pathway“
New paper on bioRvix
February 26, 2019Check the preprint on bioRviX of new collaborative paper!
Thanks to Matt Simmons (Bucci Lab) and Matt Bond (Nadell Lab) for the amazing computational and experimental work, and of course to my dear friends and collaborators Carey Nadell (Dartmouth College) and Knut Drescher (Max Planck Institute for Terrestrial Microbiology).
https://www.biorxiv.org/content/10.1101/552265v1.abstract
“Evolutionary dynamics of phage resistance in bacterial biofilms”
Paper in Nature
January 24, 2019I am happy to announce to have contributed to the new paper from Kenya Honda lab published today in Nature: https://www.nature.com/articles/s41586-019-0878-z
“A defined commensal consortium elicits CD8 T cells and anti-cancer immunity“
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