Purdue Applied Microbiome Sciences

Our Mission

PAMS is an interdisciplinary community of microbiome scientists unified by the mission to develop the knowledge and tools required to predict and control microbiomes for improved health, economic benefit, and environmental sustainability.

PAMS in the news:

Purdue team gets $1 million to develop rapid sensor technology for cattle disease; affiliated startup nets $100,000 from Purdue Ag-Celerator program

Purdue University researchers, led by Mohit Verma, an assistant professor of agricultural and biological engineering, are developing technology to reduce diagnosis for Bovine Respiratory Disease – one of the most prevalent and costly illnesses in the beef and dairy industries – time to about 30 minutes. Their work is being funded by a $1 million U.S. Department of Agriculture National Institute of Food and Agriculture Inter-Disciplinary Engagement in Animal Systems (IDEAS) grant, as well as $1.4 million from the Foundation for Food and Agriculture. Dr. Verma’s startup company – Krishi LLC – also recently secured $100,000 from Purdue’s Ag-Celerator program to commercialize the technology.

NSF-funded Purdue-led project aims to understand community, cooperative effects in microbial carbohydrate metabolism – may lead to improvements in biofuel production

Microorganisms can be neighborly – when breaking down complex plant fibers they divide the labor and are able to sustain a diverse community, as each member gets its share of food. Understanding how they are able to adapt in this way could lead to improved biofuels processes and is the focus of a new $2 million project led by Stephen Lindemann at Purdue University. The National Science Foundation funded the project, which aims to uncover the mechanisms behind the division of labor among microorganisms, single-celled living organisms, including bacteria and fungi, which are too small to be seen without a microscope and naturally live in communities. The team also will develop a theory that describes how microbial interactions maintain diversity and influence the productivity and stability of a community.

PAMS authors contribute high-profile review articles as part of Purdue’s 150th anniversary celebration

To mark the 150th anniversary of Purdue University, the College of Agriculture sponsored competitive awards to teams of researchers to write and publish high-visibility, high-impact review articles. As part of this effort, three PAMS member faculty received awards. Mohit Verma co-authored a paper entitled Process Analytical Technologies and Data Analytics for the Manufacture of Monoclonal Antibodies (Trends in Biotechnology), while Laramy Enders and Cindy Nakatsu were authors on Emerging Strategies for Precision Microbiome Management in Diverse Agroecosystems (Nature Plants).

Milestones/Accomplishments

*Multiple PAMS students won poster awards at the recent Indiana Branch of the American Society for Microbiology (IBASM) meetings. Yiying Zhao (Nakatsu lab) placed first among Ph.D. students, Eunice Centeno (Johnson lab) second among M.S. students, and Abby Simpson (Nakatsu lab) second among undergrads.

*Audrey Goldbaum (Cross lab) was awarded Purdue’s prestigious Bilsland Fellowship.

*Paul Oladele (Johnson lab) was selected as a 2021 Foundation for Food and Agriculture Research (FFAR) Fellow.

*Johnnie “Junior” Cheng (Johnson lab) was selected to receive the 2021 France A. Cordova Leadership In Action Award.

*Ariana Romero (Lindemann lab) successfully defended her MS this semester, as did Eunice Centeno (Johnson lab), and Josiah Davidson and Jiangshan Wang (Verma lab).

*Carmen Wickware (Johnson lab) passed her PhD prelim exam this semester.

*Javier Muñoz (Brubaker lab) passed his PULSe Preliminary Exam

*Steve Lindemann was promoted to Associate Professor, effective 8/16/21.

Congratulations to all!

Student Spotlight

Thorsten (Thor) Hansen, Entomology
Read more on Thor’s research into how milkweed toxins shape the microbiomes of the plants and the monarch butterflies that feed on them.

Selected recent PAMS publications:

Davidson, JL, Wang, J, Maruthamuthu, MK, Dextre, A, Pascual-Garrigos, A, Mohan, Putikam, SVS, Osman, FOI, McChesney, D, Seville, J, Verma, MS (2021). A paper-based colorimetric molecular test for SARS-CoV-2 in saliva. Biosensors and Bioelectronics https://doi.org/10.1016/j.biosx.2021.100076

Lindemann, SR (2021). A piece of the pie: engineering microbiomes by exploiting division of labor in complex polysaccharide consumption. Current Opinion in Chemical Engineering. Invited review (In press).

Tuncil, YE, Thakkar, RD, Arioglu-Tuncil, S, Hamaker, BR, Lindemann, SR (2020). Subtle variations in dietary fiber fine structure differentially impact the composition and metabolic function of gut microbiota. mSphere 5(3):e00180-20.

Cantu-Jungles, TM, Bulut, N, Chambry, E, Ruthes, A, Iacomini, M, Keshavarzian, A, Johnson, TA, Hamaker, BR. (2021). Dietary fiber hierarchical specificity: The missing link for predictable and strong shifts in gut bacterial communities. mBio e0102821. http://doi.org/10.1128/mBio.01028-21

Kaplan, I, Bokulich, NA, Caporaso, JG, Enders, LS, Ganem, W, Ingerslew, KS (2019). Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome? Evolutionary Applications DOI: 10.1111/eva.12956

Maruthamuthu, MK, Raffiee, AH, De Oliveira, DM, Ardekani, AM, Verma, MS (2020). Raman spectra-based deep learning – a tool to identify microbial contamination. MicrobiologyOpen DOI: 10.1002/mbo3.1122.

Mohan, S, Pascual-Garrigos, A, Brouwer, H, Pillai, D, Koziol, J, Ault, A, Schoonmaker, J, Johnson, T, Verma, MS (2021). Loop-mediated isothermal amplification for the detection of Pasteurella multocidaMannheimia haemolytica, and Histophilus somni in bovine nasal samples. ACS Agricultural Science and Technology doi.org/10.1021/acsagscitech.0c00072

Wickware, CL, Johnson, TA, Koziol, JH. 2020. Composition and diversity of the preputial microbiota in healthy bulls. Theriogen https://doi.org/10.1016/j.theriogenology.2019.11.002

Enders, LS, Miller, NJ (2016). Stress-induced changes in abundance differ among obligate and facultative endosymbionts of the soybean aphid. Ecology and Evolution DOI: 10.1002/ece3.1908

Nakatsu, CH, Byappanahalli, M, Nevers, M (2019). Bacterial community 16S rRNA gene sequencing characterizes riverine microbial impact on Lake Michigan.  Frontiers in Microbiology doi.org/10.3389/fmicb.2019.00996

Duttlinger, AW, Centeno Martinez, RE, McConn, BR, Kpodo, KR, Lay, DC, Richert, BT, Johnson, TA, Johnson, JS (2021). Replacing dietary antibiotics with 0.20% L-glutamine in swine nursery diets: Impact on intestinal physiology and the microbiome following weaning and transport. Journal of Animal Science. http://doi.org/10.1093/jas/skab091

Chehab, RF, Cross, T-WL, Forman, MR (2020). The gut microbiota: A promising target in the relation between complementary feeding and child undernutrition. Advances in Nutrition DOI: 10.1093/advances/nmaa146

Muurinen, J, Richert, J, Wickware, CL, Richert, BT, Johnson, TA (2021). Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential. Scientific Reports http://doi.org/10.1038/s41598-021-84759-9

Cladis, DP, Simpson, AMR, Cooper, KJ, Nakatsu, CH, Ferruzzi, MG, Weaver, CM (2021). Blueberry polyphenols alter gut microbiota and phenolic metabolism in rats. Food and Function DOI: 10.1039/d0fo03457f.

Proctor, CR, Rhoads, WJ, Keane, T, Salehi, M, Hamilton, K, Piepe,r KJ, Cwiertny, DM, Prévost, M, Whelton, AJ (2020). Considerations for large building water quality after extended stagnation. AWWA Water Science 2(4). https://doi.org/10.1002/aws2.1186

French, E, Kaplan, I, Iyer-Pascuzzi, A, Nakatsu, CH, Enders, LS (2021). Emerging strategies for precision microbiome management in diverse agroecosystems. Nature Plants https://dx.doi.org/10.1038/s41477-020-00830-9

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