New Bolton Center Kennett Square, PA
Emergencies & Appointments:
Ryan Hospital Philadelphia, PA

ASMG Laboratory - Microbial Genomics

asmg-lab-new-bolton-center 500

PLOS ONE Paper Among 100 Most Read Worldwide

Editors have selected Dr. Pitta's PLOS ONE paper, “Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet,” to be highlighted on the journal homepage. The journal's editor, Nicola Stead, PhD, Senior Editor, PLOS ONE, states, "We very much enjoyed reading about your work and would like to thank you for submitting your paper to PLOS ONE."

The Agricultural Systems and Microbial Genomics Laboratory (ASMG Laboratory) was established to support Dr. Dou and Dr. Pitta in their research endeavors.

Dr. Pitta is the ruminant nutrition and microbiologist at the Center for Animal Health and Productivity (CAHP), New Bolton Center, University of Pennsylvania.

new-bolton-center-asmg-lab-microbial-genomics 400

Research at the ASMG lab focuses primarily on the gut microbial composition of ruminants utilizing advanced molecular methodologies. The alimentary tract of a ruminant is colonized by millions of microbes living in a symbiotic relationship with the host. Therefore, knowledge of the microbial composition of the entire gut can provide insights into improving the overall health and productivity of the animal. Our research  also has broad environmental implications into such diverse applications as methane mitigation, reduction of the spread of antibiotic resistance, and human health.

The recent advent of next generation sequencers has greatly enhanced our ability to explore community microbial populations. The ASMG lab has the capabilities to perform genomic, metagenomic, and metatranscriptomic studies including sample preparation, genomic DNA and RNA extraction, and generation of 16S amplicon libraries for sequencing on next-generation platforms. The sequenced data is analyzed at the ASMG laboratory utilizing the appropriate bioinformatics tools for data interpretation.

The ASMG group collaborates with other researchers and clinicians both within the University of Pennsylvania as well as at other institutions. Our research is routinely published and presented at conferences. We also work with students from multiple backgrounds, ranging from high school through postdoctoral, who have used their time in our lab to further develop their knowledge of microbial genomics and its applications. 

Contact Information

Dr. Dipti Pitta, Penn Vet

Dr. Dipti Pitta, MVSc, PhD

Ruminant Nutrition and Microbiologist

Center for Animal Health and Productivity
School of Veterinary Medicine
University of Pennsylvania

Phone: 610-925-6165

ASMG Lab ResearchTeam
Dr. Dipti Pitta, Penn Vet New Bolton Center
  •  Ph: 610-925-6165
Meagan Hennessy, Penn Vet
  • Meagan Hennessy, MS, RDN
  • Research Specialist
Kapil Narayan, PhD, ASMG Lab
  • Kapil Narayan, PhD
  • Postdoctoral Researcher
Nagaraju Indugu, Penn Vet
  •  Nagaraju Indugu, PhD
  • Bioinformatics Analyst
Bonnie Vecchiarelli, Penn Vet
  • Bonnie Vecchiarelli, BS
  • Technician
John Toth, Penn Vet
  • John Toth, MS
  • Research Specialist


ASMG Lab Alumni
Veronica Shabtai, Penn Vet
  • Veronica Shabtai, DVM
  • Research Scholar


Research projects at the ASMG Laboratory include (PI: Dr. Pitta):

A. Methane emissions from dairy cattle

  1. Deciphering the crosstalk between bacteria-archaea interactions in the rumen and methane-yield phenotypes of dairy cows. Project sponsor: USDA-NIFA Foundational Program.
  2. The effect of 3-nitrooxypropanol, a persistent methane inhibitor, on ruminal microbial gene expression profiles in dairy cows. Project sponsor: DSM Nutritional Products.
  3. The effect of feeding Asparagopsis taxiformis, a seaweed, on ruminal microbial gene expression profiles in dairy cows. In collaboration with Penn State University.
  4. Understanding the role of Methanomassiliicoccales, a gut-archaea symbiont, in the reduction of trimethylamine-N-oxide-associated obesity. Project sponsor: Penn CHOP Microbiome Feasibility Program.
  5. Exploring the potential of using cow’s waste as a goldmine for energy conservation. Project sponsor: Kleinman Center for Energy Policy.

B. Antimicrobial resistance connecting animals, environment, and people

  1. Identification and mitigation of antibiotic resistant genes in the fecal microbiome of dairy cattle and humans. Project sponsor: Penn CHOP Microbiome Feasibility Program.
  2. Understanding microbe-microbe interactions and the impact on antimicrobial resistance agents during manure composting and anaerobic digestion. Project sponsor: Pennsylvania Department of Agriculture.
  3. Developing novel mitigation strategies to reduce microbial pollutants on dairy herds. Project sponsor: Pennsylvania Department of Agriculture.

C. Animal health and production

  1. Understanding the role of rumen microbes in diet-induced milk fat depression in dairy cows. In collaboration with Penn State University.
  2. Understanding the shifts in the fecal microbiome in neonatal calves with diarrhea. Project sponsor: USDA Formula Funds.
  3. Deciphering soybean-microbe interactions in the rumen of dairy cattle. Project sponsor: Pennsylvania Soybean Board.
  4. Understanding the effect of withholding feed for 24 hours on the equine fecal microbiota. Project sponsor: Raymond Firestone Trust Research Grant.           

DNA Extraction, ASMG Lab, Microbial Genomics

Dairy Cows at New Bolton Center

Hennessy, M., Indugu, N., Redding, L.k Vecchiarelli, B., Pappalardo, C., Toth, J., Stefanovski, D., Garapati, S., Pitta, D. 2021. Short communication: Comparison of the fecal bacterial communities in diarrheic and non-diarrheic dairy calves from multiple farms in Southeastern PA. Journal of Dairy Science. In press. doi: 10.3168/jds.2020-19108.

Lage, C.F., Raisanen, S.E., Melgar, A., Nedelkov, K., Chen, X., Oh, J., Fetter, M.E., Indugu, N., Bender, J.S., Vecchiarelli, B., Hennessy, M.L., Pitta, D., Hristov, A.N. 2020.   Comparison of two sampling techniques for evaluating ruminal fermentation and       microbiota in the planktonic phase of rumen digesta in dairy cows. Frontiers in      Microbiology. doi: 10.3389/fmicb.2020.618032.

Stefenoni, H.A., Raisanen, S.E., Welchez, S.F., Wasson, D.E., Lage, C.F.A., Melgar, A., Fetter, M.E., Smith, P., Hennessy, M., Vecchiarelli, B., Bender, J., Pitta, D., Cantrell, C.L., Yarish, C., Hristov, A.N. 2020. Effects of the macroalga Asparagopsis taxiformis and       oregano leaves on methane emission, rumen fermentation, and lactational performance of dairy cows. Journal of Dairy Science. In press. doi: 10.3168/jds.2020-19686.

Willette, J.A., Pitta, D., Indugu, N., Vecchiarelli, B., Hennessy, M.L., Dobbie, T., Southwood, L. Experimental crossover study on the effects of withholding feed for 24 hours on the equine faecal bacterial microbiota in healthy mares. BMC Veterinary Research. 17(3).      doi: 10.1186/s12917-020-02706-8.

Stewart, H.L., Pitta, D., Indugu, N., Vecchiarelli, B., Hennessy, M., Engiles, J.B., Southwood, L.L. 2020. Changes in the faecal bacterial microbiota during hospitalization of horses with colic and the effects of different causes of colic. Equine Veterinary Journal. doi:  10.1111/evj.13389.

Pitta, D.W., Indugu, N., Toth, J.D., Bender, J.S., Baker, L.D., Hennessy, M.L., Vecchiarelli, B.,   Aceto, H., Dou, Z. 2020. The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania. Environmental Microbiome. 15(21). doi: 10.1186/s40793-020-00368-5.

Hennessy, M.L., Indugu, N., Vecchiarelli, B., Bender, J., Pappalardo, C., Leibstein, M., Toth, J., Katepalli, A., Garapati, S., Pitta, D. 2020. Temporal changes in the fecal bacterial community in Holstein dairy calves from birth through the transition to a solid diet. PLoS One. 15(9): e0238882. doi: 10.1371/journal.pone.0238882.

Pitta, D.W., Indugu, N., Vecchiarelli, B., Hennessy, M., Baldin, M., Harvatine, K.J. 2018. Effect of 2-hyroxy-4-(methylthio) butanoate (HMTBa) supplementation on rumen bacterial populations in dairy cows when exposed to diets with risk for milk fat depression. Journal of Dairy Science. doi: 10.3168/jds.2019-17389.

Pitta, D.W., Indugu, N., Baker, L., Vecchiarelli, B., Attwood, G. 2018. Symposium review: Understanding diet-microbe interactions to enhance productivity of dairy cows. Journal of Dairy Science. 101(8): 7661-7679.

Stewart, H.L., Southwood, L.L., Indugu, N., Vecchiarelli, B., Engiles, J.B., Pitta, D.W. 2018. Differences in the equine faecal microbiota between horses presenting to a tertiary referral hospital for colic compared to an elective surgical procedure. Equine Veterinary Journal. 51(3): 336-342. 

Stewart, H., Pitta, D.W., Indugu, N., Vecchiarelli, B., Engiles, J.B., Southwood, L.L. 2018. Alterations in the equine fecal microbiome using different sampling times and sites. American Journal of Veterinary Research. 79(8): 811-819.

Pitta, D.W., Indugu, N., Vecchiarelli, B., Rico, D.E., Harvatine, K.J. 2017. Implications of rumen inoculation on the ruminal bacterial populations in dairy cows with diet-induced milk fat depression. Journal of Dairy Science. 101(1): 295-309.

Indugu, N., Vecchiarelli, B., Baker, L.D., Ferguson, J.D., Vanamala, J.K.P. 2017. Comparison of rumen microbial communities in dairy herds of different production. BMC Microbiology. 17(1): 190.

Fecteau, M.E., Pitta, D.W., Vecchiarelli, B., Indugu, N., Kumar, S., Gallagher, S.C., Fyock, T.L., Sweeney, R.W. 2016. Dysbiosis of the fecal microbiota in cattle infected with Mycobacterium avium subsp. paratuberculosis. PLoS One. 11(8): e0160353.

Pitta, D.W., Pinchak, W.E., Indugu, N., Vecchiarelli, B., Sinha, R., Fulford, J.D. 2016. Metagenomic analysis of the rumen microbiome of steers with wheat-induced frothy bloat. Frontiers in Microbiology. 11(7): 689.

Pitta, D.W., Dou, Z. Kumar, S., Indugu, N., Toth, J.D., Vecchiarelli, B., Bhukya, B. 2016. Metagenomic evidence of the prevalence and distribution patterns of antimicrobial resistance genes in dairy agroecosystems. Foodborne Pathogens and Disease. 13(6): 296-302.

Indugu, N., Kumar, S., Pitta, D.W. 2016. Comparisons of Roche 454 and Ion Torrent PGM sequencing platforms for rumen bacterial profiling of dairy cows. Peer J. 4: e1599.

Pitta, D.W., Indugu, N., Kumar, S., Vecchiarelli, B., Sinha, R., Baker, L.D., Bhukya, B., Ferguson, J.D. 2016. Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows. Anaerobe. 38: 50-60.

Bhima, B., Reddy, Y.R., Pawani, M., Reddy, S., Rao, L.V., Pitta, D.W. 2015. The influence of stress-resistant yeast culture (OBV9) supplementation on the productive performance of water buffalo. Asian Journal of Animal and Veterinary Advances. 10(6): 260-270.

Kumar, S., Indugu, N., Vecchiarelli, B., Pitta, D.W. 2015. Associative patterns among anaerobic fungi, methanogenic archaea and bacterial communities in response to changes in diet and age in the rumen of dairy cows. Frontiers in Microbiology. 6: 781.

Students at the ASMG Microbial Genetics LabWe have an established summer student program that allows students from various disciplines to learn multiple skills, and participate in:

  • Lectures and discussions: Students attend classes and conversations with scientists, clinicians, and faculty from the Department of Clinical Studies to learn about the research experts are performing at the bench and the solutions they are seeking to apply in the field.
  • Lab access: Through guided, inquiry-based experiments, students get a hands-on introduction to some of the tools and techniques commonly used in biomedical research. These include wet lab techniques such as DNA and RNA extraction, in vitro fermentation, and PCR. 
  • Journal Clubs and individual projects: Students discuss peer-reviewed research articles in small group journal clubs, where lessons from lectures and labs are applied to current biomedical research. Skills such as scientific writing, presentation skills, and targeted projects will provide the students with valuable abilities for their future. Students will be involved in bioinformatics and data analysis using a variety of programs and analysis tools from the most cutting-edge platforms. 

Students at ASMGThe central focus for all students is to better understand the role of microbiota and how this information can be linked to problems faced by livestock production systems integrated with the environment and human health.

Students are assigned their own projects to undertake under supervision from our research technicians and scholars and are included on relevant publications.

In 2020, due to the COVID-19 pandemic, we held our summer internship program entirely virtually, with students participating in lectures on topics related to anaerobic microbiomes, as well as learning about how to conduct a literature search, the basics of bioinformatic analysis for microbiome-related research, and how microbiome-related research is performed in the lab. They also participated in journal clubs and group discussions, and completed a group project in which they selected a research question related to anaerobic microbiomes, performed an in-depth literature search, and presented their research to the group. We are currently unsure of the status of the 2021 program due to COVID-19, but interested students can email Meagan Hennessy ( to be contacted as the summer gets closer.

Testimonials from previous students:

“Working in the ASMG Lab at New Bolton Center has provided me with an experience that has enhanced my education in the sciences and has better prepared me for my future career as a large animal veterinarian. The work done at ASMG allows me to take part in graduate level research that I otherwise wouldn't encounter as a high school student, allowing me to practice and perfect laboratory skills that I would learn as an undergraduate and/or graduate, along with learning new information about animal care and nutrition (specifically dairy cows), through others in the lab. The lab work is primarily independent (working on smaller portions of larger projects), however the community of people in the lab itself provides a supportive and efficient net for people such as myself who are working in a lab for the first time.”

“This summer I worked under Dr. Dipti Pitta at the Agricultural Systems and Microbial Genomics Lab at PennVet’s New Bolton Center. My project was to investigate the effects of withholding feed on the equine fecal microbiota, and my time in lab was primarily spent extracting RNA from equine fecal samples. I learned many valuable techniques such as RNA extraction using a protocol of chloroform and isopropanol, using commercially available kits such as VILO to convert mRNA to cDNA, PCR amplification, running gel electrophoresis, and I also learned the steps involved in statistically analyzing sequencing data in R software. This experience exposed me for the first time to working in a benchtop laboratory, and I really enjoyed the persistence and determination involved in this kind of research. This experience has further encouraged me to pursue a career in academia after I graduate veterinary school, so that I can split my time practicing clinically and working in a laboratory.”

“During my time at the ASMG lab, I worked on a project studying the effects of feeding time on ruminal community dynamics and methane mitigation. This project included objectives studying the rhythmicity of ruminal archaeal communities, the effect of feeding time on said dynamics, as well as studies on inhibiting the MCR enzyme and how enzyme levels could possibly be used as a proxy to monitor methane emissions. Through this research I learned new techniques of nucleic acid extraction, utilizing barcoded primers in PCR amplifications, PCR quantification, as well as some basic knowledge regarding qPCR. This experience provided me with a solid foundation in microbial and nutrition research. If my current career plans of pursuing a nutrition residency continue to grow, this experience will give me a great advantage and will serve to set my application apart from other candidates that lack a similar research opportunity or experience.”

For more information contact Meagan Hennessy at