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ASMG Laboratory - Microbial Genomics

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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 (ASMG) Laboratory was established to support Dr. Dou and Dr. Pitta in their research endeavors.

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

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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.

The advent of next generation sequencers has greatly enhanced our ability to explore community microbial populations. The ASMG lab has the capabilities to isolate bacteria and methanogens from the gastrointestinal contents of different ruminant species as well as apply multi-omic approaches to better characterize and understand the functional potential of rumen microbiota. The primary areas of focus include deciphering dietary-microbe, microbe-microbe and host-microbe interactions that play essential roles in maintaining health and production while also minimizing negative impacts on the environment. Research efforts at ASMG are to understand the role of microbiota in ruminal methanogenesis and determine the impacts of different inhibitors on enteric methane inhibition, application of precision technologies to advance animal productivity, and early life microbial interventions to improve health and welfare, and productivity of dairy cattle. Please see Research Projects below for further details.

In addition, The ASMG group collaborates with other researchers and clinicians both within the University of Pennsylvania as well as at other institutions. Research findings are disseminated via publications and are presented at conferences. The ASMG group strives to educate and train next generation students in application of microbial genomics to help address global issues such as Food Insecurity, Climate Change, Sustainable Agricultural Systems, and Mitigation of Antimicrobial Resistance. Opportunities for students from diverse backgrounds, ranging from high school through postdoctoral are available at ASMG laboratory to further their careers in microbial genomics and its applications. 

Contact Information

Dr. Dipti Pitta, Penn Vet

Dr. Dipti Pitta, MVSc, PhD

Associate Professor
Ruminant Nutrition and Microbiologist

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

Phone: 610-925-6165
Email: dpitta@vet.upenn.edu

ASMG Lab ResearchTeam
Dr. Dipti Pitta, Penn Vet

Dr. Pitta completed her Bachelor of Veterinary Science and Master of Veterinary Science programs in India. After graduation, she received her specialty training in ruminant nutrition and microbiology as a part of PhD degree program from Massey University in New Zealand. She then moved to Texas A&M University in the United States to explore the role of rumen microbes in the incidence of wheat-induced frothy bloat before joining as a faculty member at University of Pennsylvania.

During her research career, Dr. Pitta has worked on several projects involving forages, environmental issues, nutritional aspects, microbial ecology, biometrics and food safety. At Penn, Dr. Pitta established the Agricultural Systems and Microbial Genomics (ASMG) Laboratory which became functional since 2012. Her research projects aim to decipher the functional role of microbes in the rumen associated with nutrient metabolism, milk fat depression, methanogenesis and mitigation of enteric methane emissions, antimicrobial resistance and early-life microbial interventions in dairy cows.

Dr. Pitta is one of the few international scientists who works on understanding the role of rumen microbiome in enteric methane mitigation which is sponsored by USDA-NIFA and industry grants. In addition, she is also involved in several collaborative projects at Penn Vet to investigate the role of gut microbiome in health and disease in equine, swine and honeybees. 

Nagaraju Indugu, Penn Vet
  • Nagaraju Indugu, PhD
  • Senior Investigator in Bioinformatics 

Dr. Indugu is a Microbiome Bioinformatics specialist. He received his Master of Science and his Ph.D in Bioinformatics from India. During his PhD, he got a chance to join Wistar Institute in Philadelphia and worked on bioinformatics approaches to identify biomarkers in lung adenocarcinoma. In 2014, he joined Dr. Pitta’s group at Penn Vet.

During his research career, Dr. Indugu worked on several research projects under Dr. Pitta’s supervision and was responsible for analyzing high throughput sequencing data from both microbial and host genomes derived from next generation sequencing platforms. He also applies statistical modeling approaches to compare and visualize different types of data from multiple animal species.

Recently, he has been applying data science concepts to analyze big data derived from precision technologies. He contributes immensely to manuscript preparations, grant submissions, and is responsible for data management. In addition, he is also involved in several collaborative projects at Penn Vet and other University researchers to investigate the role of gut microbiome in health and disease in bovine, equine, swine, honeybees, poultry, and shrimp. 

Kapil Narayan, PhD, ASMG Lab
  • Kapil Narayan, PhD
  • Postdoctoral Fellow
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  • Terry Webb
  • Research Technician
Bonnie Vecchiarelli, Penn Vet
  • Bonnie Vecchiarelli, BS
  • Research Technician

Bonnie Vecchiarelli has over 25 years of experience working with dairy cattle. She has 5 years of experience with handling various sample types (rumen, fecal, saliva) for DNA and RNA extraction and preparing libraries for PCR amplicon, metagenomic and metatranscriptomic sequencing on next generation sequencing platforms. 

Dr. Sarah Rassler, Pitta Lab
  • Sarah Rassler
  • Dairy Intern

Dr. Rassler graduated from Penn Vet in May 2022. Her involvement with the dairy industry began in high school, during which she worked on her aunt’s family dairy farm and showed cattle in 4-H. During her undergraduate education at Penn State, she was active in pre-veterinary and livestock clubs, and worked with the Penn State Veterinary Extension team on various research projects and educational outreach programs.

While completing her veterinary degree, she served as Food Animal Club President and AABP Student Representative, while also working at the Marshak Dairy. Her interest in dairy medicine led to an internship at Penn Vet, through which she is learning to formulate dairy rations, assisting with various research projects, teaching clinical courses, and working with local dairy producers to improve productivity and profitability. 

Alejandro Castaneda, Pitta Lab 
  • Alejandro Castaneda
  • Graduate Student

 

I discovered my passion for greenhouse gases and climate change very early. I started my research career by investigating the effect of the essential oils carvacrol and thymol on methane production and rumen methanogens in vitro as part of my master’s at the University of Chihuahua, Mexico. During my master’s, I lead a research project to investigate the effect of the nitro-compounds nitrate and 3-nitropropionic acid on methane production and fermentation parameters in vitro. I performed this research project with the guidance and collaboration of scientists from the USDA at College Station, Texas. The results obtained from these investigations were published in the Journals of Bioresource Technology and Environmental Science and Health.

Now, I am enrolled at McGill University as a PhD student and am performing world-class research at the ASMG lab under Dr. Pitta. My objectives are 1) to determine the contribution of individual methanogens to total methane production and 2) to explore the inhibiting effect of methanogenic inhibitors on methane production in the rumen of dairy cattle. My overarching goal is to generate first-class research to mitigate the environmental and economic costs of dairy production systems while producing sustainable and healthy food.

Dr. Moolchand Malhi, Pitta Lab 
  • Dr. Moolchand Malhi
  • Postdoctoral Fellow

Dr. Malhi is Associate Professor, at Department of Veterinary Physiology & Biochemistry, Faculty of Animal Husbandry & Veterinary Sciences, Sindh Agriculture University (SAU) Tandojam, Pakistan. He did his DVM and MSc from SAU Tandojam, and PhD from Nanjing Agricultural University, China. His area of interests are Nutritional and Gastrointestinal Physiology, Fermentation and Fate of SCFA in the animal body. He received scholarship under HEC-Postdoctoral Fellowship Program.

To get further insight into Rumen Microbiology, he joined Agricultural Systems & Microbial Genome (ASMG) lab as Postdoctoral Fellow under Dr. Pitta’s supervision at Department of Clinical Studies, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania in September 2022. He will be working on role of dietary-microbiome interactions in rumen development in calves. 

John Toth, Penn Vet
  • John Toth, MS
  • Research Specialist

 

Part-Time Scholars
Max Lewis, Pitta Lab
  • Max Lewis
I am a 3rd year undergraduate student at Temple University studying biology on a pre-vet track. I recently started to help out at Marshak Dairy on a research project regarding methane emissions from dairy cows. I am contributing to this project by aiding in the feeding and collection of feed refusals as well as measuring methane emissions of individual cows and processing biological samples

In my free time, I like to play table tennis, hiking, and backpacking.

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  • Dheeraj Dhanthuluri
  • High School Student Intern

I am Dheeraj Danthuluri, a senior at Newark Charter High School passionate about biotechnological research. I am a research intern at the ASMG lab, and my time working under Dr. Pitta has been invaluable in my progression towards a career in biological research. Not many students have the opportunity to conduct biotechnological research in high school, and through this internship, I learned commonly used lab skills such as DNA extraction, PCR, and gel electrophoresis and applied these lab skills toward applicable research combating climate change.

In addition, I learned niche anaerobic cultivation techniques, utilized by few laboratories across the world, and relevant bioinformatics skills on the topic of transcriptomics. I was also given the opportunity to be involved in data collection on the dairy farm, helping to process rumen samples and measuring feed samples.

Outside of lab work, I enjoy playing basketball, hanging out with my friends, and being involved in extracurricular activities in my school. This internship has greatly expanded my knowledge in regard to the research process, allowing me to gain experience in applied sciences and wet-lab research. In the future, I aspire to continue to further my research career by tackling the world's most pressing issues. 

Ojas Purandare, Pitta Lab 
  • Ojas Purandare
  • High School Student Intern 

I am Ojas Purandare and I am a senior in high school, passionate about the intersection of sustainability and technology. I enjoy playing the viola, doing robotics, hiking and reading. My time at the ASMG lab has been incredible. I've had the early opportunity to learn lab skills and procedures like DNA extractions and PCR and apply them to do meaningful research.

Part of my time has included helping with feed management and data and sample collection at a dairy farm. This has provided me with a unique perspective on my work. Both of these opportunities have allowed me to actively engage with the research process. I hope to continue working on innovative projects that make a positive impact on society.

David Chai, Pitta Lab 
  • David Chai
  • High School Student Intern 
I am David Chai, grade 12, and I was a lab and farm researcher at the New Bolton Center this summer 2022. I enjoy piano, swimming, choir, marching band, and volunteering at my church, and I am interested in engineering in college. During my internship, I learned many lab procedures like gram staining, reviving bacteria, preparing media, PCR, ELISA, DNA extraction, and much more. I also helped prepare and measure feed for the cows in our study and gather samples. I had a wonderful experience exploring a new scientific field and contributing to relevant impactful research for our planet, and I am excited to see the future innovation in store for this lab! 

 

ASMG Lab Alumni
Meagan Hennessy, Penn Vet
  • Meagan Hennessy, MS, RDN
  • Research Technician  
Meagan Hennessy worked as a research technician in Dr. Pitta’s lab and her work involved processing various sample types for DNA and RNA extraction and prepares libraries for PCR amplicon, metagenomic, and metatranscriptomic sequencing on next-generation sequencing platforms. She was instrumental in organizing on-farm animal experiments and collaborate with other research team members on scientific papers and other publications.              
Veronica Shabtai, Penn Vet
  • Veronica Shabtai, DVM
  • Research Scholar
 
Research projects at the ASMG Laboratory include (PI: Dr. Pitta):

Research Projects

  • Improving efficiency and reducing methane emissions of dairy herds by bridging the gap between animal and data science. Sponsor: USDA-NIFA-IDEAS-2021-10918
  • Deciphering the role of individual methanogens and their inhibition on hydrogen metabolism in the rumen of dairy cows. Sponsor: USDA-NIFA-AFRI-2020-02672
  • The effect of 3-nitrooxypropanol (3-NOP), a persistent methane inhibitor, on the ruminal microbiota in dairy cows with distinct microbial syntrophic clusters. Sponsor: DSM-Nutritional Products-2021
  • Deciphering the role of gut microbiome in reducing Haemonchus contortus infection in PA’s small ruminant herds. Sponsor: Center for Livestock and Poultry Excellence
  • A novel method to measure and predict enteric methane emissions in dairy cows. Sponsor: Pennsylvania Department of Agriculture
  • Understanding the role of the microbiome-gut-brain axis to improve the health and welfare of dairy calves. Sponsor: Pennsylvania Department of Agriculture
  • Precision data integration to assess rumen health in dairy cows with postpartum metabolic disorders during the transition period. Sponsor: USDA-Formula Funds

Collaborative Projects:

  • Developing novel feeds via bioprocessing of food waste and crop residue biomass to support sustainable dairy production. Sponsor: USDA-NIFA-IDEAS-2021-
  • Modulating Inflammation during the Peri-Parturient Period: Understanding the Link Between Rumen Microbiome and Inflammation. Sponsor: USDA-NIFA-AFRI- 2021-06929
  • Temporal changes in swine vaginal and fecal microbiome and resistome before and after antibiotic therapeutic intramuscular treatment or artificial insemination with semen extender containing preservative-level antibiotics. Sponsor: Center for Livestock and Poultry Excellence
  • Sharing is caring: Can pets protect their owners against antibiotic-associated disruption of the gut microbiome? Sponsor: The HABRI Institute
  • Impact of pet contact on antimicrobial-associated dysbiosis and Clostridioides difficile infection. Sponsor: NIH-NIAID PA-20-205
  • Equine guttural pouch microbiome in health and disease. Sponsor: Boehringer Ingelheim Animal Health USA, Inc.        

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 (hmeagan@vet.upenn.edu) 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 hmeagan@vet.upenn.edu.