ASMG Laboratory - Microbial Genomics

The Agricultural ASMG Lab, New Bolton CenterSystems 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.

Microbial Genomics

Research in the Microbial Genomics section of the ASMG lab focuses primarily on the New Bolton Center, ASMG Lab-Microbial Genomicsgut microbial composition of ruminants, utilizing both culture-based and 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.

Microbiology Component

The recent advent of next generation sequencers has greatly enhanced the ability to explore community microbial populations. The ASMG lab has the capabilities to perform metagenomic studies including sample preparation, genomic DNA extraction and generating 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 lab is in the process of streamlining the protocols for generating 18S libraries for protozoa and fungal communities.

Research Team
  Name Title
 Contact Information
Dipti Pitta, MVSc, PhD
  • Ruminant Nutrition and Microbiologist
  •  Ph: 610-925-6165
  • Email: dpitta@vet.upenn.edu
Sanjay Kumar, PhD
  • Post-Doc (Dairy Microbiologist)
  • Email: kusanjay@vet.upenn.edu
Bhima Bhukya, PhD
  • Post-Doc (Microbiologist)
  • Email: bbhukya@vet.upenn.edu
 I. Nagaraju, MSc
 Bioinformatics Analyst, PhD Candidate
 Email: indigun@vet.upenn.edu
 Bonnie Veccharelli, BS
  • Technician
  • Ph: 610-925-6334
  • Email: bvechia@vet.upenn.edu
Research projects at the ASMG Laboratory/Microbial Genomics, include:
  • A novel approach to enhance the production efficiency of dairy cows through the application of metagenomics to the rumen microbiome
  • Microbial diversity associated with bloat – a metabolic disorder in stocker cattle
  • A novel approach to enhance the production efficiency of dairy cows through the application of metagenomics to the rumen microbiome
  • Metagenomic analysis of the rumen microbiome in dairy cows with postpartum
  • metabolic disorders during the transition period


content content content

DNA Extraction, ASMG Lab, Microbial GenomicsDairy Cows at New Bolton Center 

  • In-Vitro ruminal fermentation assay
  • PCR assays
  • Microbial Diversity assays
  • Bacterial
  • Fungal
  • Protozoal


ASMG Lab, Microbial Genetics
  PCR Prep Work PCR Prep Work, ASMG Lab-Microbial Genomics
Imager, ASMG Lag, Microbial Genomics
  Thermal Cycler
Thermal Cycler, ASMG Lab, Microbial Genomics


  • Multi-disciplinary group investigation of the role of equine colonic microbiome in clinical disease (Equine team, NBC)
  • Metagenomic analysis of gastrointestinal flora in cattle with Mycobacterium avium subsp. paratuberculosis infection: Dysbiosis of fecal microbiota as a model for Crohn's Disease in humans? (Johne’s Laboratory, NBC)
  • Influence of the oral microbiome associated with periodontal disease on the initiation and progression of trauma induced osteoarthritis using a miniature swine model (Orthopaedic Laboratory, NBC)
  • Understanding the rumen microbiome of a transition cow (Dr. Bushman’s Laboratory, School of Medicine, Upenn and Dr. Hess, Washington State University)

 International Collaboration:


  • Metagenomic analysis of the buffalo rumen (Bubalis bubalis)