• Photo: The CHOP Microbiome Center Group

    The CHOP Microbiome Center

    The CHOP Microbiome Center supports planning microbiome projects, DNA purification, library preparation, high throughput sequence analysis, and bioinformatic analysis of the output.



  • Photo: Analytics Core

    Analytics Core

    The Analytical Core provides expertise in large-scale bioinformatics analysis of microbiome datasets. Core services start with a thorough quality check and review of sequencing results. This includes removal of host genomic sequences and other DNA added during the sequencing protocol. Automated pipelines assess the bacterial, fungal, and viral taxa found in each sample. Alignments to genes of known function are summarized, and the data are queried against a curated collection of full genomes for microbes of interest.

  • Photo of test tubes.

    High-Throughput Screening Core

    The High-throughput Screening (HTS) core provides the Perelman School of Medicine community with professional HTS screening services to identify genes or organic small molecule modulators of signaling pathways, cellular phenotypes, and protein function in models of human disease.

  • Photo: microaerobic chamber

    Microbial Culture and Metabolomics Core

    Many trillions of microbes—too small to be seen by the naked eye–live in our guts and elsewhere on our bodies. These microbes contribute to health by helping with digestion, guiding growth of our immune systems, and shouldering out invading pathogens. People differ greatly in the composition of their microbiota, influencing us each in unique ways.

  • Photo of High-Throughput Sequencing Core Group

    High-Throughput Sequencing Core

    The Sequencing Core provides expertise in next-generation sequencing of microbiome samples. Services include sample aliquoting, DNA extraction, quantitative PCR, library preparation, and sequencing. All protocols and workflows are optimized for individual sample types.

  • Photo chart of Acute Care Biobanking Core

    Acute Care Biobanking Core

    The goals of the Acute Care Biobanking Core are to encourage and facilitate microbiome- focused research in the pathogenesis, diagnosis and treatment of patients with critical illness. Many patients who are critically ill are subject to processes and complications with microbially-driven or infectious mechanisms.

  • Photo of proteomics core equipment

    Proteomics Core

    The Quantitative Proteomics Resource Core (QPRC) provides investigators access to the most advanced high resolution mass-spectrometry-based proteomics technologies. These approaches are implemented with a broad variety of mass-spectrometry-based experiments to characterize and quantify proteins from complex biological samples.

  • Photo of Microbiome human Intervention Core Group

    Microbiome Human Intervention Core

    The Human Intervention Core offers a wide array of services to assist with the design and implementation of microbiome studies. The core can assist with longitudinal studies as well as pilot studies. Pilot studies can be rapidly implemented with human intervention core staff, project managers and research coordinators, to conduct these studies.

  • photo of cientific equipment

    Gnotobiotic Mouse Core

    Some 100 trillion beneficial microorganisms populate your body inside and out. Various species are healthy, and aid in processes like digestion, and strengthening the immune system. However, what would happen if humans did not have this symbiotic relationship with commensal bacteria? The University of Pennsylvania has launched The Penn Gnotobiotic Mouse Facility (PGMF) in order to aid new research in this area, and provide investigators with germ-free mice.


The CHOP Microbiome Center has suspended non-essential lab operations due to the SARS-COV-2 pandemic. We are currently only accepting samples for COVID19-related projects. Our bioinformatics team remains fully operational and we are still available for consultations. If you would like speak with us about your project, please fill out this form. We hope to continue serving you soon.

Wednesday, April 8, 2020

The mission of the PennCHOP Microbiome Program is to facilitate research across campus focused on understanding the microbiome and altering its composition and activity to improve health. Pilot/Feasibility grants are designed to bring together microbiome investigators and to stimulate other researchers to enter the field and investigate the influence of the microbiome in their subject areas. The Pilot/Feasibility Projects can focus on the microbiota at any body site of the human or animal hosts.

Tuesday, January 28, 2020

Dr. Kelsey Jones
University of Oxford, UK
Malnutrition and diarrhea: a case for treating the immune system
10 am, Wednesday, 2/5/20, 132 Hill Pavilion, Penn Vet
380 South University Ave

Thursday, January 23, 2020

Check out an interview from one of our Co-Directors, Gary Wu MD, on the Gastronauts Podcast. In the episode, he shares his experiences as both a physician and scientist and how we can develop the skills to think creatively and communicate effectively.

Find the episode and transcript here: http://thinkgastronauts.com/the-gastronauts-podcast-season-2/

Thursday, January 23, 2020

Dear Colleagues,
We are pleased to announce the 2020 Symposium on High-throughput Screening Technologies at Penn will take place in the Biomedical Research Building (BRB) Gaulton Auditorium on:

Thursday, April 30th from 9 am to 3:30 pm

Join us to learn about high-throughput screening projects and platforms available at Penn and how high-throughput screening can be used in basic and translational medicine.

Tuesday, November 12, 2019

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