• 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

    The Microbial Culture and Metabolomics Core supports microbial culturing projects under various physiological conditions (e.g., aerobic/microaerobic/anaerobic) using multiple model systems (e.g., batch and continuous flow systems), as well as targeted metabolomics services.

  • 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.


Program Director, Dr. Frederick Bushman, and the Penn Center for Research on Coronavirus and Other Emerging Pathogens has been featured in this Philadelphia Inquirer article on the emerging Omicron variant.

Thursday, December 2, 2021

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.

Thursday, September 16, 2021

Dear Microbiome Center Colleagues and Collaborators,
We are sad to announce that Dr. Lisa Mattei will be leaving after successfully managing the laboratory of the CHOP Microbiome Center.

Lisa has made huge contributions to the microbiome field during her six year tenure. She led the Sequencing Core, oversaw all sequencing projects, and developed new microbiome-oriented technologies. We wish her the very best in her future endeavors.

Best wishes,
Drs. Bob Baldassano and Rick Bushman, Jessi Erlichman

Wednesday, May 26, 2021

The CHOP Microbiome Center is open to receive general inquiries for microbiome projects. Please complete the following form to be contacted for a free consultation with our Microbiome Center Core managers.

Wednesday, February 24, 2021

Rutgers University has just posted a new faculty position for “Tenure-Track Assistant Professor in Microbiome Bioinformatics” which is now live on the Rutgers Jobs Site. It is Faculty Posting #21FA0168. Here is the posting link:


Tuesday, February 23, 2021

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