The CHOP Microbiome Center consists of Sequencing and Analytical Cores that work together to provide end-to-end solutions for microbiome research.

Types of projects supported by the CHOP Microbiome Center

  1. 16S rRNA and ITS amplicon sequencing.
  2. Shotgun metagenomic sequencing.
  3. Whole genome sequencing of microorganisms and viruses.
  4. Bacterial and fungal quantification.
  5. 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.

    Infrastructure for deep sequencing includes two Illumina HiSeq 2500 instruments, a MiSeq instrument, and a Pacific Biosciences RS II Single Molecule Real-Time (SMRT) instrument. The sequencing facility is housed in the Colket Translational Research Building at CHOP. The wet lab is located in the adjoining Abramson Research Center and it includes dedicated pre- and post-PCR spaces. The labs are well equipped with the latest instruments including two automated liquid handling robots for high-throughput processing. The Sequencing Core is staffed by a laboratory manager and two research assistants.

    Analytical 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.

    The primary mission of the Analytical Core is to follow up basic bioinformatics analysis with targeted bioinformatics and statistical approaches that are unique to each study. Rather than applying a one-size-fits-all approach, our goal is to collaborate with other researchers and draw conclusions from the sequence data about which we have high confidence and which reflect the original goals of the experiment.

    The Analytical Core located at 3535 Market Street. High capacity network lines connect the Analytical Core to the Sequencing Core, and to the CHOP supercomputing facility in Allentown, PA. The Core is staffed by two full time programmer/analysts and is supported by a network of consulting statisticians.

    Center Services

    Interacting with the CHOP Microbiome Center can take two forms.


    Customers submit samples for sequencing and sequencing data are returned. In this setting, customers will independently analyze the sequencing data.


    Customers collaborate with the Center to design and carry out complete projects. Customers will begin by meeting with staff, who will consult on study design. The analysis will be fully planned, including sample size assessment and construction of the statistical framework for analysis. Customers will complete metadata tables for the analysis and present written documentation of IRB approval. Samples are then sent to the Center, sequenced, and analyzed according to the pre-specified plan. The results are reported to customers and any unused samples are returned. Aside from an initial free consultation, all work will be carried out according to our cost schedule.