TGen Integrated Microbiomics Center

The TGen Integrated Microbiomics Center is an efficient, cutting-edge, multi-omic microbiome research and service center that will empower clinicians and researchers to integrate microbiome analysis into cancer-based research studies. The Center uses state-of-the-art sequencing technologies and bioinformatics tools and delivers custom, interactive microbiome summaries that are directly interpretable, and which can optionally be used with collaborator-preferred tools for further downstream analysis. Additionally, the Center includes a CLIA laboratory and integrates rigorous quality control that is often lacking in many microbiome services.

We provide comprehensive microbiome services, including: 

  • Custom end-to-end service, including consulting on study design, appropriate sample collection handling, and optimal analysis approaches
  • Nucleic acid extraction
  • Analysis-appropriate library preparation
  • High-throughput sequencing
  • Delivery of publication-quality bioinformatics analysis, statistics, and visualizations
  • Post-analysis consult on interpretation and future studies

Our sequencing applications for microbiome analysis include:

  • Standard 16S (bacterial) and ITS (fungal) gene sequencing
  • Multiplexed targeted sequencing (e.g., specific toxin or drug resistance genes)
  • Shallow and deep whole metagenome sequencing to understand full microbial gene composition
  • Whole transcriptome sequencing to understand microbial and host transcription
  • Microbial whole genome sequencing (for cultured microbes)
  • Tiled genome sequencing for specific uncultured targeted microbes (e.g., select viruses)
The Center will assist with bioinformatics analysis and interpretation, including:
  • Quality control and identification and removal of human genome contamination to protect your study participants’ identities.
  • Identification and annotation of amplicon sequence variants and other microbiome features.
  • Standard and customized microbiome analyses, including alpha and beta diversity analysis and visualization, differential abundance testing, longitudinal microbiome analysis, and more.
  • Key data files will be provided, facilitating collaborator analysis with the QIIME 2 platform or other tools.
  • Generation of interactive visualizations that can be explored in your web browser.
  • Full annotation of all QIIME 2 analysis steps performed by our team, providing full transparency and enabling you to reproduce our workflow on the same or different microbiome data.

David Engelthaler Ph.D.

Professor and Director
Pathogen and Microbiome Division

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J Gregory Caporaso Ph.D.

Associate Professor (Adjunct)
Pathogen and Microbiome Division

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Keehoon Lee Ph.D.

Research Assistant Professor
Pathogen and Microbiome Division

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TGen Integrated Microbiomics Center

TGen North scientists discuss the Integrated Microbiomics Center and the fascinating world of the microbial universe.