Microbiome

Microbiome Core

Jonathan P. Jacobs, MD, PhD

This core offers a range of services for studying the microbiome in human and animal model studies. These include study design, sample collection, sequencing-based assays such as 16S rRNA gene sequencing or shotgun metagenomics and data interpretation. The Microbiome Core has experience with a wide variety of human and animal sample types including, but not limited to, feces, tissues, swabs, saliva and intestinal lavage.

For more information, contact Jonathan P. Jacobs, MD, PhD, Core Director, at [email protected]

Services of the Microbiome Core

1. Microbiome study design, sample collection, and processing

  • Consultation to plan microbiome studies, including sample collection strategies
  • Grant proposal development
  • Stool collection kits for home sampling
  • Aliquoting of frozen feces under liquid nitrogen
  • Processing of swabs (rectal, cervical, ocular, etc.)
  • Microbial DNA extraction by bead beating

2. Sequencing-based assessment of microbiome composition and function

Samples can be delivered frozen, at room temperature in a preservative such as 95 percent ethanol, or as extracted DNA. Sequence data are provided as fastq files and count tables of taxa, genes or transcripts

  • 16S ribosomal RNA gene sequencing, V4 region (bacteria)
  • 16S ribosomal RNA gene sequencing, V1-V3 region (bacteria)
  • ITS1-ITS2 sequencing (fungi)
  • Shotgun metagenomics
  • Metatranscriptomics

3. Additional services

  • Total bacteria quantitation by 16S rRNA quantitative PCR
  • Fecal calprotectin or lipocalin measurement
  • Salivary cortisol measurement
  • Analysis of microbiome sequence data (on a collaborative basis)
  • Coordination with other Goodman-Luskin Microbiome Center cores (e.g. bioinformatics, neuroimaging, clinical studies, etc.)