Microbiome Core Facility

The primary goal of the Microbiome Core is to facilitate microbiome studies for researchers at Columbia University Irving Medical Center (CUIMC). The facility is a centralized and cost-effective resource for processing and storing biological specimens, and sequencing and analysis of microbial communities for various research studies, including basic science, clinical, translational, and epidemiological projects.

We provide consultation on all aspects of study design and sample collection. The core receives, processes, and stores coded samples as needed. We provide DNA and RNA extraction and prepare and sequence samples with the Illumina Miseq platform and Oxford Nanopore platform. We also perform bioinformatics analyses on sequencing data. As a centralized core, we have higher sample volaumes, which enables more cost-effective sequencing for investigators.

The core also fosters informal interactions of investigators from varied research backgrounds and discussions regarding best practices and novel techniques in order to enhance microbiome studies at CUIMC. Through the Microbiome Working Group, we host informal Microbiome Core Data Club meetings, as well as the Microbiome Seminar Series featuring invited internal and external speakers.

Consultation and study design

  • Optimal sample collection
  • Sample size caculations¬†

Storage of clinical specimens

  • Maintenance of a sample inventory
  • Sample processing/aliquoting of liquids, body fluids and stool specimens
  • Swab storage
  • Microbial cultivation and freezing of bacterial isolates

Nucleic acid isolation and quantification

Next generation sequencing in-house

  • 16S rRNA
  • ITS (Mycobial)
  • Whole genome sequencing of single isolates (WGS)
  • Metagenomics
  • RNA-seq
  • Long-read sequencing (Oxford Nanopore)

Data Analysis and Bioinformatics

  • Standardized basic 16S rRNA analysis
  • Advanced bioinformatics capabilities available by request

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  • Anne-Catrin Uhlemann, MD, PhD

    • Associate Professor of Medicine

    Department of Medicine, Division of Infectious Diseases

    Headshot of Doctor Uhlemann


Microbiome Core
630 West 168th Street
Physicians & Surgeons Building, PS 9-428
New York, NY 10032
United States