The Gnotobiotics, Microbiology and Metagenomics core assists investigators evaluating the host microbiota and its role in normal physiology and disease. The core includes a number of resources for groups studying the role of the microbiota in human health and disease, including:

  • Administrative Unit:  Manages the core’s LIMS, invoicing and provides assistance to investigators who need to obtain IRB, Biosafety and IACUC protocols for studies.
  • CLIA (Clinical Laboratory) Unit: Handles sample collection and logistics for research and human trials, performs clinical-lab/CLIA-level testing of materials for microbiology and/or molecular analyses.
  • Molecular Unit: Handles sequence-based studies of microbiome samples including nucleic acid extraction, amplification, next-generation sequencing and quantitative PCR studies.
  • Microbiology Unit: Includes dedicated microbiologists who handle culturing of primary materials, biochemical and resistance phenotyping of defined isolates, and production of short chain fatty acids (SCFA).  The microbiology unit also maintains a large strain bank of human and animal commensal strains and assists with the development of defined microbiota for functional applications.
  • Computational Unit: Includes bioinformaticians and computer scientists who can assist in experimental design and the analysis of microbiome and other datasets integrating hosts or environmental covariates.  Novel algorithms developed by core staff support longitudinal analyses of microbiota dynamics and prediction of host outcomes with microbiome datasets.
  • Germfree animal facility: Maintains active breeding colonies of gnotobiotic mouse strains and isolators used for experimental manipulations under germfree or specifically colonized states. The facility also manages high-throughput cage containment systems that can be used for short-term germfree experiments or long-term experiments with transfer or human or other donor flora to gnotobiotic mice.

The Gnotobiotics, Microbiology and Metagenomics core is located at Brigham and Women’s Hospital.

Core Director: Lynn Bry, MD, PhD
Co-Director: Georg Gerber, MD, PhD, MPH
Microbiology Unit Director: Andy Onderdonk, PhD
Corporate Manager: Neil Herring, MBA
Core Manager: Vladimir Yeliseyev
Grants Contact: Tim Janicki
Administrator: Selsebil Slijvo

Services

  • Project management and experimental design
  • Patient consent and sample collection logistics
  • Aerobic and anaerobic culture
  • Microbial identification and analysis
  • Phenotypic analyses include short-chain fatty acid (SCFA) profiles in primary samples or cultured isolates
  • Preparation of materials for 16S rRNA microbiome analyses
  • Bioinformatic and computational analyses of metagenomic datasets
  • Time series analyses of complex microbial ecosystems leveraging novel Bayesian models developed by core faculty

Equipment and instrumentation

  • Laboratory Information Management System (LIMS) for patient registration, sample submission and viewing of datasets
  • The core maintains a complement of 22 isolators of various configurations for breeding and experiments under germfree, BL1 or BL2 conditions
  • 100-cage containment system for short-term GF and long-term defined colonization studies
  • Anaerobic hood and automated microbiological identification systems
  • Automated DNA extraction and library preparation equipment
  • qPCR and Illumina NGS platforms
  • HIPAA-compliant computational cluster
  • Gnotobiotic (germfree) mice
  • Gnotobiotic and defined colonization experiments in gnotobiotic isolators or high-throughput cage containment systems
  • Assistance with mouse necropsy and tissue preparation for histopathology

Fees

To receive a quote for utilization of services please contact the core’s Project Manager Vladimir Yeliseyevor fill in the Core’s request form.

Project Manager:  Vladimir Yeliseyev
Telephone number:  (617) 525-7180
Email: VYELISEYEV@PARTNERS.ORG