The Microbiology Unit, Directed by Drs. Lynn Bry and Andy Onderdonk is staffed by dedicated microbiologists with many years of experience working with gut anaerobes, clinical pathogens, and microbial genetic systems. Core services include the quantitative and qualitative culturing of primary materials for the presence of aerobic and anaerobic microbial species. Analyses can include identification of specific members within complex communities or be

limited to specific commensal or pathogenic organisms.  Microbial identifications are performed using established methodologies including phenotypic characteristics, biochemical reactions, and analyses of microbial fermentation products including short- medium- and long-chain fatty acids. Custom bacterial antibiograms are also provided by the unit. 

Center identified microbial species also be used for sequence based identification by 16S rRNA gene sequencing or genomic analyses performed in the Center’s Molecular Unit.  Analysis of primary samples and in vivo-collected materials for short chain fatty acids (SCFA) are used to identify profiles of microbial products of fermentation. The unit also maintains a large strain bank of human and animal commensal strains that is available to investigators as single organism cultures or mixed communities.

The unit maintains dedicated anaerobic hoods for BL1 and BL2 culturing, and for clean preparation of microbial consortia to be used in in vitro or in vivo models. Additional high-throughput equipment supports microbial biochemical identifications, GC/LC quantitation of short chain fatty acids and other small molecules metabolites from microbial fermentations, and preparation of microbial consortia and stocks.

Continuous chemostat fermenters maintained by the unit support batch and longitudinal studies of single or defined microbial communities with capacity for real-time monitoring of temperature, pH, redox, dissolved O2 and biomass, and means to add/alter fermentor conditions and sample materials.

The unit also support the microbiology and sterility program for the MHMC gnotobiotic facility and for other area germfree facilities.

Dr. Lynn Bry’s lab also has developed genetic systems for commensal species and works in collaboration with many groups to develop defined consortia for functional applications.

Example Projects:

  • Development of the MHMC GnotoComplex toolkit for developing therapeutic microbiota in target areas such as Clostridium difficile infection and to promote immunomodulation.
  • SCFA studies of mice fed different diets to develop formation that promote butyrate production or other end products of microbial fermentation.

Case studies:

EndOclear Study

MDSINE: Microbial Dynamical Systems Inference Engine for microbiome time-series analyses

Pathogen Genomic Surveillance Program

Microbiota Drug Metabolism 

To inquire further please fill out our online request form or contact us at microbiome@bwh.harvard.edu.