The Massachusetts-Host Microbiome Center’s Gnotobiotic (germ free) Facility supports studies evaluating in vivo effects of the host’s microbiota on health and disease. The core maintains 60 flexible film isolators of different configurations to support small and large scale experiments under BL0, BL1 and BL2 conditions. Experiments may include colonizations with defined associations or complex microbiota, dietary and other perturbations to define causal effects of microbial communities in vivo. In addition, the facility maintains multiple 700-cage capacity cage-containment units to support conventional studies and short-term germfree or defined associations.

The facility’s breeding program provides gnotobiotic stocks of  mice to investigators and is able to maintain dedicated lines for users. Facility staff will also work with groups who need to derive specific lines to a germfree state.

Facility staff manage all routine husbandry and are available to work with investigators on defining experimental plans, submitting IACUC protocols, and performing in-isolator procedures to insure success of ongoing studies. For external users, Center staff will evaluate if studies may be conducted under the Center’s IACUC protocol as a collaboration, else both external academic and industry users may obtain dedicated IACUC protocols through the BWH IACUC.

Integration with other Center Units:

Collaboration with the Functional Metabolism unit has developed CLAMS cages rigged for gnotobiotic operation to support detailed metabolic studies for evaluating effects of microbial colonization on host metabolism, body tissue composition, and thermogenesis. CLAMS units can be operated to support gnotobiotic, defined associations and studies with adoptive transfer of donor microbiota from human or other sources.

The Center’s Microbiology Unit manages the gnotobiotic facility’s sterility program, monitoring of gnotobiotic stocks, defined colonizations, and sterilization of supporting supplies. In addition, microbiology staff can also prepare defined microbial consortia, from existing or external sources, to be used in association experiments.

Facility resources:

  • 40 X 5 cage isolators for experimental studies
  • 6 X 18 cage isolators for experimental studies
  • 4 X 18 cage negative pressure BL2 isolators for experimental studies
  • 3 X 55 cage capacity breeding isolators
  • 7 X 18 cage isolators for breeding programs
  • 700 cage capacity containment system for conventional studies including colonizations with donor human or other origin microbiota, or short-term germfree and defined association studies
  • Dedicated autoclaves and EtO sterilizers
  • In-isolator equipment to support experimental procedures such as obtaining body weights, sample collection, blood glucose measurements, introduction of specific microbes, small molecules by gavage or injection, or adoptive transfer of donor cells for immunologic studies
  • Availability of different diets and means to sterilize for gnotobiotic or defined association studies

Dedicated BL0/1 and BL2 procedure rooms with biolaminar flow hoods.

Case studies:

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

Microbiota Drug Metabolism 

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