Skip to main content
Center for Gastrointestinal Biology and Disease

Considerations for Your Gnotobiotic Experimental Design

There are special issues to consider when planning gnotobiotic experiments beyond those of routine scientific design.

Please contact us using our Request/Inquiry Form to start a discussion about experimental plans, mice, services, and feasibility. The purpose of these discussions is to design experiments that are practical and efficient in the gnotobiotic setting and meet your research needs.

Number of isolators:

Each germ-free study or selective colonization, whether with a single strain or combination of strains, need to be housed in a separate isolator, since the transfer of microbes can occur between cages within an isolator.  Larger Trexler isolators can house up to 12 cages of mice, although we recommend no more than 8 for technical reasons.  Small Trexler isolators can house up to 6 cages of mice.  It is possible to house several mouse strains colonized with identical microbes within different cages in the same isolator.

Type of housing

Germ-free or selectively, gnotobiotic mice need to be maintained under gnotobiotic conditions.  Options include large or small Trexler isolators (maximum 12 vs 6 cages, respectively, see above “Number of isolators”) or individually contained cages (IsoCage system) where each cage is a functional isolator.  We currently restrict IsoCage housing to 4 weeks, preferably 2 weeks, and suggest that studies requiring longer colonization or frequent manipulations (serial gavages, injections, etc) be done in Trexler isolators.  Fecal transplant studies into ex-germ-free are best done in our BSL2 cubicle or IsoCages rather than gnotobiotic isolators.

Constraints on numbers

We are able to accommodate requests for fewer than 24 mice without limitations on sex and tight age distribution more rapidly than those with limitations. Requests larger than 24 mice require careful planning, as do those with sex and tight age restrictions.

Location of studies

We offer 4 options for services:

  • Shipping germ-free mice to an investigator;
  • On-site experiments with mice shipped to the investigator at the end of the experiment;
  • On-site experiments with local (UNC) harvest of tissues by our trained technicians. The tissues are then sent to the investigator;
  • On-site experiments with tissues locally harvested by the investigator’s staff in conjunction with our trained technician.

The decision on which option is optimal is best reached by a discussion with the NGRRC leadership, taking into account the requesting investigator’s access to gnotobiotic facilities at their own institution, duration of the experiment and the experimental design.  It is often less costly to fly an investigator or team member to our facility to harvest mice than to ship germ-free or gnotobiotic mice by air freight.

Keep it simple!

The realities of gnotobiotic experiments are that manipulations are difficult in the isolator where bulky gloves are required that limit dexterity of the manipulator and each isolator is expensive to maintain. Thus, we recommend the use of no more than 3 concurrent isolators (3 separate microbial colonization or 2 groups + germ-free controls), low numbers of mice, and relatively simple manipulations.