The Massachusetts Host-Microbiome Center core facilities provide support to groups around the world who study effects of the microbiota on the host. Core staff and equipment handles materials from in vitro systems, animal models and human studies. The core provides personnel, resources and equipment for:

(1) Gnotobiotic (germfree), defined association and conventional housing for mice.

(2) Gnotobiotic mice and breeding programs
(3) CLAMS metabolic caging units, including capacity to operate under germfree or defined-colonization conditions
(4) Quantiative microbiology and microbiological assessment of complex samples
(5) Technical sequencing for 16S rRNA gene analyses (phylotyping)
(6) Bacterial whole genome sequencing
(7) Short chain fatty acid (SCFA) and other microbial metabolite analyses in primary gut samples or culture supernatants
(8) CLIA-level (clinical laboratory) testing for clinical microbiology, Clostridium difficile detection (antigen, PCR and cell-culture based assays), fecal calprotectin, and screening of human or animal samples for multi-drug resistant organisms (MDROs).

The core maintains 60+ gnotobiotic/germ free isolators for housing of mice under germfree conditions, and biohazard levels 1 and 2 for specifically-associated mice. In-house bred germfree mice are also available to investigators for experiments. In addition the core maintains a 700-cage containment system for idefinite housing of BL1 or BL2 conventional mice with complex flora, and short term gnotobiotic or defined-colonization experiments.

Microbiologically, the core maintains an extensive repository of human and animal commensal isolates and BL-2 pathogens for use in specific-associations as well as for in vitro studies. Experienced microbiologists routinely cultures primary samples from humans and/or animals to study complex samples using culture and/or sequencing-based methods.

Addition core platforms support analyses of short-chain fatty acids (SCFA), microbial products of fermentation, next-generation sequencing-based methods for 16S rRNA gene phylotyping and bacterial genome sequencing. In addition, core staff manage continuous chemostat fermenter systems for robust in vitro studies that may be run under aerobic or anaerobic conditions, and routinely develop defined microbial consortia for experimental and pre-clinical studies.