The CGIBD Gnotobiotic Core, an integral Center component since 1988. The Core provides germ free (GF) wild type (WT) and genetically-engineered gnotobiotic mice to CGIBD members and national DDRCC investigators at heavily subsidized costs, and provides technical support and expertise to facilitate optimal study design. This resource allows our investigators to examine a) physiologic and pathogenic differences between GF, gnotobiotic (selectively colonized), conventionally raised and fecally-transplanted ex-GF mice; b) functional relevance of microbial genes; and c) host/microbe, microbe-microbe and dietary-microbe interactions. Gnotobiotic technologies enable precise microbial manipulation by colonizing GF WT, knockout (KO) or transgenic (TG) inbred mice with single or combinations of resident or pathogenic bacterial, viral or fungal species. To this end, this resource also includes genetically engineered bacterial strains, and fecal bacterial communities derived from normal or diseased human or experimental animals.


  1. Provide GF or selectively colonized (gnotobiotic) WT and mutant mice, their tissues and cells.
  2. Derive additional GF WT and genetically engineered mouse strains.
  3. Consult with investigators to optimize experimental design and implementation and provide technical services.
  4. Support studies for new investigators to generate key data for grant applications.
  5. Develop a library of fully characterized bacterial strains and complex human and murine fecal communities to facilitate reproducible results in gnotobiotic studies.

This facility and the combined expertise of the Directors, Balfour Sartor, UNC-CH and Sue Tonkonogy, NCSU provide Center members an unparalleled resource to perform innovative functional studies to explore microbially-driven mechanisms of GI homeostasis, injury and repair.

More information or request services.


UNC-Chapel Hill Gnotobiotic Core

Core Director: R. Balfour Sartor, MD. Dr. Sartor brings 30 years of experience performing internationally recognized scientific research with gnotobiotic rats and mice and innumerable contacts and scientific interactions with regional, national and international investigators. Dr. Sartor will oversee management of the UNC-CH facility and interact with UNC investigators to coordinate gnotobiotic mouse experiments and distribution of bacterial strains.

Core Co-Director. Andrea Azcarate-Peril, PhD, is a microbiologist who is the director of the UNC Microbiome Core.  The Microbiome Core was previously a CGIBD core, but as described in the overall section of this application, the Microbiome Core has been spun off as a stand-alone facility no longer funded by the CGIBD. For the CGIBD Gnotobiotic Core, Dr. Azcarate will be responsible for isolation of new bacterial strains by fecal culture. The UNC Microbiome Core partnered with the Carolina Donor Services (CDS) to receive intact intestines from organ donors. Processing of 4 organ donor intestinal samples has generated over 350 mucosally-associated bacterial isolates currently preserved in the UNC Microbiome Core (Table 3).

Core Facility Manager: Josh Frost, BA, RLATG. Mr. Frost was hired after a national search to replace our first Core Manager, Maureen Bower, who retired 14 yrs after setting up and managing the UNC gnotobiotic facility. Mr. Frost brings >7 yrs experience in gnotobiotic technology and management of large animal facilities at the Univ. of Michigan. He is responsible for managing all aspects of facility operation. He supervises and trains all technical staff and is responsible for daily management of the facility, including planning the 7 technical staff’s daily activities, monitoring and managing breeding to ensure maintenance of unique mouse lines and generation of adequate mouse numbers for current and requested experiments. Mr. Frost is also responsible for allocating gnotobiotic rodents to requesting investigators based on priorities established by the online ordering application and the Gnotobiotic Steering Committee. In addition, he is charged with upkeep and repair of Trexler isolators and documenting facility activity with monthly use records and billing statements.

Core Derivation Specialist: Fengling Li, MD, PhD, performs GF derivations of mice and assists with cryopreservation of embryos and sperm. After becoming our derivation specialist in 2010, she has dramatically improved our embryo transfer success rate. In 2018 she used hysterectomy rederivation (C section) to derive 2 new GF mouse strains that proved refractory to derivation via embryo transfer, accomplished successful transfer of cryopreserved embryos, and derived a Collaborative Cross strain by in vitro fertilization.

Core Culture Collection. Kshipra Chandrashekhar, PhD., Research Associate in the UNC Microbiome Core (Azcarate-Peril lab) will isolate bacterial strains from the collected samples and perform quality control, plating, and preliminary characterization of bacterial strains. Dr. Chandrashekhar has processed small and large intestines from four organ donors for isolation of bacterial strains. Bacterial strains isolated from fecal specimens will be assigned to taxonomic groups by 16S Sanger sequencing and stored for future studies.

Lab Manager: Lisa Holt, BS, coordinates activities, compliance, orders supplies, prepares amendments for IACUC renewals and prepares for annual inspections. She will send bacterial strains stored in Dr. Sartor’s lab to requesting investigators and culture strains for gnotobiotic inoculation.

Research Specialist: Jeremy Herzog, BS, performs gnotobiotic experiments designed by Core investigators. He communicates with investigators, performs the experiments, including colonization of gnotobiotic mice, gavages, weighs mice within isolators and collects feces for analysis.  If requested, he can assist with conducting necropsies, collecting, processing and storing tissues, collecting and analyzing data for requesting investigators.  These studies are conducted under the close supervision of Dr. Sartor.

Animal Technician III: Michael Waldrop, BS, performs day-to-day animal care duties, including cage changes, providing fresh food and water, stocking of sterile isolators with autoclaved food, bedding and water, confirming sterility every 2 weeks by obtaining fecal pellets and bedding for culture, transfer of animals to study isolators for experimental studies, separate offspring at weaning, cut tails of weanings for genotyping (DNA analysis), set up breeders, monitor pregnancies, and identify ill or injured rodents. He is primarily responsible for 12-15 isolators. The remaining 50% of his salary will be paid by program income or other grant sources.

NCSU Gnotobiotic Core

Core Director: Susan L. Tonkonogy, PhD. Dr. Tonkonogy, a cellular immunologist, is the Scientific Director of the North Carolina State University (NCSU) component of the Gnotobiotic Core. She has over 25 years of experience in using GF and gnotobiotic rodents as models of chronic intestinal inflammation. Dr. Tonkonogy oversees all aspects of NCSU Core administration and supervises the technical staff.

Core Technical Manager: Karen Flores, BS, RLATG. Ms. Flores is the technical director and supervising technician, responsible for mouse care, breeding, organizing and implementing all experimental protocols, isolator maintenance, quality assurance, record keeping, and training new Core personnel. This senior technician position is essential for the Core to meet its goals and to provide stability of leadership.

Core Assistant: Nicole Gagnon, BS. Ms. Gagnon assists with all Core operations including mouse care, assisting with implementing experimental protocols, changing bedding, transferring rodents between isolators and autoclaving food, bedding and supplies.

Wild type miceKnockout mice (background)Knockout mice (background)Reporter, transgenic, other
C57BL/6JIL-10-/- (129S6/SvEv)MDR2+/-; IL-10-/-*IL-10EGFP transgenic
BALB/cIL-10-/- (C57BL/6)NLRC3-/-(C57BL/6)*NFkBEGFP transgenic
CB6F1*Rag 2-/- (129S6/SvEv)NLRC3-/- x IL-10-/- (C57BL/6)*Sccn1b-transgenic
129/S6SvEvRag 2-/- (C57BL/6)NLRP12-/-(C57BL/6)*P48Cre/Kras
Swiss WebsterRag 2-/- IL-2Rg-/- (C57BL/6)*NOD SCIDCC027(Collaborative Cross)*
IL-10-/- x Rag 2-/- (129S6/SvEv)NOD SCID IL-2Rg-/- (NSG)
IL-10-/- x Rag 2-/- (C57BL/6)PlgR-/- (C57BL/6)
ATG 16L1 hypomorphTL1A-/- (C57BL/6)
*Derived 2014- 2018