Germ-Free Mouse Health Monitoring
Diagnostic testing must be comprehensive enough to screen for standard pathogens, as well as microbial contaminants that may be finnicky or non-cultivable on cell-free media. Anaerobic agents are the most difficult to detect from environments containing oxygen, so it is critical that anaerobic collection culture media, anaerobic chambers, and powerful microbial identification technologies can be utilized to ensure accurate results in your microbiome research.
We offer comprehensive, accurate, and sensitive detection of infectious agents using both aerobic and anaerobic cultures of samples obtained from the isolator environment, individual cages, and directly from colony animals.
The C57BL/6-Germ-Free Mouse
for Microbiome Research
This model is indispensable for research into the host-microbiome interaction, including type 1 diabetes and inflammatory bowel disease.
Our microbial cultures can confirm the absence of bacteria in samples from germ-free mouse models. If bacterial growth is detected, we will work to identify the bacteria and assist in preventing the same agent from showing up in the future. Our microbiome services experts are available to provide guidance on establishing a germ-free screening program specific to your colony and research, and custom test panels can be developed to suit your specific needs.
Key Microbiome Services
Diagnostic Microbiome Screening
- Rodent feed sterility test
- Germ-free water testing
- Bedding sterility
- Environmental swab
- Sterility test – broth cultures
- Environmental swab
- 16s rRNA PCR
Next Generation Sequencing (NGS)
Next generation sequencing (NGS) analysis of your microbiome research samples makes it easy for you to assess the biodiversity of bacterial composition of your animal colony and research experiments. Our laboratory will extract genetic material from submitted samples, confirm the presence of 16S ribosomal RNA sequence, and use NGS technology to collect, sequence, and conduct bioinformatics microbiome analysis.
Request complimentary sample shipping supplies (e.g., swabs, vials) via our online order management platform, Laboratory Testing Management® (LTM™). Further, use LTM™ to generate submission forms and schedule your samples for submission. By creating orders ahead of time in LTM™, our laboratory will know when to expect your samples for testing, and you can track your samples online throughout the entire testing process.
Additional Microbiome Services
Germ-Free Mouse Colony Health Screening
Anaerobic agents are the most difficult to detect from oxygen-containing environments and, therefore, it is critical that anaerobic collection culture media, anaerobic chambers, and powerful microbial identification technologies be utilized to ensure accurate results. Charles River offers comprehensive, accurate, and sensitive detection of infectious agents using both aerobic and anaerobic cultures of samples obtained from the isolator environment, individual cages, and directly from colony animals.
Our microbial cultures can confirm the absence of bacteria in samples from germ-free animals. If bacterial growth is detected, we will work to identify the bacteria and assist in preventing the same agent form showing up in the future. Our health monitoring experts are available to provide guidance on establishing a germ-free assessment program specific to your colony and research, and custom test panels can be developed to suit your specific needs.
Whole Animal Monitoring: Axenic Mouse HM Plus with Anaerobic Cultures and PRIA®
PCR Rodent Infectious Agent (PRIA®) testing of feces for viral, bacterial, and fungal/parasitic agents
Aerobic culture of upper respiratory and gastrointestinal tracts with identification via MALDI-TOF mass spectrometry
Anaerobic culture of cecal contents with identification via MALDI-TOF mass spectrometry
Necropsy (with histology of gross lesions upon requests)
Serological viral antibody detection
Environmental Monitoring: Surveillance Plus PRIA®
PCR Rodent Infectious Agent (PRIA®) testing of cage/isolator swab for viral, bacterial, and fungal/parasitic agents
16S next generation sequencing
Direct Submission of Samples
Anaerobic (germ-free) fecal screening
Germ-Free Mouse Isolators
Microbiome research that require animals to be maintained at a germ-free health status need specialized isolators that are capable of excluding all contaminants are required. Germ-free isolators are available in various sizes, easily transportable, and can be connected to one another to support colony expansion.
Scientific Staffing and Training for Microbiome Research
There are added levels of complexity associated with maintaining a vivarium that supports microbiome research. Unlike standard animal care and maintenance programs that adhere to a strict but selective biosecurity program, a vivarium designated for microbiome study needs expanded biosecurity to ensure that all agents (pathogenic or not) are accounted for or excluded. Therefore, it is critical that vivarium staff have the necessary qualification and expertise to maintain this level of biosecurity.
Customized solutions for staffing needs whether you are looking for technicians or a management partner. In addition to recruitment and training, we can also provide performance assessment and career guidance.
Provide training and continuing professional development for scientists, veterinarians, lab technicians, and more. We offer hands-on instruction in actual and simulated research environments, as well as an e-learning course design.
Vivarium Program Design for Microbiome Research
Clients can leverage our scientific and engineering expertise to plan and design a vivarium specific for microbiome research. Consultation is available on a number of design aspects including development of mechanical and electrical systems concepts, equipment lifecycle cost analysis, staffing, and options to maximize space. A review of your existing program(s) is also available.
Frequently Asked Questions (FAQs) About Microbiome Research
What is the microbiome?
The microbiome is the group of bacteria, fungi, and viruses contained within a sample. Several different spots on an animal contain microbiomes. A mouse has a different microbiome on its fur/skin than it does in its mouth or in its gastrointestinal tract.
Why is the microbiome research important?
The microbiome plays an important role in food metabolism, protection from infection, drug metabolism, hormone production, amongst others. As such, the microbiome has been identified as an important contributor to a number of disease phenotypes, including obesity and non-alcoholic fatty liver disease. Monitoring the microbiome offers insight into the changes occurring in the bacterial communities of your animal colony.
What is microbiome screening?
Microbiome screening captures a snapshot of the bacterial communities contained within a sample. Our microbiome services covers amplicon-based analysis of the bacterial communities present in your sample. Our team will perform everything from nucleic acid extraction to sequencing, ultimately delivering a report breaking down your microbial community composition.
What kind of data do you receive?
We've partnered with OneCodex, a leading bioinformatics provider to deliver your data in a presentation-ready format. OneCodex will host access to your raw data in FASTQ format, as well as provide you with publication-quality figure located in their web interface and a report in PDF format.
What type of samples do you accept and from what animal?
We accept a variety of sample types and origins. Please reach out to us at [email protected] to discuss your interests.
Fecal, Cloacal swab
Can I view a sample standard report? What data is included?
The standard report includes relative abundance data for each sample submitted, broken down by taxonomic level. It also contains alpha and beta diversity, PCA and PCoA analysis, and rarefraction analysis. Additional microbiome analysis is available through our bioinformatics partner, One Codex.
Please email [email protected] and we will provide you with a copy of our sample report.
What is amplicon testing?
Amplicon testing is a strategy in microbiome research that focuses on a specific region of the bacterial genome to identify the bacterial genus. In some cases, both genus and species level identity is possible.