Microbiome & Germ-Free Monitoring

Microbiome research has primarily focused on the gut as it has been found to be the most diverse and constitutes the densest number of microbe cells in the human microbiota. Recent studies using germ-free animals have provided further insight into how the gut microbiota are specifically linked to autoimmunity. Charles River provides a full range of services for your microbiome research needs.

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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.

Download the Data Sheet

Microbiome Service Offerings

  • Germ-Free Animal Models

    Germ-free rodents have been essential to microbiome research and the production of specific pathogen-free (SPF) rodent models. Bred in an axenic environment free of all microorganisms, our C57BL/6NCrl (B6N) germ-free mouse can aid research projects studying conditions involving host-microbiome interactions, including type 1 diabetes, inflammatory bowel disease, obesity, and autism.

  • Germ-Free Housing (Isolators)

    Microbiome research requires animals to be housed in specialized isolators that are capable of excluding any contaminants, in order to maintain their “germ-free” health status. Germ-free isolators are available in various sizes, can be transported easily, and can be connected to each other, supporting colony expansion.

  • Comprehensive Environmental & Germ-Free Model Screening

    It's crucial to establish a robust health surveillance program to maintain germ-free animals. Any testing that is performed should not only be screening for standard pathogens, but also microbial contaminants that may be fastidious or non-cultivable on cell-free media (like much of the indigenous microbiota).

    Since anaerobic agents are the most difficult to detect from oxygen-containing environments, their collection culture media and chambers, and powerful microbial detection identification technologies should be used to obtain accurate results.

    Our microbial cultures can confirm the absence of bacteria in samples from germ-free animals. If bacteria is detected, we will work to identify it and assist in preventing the same agent from reappearing in the future.

    We offer several screening options to ensure your germ-free animals maintain their health status. Our laboratory scientists will work with you on developing and implementing a health monitoring program that fits your research needs and budget.

  • Microbiome Sequencing (NGS)

    Microbiome sequencing captures a snapshot of the different bacteria in a laboratory animal. Whether you’re monitoring the health of your vivarium or interested in an effect-driven change in community composition, it can give you the insight you need to identify any changes in the bacterial communities that are present in laboratory animals.

    Our microbiome laboratory offers start-to-finish bacterial 16S ribosomal RNA sequencing, enabling investigators to take a hands-off approach to analysis. Once your sample is received, we’ll take care of the extraction, library preparation, and sequencing. OneCodex, a leading industry partner in bioinformatics, will then analyze the generated data and compile a comprehensive report, including parameters such as alpha and beta diversity and relative abundance. You’ll also gain access to their carefully curated 16S rRNA database, dynamic web interface, and hosting of your raw and analyzed data.

Germ-free mouse models are available for microbiome research

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.

View the Model


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.

    Sample Type
    Skin Swab
    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.