What Are Germ-Free Mice and How Are They Sourced?

by Phil Dubé, PhD | Updated: January 16th, 2025

Key TakeawaysKey Takeaways

  • Germ-free mice, devoid of all microorganisms, offer unique research advantages as "clean slates" for studying microbiome impacts on health, immune function, and disease causality.
  • These mice enable researchers to explore specific microbiome-host interactions, disease mechanisms, and therapies targeting the microbiome across fields like immunology, oncology, and neuroscience.
  • While germ-free mice are available from academic, government, and commercial sources, Taconic Biosciences is the sole comprehensive provider with consistent availability, IVF derivation, and robust microbiome services.

Understanding what germ-free mice are, the opportunities that they offer, and how you can obtain them will help you decide how best to incorporate these models into your research program.

The body is inhabited by trillions of microorganisms (the microbiome, consisting of bacteria, fungi, viruses, etc.) which play major roles in health and disease. Axenic or germ-free mice, specially-raised animals devoid of all microorganisms, are increasingly powerful tools for biomedical research and drug discovery in the microbiome space.

What are Germ-free Mice?

Germ-free mice lack all microorganisms (as determined within the limitations of the detection methods available) and are housed in tightly controlled and monitored isolators to prevent contamination. They are microbiologically sterile; no living organisms can be cultured from germ-free mouse specimens. Strict husbandry protocols and stringent testing regimens are required to maintain and confirm the germ-free state.

Other related terms:

  • Gnotobiotic Mice (from the Greek gnotos for known and bios for life) refers to mice in which every microorganism present is defined. Germ-free mice are one class of gnotobiotic animals, but mice associated with defined bacterial communities (e.g. Altered Schaedler's Flora) are also considered gnotobiotic. Gnotobiotic animals are kept in isolators for long-term maintenance of their microbiological status, although various caging systems can allow for alternate husbandry solutions.
  • Conventional is an often used, but poorly defined term in microbiome research. A conventional mouse is colonized with a diverse and largely undefined microbiome containing ~1011 bacteria within the gut alone. The exact microbial composition of a "conventional" mouse can vary widely, and there is no standardized "conventional microbiome." The microbiome of a wild mouse differs widely from that of laboratory mice, which themselves can have very different microbiomes depending on how and where they are raised. A conventionalized mouse generally refers to a germ-free mouse that is colonized with the fecal or intestinal microbiome of a non-germ-free mouse.
  • Modern laboratory mice are often referred to as specific-pathogen free (SPF), meaning that a defined list of mouse pathogens is excluded from these animal colonies. These specified pathogens vary between institution, making SPF itself a vague term. Vendors often raise mice at defined health standards that provide various levels of exclusion for pathogens, opportunistic bacteria, and commensals. Apart from these excluded microorganisms, the exact microbiome of an SPF mouse is not generally known or controlled, and is determined by the husbandry methods established for each health standard.

How are Germ-Free Mice Used in Research?

Work on germ-free mice began in the 1940's to understand how microorganisms contribute to physiology and disease. Since this pioneering work, researchers have identified key roles for the microbiome in metabolism, immune function, and resistance to pathogens.

In the past decade, the development of high-throughput sequencing technologies to characterize the microbiome has led to a revolution in our understanding of microbiome associations to disease. However, these studies can only identify associations and cannot prove causation or uncover the underlying biological mechanisms behind these interactions. In order to target the microbiome with novel interventions, it is necessary to understand its interactions with the host.

Germ-free mice are a critical tool to uncover the causal relationship between the microbiome and disease, and to determine the mechanistic basis through which microbes influence the host. Completely devoid of all microorganisms, germ-free mice offer a "clean slate" that can be studied as-is, or experimentally associated with microbes to test specific hypotheses.

Applications of germ-free mice include:

  • Identifying disease causality by comparing germ-free to conventionalized mice.
  • Determining how specific microbiomes protect from or contribute to disease.
  • Testing how patient-derived microbiomes affect pathology.
  • Analyzing how specific microbes, alone or in combination, regulate the host.
  • Discovering drug strategies to target the microbiome.
  • Understanding how drug responses are modulated by the microbiome.

Therapeutic research areas benefiting from germ-free mice include:

  • Immunology
  • Metabolism
  • Gastroenterology
  • Infectious disease
  • Oncology
  • Neuroscience
  • ...and more

Where Can You Obtain Commercial Germ-Free Mice?

Germ-free mice are available from several sources. Many are academic- or government-based centers, while Taconic Biosciences is the only comprehensive provider of microbiome products and service solutions. Academic and government cores may be less expensive, but generally have limited production capacity, long wait times, and, in some cases, may carry restrictions for end users (particularly for those in industry).

In contrast, commercial germ-free mice are available on demand and in cohort sizes suitable for any sized study. A commercial source allows you to reliably obtain germ-free cohorts when you need them, with consistent genetic quality and guaranteed Germ Free health status.

Germ-free mice are a critical tool to uncover the causal relationship between the microbiome and disease, and to determine the mechanistic basis through which microbes influence the host.

Custom germ-free derivation of novel mouse lines is offered by many of these same providers. One limitation of smaller academic cores is their inability to derive germ-free mice through in vitro fertilization (IVF), instead relying on cesarean delivery.

Although technically-demanding, IVF followed by embryo transfer is the preferred method for germ-free derivation as it reduces the likelihood of microbial contamination. Cesarean delivery carries an increased risk for contamination with microbes that cross the placental barrier (e.g. Lymphocytic Choriomeningitis Virus (LCMV), Lactate Dehydrogenase Elevating Virus (LDHV), Pasteurella pneumotropica, or Mycoplasma spp.). The IVF method for germ-free derivation is only available through larger centers and the single commercial provider of germ-free mice, but the capacity, delivery timelines, and husbandry support may differ widely between these sources.

Sources for Germ-Free Mice

Commercial source for germ-free mice and germ-free IVF derivations and husbandry:

Non-Commercial Sources for Germ-Free Mice and Germ-Free Derivations:

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