Rise in Usage of Germ-Free Mice

Germ-free mice are not new. Taconic Biosciences first started raising germ-free mice in 1960, after learning axenic husbandry techniques from the Laboratories of Bacteriology at the University of Notre Dame (LOBUND), where the first germ-free facility was established. Researchers have been using germ-free rodents since the '60s, producing a steady level of publications ...until recently. The use of germ-free animals in research grew dramatically within the last few years, driven by the surge of interest in microbiome science.

Surge in Demand Drives Production of Germ-free Mice

Taconic has seen this increased research focus reflected in usage of commercially available germ-free mice. Although Taconic has provided germ-free mice for decades, sales have been limited to a core group of users and fairly modest quantities. With the explosive growth of research using germ-free mice, that is no longer the case. The number of users has grown dramatically, but a shift in user demographics is even more telling. Prior to 2016, the vast majority of germ-free mice sold by Taconic were to non-profit users. In 2016, nearly 40% of germ-free mice were used by pharma and biotech researchers. These figures demonstrate the transition of germ-free and microbiome research from a niche research field to big business.

This transition is linked with an emerging realization that the microbiome's impact is not limited to immune system development and function, but affects a wide range of therapeutic areas. Taconic has increased germ-free production to meet this increased market demand and is introducing a new germ-free strain, BALB/c, to meet demand for broader applications.

Academic Gnotobiotic Core Facilities Expand

The growth in germ-free and gnotobiotic research has been felt in university cores, as well. Trenton Schoeb, Director of the University of Alabama at Birmingham Gnotobiotic Facility, commented that "There has been a general upward trend in the number of users," and that "we have received several inquiries about conducting projects with investigators from institutions that don't have gnotobiotic facilities. Our 2015 renovation and expansion increased our capacity significantly, so I expect we will be undertaking more such projects than we have in the past. This will not only lead to productive research collaborations, but also help us recover some of the high fixed costs associated with operating a gnotobiotic facility."

The Germ-Free Oeiras Service (GFOS)/Instituto Gulbenkian de Ciência, part of EMMA (European Mutant Mouse Archive)/Infrafrontier, has maintained a germ-free facility since 2005 for use by that community, and recently expanded to open a gnotobiology facility for experimental use of germ-free mice. According to GFOS staff, this expansion was "prompted in our Institute by ecologists interested in population dynamics, studying bacteria interactions. These researchers desired to move from in vitro to in vivo assays". In terms of research trends, GFOS has seen "a progression from immunology to developmental biology (in relation to the immune system). Also, research areas such as inflammation, ecology, population dynamics, and Darwinian evolution have been very active in the use of the germ-free and gnotobiotic facilities."

Julia Krout, Assistant Operations Manager, Division of Comparative Medicine at NYU School of Medicine, sees a shift in the expectations investigators have of institutional support. "I have seen more lab animal departments setting up gnotobiotic research. For many years, this was something that was run by the scientist... Some institutions did take ownership, historically, but in the past four years scientists are now looking to the lab animal department to run them... I see this merging into mainstream lab animal work more and more." She has seen growth in gnotobiotic research driven by "a much larger emphasis on personal microbiota that have led to research that must be more refined and defined."

University of Washington set up a gnotobiotic core three years ago, driven by investigator demand. "My research interests were really leading me towards the need for gnotobiotic study capabilities, and there were other University of Washington faculty with the same need," said Lynn Hajjar, Director of the University of Washington Gnotobiotic Animal Core. "The chair of the Comparative Medicine department, Denny Liggitt, really had the vision to see microbiome research as a growing area," said Charlie Hsu, Co-Director of the University of Washington Gnotobiotic Animal Core, "including serving as a resource for both within and beyond the UW community." Hsu notes, "It's been really exciting to work in this growing field and work with so many different investigators on their gnotobiotic projects."

Microbiome Research Funding a Challenge

The growth in gnotobiotic research is not without challenges. In particular, Krout notes that, "This community needs training assistance and a knowledge base at a grander scale. I have been a part of a team that has been bringing new workshops to the AALAS meetings that supplement other trainings present during the meeting and outside. Also, more needs to be published about general husbandry and operations so that new users may have a reference. Right now, Trenton Schoeb of UAB has set up a gnotobiotic listserv that has allowed people to ask these questions. There has been a new Gnotobiotics Guide published that is called Gnotobiotic Mouse Technology: An Illustrated Guide that is a great help."

User expectations must also be realistic. Krout says, "Programs and scientists need to understand that breaks will happen. When I was starting, a large program told me that they had a 10% contamination break annually. Also, gnotobiotics costs more than a traditional program. Everything takes longer because you are working under germ-free status....Programs cannot start overnight. Take your time and setup the program right from the start. Ask questions, see if you can take tours, and read available literature."

Schoeb calls funding critical: "I would list funding as the fundamental bottleneck for our investigators, and this is of course exacerbated by the high costs of gnotobiotics." At University of Washington, Hajjar also highlights finances as a challenge, "It's expensive to start a gnotobiotic core, and more funding is always needed." Hsu credits the gnoto community for an open spirit. "Other gnotobiotic researchers and cores were very helpful to us as we got started, and we have been trying to pass on the favor to new researchers starting facilities now," he said.

Where is Germ-Free and Gnotobiotic Research Going?

Taconic expects germ-free and gnotobiotic research to continue expanding, with pharma increasingly utilizing these tools for drug discovery and development. GFOS staff state that "the increasing availability of germ-free/gnotobiology facilities and the increasing evidence described in the literature, that the microbiota has a crucial role in health and disease, open new possibilities for new research areas (obesity, nutrition, neurodegenerative diseases and many more)".

UAB's Schoeb says, "As far as the role of gnotobiotics in research goes, I think it can be said with some confidence that interest will remain strong for some time, given that not only is the microbiota an important factor in major human health issues, but also is involved in just about every process that has been investigated so far."

GFOS staff believe "Germ-free and gnotobiology are already integrated in many branches of biology that are 'beyond the cells', i.e. organism/population centered. It is trendy today and it will hold for the next five-to-ten years, with more of the same, at increasing scale and covering more domains of biology. As it will be associated with even more very large data analysis, it is expected that we will get even more confusion...[but] when it will calm down and theories will be lay down, we will have gained reliable novel and useful concepts."