Trusting Their Guts: OSU's germ-free mice research identifies new generation probiotics, trains next generation of scientists

Tuesday, October 8, 2024

Media Contact: Sydney Trainor | Communications and Media Relations Specialist | 405-744-9782 | [email protected]

While some people perceive mice as pests to be eradicated and others see them as cute and cuddly symbols of Disney magic, Dr. Joy Scaria sees something entirely different.

At the forefront of microbiome research as Oklahoma State University's Walter R. Sitlington Endowed Chair in Infectious Diseases, Scaria views germ-free and humanized mice as innovative tools to enhance human health, opening doors to groundbreaking medical advancements.

When it comes to research funding, prestigious National Institutes of Health grants are highly competitive. Universities such as OSU vie for these grants alongside large medical schools like Harvard, Johns Hopkins University and Stanford University. Competitive applications for grant funding showcase a combination of innovative instruments and expertise to demonstrate the future of science.

At OSU, Scaria's lab is trying to understand how a gut microbiome host interaction shapes health and disease. He uses germ-free mice to understand the fundamental makeup of the healthy microbiome to devise better therapeutics.

Conventional mice harbor other bacteria or species that make it difficult to clearly know whether the effect is because of the resident species or the one added. Germ-free mice provide a clean slate to conduct studies without resident species and show the cause conclusively.

OSU's facility is unique because it has germ-free mice and microbial culturomics expertise - it's rare for universities to have both.

"Our expertise and tools also allow transdisciplinary studies with other disciplines to use these kinds of tools and ask questions otherwise not possible by a group alone," Scaria said. "I'm hoping that other faculty at OSU and in the region would benefit from the full spectrum tool set that we have established."

Gut bacteria exist in unequal proportions and many studies focus on understanding the role of microbes high in abundance. Scaria's team believes for the ecosystem to work properly, the roles of both high- and low-abundance bacteria are essential.

Using unconventional methods, Scaria's team cultured extremely low-abundant bacteria and studied if they could substitute functions of higher abundant species when they are lost.

For example, if only one species had a particular metabolism in the gut and that species was lost, would that function be lost?

"Insurance hypothesis says we keep multiple species in our gut as a backup to prevent loss of function," Scaria said. "If one species is dormant or one is lost, we have a spare one who can take over and then do it."

These anaerobic microbes need to be cultivated using microbial culturomics - utilizing techniques to isolate and identify microorganisms not easily cultured using traditional methods.

One of Scaria's studies, recently accepted in Gut Microbes, a prestigious journal in the microbiome field, would not have been possible without the germ-free and humanized mice as tools.

Achuthan Ambat was a Ph.D. and postdoctoral student in Scaria's lab and the lead author on this study. He and Scaria looked at the role of low-abundant bacteria in producing short-chain fatty acids. These small molecules, secreted by gut bacteria when they ferment fiber, are then absorbed and form approximately 15% of the energy of the gastrointestinal tract, as well as stimulate immune cells and a host of other functions.

The team designed an experiment that isolated low-abundant, short-chain fatty acid-producing bacteria from a healthy human gut and tested its effect on host health using germ-free and human microbiota-associated colitis mouse models.

They hypothesized that low-abundant, short-chain fatty acid-producing bacteria could reestablish the normal state of microbiome and reduce the severity of colitis.

These bacteria prevent the loss of function when the high-abundant bacteria-producing butyrate is lost.

"We are one of the groups that, for the first time, is showing that extremely low-abundant bacteria can reduce diseases like colitis and then mechanistically showing that extremely low numbers of those species do have function and they can serve as a backup of the other species when they are lost," Scaria said.

The same concept now probably applies to other diseases or healthy states and will continue to do so. Moving forward, to be competitive in the NIH grant application space, using tools like germ-free mice is becoming a requirement.

Scaria has one NIH grant where the germ-free mouse model is a component. This study was used for preliminary data. Since then, they have clearly shown that low-abundant bacteria are important for overall ecosystem function and disease prevention. This leads to the possibility of developing low-abundant bacteria as new-generation probiotics to prevent diseases such as inflammatory bowel disease. They plan to submit a new NIH application based on the results to continue research in this area.

Research in Scaria's lab is a collaborative effort between postdoctoral and graduate students. Some individuals specialize in maintaining the germ-free mice and doing mice experimentation. Then, there are others who specialize in bioinformatics or culturomics.

"In terms of OSU, as a university, it's our mission to train the next generation in modern techniques," Scaria said.

And that's exactly what he does.

Culturomics is critical for functional studies in mice models and therapeutic developments. Still, since it's such a new microbiology science, expertise is limited making that skill high in demand in academia and industry.

Scaria mastered the technique and created a culture library with approximately 120 species - one of the largest in the country - and trains his students to be critical assets to this area of research at major medical schools.

With a background in microbiology, Prabhjot Sekhon joined Scaria's lab in 2020, where she first encountered working with gut microbes that require anaerobic conditions. She learned about the varying nutrient requirements of bacteria and how to prepare specialized media to meet these needs.

In March 2024, Sekhon left OSU to join the Mayo Clinic, where she will establish the media preparation process for culturomics. Given the Mayo Clinic's high volume of patient samples and the need to isolate and compare specific bacteria, Sekhon's expertise is crucial.

Going from OSU to one of the leading medical institutions in the world is like a dream come true for Sekhon, a dream she hopes other students chase.

As a first-generation student, Ambat grew up in rural India where he completed his undergraduate and master's degrees at the Amrita School of Biotechnology, which is where he connected with Scaria.

For four years with Scaria, Ambat trained to maintain and breed germ-free mice, worked with other germ-free models and collaborated with prestigious research institutions like Stanford and the Mayo Clinic.

It's critical for germ-free facilities to have personnel who can properly maintain germ-free mice and breed them to establish a colony. Many labs that do germ-free studies buy germ-free mice from commercial vendors for each project.

"That's exactly where Joy's lab is peculiar," Ambat said. "He usually buys the initial parent, but apart from that, everything is bred inside, which means all the germ-free mice we get are from in-house breeding."

The germ-free techniques Scaria taught Ambat made him an invaluable asset to microbiome research, leading principal investigators at Stanford to invite him to join their research group. Now a postdoctoral researcher at Stanford, Ambat acknowledges that his journey from a state school to such a prestigious university was rare but not impossible.

"I never thought I would end up in Stanford or get an offer from Cambridge," Ambat said. "Seriously, I didn't have any hopes for that. I was just going with the flow ... The time I spent in Joy's lab, he never had any restrictions on me. He was very open to me exploring anything I wanted. He was also very supportive in giving constructive criticisms in whatever work I was doing, which eventually ended me becoming a good scientist and getting a position at Stanford."

This all goes to show not only is Scaria shaping the future of medical research and therapy development through his research but also by training the next generation of scientists and fostering a culture of innovation.

What some might dismiss as a small rodent, Scaria demonstrates, is a crucial component in groundbreaking research advancements.

Just like Disney World, Scaria's lab is a place "Where Dreams Come True."

Photo By: Gary Lawson

Story By: Sydney Trainor | Research Matters Magazine