BOZEMAN — A biochemist focusing on microbiology is the latest Montana State University researcher to have their work recognized and funded through a National Institutes of Health program emphasizing the investigation of broad scientific questions.

Roland Hatzenpichler, an assistant professor in the Department of Chemistry and Biochemistry in MSU’s College of Letters and Science, received the Maximizing Investigators’ Research Award, or MIRA, through the NIH’s National Institute of General Medical Sciences in August to support his fundamental research into developing new single cell resolving tools to better understand the human gut microbiome. The grant will fund Hatzenpichler’s work with $1.7 million over five years.

Hatzenpichler’s research interests fall under environmental microbiology; historically his studies have focused on microorganisms inhabiting Yellowstone National Park hot springs, salt marshes, or the deep sea. This is the first time he will be turning his attention toward the microbiology of the human body.

“The expertise my lab has is mostly lacking from the human gut microbiome field simply because the people who do human gut research typically don’t use those techniques,” Hatzenpichler said “So, this will be very exciting to apply them and use these tools for the first time in microbiome research.”

According to Hatzenpichler, the human gut microbiome is not well understood due to the small number of techniques that can be used on a living human and the type of samples used in analysis. The most common samples used for gut research are fecal, but because the samples are outside of the body and do not contain all the microbes living in our gut, they do not give the full picture of what the gut’s microorganisms are doing and how they interact with each other or human cells in their natural habitat.

The best way to understand the gut, Hatzenpichler said, is to use endoscopy samples, and Hatzenpichler’s lab will work with the Metrodora Institute in Salt Lake City to retrieve these types of samples. The institute, which will open in 2023, will focus on the care and research of complex multisystem disorders that are driven by dysfunctions of the “neuroimmune axis” — that is, the interaction between the nervous, immune and endocrine systems. Many gastrointestinal, neurological and immunological disorders fall under this umbrella.

Hatzenpichler said one of the biggest issues in studying the human gut microbiome is the time between retrieving samples and taking them to a lab for analysis. The more time elapses, the more microorganisms in a sample will either die or change from how they lived in the gut, thus affecting the accuracy of how the sample represents the host.

To bridge that gap, Hatzenpichler found a solution to the problem through a unique partnership with Metrodora Institute. The institute has an anaerobic microbiology lab and biobank directly connected to the surgery suites where the endoscopy samples will be taken, significantly reducing the time from sample collection to sample processing. Researchers from Hatzenpichler’s lab will visit the institute in regular intervals to process the samples in real time, then bring them back to his lab at MSU for further analysis with the tools he is creating.

“You can never replicate the human gut, but this is as close as you can get as possible because we are on the same floor as where the sample is taken,” Hatzenpichler said.

The tools that Hatzenpichler and his lab will work on with the MIRA funding revolve around imaging. Hatzenpichler is developing new microscopy approaches to study microbes at a single-cell level to understand where they are located, such as the mucosal surface or deeper within the layers of the gut; how they interact metabolically or physically with each other or human cells; and what kinds of genes and proteins are expressed and at what level of activity they function. To achieve this, his team will build on recently developed workflows that combine light, electron, fluorescence and Raman microscopy approaches into a single workflow. Their ultimate goal is to visualize different microbial species directly in endoscopy samples taken from the entire length of the human gut and visualize which cells take up certain foods.

“Roland is one of the top microbiologists in the world and leading expert in microbial physiology, which is why we are so excited to work with him,” said James Hemp, Chief Scientific Officer and co-founder of the Metrodora Institute. “The impact of the tools that the Hatzenpichler lab is developing will be massive for the human microbiome field. The discoveries facilitated by these single cell ecophysiology techniques will lead to a deeper understanding of host-microbe interactions, as well as the development of new diagnostics and therapeutics for neuroimmune axis disorders.”

Currently, most human gut research uses “omics,” or bulk, techniques – DNA, RNA and protein sequencing techniques that look at what kinds of genes are present in populations of microbes in either fecal or gut samples. These techniques show what genes are present in the community, and which genes and proteins are expressed at a given time.

While this is a powerful technique and currently the forefront of human gut research, Hatzenpichler said the problem with omics techniques is that one sample is not completely representative of the whole and that these samples take averages of millions of cells at a time.
“Samples processed for these approaches typically contain billions of cells,” he said. “The assumption is that the genes and protein that are expressed in that bulk sample represent what the average cell is doing.”

Hatzenpichler added this is not the case, and the only way to solve this is to work on a level where you can distinguish individual cells from each other. So rather than taking an average of 100,000 to 1 billion cells, you measure each cell separately.

“The solution to the problem, even though it’s technically complicated but conceptually simple, is to preserve the architecture of where and how the cells typically work,” Hatzenpichler said. “If you bring in imaging techniques that allow you to preserve the sample as close as possible to natural conditions, the images you are taking will allow individual cells to be distinguished.”

Hatzenpichler’s MIRA grant is the fifth for MSU. According to Alison Harmon, vice president for research and economic development at MSU, receiving these prestigious grants is testament to the pioneering, cutting-edge research occurring on campus.

“I congratulate Roland on this achievement and on developing the critical partnerships that will make this very relevant research fruitful. Better understanding the gut biome is work that has the potential to benefit every one of us,” Harmon said.