Journey to the Microbiome

Journey to the Microbiome
Keehoon Lee, Ph.D., investigates the vast and intricate ecosystem of the human body

In a world teeming with organisms too small to see with the human eye, a deeper understanding of microbiology has long fascinated scientists. These tiny life forms, collectively known as microbes, have an outsized impact on our planet’s ecosystems, our health, and even our daily lives. For scientists such as TGen’s Keehoon Lee, Ph.D., the relatively new field of integrated microbiomics seeks to fully understand the microbial realm by shedding light on the intricate web of connections between microorganisms and their hosts. “We often speak of the microbes that cause disease as free-floating, solo agents of destruction, whether it’s the bacteria behind a hospital infection or the fungus that infects the lungs in Valley fever,” says Lee, a research assistant professor in TGen’s Pathogen and Microbiome Division and co-director of the TGen Integrated Microbiomics Center (TIMC), “but the way we study microbes in the lab differs vastly from how they appear in nature.” Microbes are microscopic organisms such as bacteria, viruses, and fungi. They are ubiquitous, found everywhere from the depths of the ocean to the human gut, from the soil beneath our feet to the skies above. While many are harmful and cause diseases, a vast majority are beneficial, playing essential roles in various ecosystems and supporting life as we know it. “Before, all of microbiology study was of the single, pure forms,” says Lee. “Scientists would study one microbe at a time, such as E. coli, rarely, if ever, considering that microbe as part of a larger microbial community.” Today, the microbiome is the focus of intense clinical interest. But 15 years ago, it was a word that was only just appearing in the scientific literature. For Lee, it all began with a sticky film of bacteria he encountered in a Northern Arizona University lab. Sometimes bacteria from one or two species will aggregate in a slimy matrix, called a biofilm. Most often studied in medicine, biofilms also cause problems in places like the oil and gas industry where they can clog pipelines, and in transportation where they cling to and corrode the hulls of ships. At NAU, Lee learned more about how biofilms cause chronic infections. For example, Pseudomonas aeruginosa bacteria, commonly found in burn victims, results from Pseudomonas biofilms, which adhere to the skin’s surface and contribute to persistent infections. “It’s hard to clear or kill these biofilms with traditional antibiotic treatment, as the antibiotic resistance increases on the order of 1000-fold,” Lee says. “That really caught my interest, to see how they act differently in their community.”

The Early Years
When Lee first started his research, the primary method for studying biofilms required him to take on the role of an amateur gardener, skillfully encouraging different species to thrive together and form new biofilms within the laboratory setting. “But it’s a lot harder than it sounds,” he says. “Biofilms that form in nature are usually not just one species, they also have all kinds of bacteria, fungus or other microbes in there.” Luckily, genomic sequencing was coming into its own at that time, sparing Lee from those tedious experiments. Sequencing could swiftly identify and analyze not just the few genomes contained in a biofilm but the entire microbiome of an environment, such as the nose, throat or gut. “Whether skin or slime on a river rock, sequencing allows us to define what’s in there,” he explains. “We changed the method of study by looking at their genomes instead of actually growing samples to analyze.” Lee and his colleagues now had a new way to glimpse the complex workings of a mostly hidden and poorly understood microbial world. But what would they see?

The Brain, the Gut and Everything In Between
The TIMC is a research service center, explains Lee, who has served as its co-director for almost two years. He and his colleagues work with scientists and clinicians to design studies that look deeper into a particular microbiome contained in fecal matter and urine and in the case of medical studies, tissue. Staff at the center sequence the genomes of the microbes that make up that microbiome’s community and sometimes analyze the function of specific genes within those genomes. Often the goal is to compare and contrast: what does a healthy gut microbiome look like compared with the gut microbiome of a person with colitis, for example? If researchers can pinpoint differences in the types of microbes or the way the microbes behave in each community, they could design therapies to nudge the diseased microbiome back toward health. At the moment, there is only one FDA-approved microbiome treatment, to treat infection of the colon by C. difficile bacteria. Patients with this condition, sometimes called C. diff, receive a donor’s fecal transplant that carries a healthy gut microbiome. Treating C. diff with surgery or antibiotics proved successful 30- to 45 -percent of the time. “With the microbiome transplant, we saw a 90- to 95 -percent cure rate,” Lee says. “It was extremely effective and resulted in few relapses.” A recent surge in microbial studies revealed the sophisticated connection between the gut microbiome and various diseases extends beyond the gastrointestinal tract, encompassing the central nervous system, conditions such as depression, and even cardiovascular diseases. The link between brain and gut has been one of the more astonishing connections discovered in microbiome studies. Scientists have found that bacteria in the gut can produce chemicals like serotonin, for example, that travel the long vagus nerve connecting the gut and brain to impact illnesses such as depression. Some scientists believe that disruptions in the gut microbiome may initiate or worsen the inflammation observed in disorders like Alzheimer’s disease and heart disease. Some gut bacteria produce molecules known as short-chain fatty acids, which possess protective and anti-inflammatory properties. “These molecules can reinforce the barrier that the brain uses to protect itself,” says Lee. “But if you have an unhealthy gut microbiome that has low short-chain fatty acids and more inflammatory molecules, they can go to the blood-brain barrier and increase its permeability.” Is there a way to tilt the health of the gut microbiome back toward normal? The scientists who collaborate with TIMC want to answer that question. They are looking at possible probiotic treatments that add an essential microbe, or the molecules it produces, back into a microbiome. But they are also studying prebiotic approaches, looking for diets that lead to a healthy microbiome. For instance, the TIMC is helping a team of Finnish and City of Hope researchers determine whether a high-fat diet —like the Ketogenic diet— can be beneficial for patients with bowel disease.

Cancer and Valley fever
Researchers from TGen and City of Hope recently collaborated to examine how the microbiome can trigger certain cancers, such as the link between the HPV virus and cervical cancer, or how cancer drugs or immunotherapy interact with these microbiomes. At City of Hope, for instance, Sumanta Pal, M.D., co-director of City of Hope’s Kidney Cancer Program, has been collaborating with Lee and Center researchers to learn how a patient’s microbiome might respond to immunotherapy for metastatic renal cell carcinoma. “We know that some microbiome members render these therapies very inactive, but some microbiomes can enhance the efficacy of these drugs,” says Lee. One example is the role of short-chain fatty acids in colon cancer. Scientists are also exploring the restoration of the microbiome after radiation therapy in rectal cancer and assessing whether probiotics can reduce side effects and enhance outcomes in immunotherapy for multiple cancers. Physicians also share information about the inflammatory molecules they see in their patients, or patient outcome data, for a particular type of cancer or treatment. This allows TIMC staff to dig deeper into the exact relationship between a specific cancer and the microbiome data. The center also actively partners with public health officials throughout the Southwest, actively monitoring the spread of the fungus responsible for causing Valley fever in both people and dogs. In Arizona’s Maricopa County, the Center conducts air microbiome sampling at various locations to actively track potential outbreaks. Fungal genome sequencing is a challenge, Lee says, capturing only about 50 percent of the data in a sample. But the center is working on a new sequencing technique, “and I’m confident that we’re going to increase the accuracy of fungal microbiome studies,” he notes. Beyond cancer and Valley fever, Lee and his colleagues are proactively seeking new opportunities to apply their expertise. He sees potential in collaborating with TGen’s Center for Rare Childhood Disorders, or maybe offering a microbiome sampling kit to patients enrolled in the precision aging studies led in part by TGen researchers. In an era where the smallest entities are making the biggest impacts, integrated microbiomics provides a gateway to unlocking the secrets of the microbial world—a world that has always been with us yet remains largely unseen. “With each breakthrough,” says Lee, “we inch closer to a deeper understanding of the tiny organisms that shape our lives in ways we could never have imagined.”