She's Got Guts
Feb 25, 2019 Diane Krieger
How rising star Suzanne Devkota, PhD, is building a career at the convergence of her passions: food, health, and the bugs that live in our guts.
At 8:30 on a Wednesday evening, Suzanne Devkota wraps black tape around her hands as electronic dance music reverberates through the West Hollywood gym where she works out. Her fists now protected, she pulls on boxing gloves.
At 5 feet, 4 inches, she’s petite and slender, dressed in compression shorts and a muscle shirt. Normally her almond eyes are framed by an elfin bob and she wears a bright smile. But now, with her hair pulled back in a no-nonsense ponytail, her expression is focused and serious. She pounds the heavy bag with steely focus. Bap-pa-pa-bap-bap. In a choreographed dance of fist blows, she powers through a high-intensity, 45-minute routine.
Toward the end of the class, she spars with instructor Mark Lawson. He wears body armor to absorb her precise jabs.
“Oh, she knows what she’s doing,” Lawson says, stopping to chat afterward. “I model Suzanne for what I want the class to do.”
A self-described adrenaline junkie, Devkota has a black belt in taekwondo. She works out nearly every day and, on the rare nights she skips the gym, she’ll hop on the Peloton bike in her home and join a spin class live-streamed from New York. When on vacation, she gets her endorphin fix deep-sea diving or backcountry skiing.
Devkota brings that same disciplined, thrill-seeking, high-impact energy to her research. She enjoys being out of breath, craves the rush of discovery, and punches for the gut. Literally.
I incorporate what I’ve learned through my work into my daily life, and vice versa.”
A rising star at Cedars-Sinai, Suzanne Devkota, PhD, is director of microbiome research at the F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute and an assistant professor in the Division of Gastroenterology.
Led by the 37-year-old scientist, the Devkota Research Laboratory’s primary target is inflammatory bowel disease (IBD), a group of disorders that involves chronic inflammation of the digestive tract. However, her scope is expansive and she has made several important discoveries in her three years at Cedars-Sinai, including an explanation for why some vegans may be protected from amino acid deficiency. It turns out certain gut bacteria can produce essential amino acids from vegetable fibers during periods of dietary protein restriction.
So why does a multitalented, intellectually voracious scientist spend her days poring over stool samples?
Because that’s where the action is. The gut is ground zero of the microbiome revolution that challenges the foundational assumptions of modern medicine.
It’s hard to overstate the importance of the bacteria, fungi, viruses, phages, and protozoa living inside us. Experts believe many diseases can be linked back to them. And more than 90 percent of these microbes are found in the gut, primarily in the colon.
To fully appreciate the magnitude of the microbiome revolution, we must acknowledge that the body is an ecosystem. While most internal organs are sterile, certain physiological “niches”—the skin, nose, mouth, gastrointestinal (GI) tract, and urogenital tract—teem with microscopic lifeforms. Think of these microbe-rich niches as a rain forest: the natural habitat for up to 10,000 unique species and 100 trillion individual organisms.
These microorganisms have evolved with humans since Paleolithic times. They are native to the body, involved in day-to-day functions. While some can cause disease, the majority are beneficial—and some downright essential.
“Microbes have enzymes we don’t have. They are responsible for producing about 10 percent of our daily caloric energy intake,” Devkota says. “They’re absolutely critical for proper processing of foods and maximizing the nutrition we get from them.”
The microbiome is the collective genes of these microbes and, with the help of sequencing technology, big-data archives, and machine learning, Devkota has the tools to sift through the information avalanche hurtling toward her.
The field is still in its infancy. Ten years ago, the microbiome was virtually unknown. Researchers now believe diet and other external factors can switch harmless gut bugs into harmful ones. The downstream effect of microbial byproducts is huge. A raft of studies shows that microorganisms play a role far beyond the GI tract, affecting everything from brain function to the immune system. Cancer, depression, obesity and diabetes, skin diseases, Parkinson’s, multiple sclerosis, and even autism leave microbial footprints. At Cedars-Sinai, investigators across multiple disciplines are studying microbiome interactions with digestion, disease, and human development.
Devkota has the advantage of being both a microbiome specialist and a disease generalist.
“Dr. Devkota lives with a sense of adventure,” says Dermot P. McGovern, MD, PhD, director of Precision Health and the Joshua L. and Lisa Z. Greer Chair in Inflammatory Bowel Disease Genetics. “She combines a thrill-seeking spirit with focused discipline to achieve high-impact research.”
Optimal health is where Devkota, the microbiologist, and Devkota, the adrenaline junkie, converge.
“I incorporate what I’ve learned through my work into my daily life, and vice versa,” she says. “It’s a bidirectional relationship. The things I do in my life, in terms of food and fitness, also inform the research projects we do in the lab.”
A good example is a new project comparing the benefits of intermittent fasting with a liquid nutrition diet. Patients with IBD and Crohn’s disease are periodically put on “bowel rest,” enduring meal-replacement drinks for weeks at a time. Devkota’s laboratory participated in a challenge with several other physicians and dietitians, adopting the liquid diet in solidarity with their patients. Her conclusion after 24 hours on the nutrition drinks: “They’re disgusting. These poor patients!” So she is seeking alternatives.
In a previous position, she studied the effects of fasting on healthy mice and mice with IBD, documenting dramatic improvements in the rodents’ microbiomes and gut physiology after a 24-hour fast. She continues those investigations at Cedars-Sinai.
Certain bacteria species, she says, are acutely responsive to the presence or absence of food. The microbial community quickly rebounds when the normal diet is restored, but some positive changes persist.
Could a weekly or twice-a-week modified fast do as much as the drinks to relieve IBD symptoms? To find out, Devkota is considering a study of inpatient volunteers.
Devkota craved being at the center of the action as a young athlete growing up in Columbia, Missouri. “I picked the positions that were the most physical. In softball, I played catcher. I liked blocking people from stealing home. I loved the adrenaline and the endorphins,” she says.
In high school, she won state championships in tennis. In college, she worked up to a black belt in taekwondo.
Balancing out her athletic childhood was a university-centered, multicultural family life. The third of four children, Devkota was raised in an immigrant home. Her father is a retired university radiologist originally from Nepal; her mom emigrated from Egypt.
As a chemistry and biology major at the University of Illinois at Urbana-Champaign, she found exhilaration at the laboratory bench working with her first scientific mentor, Carl Woese, PhD. His discovery of archaea, the “third domain” of life—a group of single-cell organisms that had previously been lumped in with bacteria—revolutionized microbiology and led directly to the creation of the microbiome field. For Devkota, a research tech job at the Medical College of Georgia sealed her vocation in academic medicine, after which she returned to Urbana-Champaign for her master’s in nutritional science. She earned her PhD in molecular metabolism at the University of Chicago, where she turned her attention to the microbiome, earning an invitation to the prestigious Lindau Nobel meeting that sent her to Germany to represent her university at a gathering of 25 Nobel laureates. She completed her postdoctoral fellowship at Harvard Medical School, where she was again handpicked for an elite, international program, the Branco Weiss Fellowship.
Poop Pillow Talk
The tools to investigate the links between gut microbes and health are readily available. Stool samples can be obtained noninvasively and studied via DNA sequencing at relatively low cost. Yet every day, we literally flush tons of medical and scientific data down the toilet. Devkota believes fecal panels should be a routine part of every patient workup.
If only people weren’t so squeamish.
“There are huge cultural differences in how people perceive these things,” she says. “America is by far the most prudish.”
Most of us would rather have blood drawn than produce a stool sample, though the latter is an everyday event. Because patients are reluctant, doctors only order fecal studies when there’s a serious health problem—say, blood in the stool or persistent diarrhea. Even patients with a diagnosed gastrointestinal disease are reluctant to discuss “bathroom issues” with their doctors.
Devkota is on a personal mission to destigmatize fecal matter. She educates nurses and doctors about the best way to ask for and receive stool samples. She brings a “poop pillow” prop to all her public speaking engagements. The larger-than-life plush version of the familiar emoji gets instant laughs and breaks the ice.
“I work with poop every day and I look like this,” she tells audiences, referencing her impeccable feminine attire. “I’m not grossed out by it, and you shouldn’t be either.”
Gus Hendrick, a tech in Devkota’s lab, sets a collection tube under the fume hood. Smiling genially, Hendrick opens the vial and spoons out micro-portions of human feces. He divides the contents into three samples, lays them on a tiny scale, and adjusts until each weighs 0.2 grams. He delicately transfers them into test tubes filled with preservative solution. Once sealed and labeled, they go into the freezer; Devkota can decide later which DNA tests to order.
The hood’s ventilation doesn’t completely eliminate the faint toilet odor but, after a year on the job, Hendrick and the two postdoctoral fellows who share this lab space hardly notice. Besides, it’s a small price to pay for working at the frontier of scientific discovery.
Today’s sample came hand-delivered by one of the subjects whose gut microbes Devkota monitors. This particular individual is a Cedars-Sinai doctor who, somehow, has never taken antibiotics. A childhood spent in rural areas of developing countries also contributes to a microbiome that, in Devkota’s opinion, is the paradigm of gut health. Others she follows include a youngster newly fitted with a colostomy bag, and a Crohn’s disease patient who has undergone a fecal microbiota transplant. (The latter procedure entails exactly what one might imagine: A solution of fecal matter is transferred from a donor into the intestinal tract of a patient whose health may benefit from an internal microbial makeover.)
Devkota has a particular interest in Crohn’s patients. Her team just received a $1.9 million, three-year grant from the Helmsley Charitable Trust to study “creeping fat,” an unexplained signature of the chronic disease. Devkota gravitates toward medical mysteries, and creeping fat is a real puzzler. The north star of Crohn’s inflammations, gut surgeons recognize it as a flashing arrow instructing them to “cut here.”
Everyone has at least a little bit of fat in their abdomen but, in many Crohn’s sufferers, the intestines become partially encased in it. Until Devkota started investigating creeping fat, no one knew why ordinary abdominal fat invariably migrated to the sites of severe intestinal inflammation or fibrosis in these patients. Her lab performed single-cell RNA sequencing—a analysis that looks at the expression of all genes in thousands of individual cells—on tissue taken from patients during intestinal surgery. Her findings indicate that creeping fat begins as a protective mechanism preventing bacteria from spilling into the bloodstream. But in the long run, the fatty barrier turns fibrotic, or rigid, due to continual signals from certain bacteria. This ultimately compounds the problem in underlying gut tissue that is already damaged.
“When a doctor says, ‘We see this all the time, and we have no idea what it is,’ I know there’s a real utility to studying it,” Devkota says.
Doctors saw a 74 percent growth in Crohn’s cases between 1992 and 2004. Today, nearly 800,000 Americans have the hereditary disease. Yet few investigators are working on creeping fat, probably because it can only be studied in human populations. Crohn’s mice don’t develop the anomaly, so there’s no animal model to study. As a hospital-based microbiome specialist working in a research powerhouse, Devkota finds herself in a unique position to crack this nut.
“She’s absolutely phenomenal,” says Phillip Fleshner, MD, the Shierley, Jesslyne, and Emmeline Widjaja Chair in Colorectal Surgery. As director of Colorectal Surgery Research, Fleshner collaborates with Devkota on her creeping-fat research. “She is using very sophisticated techniques to delve into what we see at the bedside or in the operating room, and to study phenomena that no one yet understands. Her work brings the study of disease full circle and potentially could result in new treatments for our patients.”
Lab and Life Partners
Devkota orders a messy burger at a busy restaurant near the hospital but eats only half of it. She swaps out the fries for apple slaw. It’s lab lunch day—a regular ritual that precedes her team meeting.
Postdoctoral fellow (and trained chef) Anthony Martin expertly twirls his short-rib tagliatelle, while postdoc Connie Ha debones the Jidori rotisserie chicken. Hendrick polishes off the prime steak sandwich. They’re all unabashed foodies and enthusiastic meat eaters—in moderation.
They have a lot of catching up to do at today’s mobile lab meeting/food fest. The week before, Ha and Martin presented simultaneously in Atlanta and Boston.
It wasn’t long ago that Devkota was a postdoc herself. She joined the Cedars-Sinai faculty in 2015, straight from her Harvard fellowship in microbiome and metabolic diseases. Her PhD from the University of Chicago was awarded three years earlier, under the wing of digestive diseases expert Eugene Chang, MD.
It was Chang who introduced Devkota to her husband, Shehan Dissanayake, a former PhD student of his who had left the research bench for a successful career in private investment.
Today, when the conversation turns to biomedical science, Devkota does the talking and her husband mostly listens.
“She’s much smarter than I am,” Dissanayake says, sipping coffee in the couple’s living room.
When Devkota isn’t working up a sweat, research commands her undivided attention. Dissanayake’s work demands that he travel continually and interact with associates in multiple time zones.
“Time is precious to us,” says Dissanayake, a Sri Lankan-born senior managing director of Tavistock Group, in a lilting British-infused accent.
Food is the unifying theme in their busy lives; coffee is a shared passion. A couple of years ago, in a nod to his wife’s scientific fervor, Dissanayake undertook a comprehensive investigation into the optimal mineral content in water for brewing the perfect cup from Devkota’s favorite bean.
Collaboration and Proliferation
Time’s crunch factors into Devkota’s professional as well as personal life, as she strives to maximize every available minute.
She applies the teamwork she learned as a kid playing softball to working with colleagues across disciplines. She regularly attends grand rounds, ears pricked for enigmas that puzzle the clinicians.
Partnering with Cedars-Sinai oncologists, she is collecting tissue and stool samples from patients treated for rectal cancer. Everyone knows antibiotics wreak havoc on the microbiome, but no one knows how chemotherapy and radiation affect gut bacteria in this densely colonized part of the bowel. Likewise, can an individual’s baseline microbiome determine how well a treatment works? Devkota means to find out.
Another collaboration plans to explore the innate microbiome of preterm babies, with the goal of benchmarking optimal gut health for the most fragile patient population in Cedars-Sinai’s Neonatal Intensive Care Unit, part of the Maxine Dunitz Children’s Health Center.
Her focus on collaboration is essential to meaningful progress in her work. According to one estimate, the totality of medical knowledge now doubles roughly every two months. “No one person can learn everything,” she says. “We don’t have two-author papers anymore. We have 20 authors on papers.”
“I really like unexplained phenomena,” Devkota says, and, as ranks of scientists turn their attention to the microbiome, intriguing questions are piling up.
She has mountains to climb, both figuratively and literally. Ascending Sagarmãthã (aka Mt. Everest) is on her to-do list.
Her Nepalese relatives will cheer her on. Their interpreter skills may come in handy. Devkota will need all the help she can get cajoling the Sherpa guides to produce stool samples.
Oh, yes. She plans to ask.
“They’re bound to have really interesting microbiomes,” Devkota says. “Probably lots more oxygen-sensitive bacteria than you would normally see.”
Getting the samples past the sniffer dogs at LAX remains a challenge for another day.