Over the last five to 10 years, grocery store shelves have become increasingly crammed with probiotic sodas, drinkable yogurts and fermented beverages marketed toward supporting your gut microbiome — the microscopic community of bacteria and other living organisms that live in your gastrointestinal tract.
Some local businesses have even built brands around this gut health boom.
Happy Gut Foods, for example, is a Leon-Valley-based pop-up grocer offering probiotic drinks and fermented produce. On the East Side, a taproom bar called Fermenteria brews its own water kefir, a bubbly fermented drink. EndoMune Probiotics, started by San Antonio gastroenterologist Dr. Lawrence Hoberman, has grown into a national probiotic supplement business.
Research into the gut microbiome has accelerated quickly over the last two decades, as scientists have uncovered more and more connections between this community of microorganisms, our overall health and various diseases, including in San Antonio.
UT Health San Antonio researchers recently found a link between a specific bacterium in the gut and lupus, an autoimmune disease with no cure that affects an estimated 1.5 million Americans, a finding that could potentially lead to more effective treatments.
But how much of the gut health food and supplement boom is rooted in evidence versus wellness hype? According to the UT Health researchers behind the recent lupus findings, it’s complicated.
“I just had an email from a colleague asking me, ‘I have a friend who just got diagnosed with lupus, should she take probiotics?’” said Laurence Morel, an immunologist who co-led the lupus study and heads UT Health’s microbiology and immunology department. “We don’t have simple answers.”
What is the gut microbiome?
Your gastrointestinal tract is home to trillions of bacteria, fungi, viruses and parasites that float around or attach to the inner walls of the large intestine, small intestine and stomach. Scientists refer to this community of microbes as the gut microbiome, or gut microbiota.
Most of these microbes live symbiotically with us. They get shelter and food, and in turn help our bodies break down nutrients and keep harmful microbes in check. Without them, our bodies wouldn’t be able to break down certain complex carbohydrates and fibers, and we would be deprived of important nutrients like short-chain fatty acids and vitamins B1, B9, B12 and K.
Researchers have also found that the gut microbiome has implications outside of our digestive system. The gut microbiome plays an especially important role in the immune system, helping us fight disease, as well as the nervous system via the gut-brain axis, and our endocrine system, which regulates hormones.
Research has shown that patients with a wide array of diseases and conditions — ranging from obesity, depression, Alzheimer’s, eczema and colon cancer — also tend to have unbalanced gut microbiomes, or “dysbiosis,” meaning they lack an adequate number of healthy bacteria or have an overgrowth of harmful ones.
These findings alone don’t mean gut dysbiosis is causing or contributing to these diseases, explained Yong Ge, co-lead of the lupus study and gut microbiology researcher at UT Health.
“We have repeatedly seen that the microbiome is different between healthy people and diseased patients,” he said, “but the first question is whether this is a cause or a consequence.”
For some diseases, like lupus, there’s a growing body of evidence that this imbalance is contributing to the disease, Morel said. “We are not saying that it causes [lupus],” she added. “But it’s part of the amplification of the disease.”
Ge and Morel’s lupus paper, published in April in Nature Communications, found that supplementing lupus-prone mice with a specific bacterium — F. prausnitzii — alleviated disease progression. This bacterium is one of the most abundant in healthy guts, and has been shown to be depleted in lupus patients, Morel said.
The finding could potentially pave the way for human studies, and if successful, lead to a targeted probiotic treatment for lupus patients.
The growing gut health market
As research on the gut microbiome has grown, the health and wellness market has followed. A 2026 survey by the International Food Information Council suggests that interest in gut health has made its way out of wellness culture into the mainstream, with nearly two-thirds of Americans considering gut health a high or extremely high priority.
Nationally, prebiotic soda companies like Olipop and Poppi have exploded in popularity, with Coca-Cola announcing its own line of prebiotic sodas last year.
Probiotic supplements have taken off too. The U.S. gut health supplements market size was estimated at $5.19 billion in 2024 and is projected to reach $9.36 billion by 2033, according to Grand View Research.
Melissa Colunga, a San Antonio native, bought Happy Gut Foods in 2023. The fermented food and probiotic grocer has been around since 2015, selling out of its Leon Valley store and at local farmers markets.
“People will say, ‘Oh, I have been needing to focus on my gut health,’ and we have had a lot more activity … it’s like a buzz right now,” Colunga said.
Concierge clinics and online wellness retailers have also started advertising gut microbiome testing: Stone Oak Women’s Center, for example, offers a $425 GI tract assessment on their website.
But wellness marketing hasn’t always kept pace with the research itself.
Evidence vs. hype
About 10 years ago, the general assumption was that by now, all of the new gut microbiome research would have led to several targeted treatments for various diseases, Morel said. Obesity, for example.
“Obesity has strong associations with changes in the gut microbiome,” Morel said. “Maybe if you could give [patients] a pill with healthy gut bacteria, they would improve.”
But that largely hasn’t happened, Morel said, in part because the mechanisms behind how the gut microbiome influences disease are still not completely understood.
There are also so many different microbes, and everyone’s gut microbiome is different, Ge added.
What is clear, Morel said, is that diets high in fiber — like whole grains, fruit and vegetables — are generally good for your overall health, regardless of how much of those benefits can be attributed to promoting a healthy gut microbiome. Additionally, diets low in fiber and high in ultra-processed foods have been associated with a decrease in microbial diversity and lower levels of beneficial bacteria.
Fermented foods like yogurt, kimchi, kefir, sauerkraut and kombucha, to name a few, have been shown to promote the growth of good bacteria in the gut as well, and these foods can easily be part of an overall healthy diet, Morel added.
“It’s probably better than eating a hamburger, for sure,” she said. “But if you’re talking about evidence-based studies in which you’re comparing kefir drinkers to non-kefir drinkers — it’s a difficult study to do, and I don’t think it’s there, at least it’s not there with a rigorous methodology.”
When it comes to probiotic supplements and wellness clinic offerings, Morel and Ge are more skeptical. Although probiotic supplements are generally safe for healthy adults, right now there isn’t enough data to support their benefits, what doses are needed to see a benefit, or whether the same benefits could be achieved through dietary changes, the researchers said.
Morel and her colleagues are working on answering some of the unknowns regarding the gut microbiome. Some of her colleagues are working with a private company to develop an antibiotic that can target a specific class of bad bacteria that promote lupus without destroying beneficial bacteria. Others are investigating links between traumatic brain injuries, stroke and the gut microbiome.
“My hope is that we can have more specific ideas of which bacteria we could promote the growth of either by directly supplementing those bacteria or having the dietary condition that promotes this,” Morel said. “I’m not sure this is going to work, but we are trying.”
