Microbiome Study Challenges: A Microbiologist Discusses Opportunities, Hurdles at IFT 2017

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Research on the human microbiome, while exciting and infinitely promising, is still very much in its infancy. Scientists are only beginning to tease out some of the significant links between the human microbiome, bacterial populations, and human health. During the Institute of Food Technologists (IFT) Annual Meeting & Food Expo, a microbiologist from Tate & Lyle (Hoffman Estates, IL) discussed some of the most significant challenges facing researchers as they take next steps to study the microbiome in human populations on a global scale.

Mervyn de Souza, PhD, Tate & Lyle’s vice president, health and wellness, NPD, innovation and commercial development, started by telling Nutritional Outlook how Tate & Lyle, like some others, is continuing efforts to expand microbiome research using advanced in vitro study models like the human gut simulator known as the SHIME (Simulator of the Human Intestinal Microbial Ecosystem). Nutritional Outlookfirst highlighted this rising in vitro model developed by Massimo Marzorati, a professor at Ghent University in Belgium, nearly five years ago as a technology that will help expand researchers’ understanding of the microbiome and, from a nutritional standpoint, the impact of pre- and probiotic ingredients.

De Souza said that Tate & Lyle is now using SHIME to study how its own prebiotic Promitor soluble corn fiber impacts the gut microflora on a detailed scale. “We know that our fibers have twice as much of the gastric/digestive tolerance as, say, an inulin, chicory root, or FOS,” he said. “But when we do the microbiome studies, it’s very clear, when you compare inulin or FOS to our soluble corn fibers, that there’s a lot of gas formation in the ascending colon and quick metabolism [with these ingredients], which gives you that bloated feeling and some of the adverse side effects from having the inulins that you don’t see with our soluble corn fibers. [With Promitor], you get a very even metabolism in the ascending, the transverse, and the descending colon that corroborates what we see in our clinical studies,” he claimed.

De Souza said it’s “really nice to be able to do the in vitro work using SHIME” to study different dosage amounts and to conduct studies that might not always be feasible in human subjects. Still, he said, the next step is to progress to advanced in vivo microbiome studies-namely, those in a human population. “I think, at some point, you get to a point where you’ve got to stop [focusing on in vitro studies] because you really have to do the clinical studies and get to the humans.”

However, he said, challenges remain in designing microbiome studies in human subjects, largely because the vast differences between individuals’ microbiomes are huge factors that can confound study models.

“The microbiome is different if you’re in Asia versus the U.S.,” for instance, he said. “Nutritional status, geography, and health status” all result in unique microbiome profiles for each individual. “Are you immune compromised, or are you not?” he said. “Are you on medication, because any antibiotics you take are going to have an effect on the microbiome? What’s your diet like? Do you have more fibers, or do you have fewer fibers, and are you somehow selectively enriching the microbial population?”

“There’s so much cross-talk,” he added. “Bugs don’t function in isolation,” and so figuring out how to design appropriate human microbiome studies is extremely challenging.

Still, he said, he expects researchers to make progress working through these issues by continuing to study the microbiome, which will lead to discovering some of the “commonalities” that exist between individuals’ microbiota populations.

“There are differences,” he said, “and as we get more data and we’re able to dissect that, we’ll be able to get beyond those differences and look for those commonalities, because if you look at all of our microbiomes, there are common [microflora] populations, and when you have a disease state, you know that certain genera of bacteria are going to go up, and in a healthy population, certain other beneficial bacteria are going to go up.”

Meanwhile, he said, the general understanding is an overwhelming sense that the microbiome is a crucial window to human health. Researchers, he said, will take the next steps to elicit how to properly design the next generation of microbiome studies while keeping in mind the complexities involved.

“I trained as a microbiologist,” de Souza said, and “it’s really fun to see microbes taking kind of front and center stage. I think we’re at an age where there is so much information that we’re almost being inundated with these microbiome studies. A lot depends on the conditions of the study, what you’re asking for, how the data is analyzed. Everything we do impacts the microbiome, so how do we transcend some of that complexity and the confounding information to some of the real facts? It almost seems like we’re in this stage of over-communication, but I think it’s going to come down to how do we have some really robust, reliable studies where you can make some really strong correlations between specific microbes and also consortia?” he continued.

In the meantime, he said, the SHIME model will continue to be an important tool to help researchers learn about the microbiome. “The SHIME model is really getting very popular because of the ways in which you can control it,” he said. “It’s really become a very nice model, it’s well regarded with more people starting to be aware of it and wanting to use it as well.”

Today’s microbiome research is revealing “connections that we’ve never had before, like the gut-brain axis," de Souza concluded. “We know there’s a connection. It’s now trying to get more of that deep, scientific technical rigor and understanding that I think is going to truly get us moving forward.”
 

Also read:

More about the SHIME model:
Probiotic, Prebiotic Research: Taking It Outside (In Vitro)

Probiotics: Research Beyond the Belly...and to the Brain and Heart

Microbiome and Emerging Research to Unlock Probiotic Mysteries?