Doctors recommend dietary fiber for healthy digestion, but to benefit from it, people not only need specific species of gut bacteria but the right strains of those bacteria to process the starches, according to a new study that advances the promise of precision nutrition.
Dietary fiber, which comes in a variety of forms prevents constipation, fosters healthful gut microbes and slows digestion to regulate blood sugar. It is found in several legumes, nuts, seeds, vegetables, fruits and whole grains.
Previous studies examining the benefits of resistant starches found mixed outcomes, as some subjects benefited from it while others experienced no effect.
“We think that one of the reasons for that is because you need the right bacteria in your gut to process resistant starch,” said Angela Poole, assistant professor in the Division of Nutritional Sciences, in the College of Agriculture and Life Sciences and the College of Human Ecology, and the paper’s senior author.
In the study, published July 24 in the journal Microbiology Spectrum, Poole and colleagues used advanced techniques to detect different strains of a species of gut microbe called Bifidobacterium adolescentis. They found that different strains had unique responses when resistant starches were ingested, revealing that the right strain was needed to process the complex carbohydrates found in those starches.
“It speaks to future directions in the field of precision nutrition,” Poole said. “We need better tools to get more comprehensive characterizations of what the bacteria are and what they’re doing, and it does emphasize the fact that we really need to be looking at the strain level. We need high resolution.”
Most previous studies have used 16S sequencing, a technology that names bacteria and helps researchers survey bacteria to see what is present. In this study, the team used shotgun metagenomics, a more advanced technique that can identify bacteria down to the strain level as well as genes. By knowing the genes, researchers may then learn the functions of those bacteria.
For the study, the researchers collected fecal bacteria from more than 50 people to examine their gut bacterial communities. Participants were then fed three different crackers over three separate periods: two types of dietary fiber, called resistant starch 2 and resistant starch 4, and a control starch, which could be digested by the body’s own enzymes without requiring enzymes from bacteria to break it down.
When bacteria break down starch, their genes encode enzymes, and shotgun metagenomics can identify these genes. The team also used a new highly sensitive bioinformatics tool, Cayman, which identified more genes present in bacteria that degrade resistant starch.
The investigation revealed new, yet to be characterized bacteria whose genes were increased in the presence of resistant starch, meaning they appear to play a role in processing the carbohydrates. Researchers will investigate these bacteria further in future studies.
“It’s also important to know the strain the person has because imagine if you were trying to prescribe a precision nutrition diet for a patient who has diabetes, and you saw they had Bifidobacterium adolescentis, you could say, oh, this will or won’t work for you, depending on the strain you have,” Poole said.
Applying more advanced tools will be critical in helping nutritionists identify the genes associated with bacteria, and the enzymes those genes encode, in order to understand whether a patient has the necessary enzymes to break down particular dietary fibers and benefit from it, Poole said.
Other corresponding authors include Nicola Segata and Francesco Asnicar, both researchers at the University of Trento in Trento, Italy.
The study was funded by Cornell University and the European Union.
