Even on standardized diet, gut flora change from day to day

September 14, 2018 by Annie Young, Massachusetts Institute of Technology
Researchers are only beginning to understand how the gut microbiome — the vital community of microorganisms that lives in our intestines — interacts with our bodies and the food we eat. Credit: Shutterstock

Researchers are only beginning to understand how the gut microbiome—the vital community of microorganisms that lives in our intestines—interacts with our bodies and the food we eat. For doctors and scientists, the challenge lies in predicting whether changes to gut microbes are associated with either disease, diet, or both—a complex problem due to the ever-shifting nature of gut bacteria, food consumption, and the ways in which the two interact.

Students at the Center for Microbiome Informatics and Therapeutics (CMIT) and the Health Sciences and Technology program, two MIT-based initiatives, sought to discover how to stabilize the gut microbiome and separate the effects of and disease, thus allowing for deeper investigation into the link between the gut and human health. The study was recently published in Scientific Reports and led by Thomas Gurry, a research scientist at CMIT who received his PhD in computational and systems biology from MIT in 2015.

"A number of studies show the association between the compositions of gut microbiomes and diet, but the precise relationships between individual nutrients and their effect on composition are hard to pinpoint," Gurry says. "We wanted to go to a higher level of resolution than studies in the past."

Fixed diets are difficult to design and implement, especially across a group of people. Enforcing a particular eating pattern is crucial, because the absence of a single ingredient would alter the composition of that particular meal and affect the resulting stool sample, rendering results unusable.

Liquid meal replacements in the form of bottled shakes are commonly served in hospitals nationwide. They are often given as a nutritional supplement—and occasionally as the exclusive source of nutrition—to patients ranging from the elderly to those being treated for eating disorders. With this in mind, the researchers chose to use the commercially available liquid meal replacement shake Ensure as the sole food source for their subjects' fixed diet. The advantage of a liquid shake over a preportioned meal, the researchers reasoned, is that individuals cannot intentionally or accidentally leave out any part of a meal.

In the study, healthy adult participants drank only Ensure for six days. Participants could have as much of the meal replacement shake as they wanted but no other food or drink besides water. After the third day, subjects were given a large quantity of one of a sample of nutrients, referred to as spike-ins, to see what effects this single nutrient (such as the fiber pectin) had on the microbiome and whether its influence was reproducible across subjects.

To the researchers' surprise, day-to-day variability of the did not go down. Although Gurry was reluctant to say why, he was able to conclude that the standardized Ensure diet does not have the effect of creating a constant background in the gut. What was detected over the course of the study was a high degree of diet-induced stress in individual participants' microbiota, which Gurry says could be attributed to the large amounts of processed sugar in the Ensure product.

"Moving forward, hopefully more consideration will be given to the effect of these nutritional meal replacements on the microbiome in a clinical context, as some patients being treated for Crohn's disease, for example, are asked to eat only Ensure."

The team was equally surprised to find that the effects of the majority of nutrients, excluding the fibers inulin and pectin, despite being administered in high doses, produced little effect on microbiome composition and no reproducible impact across subjects. "These results suggest that the major drivers of microbiome composition are dietary fibers," Gurry says.

Ultimately, according to Gurry, more needs to be documented at the strain or subspecies level of the gut. "We now know that a standardized diet is not an effective way to clean up a signal in a study measuring associations between composition and disease, nor does it reduce day-to-day variability," he says.

"However, we do find that different individuals have different responses to the same specific nutrient, likely due to the different strains they harbor. This offers an opportunity for precision medicine."

Explore further: Changes in gut microbiome in only one subset of helminth-infected patients

More information: Thomas Gurry et al. Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort, Scientific Reports (2018). DOI: 10.1038/s41598-018-30783-1

Related Stories

Changes in gut microbiome in only one subset of helminth-infected patients

August 9, 2018
Over the last decade, it's become clearer than ever that bacteria in the human gut— collectively termed the microbiome—play a key role in health and disease. Now, researchers reporting in PLOS Neglected Tropical Diseases ...

How to feed your gut bacteria

August 21, 2018
Day 1 of the meal plan seems simple enough.

Gut microbiome showed positive response to vegetarian diet in two weeks

June 7, 2018
The research team from ITMO University and collaborators analyzed the impact of short-term changes in diet on the condition of the gut microbiome. Assessing changes in the microbiome structure of 248 volunteers, the researchers ...

What you eat while pregnant may affect your baby's gut

July 4, 2018
A mother's diet during pregnancy may have an effect on the composition of her baby's gut microbiome—the community of bacteria living in the gut—and the effect may vary by delivery mode, according to study published in ...

Recommended for you

A low-gluten, high-fiber diet may be healthier than gluten-free

November 16, 2018
When healthy people eat a low-gluten and fibre-rich diet compared with a high-gluten diet, they experience less intestinal discomfort including less bloating. Researchers at University of Copenhagen show that this is due ...

Youth dating violence shaped by parents' conflict-handling views, study finds

November 16, 2018
Parents who talk to their children about nonviolent ways of resolving conflict may reduce children's likelihood of physically or psychologically abusing their dating partners later—even when parents give contradictory messages ...

Why we shouldn't like coffee, but we do

November 15, 2018
Why do we like the bitter taste of coffee? Bitterness evolved as a natural warning system to protect the body from harmful substances. By evolutionary logic, we should want to spit it out.

Dietary fat is good? Dietary fat is bad? Coming to consensus

November 15, 2018
Which is better, a low-fat/high-carbohydrate diet or a high-fat/low-carbohydrate diet—or is it the type of fat that matters? In a new paper featured on the cover of Science magazine's special issue on nutrition, researchers ...

Low-carb diets cause people to burn more calories

November 14, 2018
Most people regain the weight they lose from dieting within one or two years, in part because the body adapts by slowing metabolism and burning fewer calories. A meticulous study led by Boston Children's Hospital, in partnership ...

Colder, darker climates increase alcohol consumption and liver disease

November 14, 2018
Where you live could influence how much you drink. According to new research from the University of Pittsburgh Division of Gastroenterology, people living in colder regions with less sunlight drink more alcohol than their ...

1 comment

Adjust slider to filter visible comments by rank

Display comments: newest first

gzurbay
not rated yet Sep 14, 2018
Well, GOLY GEE - really?? ""However, we do find that different individuals have different responses to the same specific nutrient, likely due to the different strains they harbor." Isn't this the entire idea of dysbiosis?

What the hell do the researchers think, that a shift in diet is the basis of food poisoning? I think it should be well past obvious that the metabolite and the person's reaction to it plus likely epigenetic changes due to exposure should be the line of inquiry. It's a sliding scale. Basic intestinal health - due to microbiome influenced by disease microbes that gain a temporary or semi-permanent squatters rights. Some metabolites are potent enough to kill, some contribute to long term chronic disease - lacking an immediate deadly toxicity. 12,000 diseases - 70,000 ways for the human body to fail... Diet, yes, - infectious agents, poisons, epigenetic changes....

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.