Issue: July 2019
July 18, 2019
13 min read

Microbiome’s ‘untapped extra genome’ may hold clues to prevent, treat diabetes

Issue: July 2019
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The human gut microbiome contains tens of trillions of microorganisms, including at least 1,000 different species of known bacteria with more than 3 million genes. The microbiota that inhabit the intestines are essential for key metabolic processes, such as the breakdown of indigestible dietary fibers, the biosynthesis of amino acids and the production of neurotransmitters and hormones.

“There is more and more evidence that the microbiome is an active metabolic compartment of the human body, in the way we think of the liver or the kidney as metabolic organs,” Martin J. Blaser, MD, director of the Center for Advanced Biotechnology and Medicine and the Henry Rutgers Chair of the Human Microbiome at Rutgers, The State University of New Jersey, told Endocrine Today. “As such, it may affect energy production, drug metabolism and different aspects of hormonal homeostasis — and there seems to be evidence for all of these.”

Lack of microbial diversity, which is greatly influenced by diet, is a common thread among metabolic diseases, according to Ruchi Mathur, MD, FRCP.

Photo by Jo Auger. Printed with permission.

Microbiome researchers are only beginning to understand the greater influence of gut microorganisms on the human body, which research suggests affect the pathogenesis of conditions ranging from obesity, asthma and cardiovascular disease to type 1 and type 2 diabetes. As new sequencing techniques are enabling a more comprehensive mapping of bacteria in the gut, researchers are discovering that bacterial genomes, and not individual microbes, may hold the clues for targeting diseases like type 2 diabetes.

“Until recently, a lot of emphasis has been placed on looking at bacteria based on their names: E. coli, Prevotella, Akkermansia,” C. Ronald Kahn, MD, the Mary K. Iacocca Professor of Medicine at Harvard Medical School and chief academic officer of the Joslin Diabetes Center, told Endocrine Today. “What we now know is that even bacteria that have the same names may have as much as 15% of their genes different. That is one of the bigger areas that will influence microbiome research over the next several years. It is getting down to this notion of the genetics of the bacteria, because the genes tell us what the bacteria can make and metabolize.”

Those discoveries, according to researchers, may help clinicians to better personalize diabetes treatments, potentially targeting bacterial proteins in patients with a specific cluster of metabolic derangements.

“As we move forward, we are not just going to have type 1 and type 2 diabetes,” Ruchi Mathur, MD, professor of medicine and director of clinical research in the Medically Associated Science and Technology Program at Cedars-Sinai, told Endocrine Today. “We will have type 3, type 4 and type 5 diabetes. The hallmark for each will be hyperglycemia, but the etiologies will be very different — and I think the microbiome will fit into one of those etiologies.”


Bacteria’s influence

Humans, born sterile, are initially “seeded” with their first microbes at birth, both on the surface of the skin and in the gut. That initial seeding, according to researchers, sets the stage for a person’s developing immune system, influencing the risk for future disease.

Martin J. Blaser

“You’re largely colonized by your mother’s bacteria if you are vaginally born and by the hospital’s bacteria if you are born by cesarean section,” J. Mark Brown, PhD, director of research at the Center for Microbiome and Human Health at the Cleveland Clinic Lerner Research Institute, told Endocrine Today. “Breastfeeding also plays a big role. There is a lot of data to suggest that the types of microbes that are initially seeded inform both your innate and adaptive immune system for the rest of your life.”

New research, according to Blaser, suggests that specific changes in the microbiome early in life may affect the progression to symptomatic type 1 diabetes, as well as the development of obesity and type 2 diabetes phenotypes.

“There is more and more evidence suggesting that a disturbance in the microbiome early in life may be one of the triggers or risk factors that moves people who are genetically at risk into active disease,” Blaser said. “We have evidence that if we perturb the microbiome with antibiotics, we can accelerate diabetes. We have identified both microbes and pathways that suggest how this is happening.”

In a 2015 analysis published in Cell, Host & Microbe, researchers found that a cohort of infants genetically predisposed to develop type 1 diabetes showed a drop in microbial diversity, with a disproportionate decline in the number of species that support gut health. By measuring infant stool samples, the researchers observed a 25% drop in the number of distinct species present in the microbiome 1 year before disease onset in the few infants who developed type 1 diabetes during 3 years of follow-up. The population shift involved a reduction in bacteria known to help regulate health in the gut and a rise in potentially harmful bacteria known to encourage inflammation.

“Human studies show a perturbation in the microbiome prior to the development of diabetes,” Blaser said. “It is consistent. In humans, we don’t know the exact culprit, and we don’t know whether it is an individual culprit or a community.”

By the second or third year of life, Kahn said, the microbiome establishes itself toward its adult nature; however, it continually remodels as exposures throughout life alter gut microbial diversity.

“As adults, we also take antibiotics, and we all know that sometimes when you take a potent antibiotic, you develop diarrhea or gastrointestinal (GI) side effects,” Kahn said. “This reflects the impact of the antibiotic on the microbiome more than anything else.”

Some diabetes drugs known to affect GI motility and function also affect the microbiome, Kahn said.

“The best studied example is metformin, which itself slows gastric motility,” Kahn said. “Because of that, it changes the nature of the bacteria in the gut. It is possible that some of the effects of metformin in diabetes are not due to the drug’s effects on metabolism in the individual taking it, but are due to the effects changing the microbiome.”

Another potential driver of disease, Mathur said, are gram-negative bacteria, which produce lipopolysaccharides (LPS), a marker of inflammation.

“Many gram-negatives make LPS,” Mathur said. “If these bacteria overproduce, or if they are there in abundance in the gut, they can cause inflammation.”

Certain gut bacteria also produce short-chain fatty acids, Mathur said, which can then be used for fuel.

“Nondigestible carbohydrates ultimately reach these gut bacteria, the bacteria ferment them and they produce butyrate, propionate and acetate,” Mathur said. “Some of those go on to become gluconeogenic and lipogenic precursors, and some go on to become calories absorbed by the host. There is a theory that between 100 and 200 calories per day can be produced by these bacteria for the human host to absorb.”


Targeting metabolites

Recent advances in metabolomic approaches and microbial genome mining — the process of translating secondary metabolite-encoding gene sequence data into purified molecules — have uncovered a diverse set of small-molecule metabolites, produced by intestinal microbes, that influence human health and disease, Brown wrote in a review published in the Journal of Biological Chemistry. These novel metabolites present “untapped potential” for targeting bacterial enzymology to potentially treat metabolic conditions, such as diabetes and obesity, he noted.

“With 16s sequencing, metagenomics or whole sequencing within a fecal sample, you can gain information about what types of microbes are in the gut, but you only get limited information,” Brown said. “The problem with the classic way to look at who is there is that these methods only reveal who is there. They do not tell you what genes are expressing, what metabolites or products the microbes are making. We need to understand the molecules, the metabolites, the things the microbes are actually making, because those are probably the actionable, druggable targets.”

J. Mark Brown

In a collaborative study, Brown is partnering with Stanley L. Hazen, MD, PhD, chair of the department of cellular and molecular medicine at the Cleveland Clinic, to study a small-molecule enzyme inhibitor that targets trimethylamine N-oxide, or TMAO, a circulating metabolite implicated in the development of atherosclerosis and cardiovascular disease.

“This particular drug only builds up in the bacteria and inhibits the production of TMAO at the level of the bacteria, but it doesn’t systemically circulate,” Brown said. “We are finding that it has very beneficial effects in heart disease models and in obesity and diabetes in animal models.”

Brown said other potential pathways are also being studied.

“From a pharmacology and drug discovery perspective, almost all of the targets right now are of human origin,” Brown said. “There is this untapped extra genome, and we can make small-molecule inhibitors that selectively target bacterial enzymes and receptors or transporters that could have benefit for the human host.”

Studies, conducted mostly in mice, suggest that genetics also play a role in influencing the response of microbes in the gut and the metabolites the microbes produce, Kahn said.

“When you think of the microbiome, you have to keep in mind that there is an interaction between the individual’s own genetics and bacterial genetics,” Kahn said. “The bacteria may be making substances that in one person are metabolized faster or slower or better or worse. The way these metabolic pathways occur can dramatically influence the outcomes of insulin resistance, inflammation and metabolic health.”


Role for probiotics, prebiotics

In an August 2018 analysis published in Clinical Nutrition, researchers found that a small cohort of adults with newly diagnosed type 2 diabetes randomly assigned to twice-daily, multi-strain probiotic therapy — so-called “good” bacteria — for 6 months experienced reductions in insulin resistance and endotoxin-induced inflammation vs. those assigned to placebo for the same period.

Researchers randomly assigned participants to consume 2-g sachets of freeze-dried probiotic powder with eight probiotic strains (n = 31; mean age, 48 years; mean BMI, 29.4 kg/m²) or placebo sachets containing 2 g freeze-dried maize starch and maltodextrins (n = 30; mean age, 47 years; mean BMI, 30.1 kg/m²) twice daily before breakfast and bedtime.

At 6 months, there were no between-group differences in anthropometric measures; however, compared with the placebo group, participants assigned to the probiotics group experienced a clinically significant decrease in homeostatic model assessment of insulin resistance at 3 months (0% vs. –60.4%) that persisted at 6 months (20.5% vs. –64.2%), according to researchers. Within-group comparisons also showed that all inflammatory markers decreased over time in the probiotics group, according to the researchers.

“In conjunction with a reduction in endotoxin levels in the probiotic group at 6 months, there were also associated improvements in cholesterol, total cholesterol/HDL ratio and glycemic control from baseline in group analysis, supporting the concept that probiotics can provide cardiometabolic protective effects,” the researchers wrote.

Purna C. Kashyap

While the research shows promise, Mathur said, there are still many unanswered questions surrounding the use of probiotics to promote intestinal health.

“No. 1, what are you actually getting in your probiotic? Mathur said. “Probiotics have to be alive. If they are desiccated and placed in a capsule on a shelf for months, by the time you get them as a consumer, chances are they aren’t doing what they are supposed to. No. 2, how is your probiotic getting through the acid in your stomach and to the bowel, where it can make a difference? No. 3, are the microbes in the probiotic actually going to colonize? Not only do the bacteria need to make it past the stomach, they need to seed and colonize to make a difference. No. 4, do we really know what these probiotics are doing? Probiotics have great potential for therapeutics, but we are not there just yet.”

While there are promising probiotics candidates, none are FDA-approved and their effects cannot be generalized, according to Purna C. Kashyap, MBBS, a consultant in the division of gastroenterology and hepatology at Mayo Clinic in Rochester, Minnesota.

“It is like saying, ‘We should take painkillers,’ without specifying the drug or the dose,” Kashyap told Endocrine Today. “There are hundreds of different strains and species of bacteria, each of which have a very specific effect. We can’t generalize it. We can’t say Lactobacillus acidophilus is effective in women with preterm birth, so therefore we should use it for health in general.”

Additionally, Mathur said, everyone’s microbiome is different and will respond to probiotics differently.

“The problem is that the term ‘microbiome’ is sexy and everybody wants to cash in on it,” Mathur said. “All these claims are being made and many of them are not valid.”

Brown said prebiotics — types of dietary fiber that feed the friendly bacteria in the gut — may hold greater promise because they can have greater influence in shaping microbes.

“Although there are many probiotics available commercially, the problem is those single organisms have to overcome selective pressure to grow in the gut, and many of them can’t grow very well,” Brown said. “If you give a single Lactobacillus, few of those organisms can persist after you eat them.”


Kashyap said probiotics are often viewed as an “instant cure,” whereas vaccination is a better analogy for how prebiotics work.

“With prebiotics, you are taking something so, in the long run, you have an improvement,” Kashyap said. “You are trying to restructure the entire microbe community, and that effect will not be instantaneous. If you were to think of it in terms of how we get protection from diseases, it is like passive immunity vs. active immunity. There is appealing data coming out, and we will figure out which are good, but at this point there is not good data on prebiotics.”

Role of diet

Research has suggested that the foods humans consume can induce metabolic changes by directly altering the gut microbiota, whereas microbiota, much like humans, exhibit diurnal rhythmicity that can further affect host epigenetics.

“Diet dramatically affects the gut microbiota,” Kahn said. “Every change in diet does. However, no one has found an optimal diet for the optimal microbiome, in part because we can’t yet define what is the optimal microbiome.”

Khan said research does suggest that certain components of the diet, such as dietary fiber, tend to promote what is considered a more healthy, diverse microbiome.

“But we don’t know what parts of the diversity make it healthy,” Kahn said. “Is it these 10 strains? Is it 50 strains? The important thing for people to think about is the microbes in the gut are continually remodeling as diet changes.”

A “common thread” in metabolic diseases such as obesity and diabetes is a lack of microbial diversity in stool, Mathur said — and the amount of microbial diversity is likely heavily influenced by diet.

“If you look at someone who is eating an American diet or a diet rich in plant fibers from other parts of the world, the person consuming a plant-rich diet tends to have more diversity,” Mathur said. “If you take someone who has more of a Western diet with fast food and processed food, their microbial diversity is much less. Whether that’s a predisposition to develop those diseases or whether it’s cause and effect, we don’t know.

“People always ask what makes a healthy microbiome and the answer, in one sentence, is, ‘We don’t know,’” Mathur said. “What we do know is a diverse microbiome is good. The more different players you have on the field, the better and healthier you are. Redundancy is also good.”

‘A new frontier’

In a 2017 review published in Diabetologia, Marju Orho-Melander, MD, a professor of genetic epidemiology at the department of clinical sciences at Lund University in Malmo, Sweden, wrote that the metabolic potential of the GI tract and its microbiota are increasingly recognized as promising targets to improve glycemic control and treat type 2 diabetes.


“Several potential gut-targeting, glucose-lowering treatment strategies are now emerging and show initial promise, yet a better understanding of the mechanisms underlying these effects in humans is required,” Orho-Melander wrote. “So far, human studies in this field have been limited in size, and the results have often been inconclusive and difficult to interpret.”

Kashyap said the microbiome is going to become a part of clinical practice at multiple levels of care — it is only a matter of when.

“If metformin is working with the microbiome and there are certain bacteria that are driving its effect, one strategy might be to increase those bacteria and a second might be to identify individuals who are most responsive to metformin and put them on it,” Kashyap said. “We know the microbiome has a role to play. It is not so much of a mystery, it is trying to figure out the exact signatures that may be relevant.”

Beyond probiotics and prebiotics, Kashyap said, the future may include a clinical tool or diagnostic test that can aid in precision medicine based on a person’s gut microbial diversity.

“A lot of people think of the microbiome and think, ‘Oh, I should take a probiotic,’” Kashyap said. “I don’t think it is that straightforward. The microbiome is going to be a part of both diagnostic strategies and treatment stratification strategies, as well as therapeutic strategies.”

There is still much to learn, Blaser said. Type 2 diabetes, for example, has a single common pathway but may be multiple diseases. As researchers learn to better phenotype these patients, the mechanisms behind microbiome contributions may become clearer. Conversely, he said, certain microbiome patterns may predict different constellations of disease.

“This is a new frontier,” Blaser said. “Scientists and doctors will have to take into account these concepts. Over time, scientists will provide better definitions. It may be that a physician’s choice of medications will be based, in part, on issues of microbiome composition. I don’t think we are there yet, but I don’t think it is that far off.” – by Regina Schaffer


Disclosures: Blaser reports he serves on scientific advisory boards for Dupont, Elysium, Procter and Gamble, and Seed. Kahn reports he serves on a scientific advisory board for Kaleido Biosciences, which makes customized fiber substitutes for modifying the microbiome. Mathur reports she is a shareholder of Gemelli Biotech. Blaser, Brown and Kashyap report no relevant financial disclosures.