Decoding Dysbiosis: Are Your Gut Microbes Out of Whack?


Cultivating Our Gut Microbiome to Stifle Disease Series (Part 4)

In this series, we’ll share how the latest developments in this medical frontier are transforming our approaches to illness and offering new strategies to heal and prevent disease.
Previously: Scientists are examining thousands of people’s stools in an effort to infer a “normal” gut microbiome. This would create a standard that should help clinicians and researchers figure out when someone has a microbial imbalance. 
Sometimes, microbiome terminology is like the science itself: unfamiliar, incomplete, and confusing. Dysbiosis is no exception.

Dysbiosis is often used as a synonym for “imbalanced” when describing the state of someone’s microbiome. The problem is knowing what constitutes balance when there are trillions of bacteria—not to mention viruses and fungi—in the human gut.

It’s this diversity that makes it hard to determine whether we have all the right bugs in the right amounts.

Despite being poorly understood, studies continue to link gut microbiota to diseases of the gastrointestinal tract—and beyond. Dysbiosis is a biomarker of several disorders and a priority for future therapies to prevent and treat diseases.

That’s because the human microbiome, that total collection of microbes that live inside us and on our skin, functions like a secondary set of cells. The cells that make up our body are performing thousands of biochemical reactions, transforming substances, creating compounds, and generating the very spark of life that animates our flesh. Those microbes perform many of those same actions. When we don’t have enough helpful bacteria—or too many pathogenic bacteria—problems result.

A Balance of Bugs and Disease

Research is just scratching the surface of what dysbiosis is all about. A research review published in Microorganisms in 2019 looked at 113 studies to examine the state of science around gut microbiota balances.

“Dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extra-intestinal diseases such as metabolic and neurological disorders,” the review authors wrote.

Insight about how the composition of our microbiome affects disease should help open new therapeutic options for those diseases, the researchers wrote.

The review revealed studies that drew several specific associations between dysbiosis and disease:

  • Irritable bowel syndrome is associated with a loss of microbial richness, which could affect the integrity of cellular junctions and weaken the epithelial barrier.
  • Studies of celiac disease demonstrate patients have a reduction in Lactobacillus and Bifidobacterium and an increase in potentially pathogenic bacteria compared to healthy subjects.
  • Obesity is associated with lower species diversity, as well as lower levels of genes involved in metabolism.
  • Patients with dementia have lower microbial diversity and disturbed microbiota associated with inflammatory states.
  • Studies show a less diverse gut microbiome in children with autism spectrum disorders, as well as lower levels of Bifidobacterium and Firmicutes.
  • Stress has been shown to have a relationship with gut microbiota, with specific changes that are associated with depression and others with stress.
  • The gut microbiota of colorectal cancer patients had more of some bacteria and fewer butyrate-producing bacteria.
  • Several studies found the gut microbiome is altered in patients suffering from Type 2 diabetes.

Our Microbiome Fingerprint

Correlation doesn’t equal causation. Though researchers have linked certain microbiome types to certain diseases, we don’t know if the bacterial imbalance caused the disease or was caused by the disease. Or maybe some other factor contributes to both a disease and a shift in the microbiome. Further complicating the study of dysbiosis is the fascinating fact that microbiomes are unique to cultures and even individuals.

No two people have the same microbiome, not even identical twins, although they’re quite similar, according to studies. Some researchers have even measured the human “biologic cloud,” the space around us that is picking up and emitting microbes through our skin and breath. This cloud is how pathogens—and beneficial microbes—spread.

“Your microbial space is distinct like a fingerprint basically, which interestingly brings up some forensic implications. You might even be able to solve a crime [with the microbiome] someday,” said Neil Stollman, chairman of gastroenterology at Alta Bates Summit Medical Center and associate clinical gastroenterology professor at the University of California–San Francisco.

But, right now, it seems impossible to solve the puzzle of our own health. Lab tests can confirm for doctors if you lack a certain vitamin and supplements can be prescribed. If you want to know if you have a broken microbiome, however, it’s difficult to test for and even harder to fix—although some supplement makers promise otherwise.

Divided Philosophy

Mainstream medicine tends to lean toward a more conservative approach regarding dysbiosis, only acknowledging its role in a handful of scenarios such as pathogenic infections like Clostridioides difficile (c. diff). On the other hand, researchers are continuing to link different bacterial profiles to different diseases and many functional medicine doctors will use stool tests to discern if levels of certain beneficial bacteria are low and try to increase those for disease prevention.

Dr. Akil Palanisamy, physician and author of The T.I.G.E.R. Protocol: An Integrative 5-Step Program to Treat and Heal Your Autoimmunity, told The Epoch Times that integrative practitioners tend to hone in on the subtleties and nuances of the microbiome. This is likely because these practitioners are actively engaging with patients and seeing how different protocols affect outcomes.

Though it can require a lot of detective work, Palanisamy said there are thousands of studies coming out every year and many affirm dysbiosis and its role in autoimmune diseases.

On the other hand, some clinicians such as Dr. Ari Grinspan, associate professor of medicine and director of the fecal microbiota transplant program at Mount Sinai Hospital, are a bit more cautious and say the research isn’t robust enough.

Grinspan told The Epoch Times that dysbiosis is largely a “made-up term” for when the flora is changed. It’s been proven in cases of antibiotics, which broadly kill off all sorts of bacteria including pathogens like C. diff. Anything beyond that is an association but not causation, he said.

Individualized Treatments

Most cases of dysbiosis tend not to be “lightning strikes,” meaning they aren’t often a chance event, Dr. Scott Doughty, an integrative family practitioner with U.P. Holistic Medicine in Michigan, told The Epoch Times.

Rather, he said, gut issues tend to be the result of lifestyle—stress, toxins, nutrient deficiencies, and genetic complications with an occasional lightning strike. The good news is it makes dysbiosis reversible.

He doesn’t have hard rules, such as removing all gluten and dairy that he said give him the uncomfortable feel of “conveyor belt medicine,” although he does make dietary suggestions on a case-by-case basis before introducing supplements.

On the other hand, the library is filled with books from doctors who do offer blanket recommendations for healing the gut. Clearly, there’s a market for that, and they have helped plenty of people lead a more healthy lifestyle.

Palanisamy uses the method he wrote about in his T.I.G.E.R. Protocol, with T.I.G.E.R. an acronym for toxins, infections, gut, eating, and rest.

It takes a minimum of three months to start experiencing results from the protocol, which is designed to take a committed, holistic approach to the gut, he told The Epoch Times.

Doughty said while the books and products can be useful, he often suggests patients push them to the side once they begin working with him.

“What I typically say to them is Dr. Axe is not your doctor. I’m here for you, and you’re here for me,” he said.

The Glyphosate Conundrum

Besides antibiotics and stress, another factor affecting microbial balance could be toxins that make contact with the colon through food. Studies indicate that an array of toxins can alter microbial composition, including one chemical that everyone has broad exposure to: the herbicide glyphosate.

The most widely used herbicide worldwide, glyphosate—which was originally patented as an antibiotic—is the active ingredient in more than 750 herbicide products. While the Centers for Disease Control and Prevention (CDC) has reported that the specific levels of glyphosate found in urine are higher in women and children, it doesn’t offer a threshold that’s deemed safe.

The CDC offers no toxicity, health, or regulatory guidance and states the assessment of exposure “does not by itself mean that the chemical causes disease or an adverse health effect.”

Since a research review published in Interdiscipinary Toxicology in 2013, scientists have been calling on governments to reexamine policies on glyphosate to restrict its use. Glyphosate is the active ingredient in the world’s most widely used herbicide, Roundup, a product so prolific that one of the most common genetic modifications made to major crops is to make them better able to withstand Roundup. Its maker, Bayer, is phasing out glyphosate from its residential brand.

As Dr. David Perlmutter pointed out in his book “Brain Maker,” glyphosate changes the composition of gut bacteria by:

  • comprising our ability to detoxify toxins.
  • impairing the function of vitamin D.
  • chelating iron, cobalt, molybdenum, and copper out of the body.
  • impairing our synthesis of tryptophan and tyrosine, amino acids vital to protein and neurotransmitter production.

The review focused on the link between glyphosate and celiac disease, arguing it’s a causal factor for the rise in gluten sensitivity, which tracks with the increase in glyphosate application added a few days before harvest to kill the wheat so it dries better for harvest and storage.

Perlmutter writes that the relationship between glyphosate and celiac disease is undeniable though other variables are probably at play.

“One thing we do know from recent research is that glyphosate does in fact impact gut bacteria,” he wrote.

Dysbiosis but Not Illness

It’s a frustration in science that even when a bulk of evidence looks suggestive, causation is difficult to prove, which is why vocabulary is important. As Grinspan said, one danger of using the word dysbiosis in place of imbalance is that it’s uncertain whether it’s always indicative of illness. People in urban areas have a less diverse microbiome than those who live rurally, for example.

“This really gets a little complicated. People will jump on the term ‘dysbiosis,’” Grinspan said. “The microbiome is different in every single person. There’s so many different things that can affect that.”

It’s the sort of dilemma that functional physicians like to tease out—even if the science is still in its infancy.

As research evolves, Palanisamy said microbiota “signatures” of bacterial dysbiosis are emerging—patterns that reflect specific disease states. Some of them he mentions in his book are linked to multiple sclerosis, rheumatoid arthritis, lupus, and ankylosing spondylitis.

“There are a lot of different types of dysbiosis,” he said. “We haven’t understood them all fully.”

Next: We examine some precise roles that gut bacteria play and how to pick up on your body’s early signs that your microbiome has been disrupted.

Read Part 1- Killing Bacteria with Antimicrobials and Antibiotics May Be Shortsighted, According to New Science About the Microbiome

Read Part 2- How the Gut Cures and Creates Disease

Read Part 3- Why Scientists Are Obsessing Over the Bugs in Our Stool

Important Notice: This article was also published at by Amy Denney where all credits are due.


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