Microbiome Update – New Discoveries for Gut Healing
You may be familiar with the microbiome as well as the gut-brain axis, but are you familiar with the microbiota-gut-brain axis? How bacteria and other organisms communicate with the gut and the nervous system, offers clues to treatment for gut symptoms and various diseases.
Functional Medicine always looks at the connections between systems, but now science is shedding new light on some of the underlying mechanisms. Will dive into what this new research reveals in today’s article, but first cover some of the intricacies of these connections.
Keep reading to learn more about:
- The microbiome
- The enteric nervous system
- The microbiota-gut-brain axis
- New research discoveries in this field
- Action steps for microbiome support
What Is the Microbiome?
The microbiome is a complex community living in and on the body, composed of over 100 trillion microorganisms with 80 percent of those living in the gut. Most of the microbiome is bacteria, and mostly anaerobic species that thrive without oxygen, but protozoa, archaea, fungi and viruses are a part of the mix as well. The genetics in the microbiome outnumber human genes by a factor well over 100 times.
Babies inherit their microbiome from their mother: bacteria are passed via the placenta, during delivery and through breastmilk. By the age of one, the microbiome is almost fully developed and appears adult-like in abundance and diversity. The microbiome helps with the maturation of the immune system through childhood.
The microbiome is negatively affected by many factors, including:
- Antibiotics
- Medication including birth control pills, proton pump inhibitors and NSAIDS
- Illness or infection
- Poor diet
- Stress
- Toxins including chlorine, pesticides and herbicides in food and water
- Advanced age
We often discuss how microbiome health affects systemic health. Poor microbiome health, as measured by low abundance and diversity of organisms as well as certain pathogenic infections, has been linked to autism, anxiety, obesity, Parkinson’s disease, Alzheimer’s disease, schizophrenia and more.
Not surprisingly, the microbiome also affects the health of the gastrointestinal system itself. They are in close proximity after all.
Gastrointestinal diseases are not only prevalent, but they can be hard to treat in a way that prevents the recurrence of symptoms.
These include:
- Irritable bowel disease (IBS)
- Small intestine bacterial overgrowth (SIBO)
- Inflammatory bowel disease (IBD) including Crohn’s disease and ulcerative colitis
- Chronic constipation
These conditions can be chronic in nature, respond initially to treatment and then recur. Why? Because the disease includes changes in the enteric nervous system, and we need to be able to address this nervous system component as part of treatment.
What Is the Enteric Nervous System?
The enteric nervous system, or ENS, is a part of the autonomic nervous system that contains neurons and glia cells connected to nerve fibers throughout the GI tract. It’s ultimately connected to the vagus nerve that goes to the brain, but largely can operate on its own. We don’t have to think about the ENS, it functions without our conscious control.
The ENS works independently of the sympathetic (“fight or flight”) nervous system and the parasympathetic (“rest and digest”) nervous system but is influenced by them both.
The ENS regulates:
- Motility and transit time, or the movement of food through the digestive system, and how quickly
- Absorption of nutrients
- Gut immunity
- The mucosal lining of the digestive tract
- Intestinal permeability (whether the gut is leaky, or not, or somewhere in between)
Here’s the connection: The microbiome interacts with the ENS and together they regulate gut physiology.
The Microbiota-Gut-Brain Axis
The Microbiota-gut-brain axis, goes beyond the gut-brain axis that we often discuss. This axis, also called the microbiota-brain axis, refers to the total microbiome as well as the products the microbiome produces and its connection and influence on the nervous system and brain.
This axis includes the ENS, but also the sympathetic and parasympathetic nervous systems and the central nervous system. It also connects to neurotransmitters, hormones and the immune systems in the gut and nervous system.
There is a lot of communication going on here!
Five routes of communication have been identified. These include:
- The HPA axis (hypothalamic-pituitary-adrenal axis)
- Neurotransmitters
- Mucosal barrier
- The blood brain barrier
- Gut immune system
We know that when the gut microbiome changes as a result of a gut infection or taking antibiotics, as examples, the ENS changes too. The gut microbiome regulates GI function, the gut microbiome affects brain function, and the gut microbiome influences the ENS. It’s all connected!
New Microbiome Research
We see the connections between the microbiome and the enteric nervous system, but we are still learning more about the mechanisms behind the connections.
There are potentially hundreds of microbiome molecules, made by bacteria and other organisms, that influence and help to regulate the enteric nervous system. Understanding these factors may lead to improved treatment for those with damaged gut health or gastrointestinal disease.
Molecules of interest are:
- Ligands for toll-like receptors (TLR) – proteins involved in the immune system
- Short chain fatty acids (SCFA) – fatty acids produced by bacteria that modulate serotonin and are an energy source for the cells that line the GI tract
- Lipopolysaccharides (LPS) – large molecules, known as “endotoxins” expressed by bacteria
A new study, published in the journal Microbiome, looked at some of these factors and their role in digestive function. This was an animal study where the microbiomes of mice were depleted by antibiotics and then allowed to restore.
Researchers observed that when the microbiome was depleted, the mice also experienced a loss of neurons in the ENS in areas of both the large and small intestines. The mice experienced slower transit time (more tendency toward constipation) and increased intestinal permeability (a leaky gut situation associated with food sensitivities and immune activation). After antibiotic use, the mice also experienced an elongation of their small intestine.
In short, microbiome depletion was associated with both a change in structure and of function in the gut.
Re-building the microbiome, however, had the opposite effect. As bacteria returned, it promoted the growth of new neurons (neurogenesis) in the ENS and gut function was restored. This demonstrates a plasticity of the ENS, much like the brain itself, where we see new growth and the repair of damage.
Further, it was determined that both LPS and SCFA help neurons survive through the microbiome depletion due to the antibiotics. SCFA have the additional benefit of stimulating neurogenesis. SCFA supplementation helped to restore the neurons in the ENS post-antibiotics.
The study concludes: “the microbiota is essential for the maintenance of ENS integrity, by regulating enteric neuronal survival and promoting neurogenesis.” This means that the microbiome is essential for ENS function and health.
A Functional Medicine Perspective
Functional Medicine has been talking about this connection for a long time. Now we have some more research to support what we’ve seen clinically.
Even though there are many details to still discover, it is clear when we work on microbiome health, we see gut symptoms improve, systemic symptoms improve and unlock an important root cause to disease.
Here are some tools to consider:
- Optimize your diet. There is no doubt that changing the diet changes the microbiome, often in a matter of days. Increasing colorful and fiber-rich plant foods that are full of polyphenols is key for feeding beneficial bacteria and producing a robust and diverse microbiome. Shoot to eat 40 different plant foods each week from these Paleo categories: nuts, seeds, herbs, spices, sea vegetables, vegetables, tubers and fruit. If tolerated, properly prepared beans and lentils are a fantastic food to “seed” the gut and encourage healthy bacteria and SCFA’s production. Download my free Paleo Diet – Quick Start Guide here.
- Question antibiotic use. Antibiotics continue to be overprescribed despite anti-biotic resistance and other available options. Save antibiotics for when it’s necessary and consider the use of antibacterial herbs and Functional Medicine protocols instead. Herbs like berberine, oregano, garlic and others may be supportive.
- Use gut supportive supplements. When we think of supplements for gut health, the focus is often on probiotics, which are important, but we have many other options that support microbiome health, gut function and the connections between the two. Here are some that I use in my practice:
- Practice mindfulness and relaxation around food. Bringing your body out of a stressed state and into the “rest and digest” state helps bring more blood flow to the digestive system and optimize digestive function. You can do this by minimizing distractions, taking a few deep breaths before eating, using your senses and getting the full pleasure from your meal.
The microbiome itself is incredibly complex, but the connections are clear as can be. When we use food, supplements and our daily lifestyle to nourish the microbiome, we experience better digestion as well as body wide benefits.
Work with a Functional Medicine practitioner for personalized guidance and see your health improve quickly as you support the microbiota-gut-brain axis.
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