Gut check: Biomarkers and nutrients that restore microbiome health and digestive balance

Your gut does far more than break down food. It helps produce neurotransmitters, shapes your immune response, helps keep inflammation in check, and communicates with your brain through the gut-brain axis. When the trillions of microbes living in your digestive tract fall out of balance, the effects aren’t limited to digestion—they show up everywhere.

In recent years, research has reshaped how we think about gut health. An imbalanced microbiome has been linked to mood changes, autoimmune conditions, metabolic problems, and even cognitive decline. In many cases, gut dysbiosis appears years—sometimes decades—before symptoms emerge.

This connection is why bloating may accompany brain fog, and why stress often makes digestive issues worse. 

But balance is often restorable. Targeted nutrition can support the microbiome, calm inflammation, and improve digestive function over time. And with functional testing that tracks key biomarkers, you can move beyond guesswork and make adjustments based on real, measurable data.

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Nutrients that support microbiome balance

Restoring gut health is often about providing the specific building blocks your digestive system needs to repair, regulate, and thrive. These include B vitamins, glycine, and magnesium. Below, we take a closer look.

B vitamins

B vitamins serve as essential cofactors for hundreds of enzymatic reactions in your body, and your gut is no exception. Interestingly, your gut bacteria both produce and consume B vitamins, creating a delicate ecosystem that requires consistent nutritional input.

For instance, vitamin B1 (thiamine) supports the metabolic and nervous system processes involved in digestion. When stomach acid levels are low—a surprisingly common issue—protein breakdown is impaired and harmful bacteria are more likely to survive before reaching the intestines, increasing the risk of microbial imbalance.

Vitamin B6 is also important for producing neurotransmitters, including serotonin—approximately 90% of which is produced in the gut. When B6 levels are insufficient, this production slows, affecting both mood and gut motility. In fact, research has found that adequate B6 status is associated with greater microbial diversity—a key marker of gut health.

On top of the above, vitamin B12 and folate work together to support the integrity of the intestinal lining. They’re essential for cell division and DNA synthesis, processes that happen rapidly in the gut, where the lining replaces itself every three to five days. Without adequate B vitamins, this regeneration slows, potentially increasing intestinal permeability.

For optimal absorption, B vitamins are best taken in the morning with food. Look for activated forms like methylcobalamin (B12), methylfolate, and pyridoxal-5-phosphate (B6), which are more readily utilized by the body.

Glycine

As a primary component of collagen, glycine helps maintain the structural integrity of the intestinal lining—your first line of defense against pathogens and undigested food particles entering the bloodstream.

Beyond its structural role, glycine supports bile acid production, which is essential for fat digestion and the absorption of fat-soluble vitamins A, D, E, and K. Poor bile production can lead to undigested fats that often cause bloating, discomfort, and changes in stool consistency.

Glycine also demonstrates anti-inflammatory properties in the gut. Research has found that glycine supplementation reduced intestinal inflammation markers and supported the growth of beneficial bacterial species. This makes it particularly valuable for those dealing with chronic bloating or inflammatory digestive conditions.

Notably, glycine acts as an inhibitory neurotransmitter, calming the nervous system. Since stress directly impairs digestion by shifting the body into sympathetic (“fight or flight”) mode, glycine’s calming effects can indirectly improve digestive function by helping you stay in the parasympathetic (“rest and digest”) state.

Because glycine has a naturally calming effect, many people find it works best in the evening. Taken before bed, it may help ease digestion after your final meal while also supporting the body’s overnight repair and recovery processes. Typical doses range from three to five grams.

Magnesium

Dietary surveys suggest that a large portion of the U.S. population does not meet recommended magnesium intake levels. Because magnesium is absorbed in the gastrointestinal tract and plays a key role in gut motility, enzyme activity, and electrolyte balance, low intake can directly affect digestive function. 

In people with compromised digestion or chronic GI stress, magnesium insufficiency may develop quietly and systemically—often long before it’s detected on routine blood tests.

However, this mineral is essential for smooth muscle function throughout the digestive tract, regulating the rhythmic contractions (peristalsis) that move food through your system. When magnesium is low, motility slows, potentially leading to constipation, bloating, and bacterial overgrowth.

Beyond motility, magnesium supports the production of digestive enzymes released by the pancreas. These enzymes break down proteins, fats, and carbohydrates into absorbable components. Insufficient enzyme production means undigested food sits in the gut longer, fermenting and feeding less desirable bacterial species.

Magnesium also modulates the stress response by regulating cortisol and supporting GABA activity in the brain. Since chronic stress is one of the most significant disruptors of gut health—altering microbial composition, increasing intestinal permeability, and slowing motility—magnesium’s stress-buffering effects provide indirect but powerful digestive support.

Yet, there are plenty of different forms of magnesium; thus, it can be confusing regarding which one to take. Here’s a quick breakdown to help you best determine what’s right for you:

• Magnesium glycinate combines magnesium with glycine, offering the benefits of both nutrients while being gentle on the stomach. 
• Magnesium citrate has a mild laxative effect, making it useful for those dealing with constipation. 
• Magnesium L-threonate crosses the blood-brain barrier more effectively, supporting the gut-brain connection.

Evening supplementation typically works well for most people, as magnesium’s relaxing effects support both digestion and sleep quality. Doses typically range from 200 to 400 mg, though individual needs vary based on dietary intake and stress levels.

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Building your gut health protocol

Restoring microbiome balance is a gradual process that unfolds over weeks and months with consistent support. With the right approach, it is, however, possible to feel good again.

Looking for more support and guidance? Welle’s functional testing approach tracks key biomarkers that provide a clear snapshot of your gut and overall health. In turn, these help guide targeted support appropriate for you and your needs. Along the way, we can also help you adjust your protocol as needed.

When you support your microbiome strategically, you’re not just improving digestion—you also support your mood, immune function, and so much more!

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Sources

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