The Gut Microbiome: Key Steps for Healthy Gut Flora


The “microbiome” is not a myth the populations of bacteria in your gut, good and bad, are absolutely integral and essential to overall health and wellness and are inexplicably linked to important bodily processes. How you sleep, how you eat, how you digest, and how you respond to infection are all things that can be impacted by the gut biome and also impact the gut biome itself. Infections, stressors, or sleep schedules can all impact the diversity and species of bacteria in your gut ecosystem.

Until fairly recently, bacteria were always perceived as inherently “bad” and that sanitation or elimination of bacteria was essential to health. As we discover more about the ecosystem of the gut and the impact of antibiotics and diet, we are starting to realize the absolute importance of gut flora as one of the pillars of being healthy.

How to Easily Restore Gut Microbiome After Antibiotics, High-Stress, or Poor Dietary Choices

Not everyone has a poor digestive system or flora by choice – many have sleeping issues, high-stress jobs or home environments, or have been stricken by poverty and cemented into a lifestyle that features unhealthy dietary choices or things that may impact the digestive system (NSAIDs, processed food, alcohol, cigarettes). However, it is a choice to take action to remedy the root causes of digestive distress—be it by short-term antibiotics or long-term lifestyle & environmental factors.

The most plain-and-simple way to restore gut health and improve overall markers of health is through a fiber-rich, nutrient-rich diet that is primarily plant-based and whole-food-based.

1. Avoid processed foods, refined foods, sugars, and low-fiber foods. Instead, look to prioritize vegetables, nuts and seeds, legumes, whole grains, fruit, and seafood. The evidence is clear that a highly processed and refined diet is not only terrible for overall health but especially for the gut bacteria in your digestive ecosystem. Sugar and refined foods can help feed bad or pathogenic bacteria while depleting us of the stuff that fuels good bacteria (fiber – both soluble and insoluble). This can not only lead to chronic low-grade inflammation in the body but also put you at risk of metabolic and cardiovascular disorders later in life.

Gut Microbiome

2. Fermented foods. Consume more fermented foods, which will provide numerous bioactive effects, and are more beneficial than consuming a singular strain of probiotic bacteria in the form of a capsule. These include things like sauerkraut, kimchi, and kefir. But not all fermented foods contain live bacteria that are beneficial for the gut.

Depending on what the actual food is, types of bacteria, mold, or yeast will naturally bring about the fermentation process. However, if these foods are then pasteurized, the active microbes and live bacteria are destroyed. When shopping, look for sauerkraut or kimchi that is refrigerated and in a glass jar, rather than those sitting on a grocery store shelf, as anything shelf stable or canned has been pasteurized. You can also opt for kefir or yogurt that specifically mentions “live cultures” in the ingredient list.

3. Increase the intake of probiotics and prebiotics—either through whole food sources or supplementation. Probiotics are live microorganisms, while prebiotics is foods that promote and encourage the growth of beneficial bacteria. Prebiotics can be supplemented in the form of psyllium husk, acacia gum, partially hydrolyzed guar gum, or inulin. These are sold as “fiber” supplements; in that, they are broken down by the gut and fuel the growth of beneficial bacteria like Bifidobacterium.

Prebiotics can also come from a wide array of foods like artichokes, onions, leeks, shallot, legumes, etc. Probiotics, on the other hand, provide benefits when consumed – often in the form of capsule supplements. Probiotics do not “permanently” colonize the gut, but may shift the composition of the gut towards promoting the growth of ‘beneficial’ strains of bacteria.

When choosing probiotics, ensure you look for a supplement that contains a multitude of varied, clinically studied strains, compared to one or two single ones. If you have issues with histamine, it is best to avoid strains like Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus. Bifidobacterium longum, Lactobacillus Plantarum, and Lactobacillus rhamnosus are good options for those with histamine intolerances or brain fog.

The most important caveat to all of this is that different probiotic strains and different foods may not work the same for everyone – some may feel fatigued after yogurt or kombucha, while some feel a burst of energy. This generally relates to histamine, and what’s already going on in your gut – certain populations of bacteria or yeasts can cause dysbiosis or other physical symptoms, which may worsen upon taking a probiotic supplement or eating food high in fiber.

That’s why it is always best to see what works for you through trial and elimination, opt for safe, clinically tested strains of probiotics, and ensure proper diet, nutrition, and sleep. As always, a natural practitioner such as a naturopath may be able to better determine the actual source of the digestive issue and, from there, determine the best course of action to “fix” the digestive issues be it probiotics, prebiotics, supplements like marshmallow root, or through a whole-food, plant-based approach. 

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