11 non-diet-related things that can positively modulate the gut microbiome

What if there were other ways you can improve gut health, other than diet, anti-biotics, pre and/or pro-biotics?

There are actually quite a few. Some of them will make a lot of sense and others will definitely be a surprise.

The gut is central to optimal health

If you want to be in optimal health, then you have to look after you gut.

Your gut is inhabited by trillions of bacteria and other critters. They comprise over 1000 species and they have much more DNA than us. As a matter of a fact, more than 90% of our DNA is from bacterial origin.

Gut health is been implicated in more and more health conditions because the gut influences every aspect of the body. If there is inflammation in the gut, then there will be inflammation anywhere and everywhere in the body and it manifests differently for all of us.

The most common signs are skin issues (psoriasis, acne, eczema, etc.), mood disorders (depression, anxiety, autism, Parkinson’s, etc.), low testosterone symptoms and hypothyroidism.

Lifestyle changes, tips and tricks to improve gut health

#1 Eat clean

With this, I don’t mean eat out of clean plates, or only natural foods, but actually looking out for hidden contaminants in foods. Supposedly harmless foods such as cottage cheese, yogurt or even milk can contain emulsifiers. Two emulsifiers, namely, carboxymethylcellulose and polysorbate-80, have been shown to cause gut dysbiosis, low grade inflammation and leaky gut in mice (R).

So even if your milk brands doesn’t indicate that it doesn’t contain anything else that’s not indicated on the label, doesn’t mean there isn’t harmful things in there. Food manufacturers are allowed to add things like emulsifiers, thickners, etc., and don’t have to indicate it on the label as long as it’s below 1% of the total content.

So if your cottage cheese or milk is giving you negative symptoms and you think maybe milk just isn’t for you, maybe try a cleaner brand.

#2 Don’t starve yourself

Chronic under-eating is associated with a plethora of side effects. Under-eating increases the risk of developing a protein deficiency, vitamin and mineral deficiency, slow metabolism, elevated stress hormones, low androgens, etc.

Starvation reduces antimicrobials peptides and causes bacterial translocation (R). For example, people with anorexia have gut dysbiosis (R). This is another reason why chronic caloric deficits are unfavorable.

#3 Get enough sleep

We all know the importance of proper sleep. Sleep deprivation or having poor quality sleep can lead to cognitive dysfunction, low testosterone, increased fat mass, low stress tolerance, muscle wasting, exaggerated appetite, and the list goes on.

Poor sleep and circadian disruption can negatively alter the gut microbiome (R). During sleep there is a preferential growth of highly fermentative members of Lachnospiraceae and Ruminococcaceae and a decrease of Lactobacillaceae families (R). This is associated with gut inflammation and leaky gut and all the chaos that follows that.

I quote:

The health effects of circadian disruption are increasingly recognized, and include both short and long term health decrements such as increased GI permeability (Summa et al., 2013Voigt et al., 2016b), altered immune responses (Curtis et al., 2014), increased susceptibility to inflammation and GI epithelium damage (Pagel et al., 2017), and multiple chronic inflammation-associated diseases including irritable bowel syndrome and inflammatory bowel disease.


In this animal study, melatonin supplementation improved sleep quality and significantly increased the richness of the microbial community and the relative abundance of Lactobacillus intestinalis, Lactobacillus johnsonii, and Lactobacillus reuteri, while it reduced the relative abundance of Prevotellaceae (R).

#4 Stress less

Stress is our nemesis. It’s prevalent and sneaky. Before we know if, we’re stressing about something. Chronic stress has immense detrimental effects on our health.

Stress hormones such as noradrenaline, adrenaline and cortisol negatively modulate gut bacteria. Noradrenaline and adrenaline increase the growth of gram-negative bacteria, which can lead to elevated inflammation (R).

Stress also diverts blood flow away from the intestine, so you end up with poorly digested food and leaky gut, and this leads to oxidative stress and inflammation.

HPA axis activation resulting in immunomodulation, inflammation, intestinal damage, and increased GI permeability (R).

#5 Get ample sunlight daily

Sunlight is so good for us on so many levels. Sunlight positively modulates the microbiome. And it’s not just vitamin D that has benefits, but also the UV light (R), red light (R) and most likely most of the other light spectrums of sunlight.

Vitamin D levels in humans are inversely associated with circulatory bacterial endotoxins, which will lead to lower levels of inflammation.

Vitamin D is effective against both inflammatory gram-positive and negative bacteria. It’s also effective against pathological bacteria, such as H. pylori and Streptococcus mutans, etc. (R).

Human defense peptides (HDPs), and specifically anti-microbial peptides secreted in the gut (such as cathelicidin and β-defensin), control the growth of bacteria and prevent overgrowth.

Vitamin D3 (and butyrate) are capable of inducing HDPs without provoking inflammatory responses (R). Bacteria in the gut can also increase HDPs, but this usually causes an inflammatory response. Vitamin D can help to prevent bacterial overgrowth, without inducing inflammation.

This study found that having vitamin D levels at 38 ng/ml or higher was correlated with a twofold reduction in the incidence of acute viral respiratory tract infections (R).

Low vitamin D might also lead to increased gut inflammation and leaky gut, by lowering Akkermansia muciniphila levels (R). Read more on the benefits of Akkermansia muciniphila here and how to boost their levels.

So even though vitamin D is awesome, don’t just rely on supplements for better health, or specifically gut health, but go out in nature and get some sunlight on your gut daily. The worse off your gut health is, the more you’ll benefit from prolonged sunlight exposure daily.

I like to get sunlight first thing in the morning after I wake up. This helps with increasing dopamine and circadian entrainment. I also take breaks during the day and go outside to get more sun.

#6 Heat up

Who would have thought that something as insignificant as heat could affect the gut microbiome?

Intentional heat therapy can be very therapeutic. As a matter of a fact, whole body thermal therapy is being tested for the treatment of cancer, inflammatory diseases such as rheumatoid arthritis, and even psychological conditions such as depression (R). So many people benefit from heating themselves up first thing in the day if they have a slow metabolism, either via baking in the sun, taking a warm shower, baking in the car, etc.

However on the other hand, heat stress can have the opposite effect. Heat stress, and especially exercising hard in the heat can cause leaky gut, inflammation and gut issues. Having glucose before exerting yourself in the heat can protect against heat and exercise induced leaky gut. This is because heat stress is a stressor and like any other stressor, it diverts blood flow away from the gut, which then causes leaky gut.

So keeping yourself warm, either through warm clothing or by increasing the metabolism by improving thyroid function will positively modulate the gut bacteria.

Another cool hack is to shine a brooding lamp on your gut for 10-20 minutes daily. Or alternatively, you can consume methylene blue 6 hours before your red light/heat session, because the red light and methylene blue have a synergistic effect on killing pathogenic bacteria and modulating the gut. The reason for their synergy is because red light reacts with methylene blue to creates H2O2, which has antimicrobial effects.

#7 Exercise

We all know the benefits of exercise or at least the importance of having some form of movement/activity in our lives.

Low intensity exercise increases transit time and thus the contact time between the pathogens and the gastrointestinal mucus layer. As a consequence, it seems that exercise has protective effects, reducing the risk of colon cancer, diverticulosis, and inflammatory bowel disease.

The benefits of exercise are so strong that even in the presence of high fat diet, exercise may reduce inflammatory infiltrate and protect the morphology and the integrity of the intestine. A high fat diet, accompanied by sedentary behavior, leads to increased villi width due to plasmacytoid and lymphocytic infiltrates. Exercise prevents these morphological changes by reducing cyclooxygenase 2 (COX2) expression in both proximal and distal gut.

But again, everything can be overdone.

Too much exercise can become stressful and promote leaky gut, gut inflammation and gut dysbiosis. Exercising for too long can overproduce serotonin, which can cause a common disorder amongst long-distance runners, called, runners diarrhea. However, you don’t have to be a long-distance runner to get that side effect. If you deplete your glycogen and increase stress hormones, you will experience leaky gut and gut inflammation.

Excess gut serotonin is no joke. Excess gut serotonin promotes gut inflammation and contributes to IBS, Crohn’s disease, liver disorders, insulin resistance, metabolic syndrome and all other kinds of inflammatory disorders in the body.

Proper exercise of all intensities can positively modulate the gut microbiome and increase “beneficial” bacteria, such as Faecalibacterium prausnitzii which may protect the digestive tract by producing butyrate and lowering the oxygen tension in the lumen.

But apart from your modulating the gut bacteria, one of the biggest benefits of exercise are due to increasing transit time, and not so much by modulating the gut bacteria.

We find that a long colonic transit time associates with high microbial richness and is accompanied by a shift in colonic metabolism from carbohydrate fermentation to protein catabolism as reflected by higher urinary levels of potentially deleterious protein-derived metabolites. Additionally, shorter colonic transit time correlates with metabolites possibly reflecting increased renewal of the colonic mucosa. Together, this suggests that a high gut microbial richness does not per se imply a healthy gut microbial ecosystem and points at colonic transit time as a highly important factor to consider in microbiome and metabolomics studies.


So increasing transit time is fundemental for improving gut health and health in general. So if you cannot exercise, at least make time to walk, and perferably do it in nature. This brings us to our next point.

#8 Spend time in nature

Nature is a very rich source of bacteria. You get the air, soil and water microbiome, all of which are different.

This study found that when captured mice were let go into the wild and then recaptured a few weeks later, their microbiome had rapidly changed to become like that of mice in the wild demonstrating how sensitive the microbiome is to changes in the environment (R).

If you can go for a hike in nature, that will have many health benefits. If you can swim in a river or ocean, then it will have even more benefits.

Expose yourself to clean parts of nature and your microbiome and health will thank you for it.

If you’re a busy person and can’t get out in nature often, try to do a nature hike once a week, and at least do grounding a few times a week in the park or somewhere.

#9 Noise pollution and nature noises

Another major stressor that can negatively modulate the gut microbiome is noise. Constantly hearing horns blaring, yelling, engines, etc., you’ll most likely be in a low grade stressed state.

Once you get out of that environment and get into a more quiet area where you can hear nature and birds, your stress will drop like a rock and your gut microbiome will also improve.

In this study, Cui et al. found that chronic noise increased the Firmicutes: Bacteroidetes ratio and also accelerated aging-related changes in a mouse model of Alzheimer’s disease (R). Scary stuff right?

Aside from directly affecting the ear, exposure to acoustic stress activates the sympathetic nervous system and HPA-axis, thereby eliciting a classical stress response as reflected by increased circulating concentrations of glucocorticoids and catecholamines in both animals and humans exposed to various durations and levels of noise.

When my wife and I lived in a flat that was close to the road, railway, harbor and a school (just a bit after we got married), we were chronically exposed to a huge variety of disruptive noise. And just to make it worse, there wasn’t a lot of nature so we rarely heard birds or other animals. It was awful.

Once we moved to a quiet area, we constantly told each other how fantastic it is to be in such as calm area where you can hear the wind, birds, etc. Noise stress is awful.

#10 Care for pets

Pets, especially when they’re exposed to nature more than you are, can actually improve your gut microbiome. They lick you or you pet them and thus share bacteria. Kinda gross I know, but it has health benefits. You share bacteria with your pet which alters your bacterial colonies (R).

The healthier your pet is, the healthier their microbiome will be and the more benefits you will get.

#11 Breathe clean air

If you’re surrounded by polluted air, your airway and lung microbiome as well as your gut microbiome will suffer.

If you expose yourself to clean air filled with natural particles released from trees, bushes, flowers, etc, then that will enrich your microbiome. These particles in the clean air have many anti-inflammatory and health-promoting benefits.

I quote:

Particulate matter is a component of air pollution that could trigger and accelerate development of GI diseases, particularly in genetically susceptible individuals (Salim et al., 2014). This is manifested by increased GI permeability, decreased colonic motility and clearance, and altered gut microbiota composition and function. In support, exposing mice to high doses of urban PM causes oxidant-dependent GI epithelial cell death, disruption of tight junction proteins, intestinal inflammation, and increased GI permeability.


All the more reason to get away from a dirty environment, into a clean one.


If you want to learn more about how to improve gut health and how to eat correctly, check out the Alpha Energy Nutrition Course.

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