How to Create a Healthy Microbiome.

Bacteria may not build cities or have interesting social lives, but they will be here when the Sun explodes. This is their planet, and we are on it only because they allow us to be.” – Bill Bryson, A Short History of Everything.  

How do you create a healthy microbiome?

The bacteria within your body are absolutely crucial to your health and wellbeing. So, making lifestyle choices that will benefit and promote a healthy microbiota is a great way to reduce your risk of health complications. Whilst a ‘core’ group of bacteria is assumed to exist within all healthy people, the specific numbers and combinations of microbes that are ‘optimal’ for our health will be unique to each of us and our environments (for more information on this, Click Here).

This uniqueness can make it hard to define what a ‘normal’ or ‘healthy’ microbiome looks like. However, it is generally agreed that there are certain features that are associated with a health-promoting microbiome, including diversity, stability, resilience to disturbances, and ability to perform all of the important functions required. From the research that has been carried out thus far, we are now beginning to understand the effects that our daily choices have on the microbes within us. We have explored hundreds of microbiome studies and have outlined below several key lifestyle factors that are important for an optimal and functional microbiome. Happy reading!

1. Diet

The most obvious lifestyle factor that comes to everyone’s mind when considering microbiome health is diet. This connection is because the vast majority of your microbes are found in your gastrointestinal tract, predominantly in your large intestine (known as the gut)1. Therefore, it stands to reason that the food you ingest is going to have a marked influence on the health of your microbiome. There is now a huge (and growing) body of research that demonstrates how a change in diet can alter your gut microbiota and enrich beneficial bacteria in as little as 24 hours.2 

So, what does the science say? Well, the majority of diet-related microbiome studies have a common thread of plant-based whole-foods with lots of variety3-5, as being the most important factor for promoting gut microbiota diversity and health. In fact, one of the greatest predictors of gut health appears to be a variety of antioxidant-, phytonutrient- and fiber-rich foods.3-5 Plants provide the bulk of these. That’s not to say that you must follow a vegetarian or vegan diet, but it simply means that eating a wide variety of fruits and vegetables is key to good gut health.

In 2018, a huge study6 (the American Gut Project) found that people who consumed more than 30 different types of plants each week had a more diverse microbiome than people who consume 10 different plant types or fewer. Indicating that it’s not the quantity of plant-based food you eat, or whether you consume meat or not, but the number of different types of plants that you eat, which is most important. (We all know how easy it is to fall into a routine of consuming the same foods over and over!). Diets that are rich in a wide variety of whole, plant-based foods have therefore been implicated as the best option for improving microbiome health.

The ‘Mediterranean diet’ features fish, poultry, and eggs as protein sources, but is dominated with large amounts of fruits and vegetables, potatoes, whole grain cereals, beans, nuts and seeds, and uses olive oil as a primary fat source, with only modest amounts of red meat and cow-based dairy. When researchers compared the ‘Mediterranean diet’ to a conventional ‘low-fat diet’, the Mediterranean diet treatment group were both physiologically healthier and had a more diverse gut bacterial community, with more species associated with good health.7-10 The conferred benefits of the Mediterranean diet may also be due to the high polyphenolic content of the foods10-13. Foods high in polyphenols (such as purple potato cultivars, berries, nuts and red wine!) promote microbiome health and increase beneficial Bifidobacterium and Lactobacillus species, which provide anti-pathogenic and anti-inflammatory effects as well as cardiovascular protection10-13.

High-fibre intake is also acknowledged as a high-ranking factor in good gut health. Fibre (non-digestible carbohydrates, again found in plants) encourages the growth of species that ferment fibre into metabolites such as short-chain fatty acids (SCFAs)14-16. The positive health effects of SCFAs include improved immunity against pathogens, blood–brain barrier integrity, provision of energy substrates, and regulation of critical functions of the intestine. These non-digestible food components (fibre)14-16 are also commonly referred to as ‘prebiotics’.

And on a final note: people with higher microbial diversity in their gut, also tend to have greater resistance to microbial community changes when their diets are suddenly altered17, so having a more diverse gut microbiota means you’re less likely to suffer negative impacts to your health should you occasionally indulge in ‘less optimal’ foods! Yum.

2. Activity Levels

Usually, the association between activity levels and digestion is only considered in terms of movement and muscular contractions, increasing intestinal flow-through and bowel movements. But what is often overlooked is the association between the gut microbiome and the hormones released when we indulge in light to moderate physical activity. Hormones such as serotonin, norepinephrine, epinephrine, and dopamine are released when we exercise, and these hormones interact with the bacteria in our gut, influencing gut motility, nutrient absorption and the gut’s innate immune system.18 In 2009, researchers demonstrated that sedentary animals (mice) were less able to absorb essential nutrients from their food compared with active animals on the same diet,19 showing how staying active means so much more than burning calories!

But staying active to keep your microbiome healthy doesn’t have to mean devoting huge portions of your time to high-intensity, exhausting workouts! Scientists actually found that performing just three hours of ‘light exercise’ per week – such as a short brisk walk each day – significantly increased people’s levels of beneficial bacterial species. These beneficial species are associated with reduced obesity, improved metabolic functions, and also produce the fatty acid butyrate, which supports a healthy gut lining, preventing diseases such as inflammatory bowel disease!20

3. Time Outdoors

Being outdoors is not only proven to lower stress levels, increase immune system functioning, and improve sleep patterns, but spending more time outdoors amongst ‘natural’ materials (i.e. not man-made) is also correlated with a more diverse microbiome!21-22 Scientists have found that indoor environments have their own unique microbiome23, and as most modern humans spend 90% of their time indoors24, we are continually touching and exposed to “indoor” microbes. Indoor microbes living on plastic and metal surfaces have different functions to microbes which prefer living on biological materials (like us, animals, and plants etc). They may instead have an affinity for metabolising plastic derived materials, rather than providing us with beneficial functions. Man-made materials are also more likely to have pathogens on them due to the high-touch nature of these surfaces (e.g. door handles, kettle handles), and may also contain harmful compounds which have been shown to impact gut microbiomes.25
If you (like most of the population) find yourself locked away at an office desk, don’t despair. A study in 2016 found that even short-term contact with nature-based materials, such as soils and plants, immediately changed bacterial diversity on human skin22. So much so that the authors proposed that nature-based materials might be developed as effective treatments for skin and immune disorders! Our immune system requires regular physical contact with ‘dirt’ (soils, etc) to develop optimally, for example animals (mice) raised on soil floorings had a higher level of anti-inflammatory signalling, reduced incidence of allergic responses, and a marked difference the composition of the gut microbiota,26 compared with animals raised in clean environments. People who are in regular contact with animals also have a more functional microbiome and immune systems.27-30 Studies comparing people living on traditional farms against those living on modern mechanised farms (with little animal contact), found that people in close physical contact with barnyard animals were significantly less likely to suffer from allergies, asthma, skin disorders, and other immune-related issues.27 Having household pets also lowers risk of allergies, asthma, and other autoimmune conditions in children, and dogs in particular increased the levels of 56 different classes of bacteria in the home!31

4. Stress

The gut and the brain are connected; how else would we ‘feel’ hunger, causing us to ‘go find food’. But further than just the basic ‘hangry’ feelings we sometimes have, the brain and gut also communicate on a much more detailed level. We now know that the same cells which form the brain also form the Enteric Nervous System (ENS) of the gut. The ENS spans the length of the gastrointestinal tract and connects the brain and gut. Hormones, generated and promoted in the gut, send signals to the brain via both the bloodstream and the ENS (known as the gut-brain axis) and vice versa.32 Research suggests that stress not only alters intestinal mucosal permeability and cytokine secretion (inflammation),33-34 but stress may also significantly change the community structure and activity of the commensal microbiota in the gut.35-36 In turn, considering the bidirectional interaction of the gut-brain axis, gut microbiota can potentially influence stress-related physiologic responses.37-38

Demonstrating the theory that behavioural states can be altered by changing the gut microbiome, mice displaying anti-social behaviours were found to be deficient in a specific strain of bacteria (Lactobacillus reuteri), and when supplemented with L. reuteri, the anti-social behaviour disappeared.39 Yet when the main nerve connection between the gut and the brain was cut prior to L. reuteri supplementation, the anti-social behaviour remained, indicating a nerve-dependant mechanism in bacterial communication with the brain.40 Stressed individuals also often have gut health issues or autoimmune-related conditions such as psoriasis indicating a potential relationship between stress and the gut41. I’m sure we can all recall a time when you have been extremely stressed or nervous and felt ‘butterflies’ in your gut! This is the brain-gut connection. Elucidating how stress hormones interact with the microbiome and then induce other health conditions as a knock-on effect is a relatively new area of science, and it has sparked the concept of ‘psychobiotics’: using bacterial supplementation with the intent of amending mental states.

5. Sleep

Sleep is another really important factor for microbiome health. It is unknown whether lack of quality sleep affects the microbiome, or if it is the other way around (a disturbed microbiome affects sleep), or both! Researchers found that when sleep apnoea was induced in mice their microbiome was significantly altered, but when the microbiome of the sleep apnoea-induced mice was transferred to other mice, the receiver mice began to suffer from disturbed sleep.42 Indicating that it is likely to be a two-way street. A further study also found that mice with microbiomes disrupted by a strong course of antibiotics, experienced disrupted sleep cycles, and depleted serotonin levels,43 with the team observing sleep performance using machines that monitor brain activity.

Another compelling study showed that when gut microbiota from jet-lagged humans was transferred into mice, the mice developed obesity and glucose intolerance, an effect that was not observed when microbiota was transferred from non jet-lagged humans!44 Therefore, aiming for 7-8 hours of high-quality sleep per night is a good place to start! So, sticking to a ‘bedtime routine’ as much as possible, having a defined ‘wind down’ time before bed, and switching off those screens is a simple lifestyle change that can have enormous impacts on your microbiome.

6. Consuming known beneficial bacterial strains.

What are the benefits of ingesting live bacteria? Well, a growing body of scientific evidence shows that bacterial therapy can help with several health conditions and illnesses, such as treating gastrointestinal illnesses, reducing the severity of allergies in children, decreasing the severity of respiratory infections, and treating vaginal and urinary infections in women, amongst others. Some Lactobacillus strains can shorten the course of infectious diarrhea as well as the frequency of diarrheal episodes.46 They can also reduce antibiotic-associated diarrhea by 60%, when compared with a placebo.47 Live bacterial supplementation also slows routine "gut transit time" by 12.4 hours, and increases the number of weekly bowel movements in constipated people by 1.3, as well as helps soften stools.48 Several small clinical studies have shown that bacterial therapy may also help people with Inflammatory bowel disease, with certain strains maintaining remission of ulcerative colitis and preventing relapse of the disease.49 
Other positive effects of live bacteria ingestion include preventing and reducing the severity of respiratory infections. Such as, reduction in the duration of episodes of common cold of at least 2 days and a decrease in the severity of symptoms compared to the randomised placebo-control group.50 Live bacterial therapy also improved antibody responses to influenza vaccination51 and reduced incidence of respiratory infections in individuals over 70 years.52 Last but not least, oral and topical administration of Lactobacilli may also help in the treatment of bacterial vaginosis,53 psoriosis54, and eczema and asthma.55-56
It is important to note, however, that different strains of the bacteria will have different effects and not all bacterial therapies are the same. For example, one strain may fight against cavity-causing organisms in our mouths and therefore do not need to survive a trip through our acidic stomachs to our guts! Whereas others will have adequate defences to ensure survival through or within highly acidic environments such as the stomach or the moderately acidic vagina; but may be unable to confer benefits due to other issues such as short intestinal transit times or due to the presence of other competing bacterial strains already within the body.
The field of live bacteria as medicine is still in its early stages and some strains are more ‘proven’ than others. To prove a bacteria’s efficacy, singular or specific strains must be tested at a specific dose, against specific health conditions to determine therapeutic benefits. Only when multiple, well-designed human clinical trials have been performed, can real health claims be provided. It is also necessary to remember that multiple strains combined will not necessarily provide greater benefit than that of a singular strain, and perhaps even negative cross-effects could occur when multiple strains are used in the one product. Hence why specific strains must be tested singularly and at specific doses, or at least in a modest combination number, as determining which strains are associated with health benefits would otherwise be impossible.


A balanced and varied diet containing a rich amount of whole, plant-based foods, light to modest daily activity levels, regular and restful sleep patterns, low stress levels, and increased physical contact with nature, as well as adding beneficial bacteria to your daily routine, are relatively easy daily steps you can take to improve your microbiome health! If you have any questions, don’t hesitate to message us or comment on our social media pages. You can find us on Instagram and Facebook @biomiq.




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