12 Powerful Ways to Improve Your Microbiome

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Following on from the first microbiome post presented last week here is exactly how the microbiota may impact your health and how to improve your microbiome.

Microbiota and your health

The composition of your microbiome has wide-ranging physiological implications: it can affect the growth and blood supply of your cells, regulate endocrine functions in the intestine, nervous system messaging, bone density, provide 5-10% of your energy needs, help the body produce many necessary compounds such as  vitamins and neurotransmitters, process bile salts, interact with some drugs, and help the body detox.

There is also increasing evidence of a LINK of the changing microbiome to over 25 conditions prevalent today. Let’s be clear, there is a lack of data that shows that the altered microbiome CAUSES any of these. In the absence of high-quality human evidence, animal (eg: mice) studies and lab-based studies are the best we can do. Practically speaking, it is simply easier to remove extraneous factors which may influence results in mice and petri dishes than in human studies. However, the microbial communities inhabiting humans and mice are very different. Thus, these results probably don’t accurately represent what you could expect for yourself. Instead, they are a guide for future research and an indication of potential.

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Looking across societies, we can see the changing microbiome is associated with four main consequences: antibiotic resistance, developmental diseases, middle-life illnesses, and epidemics.

  • Antibiotic resistance
    There benefits of antibiotics are obvious- eg: recovery from infection, and possibly increased growth (Studies on farm animals has shown that antibiotic use in early life leads to increased growth… It is thought that antibiotics promote the microbes that consume less of the hosts’ food, leaving more energy for them).
    However, beneficial bacteria are often knocked out, while the antibiotic resistant bacteria which survive are often harmful.
  • Developmental diseases
    There is an association between changes in children’s microbiota and diseases such as childhood obesity,  inflammatory bowel diseases, and changes in the immune system development which are linked to asthma and food allergies.
    Again, we don’t know if the microbial changes we’ve seen cause the disease/s, the disease/s cause microbiome changes, or other factors affect both.
    One example of a POSSIBLE microbiota contribution to obesity is through losses of the bacteria H. pylori. It has been eradicated in many children. On the plus side, this reduces the risk of infection developing into ulcers or even cancers of the digestive tract. On the other hand, H. pylori can also regulate the hormone ghrelin, which is involved in appetite and energy homeostasis.

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  • Middle age illnesses:
    It is believed that lifestyle and environment factors contribute to diseases via changes in  microbiome composition. At the very least, we have identfied certain microbiome compositions that are linked to several disease, such as atherosclerosis, cancer, behavioural, inflammatory and metabolic diseases.
    A specific example is the decreased prevalence of a bacteria that processes oxalate (Oxalobacter formigenes) in people. Meanwhile, we have seen increasing numbers of people suffer with kidney stones, 80% of which are composed of calcium oxalate. So, it is thought that the loss of this bacteria may contribute.
    Although as yet unproven, it is suspected microbiota changes are related to the surge in immunological conditions such as lupus.
  • Epidemics
    Gut microbiota influence the immune response to infections and protect against excess growth of pathogenic microbes.  At the population level, weakened immune defences could increase risk of epidemics.

How to improve your microbiome

Assuming that anyone who is reading this is neither in-utero nor deciding whether to suck on a bottle full of formula or a teat, there are still some factors you don’t have control of which affect your microbiome  Eg: sex, age, genetics and some health considerations. The role of genes is small but not to be sneezed at. For example, certain genes have been found to be associated with the presence of specific bacterial families such as Christensenellaceae. This family, along with other bacteria, is associated with leanness and healthy metabolism. Genes also play a role in shaping your immune system, which then effects your microbiome.

There are many other factors which you (or others) can have some level of control over. Some means of improving your microbiota may be:

1. Prebiotics or broad agents like fibre.

These dietary components support good bacterial growth and can have positive impacts on certain conditions, but their effect on the whole microbiome has not been fully elucidated.

2. Probiotics.

Eg: the famous yakult. These may introduce a specific healthy bacteria to your system, but it won’t necessarily improve the health of your microbiome overall. Also, the probiotic may not remain in your gut for a long time. The specific characteristics of your existing microbiome affects how well the introduced probiotic thrives. Further understanding of how to provide the environments necessary to support probiotic growth, and of what mixtures of microbes can contribute to this, may make probiotics more beneficial for all.

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Gut microbes have a role in digestion, so it is doubtless that they are affected by the food they are exposed to, including food additives such as emulsifiers and artificial sweeteners. However, in some cross-sectional studies diet actually contributed to <10% of variation in microbiome once confounding factors were taken care of. Further studies on this topic with different methodologies are warranted to clarify and provide more precise and long-term data.

3. Dietary changes.

Radical changes such as switching from a very meat-based to a plant based diet, or energy restriction, seem to produce the most significant shifts. In the short term, meat consumption leads to more active bile-metabolising microbes, which has elsewhere been associated with inflammatory bowel disease. On the other hand, eating more vegetables can increase the presence of plant polysaccharide-fermenting (helpful) microbes.

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On the other hand, because most of us generally consume varied diets, it is thought that minor changes to our eating habits could only lead to relatively small microbiome changes. There are few studies examining the impact of these smaller, specific, measured changes.

4. Medical restoratives

In some cases, these may be appropriate for those with a deficient microbiome, or who have a relevant condition or risk factor/s. Restoratives include faecal transplants and targeted treatments for specific microbes (still in the early development phase). Faecal transplants are exactly what they sound like: while it may not be an appealing idea, the transplant can introduce a harmonious community of beneficial microbes to the gut that needs them. We have an incomplete understanding of how the introduced microbes interact with the existing microbiomes, or HOW the transplants work at the cellular level.

Further, the benefits of faecal transplants are not universal: they have benefiited approximately 90% of patients suffering recurrent, antibiotic resistant Clostridium difficile infection (RCDI) conditions (which cause severe diarrhoea). Similar success has not been seen in cases of metabolic syndrome and ulcerative colitis (an inflammatory bowel condition), despite being associated with a deficient microbiome.

In rare cases, faecal transplants have led to harm. There’s the risk of transferring infections or unidentified ‘bad’ bacteria. The truth is we do not even know the mechanism or factors that have led to reported cases of harm, so the prospect of screening and controlling for risk is tricky at best.

5. Maintain a healthy lifestyle.

Eg: look at your smoking, alcohol, physical activity habits, trying to avoid obesity. These old culprits may affect your microbiome, too.

Other factors you that may affect your microbiome for better or worse include:

6. Medical interventions.

For example, bowel cleansing may quickly improve the overall bacterial composition. However, some specific microbes may also be lost. Surgery on the stomach also affects the microbiota and medically-induced iso-osmotic diarrhea will cause temporary alterations

7. Antibiotics.

Antibiotics kill or cripple microbes (both the composition and activity of the microbiota are key to health). When narrow-spectrum antibiotics are prescribed, they may target fewer species and have a less pronounced effect on the microbial community as a whole. However, use narrow-spectrum antibiotics successfully more accurate diagnosis is required. More general antibiotics are easier to prescribe but lead to wider-reaching losses. Some beneficial bacterial populations may not even make a complete recovery.

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8. Other medications

9. Circadian rhythms*

(not strictly controllable, but lifestyle factors can cause shifts)

10. Environmental microbe exposure and infections*

(again not always controllable)

11. Stool consistency

(can be affected by lifestyle factors, such as diet, activity and stress)

12. Environmental impacts.

These need further investigation

Hold your halophilus

You should not expect a total transformation in your health by improving your microbiome- evidence suggests that external factors appear to be linked to moderate changes in the range of 10-15%. It’s also worth keeping in mind that these changes can also have other impacts on health- for example, improving your dietary intake could exert benefits independently of its effect on the microbiome.

Furthermore, if two people make an identical change, the effect on their microbiome will likely differ. We are not able to accurately predict how your microbiome will respond, in regards to the diversity, strength or direction of any changes. Professionals may have more success in predicting effects on individual bacterial populations than the whole microbiome.

While we are making progress in our knowledge, as yet our understanding of the whole human microbiome, the interactions between its constituents and outside factors, and the variations in species is incomplete. There are mysteries that need to be solved. Thus it would be reckless to freely adopt any practice aimed at changing it. For example, you may have heard of the food poisonings which occur due to E. coli. Yet, some strains are beneficial. We don’t know about a number of other microbiome constituents and variations.

The research also has a number of other weaknesses that needs to be addressed. For instance, we know comparably little of microbes away from the gut (eg: the skin)- even when they’ve been associated with conditions. Most of our knowledge is of bacteria, but other microbes such as fungi, archeae, viruses, and eukaryotes with the digestive tract have a (quite unexplored) interacting role. There’s also some technical difficulties in assessing microbiome: several instruments used produce own biased results, and many bacteria have multiple copies of a specific unit (16S rRNA) in their genome, which makes it difficult to accurately count how many of them are.

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The Microbiome Verdict

All this goes to show that while there’s an impressive body of evidence suggesting the impaired microbiota of modern man in developed nations is linked to many prevalent health problems, we’ve some way to go to prove a clear cause-effect relationship… and to identify the intricacies involved.

In the face of this, we cannot make specific prescriptions for you to improve your health via your microbiota. Consuming plenty of plant-based foods, prebiotics and fibre seem the best bet for the average person, as this would support healthy bacteria. Consuming probiotics may help, but it may not provide a microbe you’re deficient in; even if it does, the microbe would not necessarily be integrated into your particular microbiome.

Beyond these fundamental measures, knowing how to improve your microbiome can prove tricky and is beyond the scope of this article. This is particularly true if you’ve been diagnosed with a bacterial imbalance such as SIBO. That’s why our friends at The SIBO Doctor have created educational resources such as The SIBO Success Plan.

This program is led by Naturopathic Dr Nirala Jacobi, a world-leader in gut health and SIBO. Over the course of 8 lessons, you’ll become empowered with all the tools you need to finally understand and overcome your SIBO. The SIBO Doctor also offers comprehensive training for health practitioners.

Other lifestyle factors which recurrently pop up in health recommendations (smoking, alcohol, physical activity) may play a role, so  it’s worth optimising these now as preventative measures rather than waiting for the perfect supplement or treatment. There is potential for medical restoratives to help people with specific requirements, and further research may help to ensure they are both safe and individualised for maximum benefit.

More information on the microbiome in part one.

What could you do to improve your gut health? Comment below.
  • Blaser, M.J. (2018). The Past and Future Biology of the Human Microbiome in an Age of Extinctions. Cell. 2018 Mar 8;172(6):1173-1177. doi: 10.1016/j.cell.2018.02.040.
  • de Vos, W.M., and de Vos, E.A.J. (2012) Role of the intestinal microbiome in health and disease: from correlation to causation. Nutrition Reviews. 70(Suppl. 1):S45–S56, doi:10.1111/j.1753-4887.2012.00505.x
  • Lynch, S.V., and Pedersen, O.(2016). The Human Intestinal Microbiome in Health and Disease. N Engl J Med 375:2369-79. DOI: 10.1056/NEJMra1600266
  • Schmidt, T.B.S., Raes, J., Bork, P. (2018). The Human Gut Microbiome: From Association to Modulation. Cell, 172 (6), 1198-1215. https://doi.org/10.1016/j.cell.2018.02.044.



I’m the co-founder of Evidently Healthy, the resident biohacker and a marketer’s dream. As someone who believes you can’t put a price on health. I’m passionate about improving lifespan and health span. In my spare time I enjoy traveling, snowboarding, diving, podcasts, exercise and eating in and out. #Coffee-Lover Rating global coffee bean for years..

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