The Microbiome and Trusting Your Gut

by | Nov 21, 2021 |

From butterflies in the tummy to gut-wrenching pain, most of us at some point in our lives have experienced feelings associated with the gut. Sometimes we even have the ability to immediately understand a situation without having to think it over, of just knowing; a feeling to which we have ascribed the saying ‘go with your gut’.

More commonly associated with food and digestion, the gut may also play a role in the way we think, behave and make decisions. How you feel, your mood, and your general health may be affected by the microbes dwelling in your gut.

Responsible for producing neurotransmitters, the gut microbiome’s ability to impact emotions and mood is one of the reasons why it is considered to be the ‘second brain’. Playing more of a role in brain function than previously thought, a disturbed microbiota may therefore affect your ability to think clearly, potentially impacting your ability to trust your gut.

The following will discuss the relationship between microbes and the brain as well as ways to improve gut health, which may contribute to better decision-making.

How do microbes impact how we think and feel?

Studies have shown there exist pathways between the brain and the gut collectively referred to as the gut-brain axis (8). Connected via hormonal, neural and immune pathways, the transfer of information between the gut and the brain is bidirectional.

Microbes play a key role in the gut-brain axis, influencing the brain through hormones, immune molecules and the specialised metabolites that they produce.

An example of how microbes can influence our behaviour is their role in neurotransmitter production. Microbes have the ability to produce a number of different neurotransmitters (the chemical messengers of the body) that are identical to those produced by humans (6). They can, therefore, directly alter neurotransmitter levels in the body (3), enabling them to communicate with neurons and influence brain activity.

Microbial influence on neurotransmitter levels has been demonstrated in germ-free mice who have significantly less serotonin in their blood than normal mice. Studies have shown that serotonin levels in germ-free mice could be restored by introducing spore-forming bacteria to their guts. Conversely, mice with natural microbiota, when given antibiotics, exhibited reduced serotonin production (4). This shows that gut microbiota are influencing neurotransmitters in the host.

Changes in the composition of the microbes living in the gut can change the types and levels of neurotransmitters being produced, impacting mood, pain tolerance and behaviour (1). Interestingly, dysfunction of the microbiome has been implicated in a number of neurological disorders such as depression and anxiety (2), conditions which have been shown to impair information processing and decision making.

Can the microbiome affect our ability to trust our gut?

Our ability to trust our gut and therefore make good decisions relies in part on the functioning of our microbiome.

In a healthy microbiome, our microbes work optimally with other bodily processes to help fuel good decision-making. For example, key neurotransmitters such as serotonin, 90% of which is produced in the gut, play an important role in decision making (5). However, when a reduction in microbial diversity and/or an imbalance between beneficial and harmful microbial populations occurs, our ability to trust our gut may be compromised and suboptimal decision making could ensue.

How can we improve our ability to trust our gut?

If it turns out that having a healthy gut is a factor in good decision-making, it would be prudent to suggest that we optimise for a healthy microbiome. Good gut health, according to research, can be achieved via the following approaches:


Probiotics are the type of live bacteria and yeasts we want residing in our body; they have positive benefits for our health. These microorganisms can be introduced in the form of supplements and fermented foods such as yoghurt, sauerkraut and kefir. Whilst it’s not fully understood how they work, it’s believed probiotics can help those who require them by replacing “good” bacteria when they’re lost (such as is the case when we take antibiotics), and helping to restore balance when dysbiosis occurs.

Lots of research has been carried out about the benefits of probiotics on human health including how they help alleviate mental health conditions and chronic diseases such as IBS, Crohn’s and migraine.

Each strain of probiotic has its own unique properties and thus contributes different health benefits; something to be mindful of when selecting a probiotic.

Whilst experts aren’t yet able to make recommendations on which specific probiotics can improve a particular health condition, it’s an exciting area of research with a promising outlook for future disease treatment and management.


The influence of diet on the microbiome and its implication for health is well documented (7). Eating the right food is a way to not only achieve good gut health, but desired moods and behaviours also.

Neurotransmitter production, for example, is dependent on specific proteins, vitamins and minerals. We acquire these nutrients either directly from food itself or as the byproducts of microbial metabolism. Feeding our microbes a nourishing diet (think fibre) provides them the energy and necessary materials to do their job, so we in turn can do ours; i.e decision making.

It’s important to note however, that just like fingerprints, each microbiome is unique. A specific diet that works for one person, may not work for another, hence the need for a tailored approach when it comes to using diet as a treatment for health conditions.

Fecal transplant

A fecal microbiota transplant (FMT) is when feces from a donor with a healthy microbiome are transplanted into another person in order to restore the balance of bacteria in their gut. Whilst a stomach-churning concept, inserting poo from a healthy person into a patient suffering from a serious illness, such as an antibiotic-resistant C. difficile (5), can be the difference between life and death.

For those people whom probiotics are unsuccessful at restoring gut or brain health, FMT may offer a life-changing alternative. FMT is yet to be approved by the FDA, however, clinical trials are showing promising results; poo pills may not be too far away!


For many, trusting their gut serves them well. The ability to think unencumbered and with clarity allows instinct to prevail. And it’s this feeling which can be a driving force behind good decision making. Thanks to research surrounding the gut-brain axis, we know how important a role microbes play in mental health. If it turns out that having genuine access to good instincts lies in the hands of microbes, taking care of your gut could be the best decision you ever make.

Brigid xx


(1) Borre YE, Moloney RD, Clarke G, Dinan TG, Cryan JF. The impact of microbiota on brain and behavior: mechanisms & therapeutic potential. Adv Exp Med Biol. 2014;817:373-403. doi: 10.1007/978-1-4939-0897-4_17. PMID: 24997043.

(2) Clapp, Megan et al. “Gut microbiota’s effect on mental health: The gut-brain axis.” Clinics and practice vol. 7,4 987. 15 Sep. 2017, doi:10.4081/cp.2017.987

(3) Smith, Peter. “The tantalizing links between gut microbes and the brain.” Nature news, Springer Nature, Oct 14, 2015,

(4) Yano, Jessica M et al. “Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis.” Cell, vol. 161, no. 2, 2015, pp. 264-276,

(5) Sarmiento Rivera L.F., Gouveia A. (2021) Neurotransmitters and Hormones in Human Decision-Making. In: Gargiulo P.Á., Mesones Arroyo H.L. (eds) Psychiatry and Neuroscience Update. Springer, Cham.

(6) Galland, Leo. “The gut microbiome and the brain.” Journal of medicinal food vol. 17,12 (2014): 1261-72. doi:10.1089/jmf.2014.7000

(7) Singh, Rasnik K et al. “Influence of diet on the gut microbiome and implications for human health.” Journal of translational medicine vol. 15,1 73. 8 Apr. 2017, doi:10.1186/s12967-017-1175-y

(8) Clapp, Megan et al. “Gut microbiota’s effect on mental health: The gut-brain axis.” Clinics and practice vol. 7,4 987. 15 Sep. 2017, doi:10.4081/cp.2017.987

DISCLAIMER: This article is for informational purposes only. It is not intended to constitute or be a substitute for professional medical advice, diagnosis, or treatment. 


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