Gut Health and Mood (Part 2): More on the Microbiome
- Esther Parker
- Feb 20
- 5 min read

We often think of bacteria as harmful invaders, the cause of infections, the nasty things that make us unwell. But the trillions of microbes in our gut are actually vital to our health. The bacteria in and on our bodies actually outnumber us in the trillions to one. Even if we take into account the trillions of our own cells, the essential symbiotic relationship they have with our 'own' cells makes them essential to our survival.
So, in part one I talked about the gut microbiome, but now I want to go a little deeper. This is for those who read that post already, or who may have already done a bunch of reading on this topic. It is obviously a very large area of science, which is still developing, but I want to focus on what we know about the microbiome as it specifically relates to brain health. In particular, how our microbiome affects neurotransmitters like serotonin, dopamine, and GABA, which play essential roles in mood regulation.
The Gut Microbiome and the Brain
Just a reminder, the gut and brain are connected through the gut-brain axis, a bidirectional communication system that involves the nervous system, hormones, and immune pathways. This connection means that changes in gut bacteria can directly impact mood, stress levels, and even conditions like anxiety and depression.
Certain gut bacteria help produce and regulate neurotransmitters, influencing how we feel. When the balance of these microbes is disturbed—through poor diet, stress, or antibiotics—it can lead to mental health issues.
IMPORTANT: For those who didn't endure physiology at school, it is important to explain WHERE the bacteria are in 'the gut'. When we're talking about the gut microbiome, we mean the COLON, so that last part of your digestive system.
Mini anatomy lesson - your digestive system is essentially one tube from your mouth to your anus and goes like this; mouth, down the oesophagus, into the stomach, into the small intestine, past the appendix which you may or may not have any more, then into the colon/large intestine/bowel or whatever term you feel most comfortable with. The microbiome that I'm talking about needs to be in the colon. When you have bacteria in the small intestine or elsewhere, it can cause digestive issues like bloating, pain and inflammation.
With all things microbiome, I want to make one thing very clear - it's all about BALANCE. Below, I will detail a few strains that are crucial to brain health, but that does NOT mean you go out today and buy them all in a probiotic and devour the bottle. Gut health (like many things) requires good levels in concert with others - it's not just the abundance of one, as this over-dosing could throw off levels of other important bacteria. So, as always, do your research and if you're interested in specific supplementing, speak to a health professional who knows about bacteria (aka, we love our GPs, but it probably won't be them in this instance).
Ok, back to the program.
Key Gut Bacteria Involved in Mood Regulation
1. Lactobacillus and Bifidobacterium: The Serotonin Boosters
We gotta start here. Why? Becuase Lactobacillus and Bifidobacterium species make up the largest amount of bacteria in human colons. If these are out of balance, or low, then your ability to make an appropriate amount of neurotransmitters will be impeded.
Serotonin, often called the ‘happiness hormone,’ is a neurotransmitter that regulates mood, sleep, and overall well-being. Approximately 90% of serotonin is produced in the gut, with bacteria playing a crucial role. WOW. Ok, hold your horses. That doesn't mean that all that serotonin goes straight into your brain. A large amount of this serotonin is intestinal health and peripheral metabolism (gut movement), but it does activate nerve endings that are connected directly to the central nervous system (read more here).
There are a multitude of lacto and bifido species in our colons. I will list a few of the main ones here:
Lactobacillus rhamnosus has been shown to reduce anxiety-like behaviour in animal studies by influencing GABA, a calming neurotransmitter.
Bifidobacterium longum helps to regulate the hypothalamic-pituitary-adrenal (HPA) axis, which controls the body’s response to stress. Supplementing with B. longum has been linked to lower cortisol levels and improved mood.
Lactobacillus helveticus has been associated with reduced symptoms of anxiety and depression, particularly when combined with Bifidobacterium strains.
Bifidobacterium breve may improve mood and sleep in participants with high anxiety levels and alter the gut environment by increasing pipecolic acid levels (a GABA-like substance).
Lactobacillus delbrukii has been shown to reduce depression-like behaviour in mice.
2. Faecalibacterium prausnitzii: The Anti-Inflammatory Ally
An inflamed gut is not a happy one - for the body or the brain. Inflammation has been increasingly linked to depression, and Faecalibacterium prausnitzii is one of the most powerful anti-inflammatory bacteria in the gut. It produces butyrate, a short-chain fatty acid that strengthens the gut barrier and reduces inflammation, which may help prevent mood disorders.
Studies have found that people with depression often have lower levels of F. prausnitzii, suggesting that promoting its growth could be beneficial for mental health.
3. Akkermansia muciniphila: The Gut Lining Protector
Akkermansia muciniphila plays a crucial role in maintaining gut integrity. A strong gut barrier prevents leaky gut, a condition where harmful molecules enter the bloodstream and trigger inflammation, which has been linked to depression and anxiety. It's also important for immunity, but that's a story for another day.
The takeaway here is that gut lining integrity is linked with your brain health. Think of all the things that your gut is exposed to - various foods, environmental toxins, alcohol, plastics, metals, medications etc - and now imagine if your gut was so unprotected that it let just about anything through to your bloodstream. Problematic! Gut lining and protection is a key area to reducing inflammation, and in turn, supporting immunity and mood.
4. Prevotella: The Double-Edged Sword
Prevotella or Paraprevotella species have been found in both high and low levels in individuals with depression, suggesting they play a complex role. Mostly, research has seen a correlation with high levels and depressive disorders. Back to an earlier comment about BALANCE. The way to support healthy levels of a bacteria like Prevotella, may not be to wipe it out (or supplement excessively with it), but rather to ensure balance of all your bacteria.
The impact of Prevotella (and all species) on mental health depends on overall microbiome balance.
The connection between gut bacteria and mental health is undeniable. Specific microbes, such as Lactobacillus, Bifidobacterium, and Faecalibacterium prausnitzii, play essential roles in neurotransmitter production, stress regulation, and inflammation control. By understanding the role of these bacteria, we gain deeper insight into how the gut microbiome shapes our mental well-being.
I look forward to continuing this short series, so that everyone can learn about the amazing world of their own gut microbiome.
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