Are We Slaves to Our Bacteria? Rewriting the Gut-Brain Connection – Part 2
- Jun 1
- 7 min read
Honor Tremain is an award-winning longevity nutritionist, author, and journalist whose journey into nutrition began with a personal health crisis. Determined to reclaim her life, she completed qualifications in nutrition, eventually healing herself and going on to complete a Bachelor of Science degree.
Are humans really the bound, individual selves we take ourselves to be? Until recently, it seemed obvious we were, but now that is all being questioned. The classic biological explanation of self has often been defined as one’s brain, immune system, and genetic material. However, that is being challenged by the newest discoveries on the microbiome.
As we saw in Part 1, evidence shows our microbes and their collective genetic material, known as the microbiome, can orchestrate our immune system, influence the brain, and carry out thousands more genetic functions than our own genome can. The realization that humans are not, in fact, individual, private entities, but rather a cohesive interaction with another species living within us, has consequences beyond the biological disciplines.
One of the biggest scientific questions raised at this point could be: Who are we? A deeply complex question. One I’ll leave you to ponder. But what I can explore today is: Who is actually in charge, us or them? If our gut can shape our minds, can we take control and reshape our gut and minds too?
Brief biological overview
Humans are made up of about 30 trillion human cells, along with roughly 38 trillion non-human microbial cells. The microbial genes, often collectively called the microbiome, outnumber our own human genome by 100 to 1 and roughly weigh the same amount as our brain does.
Basically, you are superhuman, carrying a larger non-human genetic counterpart of yourself that science has now discovered has 1,000 times more genetic expression variability and capabilities than your human self does. It also has abilities to hack into our own biochemical messaging systems and communicate, reset commands, and give new instructions via your hormones, nervous system, metabolites, and brain. This raises the very real question: Are we simply the body carrying around this super alien collective that alters us to feed them what they want, think how they tell us to, and design our immune system to suit them?
So, now that we understand the microbiome plays a massive role in our body and in mental health, one that can be either extremely beneficial or detrimental, here’s the empowering part: it’s not fixed.
Unlike your human genome, your microbiome is more expansive and adaptable, constantly responding and changing according to your environment, lifestyle, and the food you eat.
Research has shown how influential your microbiome is over your stress responses, emotional regulation, memory and learning, social behaviour, mental health, anxiety, and depression.
It goes both ways. While “good bacteria” are recognised as being able to treat and possibly reverse these disorders, disruptions in gut bacteria, known as dysbiosis, or swings that proliferate what is collectively termed “bad bacteria,” can fuel more depression, anxiety disorders, autism spectrum disorders, schizophrenia, and neurodegenerative diseases.
The connection is so strong between the microbiome and mental health that scientists recently coined the term “psychobiotics,” meaning beneficial bacteria that positively impact mental health and are already being used alongside antipsychotics, antidepressants, and other good mental health treatment plans.
So why is there still so much mental illness? Something is damaging the gut-brain
Several modern factors are disrupting our microbial balance and swinging it over to the “dark side.”
Processed foods: Highly processed diets feed bad bacteria due to a lack of fibre, which is crucial fuel for growing beneficial bacteria. They also contain excess sugar and unhealthy fats, which disrupt healthy gut environments, along with multiple synthetic additives, preservatives, and chemicals that can harm good bacteria and human cells. These foods don’t nourish a microbiome, they starve the good guys and feed the harmful ones.
Omega-3 deficiency: Did you know that omega-3 is an essential nutrient? Yet, up to 85% of people don’t have enough. Modern diets have shifted dramatically away from a balanced omega-3 intake and swung toward omega-6 fats, creating a ratio linked to higher inflammation and chronic disease.
Gluten sensitivity, NCGS: Non-coeliac gluten sensitivity can be harder to detect than coeliac disease, yet it affects people just as much, but in a completely different sphere: the mind and mood. Gluten can affect neurological function, alter mood and behaviour, and trigger inflammation. Removing gluten in sensitive individuals has been shown to improve symptoms in conditions such as ADHD, autism, anxiety, and depression.
Sedentary lifestyle: Exercise isn’t just for muscles. It directly impacts gut diversity, stress resilience, and mental health. Active individuals consistently show better psychological outcomes than those who are not.
We’re too sterile: The hygiene hypothesis suggests that your body evolved in partnership with your microbes, not in isolation from them. Disruptions at an early age can be damaging and may happen due to antibiotic use by the mother or baby, a lack of microbial exposure via C-section births, avoidance of breastfeeding, not playing outside in dirt as a child, and using too many antibacterial products on oneself or in the home.
These all have long-term consequences and could partly contribute to the reasons why there are increased learning difficulties, mental health issues, and allergic reactions in upcoming generations.
The inflammation connection
One of the strongest links between the gut and mental health is inflammation. Chronic low-grade inflammation is highly associated with depression, anxiety, and cognitive decline. Gut dysbiosis can increase intestinal permeability, often referred to as “leaky gut,” trigger immune responses, release inflammatory cytokines, and set up a self-perpetuating cycle between more inflammation, more leaky gut, and even more inflammation. These inflammatory signals reach the brain and alter mood, behaviour, and cognition.
How food is involved
We’re in a time when food should be viewed beyond the basic scope of simple calories, fats, carbs, proteins, vitamins, and minerals, and valued as biochemical messages too. Everything you eat sends signals through your microbiome, which then responds.
How to rebalance your inner ecosystem
Fibre, fibre, fibre. Eat more vegetables, especially raw and fibrous kinds such as celery, apples, cabbage, and carrot sticks. Include fruits such as berries, apples, and pomegranate, as well as legumes, lentils, pulses, and whole grains such as brown rice, quinoa, amaranth, and buckwheat.
These act as prebiotics, which means they feed the good microbes, helping them stay alive and grow in you. These good guys then produce more short-chain fatty acids, also known as SCFAs.
Why we like SCFAs
Short-chain fatty acids, such as butyrate, acetate, and propionate, are some of the gut microbiome’s most influential metabolites. They play crucial roles in preserving intestinal wall integrity, therefore helping to prevent leaky gut, supporting immune development, regulating cell growth, and supplying energy to the body.
Very importantly, SCFAs also exert powerful anti-inflammatory effects by suppressing common inflammatory signalling pathways, such as NF kB, and reducing all pro-inflammatory gene expression within the body. This is valuable indeed when most chronic diseases are linked to inflammation.
Support anti-inflammation
Foods that reduce inflammation through their antioxidant potential or by boosting microbiome function include organic green tea, handmade dark roasted coffee, dark chocolate with 70% cacao or higher, and antioxidant-rich plant foods and spices such as berries, turmeric, ginger, red onions, purple carrots, and pomegranate.
Omega-3 fatty acids lower inflammation and help the good gut microflora function in mega boosted ways. Microalgae, such as Nannochloropsis oceanica, are particularly promising and super high in bioavailable forms of EPA and ALA omega-3.
These omega-3s, in turn, increase the abundance of short-chain fatty acid-producing bacteria, which we like. Other helpful omega-3 foods include fatty fish, sardines, flax seeds, and chia seeds.
Apple cider vinegar and other good-quality vinegars mimic the beneficial effects of the good gut bacteria’s SCFAs, which lower inflammation and provide us with energy.
Introduce beneficial bacteria
Probiotics introduce helpful strains into your system and can come from fermented foods such as kimchi, tempeh, sauerkraut, miso soup or paste, and kombucha. They can also come from high-quality practitioner supplements with key strains such as Lactobacillus species, Bifidobacterium species, Akkermansia muciniphila, Blautia argi, Limosilactobacillus reuteri, Romboutsia ilealis, Romboutsia timonensis, and Stomatobaculum longum.
Lifestyle matters
Your microbiome also responds to quality sleep, meditation and deep breathing, exercise, and time spent in nature. Even short-term stress can alter microbial composition.
The war within
Inside you, there is a constant competition within this microbial universe. Some bacteria support your health, while others promote disease.
Whichever group dominates will set up its “house” rules and influence your brain, metabolism, immune system, mental state, cravings, mood, and ultimately, you.
So, who’s really in charge?
On one hand, it may feel startling to consider that microbes are influencing your biology, gene expression, brain, thoughts, and behaviour so profoundly, raising giant questions like: Who am I?
At this point in time, science is replying with, “You’re more complex than you ever thought you were.” But the exciting news is that you’re also responsible for designing the ecosystem that ultimately shapes you, from your brain to your mood, to how you feel, to inflammatory responses, and even what diseases you may present with or not.
You have a choice in how you want to work with this ancient, futuristic, multifaceted alien species residing within you, for good or for bad.
Read more from Honor Tremain
Honor Tremain, Nutritionist, Author, and Journalist
Honor Tremain is an award-winning longevity nutritionist, author, and journalist whose journey into health began with a personal crisis where, between the ages of 18 and 23, Honor was bedridden with multiple chronic illnesses & determined to reclaim her life, she completed a Diploma in Nutrition, eventually healing herself, and went on to complete a science degree. Honor opened a thriving nutrition practice in Sydney, Australia, became a columnist and feature journalist for national and international publications, and in 2015, Honor published her debut book, A Diet in Paradise. Most recently, she founded Daya Pet Food Co., a health-focused and sustainable dog food company that was proudly awarded Best Health-Conscious Dog Food Brand 2025.
Reference list:
Cell Press. (2019). Article in Trends in Genetics. Retrieved from Cell Press – Trends in Genetics article
Cryan, J. F., & Dinan, T. G. (2012). Mind-altering microorganisms: The impact of the gut microbiota on brain and behaviour.
Foster, J. A., et al. (2023). The microbiome-gut-brain axis and mental health.
Integrative Human Microbiome Project Consortium. (2014). The integrative human microbiome project.
NSW Government. (2021). Microbiome and the mind: How the gut influences mental health.
Sender, R., Fuchs, S., & Milo, R. (2016). Revised estimates for the number of human and bacteria cells in the body.
University of Utah Genetic Science Learning Centre. (n.d.). The microbiome. Retrieved from University of Utah – The microbiome
Additional sources:
