Understanding the Gut-Brain
Updated: May 19
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.
What if your thoughts weren’t entirely your own? What if your mood, cravings, stress responses, and even parts of your personality were being influenced by something non-human living inside you? Science is now seriously exploring this possibility. Mental health disorders such as depression and anxiety are now leading causes of disability worldwide. Rates of autism, ADHD, bipolar disorder, and schizophrenia continue to rise. While many factors contribute to this crisis, one area is rapidly gaining attention.
The Gut-Brain: Your “second brain”
Woven within the lining of your gastrointestinal tract from your mouth to your anus is a complex neural network known as the enteric nervous system (ENS), often referred to as the gut brain. Along with being considered one of the science world’s most fascinating mysteries, the gut brain is also the largest immune organ we house.
This system:
Contains over 100 million neurons
Operates semi-independently from your head brain
Communicates constantly with your central nervous system running down your spine
It’s not working alone. Meet Your Inner Ecosystem:
Microbiota, the community of microbes living in and on your body
Microbiome, the total genetic material of those microbes
These microbes help digest food, regulate immune function, produce vitamins, influence inflammation, and crucially, affect brain function and behavior. Firstly, let’s look at how the gut brain is interacting with us.
The Gut–Brain Axis
Here’s where things take an intriguing step. Your gut microbes don’t just exist passively in you; they actively communicate with your body and brain and are in constant conversation via what’s known as the gut–brain axis – a bidirectional communication system involving: The central nervous system (brain and spinal cord), the enteric nervous system (gut brain), the autonomic nervous system, the Vagus nerve, the immune system and hormonal pathways (HPA axis)
It seems they communicate by producing neurotransmitters, interacting with your nervous system directly, sending signals via the vagus nerve to the brain, influencing immune responses and inflammation, producing bacterial metabolites, such as the very valuable short chain fatty acids.
In fact, 95% of serotonin, often called the “happy hormone”, is produced in the gut with these guys, not the brain!
Your microbes have learnt to speak like you
Even more astonishing, your microbiome appears to have learnt and be able to resend their own messages coded in the same chemical “language” your body uses, effectively intercepting and influencing your internal biochemical messaging systems, sometimes to shift commands towards their own wishes and desires, and could we say intelligence, to redesign your body, mind, and cravings in ways that the microbes in power at the time deem necessary for their survival.
Cell for cell: You and your microbiome as a collective
We are made up of about 30 trillion human cells, and 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.
In other words, you are not just human. You are a super organism, essentially carrying a whole other, larger non human genetic counterpart of yourself, that has such immense genetic expression variability and capabilities, along with communication and command potentials which are sent around our entire body, giving instructions, including to our hormones, nervous system, and brains. It begs the question.
Who’s really in control?
In this study by Oxford University zoologist Dr. Manuel Berdoy, mice infected with the microbe Toxoplasma gondii lost their natural fear of cats. Some were even attracted to them.
From an evolutionary standpoint, this makes no sense unless the microbe is influencing behavior to increase its own survival. Which raises this inevitable question, “Are we just the host? Who is the boss, actually?”
Science recognizes your microbiome can:
Influence your cravings
Shape your metabolism
Regulate your mood
Impact your immune system
Communicate with your brain to impact
How you feel
What you feel like eating
How stressed you are
How emotionally resilient you are
Is this humans versus microbiome? Maybe that’s the wrong perspective. Let’s understand how it all started first.
How this alien universe set up its beginnings
In utero, initial exposure begins within your mother’s womb. At birth, major colonization occurs via the birth canal while being born. Early life, breastfeeding, diet, environment, and lifestyle shape your microbiome.
This early microbial colonization is critical and beneficial in programming and shaping your brain development, learning capacity, immune system programming, allergy responses, stress response regulation, anxiety, socializing. So, what happens when we don’t have enough, or the right bacteria? We’ll come back to that next time.
Thoughts to ponder before we go, a symbiotic relationship
Inside you lives a dynamic alien population known as your microbiome, which includes ancient futuristic genetic information that far exceeds your own, forming a complex symbiotic super organism with you.
These microbes don’t just digest food. They impact the brain in your head, its functions, your behavior patterns, and social interactions, and are responsible for producing your happy hormone, influencing your immune and stress management systems, while playing a critical role in the development and maturation of you, these systems, and your brain since before your birth.
Rather than enemies, you are partners. Instead of asking, “Are we just the slaves to our bacteria?”, a better question might be, “How do we work together better?”
Coming next: Part 2, can we control the system?
If your microbiome influences your brain, behavior, learning, and mood, can you influence it? Let’s explore these answers, what can disrupt a microbiome, how to shape your mental health, the role of inflammation in depression, and how to actively “reprogram” your gut brain. Because while your microbes may be all powerful, you still hold the steering wheel.
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.
References:
Integrative Human Microbiome Project Consortium. (2014). The integrative human microbiome project.
NSW Government. (2021). Microbiome and the mind: how the gut influences mental health.
Foster, J. A., et al. (2023). The microbiome–gut–brain axis and mental health.
University of Utah Genetic Science Learning Centre. (n.d.). The microbiome.
