In recent decades, scientists have uncovered a fascinating and vital link between gut health and mental well-being, often referred to as the gut-brain axis. This complex, bidirectional communication system involves neural, hormonal, and immunological signaling between the gut microbiota and the brain. A growing body of research shows that disruptions in gut flora—known as dysbiosis—are linked to increased risk of anxiety, depression, and even neurodevelopmental disorders.

This is what the science tells us — but correlation isn’t always causation, and it’s worth stepping back to challenge the broader narrative. Why, all of a sudden, has our gut microflora started “misbehaving”? Is it truly just about the microbes? Or are we falling into a kind of tunnel vision, where we isolate the gut as the sole culprit, simply because it’s measurable, easy and trendy to study? We rarely consider other underlying systems or external pressures that might be contributing, and yet we’re already leaping to dramatic solutions — like shit transplants — as if borrowing bacteria from a “healthy” donor can magically rebalance everything. Maybe the real question isn’t just what’s wrong with our gut, but what’s happening in our whole environment and way of life that’s throwing it off in the first place.

Lets expand the scene a little first.

It might surprise many to learn that the human body is not made up solely of human cells. In fact, microbial cells — including bacteria, viruses, fungi, and even parasites — either equal or slightly outnumber human cells in the body, depending on the measurement. A revised estimate published in Cell (Sender, Fuchs, & Milo, 2016) puts the ratio at roughly 1:1, meaning that for every human cell, there’s about one microbial cell. While older sources claimed a 10:1 ratio, newer methodologies refined that estimate — but the key takeaway remains: we’re at least half microbe, by cell count. Genetically, the picture is even more skewed — the collective genome of our microbiota (the microbiome) outnumbers human genes by over 100 to 1 (NIH Human Microbiome Project, 2012). These microbes aren’t freeloaders either; they play crucial roles in digestion, immune function, hormone regulation, and even behavior.

So who, or what, are we? If our functioning, mood, and survival depend so deeply on organisms we didn’t even evolve to recognize as “self,” then where does the boundary of identity lie? This philosophical question is being taken more seriously in science, especially as researchers explore how microbial health influences not just our physical bodies but our minds. A study in Nature Reviews Neuroscience (Cryan & Dinan, 2012) helped establish that microbes communicate with the central nervous system via the vagus nerve, cytokine production, and metabolites like short-chain fatty acids.

And it turns out the brain isn’t the only place where neurological decision-making occurs. The enteric nervous system — often dubbed the “second brain” — is a vast network of over 100 million neurons embedded in the walls of the gastrointestinal tract (Gershon, 1998, “The Second Brain”). It can operate independently of the brain and spinal cord, making its own decisions about digestion, motility, and even signaling mood-related neurotransmitters like serotonin, 90% of which is produced in the gut.

What’s more, scientists have found bacteria in places once thought sterile, including the placenta (Aagaard et al., Science Translational Medicine, 2014), lungs (Charlson et al., mBio, 2012), and even within the brain itself (Branton et al., Frontiers in Microbiology, 2013), suggesting a far deeper integration between microbes and human systems than previously assumed.

But the gut is just the beginning. The heart, too, contains its own intrinsic nervous system — about 40,000 neurons, often called the “heart brain.” This network is capable of independent reflexes, pattern recognition, and memory. Research from the HeartMath Institute and peer-reviewed journals like Neurocardiology have shown that the heart sends more signals to the brain than it receives, influencing emotional processing, attention, and even decision-making. One study published in Frontiers in Psychology (McCraty & Zayas, 2014) found that the heart’s electrical field can synchronize with the brain’s EEG patterns during emotional experiences, suggesting a deeply embedded two-way feedback system.

The liver, while not traditionally associated with cognitive processing, plays a key role in metabolic signaling that affects the brain. It detects and responds to changes in blood sugar, hormones, and microbial metabolites. According to a study in Nature Neuroscience (Yuan et al., 2022), liver inflammation can directly affect mood and cognition via immune-to-brain signaling pathways. This is particularly important in conditions like non-alcoholic fatty liver disease (NAFLD), where brain fog and depression are now recognized as secondary symptoms of liver dysfunction — a concept known as the liver-brain axis.

Even the lungs, once considered purely mechanical in function, have now been shown to engage in immunological and neurological signaling. A 2020 study in Nature revealed that the lungs produce platelet-forming cells and are heavily innervated by sensory neurons that communicate with the central nervous system about irritants, oxygen levels, and microbial presence. More surprisingly, research in Journal of Experimental Medicine (2021) identified a gut-lung axis, showing that gut bacteria can influence lung inflammation and respiratory conditions — again reinforcing the idea that bodily systems are in constant cross-talk through immune, neural, and microbial signals.

All of this suggests that intelligence in the body is not centralized. Instead, we are a networked intelligence, with multiple organs capable of sensing, responding, and influencing thoughts and feelings.

So again — why are we so fixated on the gut alone? If the same dysfunction can show up in multiple systems, why stop there? Should we start considering microbiome transplants (or a thought occurred to me with a smirky smile – shit transplants) for the heart, the brain, or even the placenta? It sounds absurd. To me, it seems clear that something much bigger is going on. These imbalances aren’t just about one isolated system misbehaving; they’re symptoms of a deeper disruption across the whole body, maybe even the whole environment we live in. But let’s face it — the gut is easier to brand, easier to test, and much easier to sell. If we frame it as the holy grail of getting better, people will pour money into probiotics, gut-targeted supplements, and high-cost procedures like fecal transplants — hoping for a fix that might only be a fragment of the story.

What has changed?

Our environment has changed radically in just the last 30 years — and it’s not just about technology or lifestyle, but about the entire ecosystem our bodies now have to navigate. Back then, you rarely heard about “waves and waves” of depression or anxiety hitting entire populations. Maybe part of that was cultural — perhaps we lacked the tools or openness to measure and discuss mental health as we do now. But what if it’s not just about better diagnostics? What if many of these problems simply didn’t exist at the scale they do today because the environmental stressors themselves weren’t there yet?

One major shift is our chronic exposure to artificial, energy-saving light, especially at night. In particular, the rise of blue-light-emitting screens. A study in Journal of Clinical Endocrinology & Metabolism (2011) showed that even low levels of light at night can reduce melatonin and impair sleep quality, leading to mood disturbances and fatigue.

Then there’s the proliferation of synthetic chemicals and vapors from modern living — especially the ones the electronic devices emit when heated (and they do heat). These toxins accumulate in the body and may contribute to neurological and hormonal dysregulation. A review in Environmental Health Perspectives (Gore et al., 2015) outlined the connection between exposure to endocrine-disrupting chemicals (EDCs) and the rise in neurodevelopmental issues, cognitive impairment, and mood disorders.

And of course, we can’t ignore the massive increase in electromagnetic field (EMF) exposure. Wi-Fi routers, smartphones, smart meters, Bluetooth — our bodies are now constantly bathed in non-ionizing radiation that simply didn’t exist at these levels a generation ago. Evidence shows that EMFs may disrupt calcium signaling in cells, alter sleep architecture, and increase oxidative stress and so much more.

And if we take into account the work of Fritz-Albert Popp and his team — who discovered that our bodies bioregulate using the electromagnetic spectrum — then that last point becomes even more unsettling.

Oh wow, no? Just in 30 years? Well … yeah.

So if we look at the cumulative effect of all these new inputs — disrupted light cycles, constant low-level toxic exposure, and artificial electromagnetic environments — it becomes harder to argue that the root of the problem lies solely with our “misbehaving” microbes. These are, after all, microbes that have coexisted with us for millions of years, adapting alongside our evolution, supporting our digestion, immunity, and even mental health long before anyone ever thought to market a probiotic capsule. It seems far more likely that these microbes — like us — are simply reacting to an increasingly hostile and unnatural environment. They’re not the enemy; they might just be the canaries in the coal mine, showing us that the internal ecosystem is collapsing in response to the external one. And as we mentioned above – they are a part of us.

Now think what happens, if your plan is to replace them?

What if their recent changes in behavior aren’t signs of rebellion — but signs of adaptation? What if, in response to a damaged and unnatural environment, they’re not turning on us… they’re actually trying to protect us?

Recent studies suggest this may not be so far-fetched. For example, in conditions of chronic stress or inflammation, gut bacteria shift their metabolic activity — not to sabotage, but to modulate immune responses and help maintain systemic balance. A study published in Cell Host & Microbe (Thaiss et al., 2016) showed that microbial communities adjust gene expression in response to host stress hormones like cortisol, in an apparent attempt to stabilize the gut environment. Another study in Nature Communications (2018) found that certain strains of gut bacteria increase production of anti-inflammatory short-chain fatty acids (like butyrate) in response to environmental stress, effectively acting like internal firefighters in the midst of chaos.

Even in disease states, some microbiota changes could be interpreted not as dysfunction, but as emergency response strategies. In Trends in Immunology (2017), Belkaid and Harrison proposed that microbes play a role in “immune education,” sometimes upregulating inflammatory responses not to harm, but to prepare the body for larger threats. It’s not sabotage — it’s survival.

So perhaps the gut is not malfunctioning after all. Maybe it’s the most sensitive and intelligent responder we have — reading the signals of the external world, adjusting internal processes, and rallying resources to keep us alive. And maybe those microbial shifts we rush to medicate or suppress… are the body’s last-ditch effort to adapt, not a flaw, but a feature.

So hey – what about the original question and mental health?

Yes — depression is real, and it’s hard. So are other mental health conditions. But imagine your body as a system suddenly forced to adjust to thousands of new signals and chemical stressors we’ve introduced at a pace nature has never experienced before. From artificial lighting and EMFs to pollutants, additives, and sensory overload — the body is constantly compensating. Think of it like a battery with a finite energy reserve: the first priority isn’t your creativity or happiness — it’s survival. Pumping blood, filtering toxins, regulating immune responses, managing inflammation — these are non-negotiables. Your higher brain functions? As far as your body’s concerned, they’re optional extras when things get tough. So yes, you’ll feel flat, unmotivated, anxious, or low. It’s not a psychological weakness — it’s a biological reallocation of energy.

The way out isn’t to start by forcing the brain to “think positively” or piling on supplements. The first step is to change the environment — reduce the burden, slow the inputs, let the system breathe. Only then can you begin to rebuild trust and balance with your body’s internal ecosystem — not by fighting it, but by listening to it. Restoring that connection might involve nutrition, breathwork, sunlight, social connection, nervous system regulation, or gentle microbiome support. But it all starts with understanding that your body isn’t broken — it’s adapting, the only way it knows how.

Think about that before planning on your next shit transplant.