The Hidden Universe Within: How Your Microbiome Orchestrates Your Health

The Microscopic Metropolis Within

I've always been fascinated by cities, the way millions of residents with different roles somehow create a functioning whole. But the most complex city I've ever encountered isn't London or New York. It's the one inside each of us. Our microbiome is a bustling metropolitan area of microorganisms. Bacteria are the main residents, but fungi, viruses, and other tiny life forms also call us home, along with all their genetic material. Before we start feeling queasy about having viruses as permanent residents, hang on. The reality is far more fascinating than frightening.

"The gut microbiome is essentially like having another organ," explains Dr. Emeran Mayer, gastroenterologist and author of "The Mind-Gut Connection." "It's about 4-5 pounds of microorganisms that are communicating with your immune system, your brain, and your metabolism every minute of every day."

Think about that for a moment. You're carrying around an entire organ you probably never considered. An organ that's as heavy as your brain and arguably just as important for your wellbeing.

Our gut alone houses over 1,000 different species of bacteria. If we're talking ecosystems, our intestinal tract rivals the Amazon rainforest for sheer complexity. Each microscopic species has its own specialised role, and when this delicate balance gets disrupted, the ripple effects can reach places we'd never expect. I often explain to my audiences that whilst our gut microbiome gets most of the research spotlight, these microscopic residents have claimed prime real estate throughout our bodies:

• Our Gut: This is the heavyweight champion of our microbial world, housing roughly 100 trillion microorganisms. Our small intestine might have fewer bacteria, but they're busy with critical tasks, helping us absorb nutrients and keeping our immune system sharp.

• Our Skin: Different areas host completely different microbial communities. The oily spots behind our ears have totally different residents than the dry stretches on our forearms. This isn't random, it's like having specialised security teams adapted to each location's unique conditions.

• Our Mouth: Over 700 bacterial species are currently residing in our oral cavity, creating complex communities that can either protect our teeth or cause problems, depending on which species dominate.

• Our Lungs: We used to think healthy lungs were sterile environments. Turns out, they maintain their own delicate microbial ecosystem, though it's far less crowded than our gut or skin.

The Invisible Workforce

One morning, as I was preparing our family’s breakfast, I found myself marvelling at the invisible workforce already at work inside me. Here's what they're accomplishing whilst we go about our day:

Our Personal Nutrition Factory: Our gut microbes tackle complex carbohydrates and fibres that our body can't handle alone, extracting additional calories and nutrients. They manufacture essential vitamins our body can't produce independently, like vitamin K and several B vitamins, plus short-chain fatty acids that maintain our gut lining's health.

Our Immune System's Training Academy: About 70% of our immune system lives in our gut, and there's a compelling reason for this proximity. Our microbiome essentially runs boot camp for our immune responses from birth, teaching our body to distinguish between dangerous invaders and harmless substances.

I often ask my clients to consider this: why do some people seem to catch every cold that circulates whilst others rarely get sick despite similar exposure? The difference often comes down to having a well trained microscopic army. A diverse bacterial community creates an immune system like an experienced security professional who can spot real threats whilst avoiding false alarms. Limited bacterial diversity, however, can result in an overreactive immune response, like an overzealous security guard who sees everyone as suspicious.

Our Living Protective Barrier: A healthy microbiome forms a protective shield across our mucosal surfaces. It's essentially microscopic "squatter's rights", beneficial microbes occupy all the prime real estate, leaving no room for troublemakers to establish themselves.

The Gut-Brain Highway

Here's where my understanding of health was fundamentally transformed: our gut bacteria are literally communicating with our brain right now. This isn't metaphorical, they're sending chemical signals that influence our thoughts, mood, and decision-making. I remember sharing this revelation with a colleague over lunch. "You mean my bacteria are affecting my mood?" she asked, looking sceptical. I nodded, explaining that about 90% of our body's serotonin, that crucial "happiness" neurotransmitter, is produced in our gut by bacteria. Our microbes are essentially running an internal pharmacy, creating mood-altering compounds based on what we've been feeding them.

Our vagus nerve, the longest nerve in our body, serves as the main communication highway between gut and brain. Our microbes have effectively integrated into this system, sending their own messages to our consciousness. The research reveals that certain gut bacteria can influence:

Our Mood: People with depression show notably different gut bacterial profiles compared to those without. Even more intriguingly, when researchers transfer microbiota from depressed humans to laboratory animals, the animals begin displaying depression-like behaviours.

Our Anxiety Levels: Gut microbes help regulate our stress response system, influencing cortisol levels and anxiety-related behaviours.

Our Cognitive Function: Emerging research links gut microbial composition to cognitive abilities, with fascinating connections to neurodegenerative conditions like Alzheimer's and Parkinson's.

As Dr. Ted Dinan, a psychiatrist and microbiome researcher, describes: "We used to think brain disorders were solely about the brain. Now we're discovering that for many conditions, we've been looking in the wrong place. The gut microbiome may be driving or worsening many neuropsychiatric conditions we previously thought were brain-centric."

Modern Life's Unintentional War on Microbes

As I've delved deeper into microbiome research over the years, I've become increasingly concerned about how our contemporary lifestyle wages constant, though unintentional, warfare against our microbial partners:

Antibiotics: Whilst lifesaving when necessary, these medications are essentially microbial carpet bombs, eliminating beneficial bacteria alongside pathogens. A single antibiotic course can alter our gut microbiome for up to two years.

Ultra-Processed Foods: Heavily processed foods lack the complex fibres that nourish beneficial gut bacteria whilst often containing emulsifiers and preservatives that disrupt microbial communities.

Excessive Sanitisation: I’m guilty of this, although getting better recently. Our obsession with eliminating all germs has consequences. Routine use of antimicrobial products disrupts the skin microbiome and may contribute to antibiotic resistance. I’ve written a bit more on this below.

Environmental Toxins: Pesticides, plasticisers, and other environmental chemicals can selectively harm beneficial microbes whilst allowing problematic species to flourish.

Chronic Stress: Psychological stress alters gut permeability and microbial composition, potentially creating vulnerability to inflammatory conditions.

Too Clean for Our Own Good?

I often share this observation with my audiences, and it invariably challenges their assumptions: we might be too hygienic for optimal health. As we've sanitised our environments: antibacterial on everything, ultra-processed foods, limited exposure to diverse microbes - we've witnessed explosive increases in allergies, autoimmune diseases, and other immune system disorders.

According to research children who grow up on farms, with animals and natural environments, tend to develop stronger immune systems and fewer allergies than those raised in ultra clean urban settings. Their immune systems receive a more comprehensive education, whilst overly sanitised environments can leave immune systems undertrained and overreactive. This doesn't mean abandoning hygiene practices, but rather recognising that some microbial exposure supports healthy immune development. It's about finding balance, something I've learned to appreciate more deeply over the years.

Building Our Microbial Garden

The encouraging news that I always share is that our microbiome is remarkably resilient and responsive to positive changes. After years of studying this field, I've developed what I call the "microbial garden" approach:

1. Diversify Our Plate Strategically

Nothing influences our microbiome more powerfully than nutrition. I learned this lesson personally when I started tracking my own dietary diversity. Different bacterial species thrive on different dietary components, making variety crucial. I now aim for 30+ different plant foods weekly, vegetables, fruits, nuts, seeds, legumes, and whole grains, to support microbial diversity. I tell my clients to think of fibre as food for our beneficial bacteria rather than just roughage for ourselves. When we eat an apple, we're not just getting vitamins, we're nourishing specific bacteria that love apple fibre. These bacteria then produce compounds that reduce inflammation, support immune function, and send positive signals to our brain.

2. Embrace Fermented Foods Thoughtfully

My morning routine now includes fermented foods, yoghurt, kefir, or sometimes sauerkraut. These foods introduce beneficial live microbes directly into our system. They've been safely consumed by humans for thousands of years and provide both probiotics and the prebiotics that feed them.

3. Feed Our Beneficial Bacteria

I've become particularly interested in prebiotic fibres that specifically nourish our helpful bacteria. Rich sources include garlic, onions, leeks, asparagus, bananas, oats, apples, flaxseeds, and seaweed. Jerusalem artichokes, chicory root, and slightly green bananas contain particularly potent prebiotics.

4. Be Strategic About Antibiotics

In my practice, I work with clients to help them collaborate with healthcare providers in determining when antibiotics are truly necessary versus when other approaches might work. When antibiotics are required, I discuss supporting microbiome recovery with appropriate probiotic supplementation and prebiotic-rich foods.

5. Manage Stress Effectively

Chronic stress damages our microbiome through multiple pathways. I've learned this from both research and personal experience. Regular stress reduction practices, meditation, nature exposure, adequate sleep, physical activity, all support microbial health alongside our mental wellbeing.

The Personalised Future

What excites me most about where this field is heading is the move toward personalised microbiome-based treatments. I envision a future where, instead of generic dietary advice, we might receive specific recommendations based on our unique bacterial profile: "Based on your microbiome analysis, increase these particular vegetables whilst reducing these specific foods." I've been following companies that are already analysing individual gut bacteria and providing tailored dietary recommendations (I’ll come with an update on this in a future article). This represents a fundamental shift from one-size-fits-all health advice to precision medicine that considers our unique microbial ecosystem.

Reframing Health: We Are Ecosystems

Perhaps the most profound insight I've gained from years of microbiome research is conceptual: we're not just individuals, but complex ecosystems. Our health depends not only on our human cells but on maintaining harmony with trillions of microbial partners that have evolved alongside us for millennia. This perspective has fundamentally changed how I approach health and disease in my practice. Many conditions we once viewed as purely "human" problems, from irritable bowel syndrome to anxiety, obesity to autoimmune disease, may actually represent ecological disruptions in our internal microbial landscape.

I now help my users understand that their daily choices, what they eat, how they sleep, how they manage stress, are essentially policy decisions for their microscopic residents. Nurture them thoughtfully, and they'll support our health in return.

Our wellbeing and theirs are inextricably intertwined. And that, I think, is beautiful!

Photo by NASA