The Science of the Gut Microbiome | Phenome Longevity

50T+

The number of microorganisms the gut microbiome is hosting.

0M+

The number of genes the gut microbiome contains, compared to about 20,000 in human DNA.

0%

Of the human immune system is located in the gut, making it one of the body’s strongest lines of defence.

0+

The number of disorders an imbalanced gut microbiome can cause.

The Intelligent Organ

The gut is one of the body’s most complex and intelligent systems. It houses trillions of microorganisms that communicate with each other and with the body through a constant exchange of chemical signals. Together, they form the gut microbiome, a living ecosystem that influences nearly every biological process.

This network supports digestion, immunity, metabolism, and even emotional balance. Every meal, thought, and environmental change can reshape it within hours, showing how deeply the gut responds to daily life. Scientists now understand that the gut is not just a digestive tube but a biological command centre that regulates how we absorb nutrients, process energy, and defend against disease.

In this guide, we explore what the gut actually does, how it keeps you balanced, what happens when that balance is lost, and how modern science can measure it.

The Four Core Functions of the Gut Microbiome

1. Digestion and Nutrient Conversion

2. Immunity and Defence

3. Endocrine and Metabolic Role

4. Neurological Communication

1. Digestion and Nutrient Conversion

How Microbes Turn Food into Fuel

The gut microbiome transforms the food we eat into the building blocks of health. While human enzymes handle most of the work, microbes complete what the body cannot. They break down complex fibres and plant compounds that would otherwise pass through undigested, turning them into short chain fatty acids that feed intestinal cells and maintain energy balance.

These microbial reactions also produce essential nutrients such as vitamin K, folate, and several B vitamins that support metabolism and cellular repair. At the same time, microbes regulate how bile acids are recycled and how fats and carbohydrates are absorbed.

When this system functions efficiently, nutrients are extracted with precision and inflammation remains low. When it falters, energy use becomes less efficient, and undigested compounds can irritate the gut lining. Understanding this process reveals how deeply microbes influence not only digestion but the body’s overall metabolism.

2. Immunity and Defence

The Gut-Immune Connection

Around seventy percent of the body’s immune cells live within the gut, constantly interacting with the trillions of microbes that line its surface. This ecosystem trains the immune system to recognise what belongs and what does not, preventing overreaction and inflammation.

A balanced microbiome helps immune cells communicate effectively and produce protective compounds that strengthen the intestinal barrier. Short chain fatty acids produced by beneficial bacteria regulate immune signalling, supporting tolerance and reducing sensitivity to potential triggers.

When microbial balance is lost, the immune system can become confused, reacting too strongly or not enough. This imbalance contributes to inflammation, allergies, and reduced resilience against infection.

Diversity is Strength.

A Varied Microbiome is Your Best Defence!

3. Endocrine and Metabolic Role

The Hormonal Intelligence of the Gut

Hormone Production

The gut is one of the largest hormone-producing organs. Specialised cells in the intestinal lining release chemical messengers that control appetite, metabolism, and stress response. More than twenty hormones originate in the gut, including serotonin, ghrelin, and GLP-1.

Microbial Regulation

Gut microbes influence how these hormones are produced and how sensitive the body is to their signals. Certain bacterial species stimulate serotonin production, while others help regulate blood sugar and energy use.

Systemic Impact

When gut and microbial balance is maintained, hormonal communication remains clear. When it is disrupted, appetite, mood, and metabolism can all shift. The gut therefore plays a central role in coordinating hormonal stability across the body.

4. NEUROLOGICAL COMMUNICATION

Signals That Shape the Mind

Early 1900s

The Gut as a Reflex Organ

Scientists first discovered the enteric nervous system, a vast network of nerves embedded in the gut wall. It could operate independently of the brain, leading to the term “second brain.”

1950s

Hormones Connect Gut and Brain

Researchers identified gut hormones such as serotonin and ghrelin that influence appetite and mood. These findings suggested that the gut was an endocrine organ communicating with the brain chemically, not just through nerves.

1990s

The Microbiome Enters the Picture

Advances in molecular biology revealed that gut microbes could affect neurotransmitter production and stress responses. The concept of the microbiota-gut–brain axis began to form.

2000s

Direct Communication Confirmed

In the early 2000s, scientists discovered that the gut and brain are in constant communication. This finding revealed that the microorganisms living in our intestines could send signals to the brain, influencing mood, emotion, and even behaviour. Since then, research has shown that this connection, known as the gut brain axis, plays a key role in both mental and physical health, reshaping how we understand the body’s internal systems.

The Gut Brain Axis Explained

Your gut and brain are in constant communication through the gut brain axis.

This system links your digestive health with your emotions, memory, and overall mental wellbeing.

Inside your gut live trillions of bacteria that produce messengers like serotonin and dopamine, the same chemicals that influence mood and focus. When your gut is balanced, your mind feels clearer and calmer. When it is not, you might experience stress, poor sleep, or low energy.

Your gut also communicates with your immune and hormonal systems, affecting everything from metabolism to how your body responds to daily stress. By understanding your gut microbiome, you can learn how to support both your physical and mental health from the inside out.

When Balance Becomes Chaos: What Happens in Dysbiosis

In a healthy gut, microbes live in a cooperative network that regulates digestion, metabolism, and immune function.

Dysbiosis occurs when this network shifts in composition or activity. It is not just the loss of beneficial species but a change in how microbial communities behave. Some start producing more inflammatory compounds, others stop generating essential metabolites like short chain fatty acids. These functional changes alter the gut environment, weaken the barrier that protects intestinal cells, and trigger immune reactions that affect tissues far beyond the digestive tract. This imbalance of bacteria can lead to symptoms such as bloating, gas and irregular bowel movements, and has been associated with conditions like irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD).

The Chain Reaction of Imbalance

The Loss of Microbial Harmony

Dysbiosis occurs when beneficial and harmful microbes fall out of balance. Helpful species decline, while opportunistic ones expand, creating an unstable environment that can disrupt digestion, immunity, and nutrient absorption.

What Triggers the Imbalance

Diet low in fibre, frequent antibiotic use, stress, and sleep disruption can all shift the microbial population. These changes weaken the gut barrier and increase the release of inflammatory molecules into circulation.

Consequences Across the Body

An imbalanced microbiome affects more than the digestive system. It influences metabolic health, immune sensitivity, and even how the body manages energy and inflammation. The effects can extend far beyond the gut.

Restoring Stability

Rebalancing the microbiome begins with diversity. Fibre-rich foods, probiotic strains, and lifestyle choices that support regularity help restore a balanced ecosystem and rebuild communication between microbes and host cells. Testing plays a key role in this process. By analysing the microbiome, scientists can identify which bacterial groups are depleted or overgrown and provide targeted recommendations to restore balance.

The Most Complete Way to Understand Your Microbiome

Shotgun Metagenomics.

We use the most advanced microbiome technology available today, powered by our partnership with Illumina. Through Shotgun Metagenomics, we analyse every microorganism in your sample with unmatched precision and depth. This technology captures the entire genetic landscape of your microbiome, revealing not just what species exist, but how they interact and influence your health. It is the most comprehensive and accurate method ever developed for understanding the invisible ecosystem within you.

Differences between Traditional Microbiome Analysis and Shotgun Metagenomics

What Shotgun Metagonmics Data Provides

The Complete Map of Your Microbial Ecosystem

Explore every microorganism that lives within you, from your gut to your mouth and vaginal microbiome. See how bacteria, fungi, and viruses work together across these systems to maintain balance and wellbeing.

The Diversity that Defines Your Health

Measure the richness and stability of your microbial communities. A diverse ecosystem across the gut, oral, and vaginal microbiomes supports digestion, immunity, hormone balance, and even mood.

Functional Insights Across Systems

Understand what your microbes actually do, from producing vitamins and neurotransmitters to regulating pH, protecting against pathogens, and supporting reproductive and metabolic health.

Personalised Microbial Profile

Gain a complete picture of how your microbiome compares to healthy patterns and where extra care can enhance balance and long-term health.

Early Signals of Imbalance

Identify shifts that may indicate inflammation, overgrowth, or loss of beneficial species in any microbiome, helping you take proactive steps long before symptoms appear.

From Data to Direction

Transform metagenomic data into actionable insights, guiding your nutrition, supplements, and daily habits for optimal gut, oral, and vaginal health.

Insights from the Longevity Hub

May 16, 2025

What Your Gut Microbiome Says About Your Skin Health

Your skin is a reflection of what’s happening inside your body-especially in your gut. While topical skincare can help manage surface symptoms, the true root of chronic skin concerns often lies within the gut microbiome. Research continues to show that...

Stories from Those Who Finally Got Answers

We are grateful to everyone who shared their journey with us. Their honesty reminds us why understanding our biology matters, because behind every test result there is a story of someone finally getting the answers they have been looking for.

I honestly did this out of curiosity, but the results were shocking. I could finally see why I kept having random breakouts and sugar cravings. It’s strange how much your gut controls without you knowing. I’ve started taking care of it differently since.
— Michael T, 41

I always thought feeling heavy after meals was just normal for me. Turns out, my gut wasn’t in great shape. After seeing what was really going on, I started paying attention to what actually works for my body. I feel more in tune now, and my stomach finally feels calm again.
— Sara L, 36