🧬 The Human Microbiome — The Hidden Superorganism

🌍 What It Is

The human microbiome is the collection of all microorganisms (bacteria, archaea, viruses, fungi) that live in and on our bodies — mainly in the gut, but also on the skin, mouth, lungs, and reproductive organs.

💡 Why It Matters

• Around 90% of human diseases are linked in some way to changes or imbalances in the microbiome.
• The microbiome has 3.3 million genes, compared to only 22,000 human genes — making it a powerful part of our biology.
• Humans are 99.9% genetically identical to each other, but our microbiomes can differ by up to 90%, explaining big variations in health and disease response.

This means the microbiome is a key to personalized medicine — understanding your microbial composition could help tailor treatments just for you.

🧫 Where the Microbiomes Live

🧠 Each body site has its own microbial community, fine-tuned for that environment’s function.

🧒 Life Cycle and Microbiome Diversity

• Infants: Microbiome depends on birth method — vaginal birth vs C-section gives completely different starting microbes.
• Adults: Diversity increases, stabilizes, then declines with age.
• Elderly: Loss of microbial diversity is linked to reduced health and immunity.

👶 Birth and Early Life

• During late pregnancy, mothers have a rise in Proteobacteria and Actinobacteria, passed to the newborn.
• Newborns start with ~16% of these; healthy adults have <5%.
• Diseases like obesity or cancer can reduce their levels.

🍎 What Shapes the Microbiome

Major influences:

• Diet 🍔🥦
• Geography 🌎
• Age and hormones ⏳
• Stress 😰
• Antibiotics and medications 💊

Different countries show distinct microbial profiles due to diet — for example, meat-heavy Western diets vs plant-based Asian diets.

⚖️ The Famous Ratio: Firmicutes vs Bacteroidetes

These two major bacterial groups dominate the gut and balance each other:

🌶️ Chili, pea fiber, cranberries, and other plant fibers can rebalance this ratio — showing diet tweaks can directly affect health.

🧠 Gut–Brain Axis

The gut and brain constantly “talk” through biochemical signals — a system called the gut–brain axis.

Key points:

• Gut microbes produce short-chain fatty acids (SCFAs) like acetate, propionate, and butyrate — critical for energy, metabolism, and inflammation control.
• Some gut bacteria even produce serotonin, affecting mood and mental health — proving a microbial link to depression and anxiety.
• These compounds cross the gut wall, reach the immune system and nervous system, and can influence behavior.

🧩 Gut health = brain health + immune balance.

🩸 Gut Leakage & Immune System

When the intestinal barrier becomes weak (“leaky gut”), bacteria or toxins can pass through the intestinal wall → trigger inflammation and autoimmune responses.

This is strongly connected to diseases like:

• Crohn’s disease
• Ulcerative colitis

💡 Research projects investigate sampling microbiomes directly from inflamed intestinal surfaces to identify disease-linked microbial signatures.

🧍‍♀️ Microbiome Gradients in the Body

• Stomach: Very acidic → kills most microbes.
• Small intestine → colon: Gradual increase in diversity and abundance.
• Respiratory tract: More microbes in the nose, fewer deeper in the lungs (cleaning mechanisms remove them).

Each system has a gradient of microbes — changing conditions = changing populations.

🐷 Experimental Models

In some research, humans are actually used as models for pigs (!) because we can control human diet history and sample collection better. This helps study how to reduce antibiotic use and inflammation via microbial management.

💩 Microbiota Transplantation (FMT)

Also known as fecal microbiota transplantation — or humorously, “crapsules” when done orally 💊💩

Process:

1. Take fecal sample from a healthy donor.
2. Wash and purify to isolate beneficial microbes.
3. Transfer to a sick person (via colon tube or capsule).

Used especially for:

• Clostridium difficile infection (C. diff) — antibiotic-resistant bacteria causing severe gut disease.

FMT success: healthy donor → patient recovers as normal microbiota reestablishes.

⚠️ Risks:

• Donor screening is critical; transferring unwanted traits (like obesity) has actually happened.

👶 Microbiome Transplant at Birth

Newborns delivered by C-section miss exposure to the mother’s vaginal microbes. Solution: hospitals now sometimes swab the newborn with the mother’s microbiota to restore normal colonization and immune development.

This simple act may reduce lifelong risks of allergies, asthma, and other diseases.

🧩 In Summary