Overview

You are not an individual; you are an ecosystem. For every human cell in your body, there is at least one bacterial cell. You are a walking coral reef. Most of them live in your gut. We used to think they were just hitchhikers, but now we know they run the show. They digest your food, train your immune system, and talk to your brain.

Core Idea

The core idea is Symbiosis. We evolved with these bugs. We provide them a warm, wet home and food. They provide us with enzymes we lack (to digest fiber) and vitamins (like Vitamin K). It is a partnership.

Formal Definition

The collective genomes of the microorganisms (bacteria, bacteriophages, fungi, protozoa, and viruses) that reside in an environmental niche (e.g., the human gut).

Intuition

Think of your gut as a garden.

  • Healthy Diet (Fiber): Fertilizer for the flowers (good bacteria).
  • Junk Food (Sugar): Fertilizer for the weeds (bad bacteria).
  • Antibiotics: Napalm. It kills everything, good and bad.

Examples

  • Fecal Transplants: If a patient has a deadly infection (C. diff), doctors can take poop from a healthy person and put it in the patient’s gut. The healthy bacteria fight off the bad ones. It has a 90% cure rate.
  • Obesity: If you take gut bacteria from an obese mouse and put them in a skinny mouse, the skinny mouse gets fat (even if it eats the same amount). The bacteria control how many calories you absorb.
  • The Gut-Brain Axis: Your gut bacteria make 90% of your Serotonin (the happiness chemical). This is why bad digestion often goes with anxiety/depression.

Common Misconceptions

  • Bacteria are germs: 99% are good or neutral. Only a tiny fraction are pathogens. We are too obsessed with being “sterile.”
  • Probiotics fix everything: Most probiotic pills (yogurt bacteria) die in your stomach acid. They don’t colonize your gut permanently. Prebiotics (fiber) are often more effective because they feed the bacteria you already have.
  • Dysbiosis: An imbalance in the microbiome (too many weeds). Linked to allergies, autism, and autoimmune diseases.
  • Hygiene Hypothesis: The idea that we are too clean. Because kids don’t play in the dirt anymore, their immune systems get bored and start attacking harmless things (peanuts, pollen), causing allergies.

Applications

  • Personalized Nutrition: In the future, diets will be tailored to your specific microbiome, not just your genes.

Criticism / Limitations

  • Correlation vs. Causation: We see that sick people have different microbiomes, but we don’t always know if the bacteria caused the sickness or the sickness changed the bacteria.

Further Reading

  • Collen, Alanna. 10% Human. 2015.
  • Enders, Giulia. Gut: The Inside Story of Our Body’s Most Underrated Organ. 2014.