Microbiome
Your internal ecosystem. The microbiome consists of 38 trillion bacteria (slightly more than your human cells), plus fungi, viruses, and archaea. This community of organisms shapes your digestion, immunity, mood, metabolism, and risk of nearly every chronic disease. You are as much microbe as you are human.
What the Microbiome Does
Digests Fiber
Ferments indigestible fiber into short-chain fatty acids (butyrate, propionate, acetate).
Makes Vitamins
Synthesizes vitamin K2, biotin, folate, B12, and other B vitamins. Supplements your diet.
Trains Immunity
70% of immune system is in gut. Bacteria teach immune cells what's friend vs foe.
Protects From Pathogens
Colonization resistance. Good bacteria occupy space and compete with bad ones.
Metabolizes Hormones
Affects estrogen metabolism (estrobolome), cortisol, thyroid hormones, bile acids.
Signals to Brain
Produces neurotransmitters, signals via vagus nerve. Affects mood, anxiety, cognition.
Diversity is Key
Why Diversity Matters
- More species = more functions and resilience
- Low diversity linked to obesity, diabetes, IBD
- Western lifestyle dramatically reduces diversity
- Hunter-gatherers have 50% more species than Westerners
- Diversity can be rebuilt but takes time
Key Beneficial Species
- Bifidobacterium: Dominant in infants, makes vitamins
- Lactobacillus: Lactic acid producers, common probiotics
- Faecalibacterium: Major butyrate producer, anti-inflammatory
- Akkermansia: Lives in mucus layer, metabolic benefits
- Roseburia: Butyrate producer, fiber fermenters
What Damages the Microbiome
Antibiotics
Broad-spectrum antibiotics devastate diversity. Single course can alter microbiome for a year.
Low-Fiber Diet
Bacteria starve without fiber. Species die off. Processed food = starving microbiome.
Artificial Sweeteners
Some (saccharin, sucralose) harm beneficial bacteria. Research ongoing.
Chronic Stress
Stress hormones directly affect bacterial populations. Reduces diversity.
Emulsifiers
Common food additives (polysorbate 80, carboxymethylcellulose) damage mucus layer.
Lack of Exposure
Over-sanitization, C-sections without seeding, formula-feeding reduce initial colonization.
Building a Healthy Microbiome
Diverse Fiber
30+ different plants per week. Variety feeds different species. Think rainbow, not supplement.
Fermented Foods
Sauerkraut, kimchi, kefir, yogurt, kombucha. Live bacteria and beneficial metabolites.
Reduce Ultra-Processed
Emulsifiers, sweeteners, preservatives harm bacteria. Whole foods feed them.
Polyphenols
Colorful plants have polyphenols that feed beneficial bacteria. Coffee, tea, berries, cocoa.
Limit Antibiotics
Only when truly needed. Consider probiotics/prebiotics during and after courses.
Get Dirty
Garden, play with dogs, don't over-sanitize. Microbial exposure builds diversity.