Micro- Microbiomes

Differences Between Mutualism, Commensalism, and Pathogenesis

• Mutualism: Both host and microbe benefit.

• Commensalism: Microbe benefits, host is neither helped nor harmed.

• Pathogenesis (Amensalism): Microbe benefits, host is harmed.

• Shared traits: All may involve host attachment, immune evasion, and gene expression changes.

• Key difference: Only pathogens damage the host.

How do mycorrhizal fungi and rhizobia benefit plants?

• Mycorrhizal fungi help plants absorb phosphate and water.

• Rhizobia fix atmospheric nitrogen and provide ammonium to the plant.

Where do mycorrhizal fungi and rhizobia live in relation to the plant?

• Mycorrhizal fungi live outside the root, wrapping around it.

• Rhizobia enter the root and form nodules inside plant cells.

What signals initiate interaction in mycorrhizal fungi vs. rhizobia symbiosis?

• Rhizobia respond to flavonoids secreted by the plant.

• Mycorrhizal fungi do not rely on flavonoids for signaling.

What nutrient exchange occurs between the plant and its microbial partners?

• The plant gives sugars to both mycorrhizal fungi and rhizobia.

• In return, mycorrhizal fungi provide phosphate and water, while rhizobia supply ammonium.

Negative Effects of Lacking Akkermansia muciniphila

• Correlated with:

  • Inflammatory bowel disease

  • Appendicitis

  • Obesity

  • Weaker mucus barrier, more vulnerability to pathogens

Flavonoids in Rhizobia/Plant Relationship

• Flavonoids = plant-secreted chemicals that attract rhizobia and trigger bacterial production of Nod factors.

• If a plant could not produce flavonoids, it would fail to attract rhizobia, so no nitrogen-fixing nodules would form.

How does getting only 5 hours of sleep affect the microbiome and health?

Poor sleep disrupts microbiome rhythms, leading to:

• Weakened gut barrier

• Reduced butyrate (affects brain/sleep regulation)

• Altered melatonin production

• Linked to inflammation, obesity, and poor cognitive performance

How the Microbiome Impacts Weight Loss

• Microbiome shifts can decrease calorie burn even after dieting.

• High-fat diets promote flavonoid-degrading bacteria, lowering metabolic benefits.

• Microbiome transplants from obese mice can cause weight gain.

• Targeting the microbiome with diet (fiber, flavonoids) or pre/probiotics may help regulate weight.

Microbiome's Role in Depression/Anxiety

• Mice given microbiomes from depressed humans showed:

  • More anxiety (in Open Field Test)

  • More depression-like behavior (in Forced Swim/Tail Suspension Tests)

• Conclusion: Microbiota directly influence emotional states via metabolic and neural pathways.

Could Probiotics Improve Sleep or Exercise?

Yes, and there’s some proof:

• Sleep: Lactobacillus gasseri helped medical students sleep better.

• Exercise: Eubacterium and Coprococcus produce molecules that stimulate dopamine release → increases exercise motivation.

• This shows microbes can influence behavior and energy regulation.

Negative Effects of Lacking Akkermansia muciniphila

• Correlated with:

  • Inflammatory bowel disease

  • Appendicitis

  • Obesity

  • Weaker mucus barrier, more vulnerability to pathogens

Role of Akkermansia muciniphila in Gut

• Main energy source: Degrades mucus

• Benefits to host:

  • Maintains thick mucus barrier

  • Feeds gut epithelial cells with byproducts

  • Recycles mucin

  • Supports immune and metabolic health

TMAO and the Microbiome

• Gut microbes convert dietary compounds (like carnitine from red meat) into trimethylamine (TMA).

• TMA → TMAO in the liver

• TMAO promotes atherosclerosis, increasing cardiovascular disease risk.

• Vegans fed steak didn’t produce TMAO → their microbiome lacked TMA-producing bacteria.