I’ve read so many things on this subject and I’m still no nearer to understanding it!
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1. Competition – It is more difficult for “bad” bacteria to gain a foothold when they have to compete with “good” bacteria. This is why people are more likely to get opportunistic infections like *C. diff* after taking antibiotics.
2. Crosstalk between immune cells and good bacteria that goes beyond the scope of ELI5, but for simplicity we’ll just say it’s practice for the immune cells. ([more information in this review article](https://www.nature.com/articles/s41422-020-0332-7))
3. The gut bacteria in particular are important for producing certain vitamins and helping us absorb nutrients, deficiencies can negatively affect health and indirectly weaken the immune system.
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