many things can kill the gut zoo
drinking alcohol especially strong drink in large amounts
taking antibiotics
some antacids (proton pump inhibitors)
diet containing glyphosate herbicide residue
there is a way to reset the immune system via a symbiotic bacteria that evolved with humans
L. Reuteri
https://www.researchgate.net/profile/Yuying_Liu2/publication/311792087_Resetting_microbiota_by_Lactobacillus_reuteri_inhibits_T_reg_deficiency-induced_autoimmunity_via_adenosine_A2A_receptors/links/585d561108aebf17d38a3279/Resetting-microbiota-by-Lactobacillus-reuteri-inhibits-T-reg-deficiency-induced-autoimmunity-via-adenosine-A2A-receptors.pdf
what could be better than having a symbiotic bacteria living in your gut that produces a very strong very selective antibiotic?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2494590/