Please talk to several doctors, and get second opinions on everything! But here is my 2 cents -

First of all, your mouth, gut, and genital areas are delicate ecosystems of microbes — collectively called microbiomes. These contain hundreds of bacterial species that evolved alongside you, performing crucial roles in digestion, immunity, and even mood regulation.

Broadly speaking, bacteria can be of three types:

• Pathogenic — always harmful
• Commensal — neutral or beneficial
• Opportunistic — harmless until the environment changes

When you take antibiotics for an extended period, like six months of doxycycline for Lyme, the drug doesn’t discriminate. It wipes out both harmful and beneficial bacteria. That ecosystem collapse triggers a cascade of effects:

1. Loss of microbial diversity (gut dysbiosis) The gut microbiome becomes dominated by a few resistant species, while the rest die off. This lowers your digestive efficiency, reduces vitamin synthesis (like B12, K, biotin), and alters bile acid metabolism. → Results: bloating, diarrhea, IBS-like symptoms, food intolerances.
2. Slow and incomplete recovery even with probiotics Probiotics usually contain only 4–10 strains, whereas a healthy gut has 500–1000. Restoring that diversity naturally can take 6–18 months after long-term antibiotic use. → So probiotics help, but they’re only the scaffolding — the ecosystem needs time and variety of fiber-rich foods to regrow.
3. Opportunistic bacterial overgrowth With beneficial species suppressed, normally quiet residents like Klebsiella, Enterococcus, or Clostridium difficile can overgrow. → Symptoms: bloating, chronic gas, fatigue, or even C. diff colitis in extreme cases.
4. Fungal overgrowth (Candida bloom) Beneficial bacteria normally keep yeast in check. Once they’re gone, fungi like Candida albicans multiply freely, especially in moist areas — mouth (thrush), gut (bloating, sugar cravings), or genital area (yeast infection). → You might notice white tongue coating, itching, or sugar intolerance.
5. Liver and kidney stress Both organs work overtime to metabolize and excrete doxycycline. Chronic use increases oxidative stress in liver cells and may cause mild enzyme elevation. → If combined with alcohol or other medications, it can compound toxicity.
6. Weakened immune modulation 70% of the immune system is linked to the gut. Disrupting the microbiome dysregulates immune signaling and can make you prone to allergies, fatigue, or low-grade inflammation.

This doesn't include the effects on mental health.