Recovery plan for 9yo following antibiotics for Lyme

ACK

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My 9 year old will be on doxycycline, a broad spectrum antibiotic, for 28 days due to Lyme infection that exhibited as fluid in the knee. This is his first ever time on antibiotics. I haven't had any since Bush was president and even then extremely rarely. His little brother has also never had any antibiotics. Everyone's breastfed with vaginal births, an unbroken chain on my maternal side. We're pretty healthy people, particularly as far as digestive, skin, and reproductive health so I'm pretty confident the microbiome in the living environment is fairly strong.

I'm hesitant to do a commercial probiotic for him as I don't think that will have anything close to the diversity of what he had prior to the antibiotic. Is it possible that simply by having his food prepared by us, bathing with his little brother, skin contact, etc., he might repopulate with the family strain organically? We're not filthy but not overly hygienic. He's not a picky eater and is happy to have high fiber fruits, veggies, and beans. Absolutely clueless as to how his gut will repopulate left to its own devices.

Any insight appreciated. Thanks!
 
Is it possible that simply by having his food prepared by us, bathing with his little brother, skin contact, etc., he might repopulate with the family strain organically?
That may result in mild improvements, but FMT is the only thing that comes close to being a complete microbiome restoration method. The FAQ page of the wiki covers this: https://humanmicrobiome.info/faq/
 
I had Lyme disease and had rocky mountain spotted fever with it. I was on doxycycline for 4 months. I did have an issue with candida afterwards and had to follow a candida diet for a month and take an antifungal. Lots of plain kefir, meat and low sugar veg. It was boring but it worked. My microbiome ultimately recovered very quickly. Even after a history of many times taking antibiotics. I took refrigerated acidopholus and lived the life of a normal 14 year old. My stomach and digestion and regularity did not suffer until 20 years later when I got c diff from clindamycin. I'm only back here again because I was given flagyl then caught norovirus a week later and have been sick ever since (6 weeks) and was hospitalized for a week over Christmas. I guess I'm saying unless it's obviously broken, it will likely fix itself. FMT is not without risks, even if you are being as safe as I have been screening your donor. I wouldn't be taking the risk myself if my life wasn't already pretty much ruined.
 
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