Hi tomie46 -
1) I don't think those things would disrupt gut flora, except maybe magnesium citrate @ very high doses... since it is used as a laxative prior to procedures.
You could try switching to chelated forms of magnesium like malate or glycinate, or possibly even try lower doses of citrate.
Are you also on vitamin k2? Magnesium needs to be balanced out with vitamin D, calcium and k2, so you may have to adjust some of those doses.
I found
this supplementation guide very useful.
2) I don't take glutamine in isolation, but I do get the complete amino acid profile from dairy products, which already have generous amounts of glutamine present.
3) Have you tried making bone broth? Bone broth has natural glucosamine and chondratin, both of which are used to alleviate joint pains.
Best.