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Exercise and diarrhea

The past few weeks I have been really trying to stay active. I was laid off from my job a few months ago and found myself struggling with weight and joint stiffness due to inactivity...my job was pretty active and you were on your feet all day. I do not do any strenuous exercising. Usually Pilates, yoga, workout DVDs and walking on the treadmill.

This morning I was on the treadmill, walking only, and had to stop because I had diarrhea all of a sudden. I also got diarrhea the other day while exercising as well. I am in remission and rarely have diarrhea so this is not normal for me at this time.

Has anyone had issues with this? Any tips on how to prevent it?

I have been job hunting and thought getting more active would help for when I head back to work as well...so that I'm not so exhausted after a full day of working.
It happens all the time to me. Just gotta plan it into your workout
Do you just pause the workout and go...then resume? Or should I take that as my body saying "that's enough of a workout for today"

This disease makes me question everything sometimes...so paranoid about throwing myself into a flare.