Just something to note about Yogurt for dogs, most importantly dogs with ME. It does not hurt( but maybe could so do be aware?)them but does not offer probiotics- humans and dogs have different bacterial flora in their intestines. You could try Fortiflora ot Prostora if you want probiotics for your dog. Yogurt also has lactose and dogs can suffer from lactose intolerance, just like humans, so you do need to be mindful of the symptoms of Lactose Intolerance- allergies, bloating, vomiting, diarrhea; some of the same symptoms you may be seeing in ME dogs cause by yogurt-just be careful with Yogurt. The other problem with human yogurt is your introducing a bacteria that the dog does not have, and this is a graver issue for an ME dog if they aspirate.

From Dr Kathy: Giving Fortiflora, Prostora, or another canine probiotic during and a few weeks after antibiotics a good idea, although, it’s not generally done by all dvm’s. We usually suggest NOT giving at same time as antibiotics; give in middle of day.

There are several premium dog foods that contain Probiotics:
The reason is cost: The probiotics themselves as well as the process utilized to add them to dog foods are expensive. As a result, it’s currently only super premium brand dog foods that contain probiotics. The following is a partial list of probiotic dog foods:
Before Grain
Blue Buffalo
Chicken Soup for the Dog Lover’s Soul
Eagle Holistic Select
Eagle Pack
Earthborn Holistic
Flint River Ranch
Fromm Four Star Nutritionals
Horizon Pet Nutrition
Nature’s Variety
Precise Plus
Taste of the Wild

It does take time for the GI tract to “balance” itself, so 6 weeks would probably be good. I wonder if you gave the probiotic in applesauce, if that would help it “slide down” more easily.