Asslamo Allaikum,
There are plenty of "Friendly" bacteria living in human body such as Lactobacillus acidophilus which naturally lives in Human intestines and other parts of the body. It is routinely added to Yogurts, Lassi and other products and to the best of my knowledge nobody has declared it Haram.
Its usually grown as a culture in labs and added to your products and not taken from guts of dead people : - )
Bifidobacterium is also in the same class of Probiotics as Lactobacillus acidophilus just discovered much later in 1960's!
If you make Yogurt at home these Probiotics naturally occur that's why in our (Indian/Pakistani) culture Yogurt is used heavily and been part of our tradition for thousands of years. Common commercially available Yogurt is stripped of these Probiotics and then they added it back to you and charge you a premium price!
There are plenty of unverified reports which explain an explosion in Autism in our times to not having a healthy balance of Probiotics in the digestive system of suffering children.
The Ayurvedic system of medicine relies on restoring the balance in the gut for many ailments and Parents report a marked improvement in the behavior of their autistic children with:
- Cutting out Gluten
- Introducing Probiotics