In more recent research, the E.coli Nissle strain was found to produce the genotoxin colibactin which is potentially linked to colorectal cancer (
https://pubmed.ncbi.nlm.nih.gov/34378987/, among others). If this is a serious problem for the probiotic use is still unclear, but there is some research on how to replace it with a genetically modified strain that does not produce the genotoxin.