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.
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.