Because it is not clear from your question which enzymes you want isolate, I have a remark: some enzymes capable to degrade alfatoxins can be exoenzymes:

. Its culture supernatant was able to degrade AFB1 effectively, whereas the viable cells and cell extracts were far less effective. Please see attached paper Cheng Ji, Yu Fan, Lihong Zhao (2016). It means that you have better determine which enzymes you want isolate.

Best regards

Vit

I strongly advocate to treat (if necessary) the contaminated feed ingredient instead of the whole mixed feed.

Most likely the proces will be time consuming and expensive and the nutritional value of the feedstuff will be altered/diminished.

Dr Mateju already indicated that your question lacks precision to give a precise answer.

I did not understand what you mean by extracting the enzyme from the bacteria because the localization of the enzyme in the bacteria will determines the method. However, the attached two review papers will answer your question:

1. Ji, C., Fan, Y., & Zhao, L. (2016). Review on biological degradation of mycotoxins. Animal Nutrition, 2(3), 127-133.

2. Loi, M., Fanelli, F., Liuzzi, V., Logrieco, A., & Mulè, G. (2017). Mycotoxin biotransformation by native and commercial enzymes: present and future perspectives. Toxins, 9(4), 111.

see this may help you

Article Degradation of ochratoxin A and other mycotoxins by Rhizopus isolates