freeze drying is very safe process to keep the products free from any microbial proliferation and i suggest you to apply freeze drying

because any bacteria cannot grow without water, the water content has a significant effect on maintaining quality of the food. This explains why

freezing, dehydration, or concentration of foods increases shelf life and inhibits bacterial growth.

The freeze drying technique is the best way for keeping the bacteria

Thank you friends. So, freeze drying don't affect the viability of anaerobic bacteria.