- Although Jiuqu will contain its own distinctive, region-specific mix of microorganisms, the temperature schemes involved in preparation directly manipulate the microbial ecology, e . g . " Aspergillus oryzae " and species of " Actinomucor " and " Mucor " prefer lower temperatures than " Rhizopus oryzae ".
- Both substrate and incubation phases can be adjusted to favour the growth of certain species of molds, e . g . " Rhizopus " and " Mucor " prefer higher water activities and temperatures to " Aspergillus ", whilst " Mucor " and " Actinomucor " prefer substrates richer in protein.
- In turn the starch ingredients used also alter the microbial ecology dictating both the type and amount of metabolites present, e . g . " Aspergillus oryzae " and " Rhizopus oryzae " both produce more starch degrading enzymes and are found commonly on 100 % flour substrates, whilst " Actinomucor " and " Mucor " produce more proteolytic and lipolytic enzymes and are more abundant when pulse flours are added.