How processing methods affect the microbial community composition in a cereal-based fermented beverage

Traditionally fermented beverages significantly contribute to food security in Africa. The nutritional and sensory quality characteristics of these beverages are closely linked to the different microorganisms they contain. We studied the effect of processing methods on the microbial composition of Munkoyo, a cereal-based fermented beverage, in three Zambian agroecological zones. In Choma, porridge was made from maize grits to which a watery extract from Rhynchosia roots was added as a source of enzymes. In Nyimba, maize meal was used to make porridge, in which Rhynchosia roots were submerged overnight. In Kitwe, porridge from maize meal was cooked until caramelization, followed by submersion of Rhynchosia roots. Irrespective of processing method, final pH was 2.5–3.5, with the lowest value for Nyimba. Presence and abundance of 16S rRNA encoding DNA sequences of the microorganisms showed no clear clustering on basis of the processing method but significantly affected the operational taxonomic unit (OTU) composition (anosim, R_3,13 = 0.407, p < 0.05). The average Shannon indices, which indicate ecological diversity, were: Choma 1.14 ± 0.64, Nyimba 1.58 ± 0.23, and Kitwe 1.07 ± 0.95. Consequently, for industrial upscaling and quality standardization, specific combinations of different bacterial species can produce Munkoyo that addresses local consumer preferences.