Sesotho
is an indigenous cereal-based fermented drink traditionally produced in the mountain kingdom of Lesotho, Southern Africa. The present study sought to examine the microbial (bacterial and fungal) community composition of
Sesotho
at five fermentation stages in five different locations. Using culture-independent (Illumina sequencing) techniques it was found that the bacterial communities followed similar successional patterns during the fermentation processes, regardless of geographical location and recipe variation between breweries. The most abundant bacterial taxa belonged to the phyla Firmicutes (66.2% of the reads on average) and Proteobacteria (22.1%); the families Lactobacillaceae (54.9%), Enterobacteriaceae (14.4%) and Leoconostrocaceae (8.1%); and the genera
Lactobacillus
(54%),
Leuconostoc
(10.7%),
Leptotrichia
(8.5%), and
Weissella
(5.5%). Most fungal taxa were from the phyla Ascomycota (60.7%) and Mucoromycota (25.3%); the families Rhizopodaceae (25.3%), Nectriaceae (24.2%), Saccharomycetaceae (16%) and Aspergillaceae (6.7%); and the genera
Rhizopus
(25.3%),
Saccharomyces
(9.6%), and
Aspergillus
(2.5%). Lactic acid bacteria (LAB) such as
Enterococcus
,
Pediococcus
,
Lactobacillus
,
Leuconostoc
, and
Wiesella
; as well as yeasts belonging to the genus
Saccharomyces
, were dominant in all breweries during the production of
Sesotho
. Several pathogenic and food spoilage microorganisms (e.g.,
Escherichia
,
Shigella
,
Klebsiella
, etc.) were also present, but the study demonstrated the safety potential of the
Sesotho
fermentation process, as these microbial groups decline throughout
Sesotho
production. The functional profiles of the different brewing steps showed that the process is dominated by chemoheterotrophic and fermentative metabolisms. This study reveals, for the first time, the complex microbial dynamics that occur during
Sesotho
production.