Spontaneous fermentation or traditional method of preserving indigenous foods using several microorganisms, is frequently practiced in the marginal world. Fermented seeds and milk are mostly consumed in the form of food condiments and desserts in Africa, Asia and others parts of world. Our previous studies deal with the production of Bacteriocin-Like Inhibitory Substances by Bacillus from fermented food and quality of fermented milk consumed in Burkina Faso. The rep-PCR and sequencing were used to characterize thirty eights strains isolated various fermented foods from Burkina Faso. Phylogenetic tree were constructed by the neighbour-joining method based on 16S or 26S rRNA genes sequences using MEGA X. Based on colonies characteristics and cells morphology, biochemical tests and gene sequencing, the isolates were identified as Bacillus cereus sensu lato (13), Bacillus pumilus group (03) with one strain (LCG1) presumed LAB was identified as Bacillus australimaris or Bacillus pumilus by 16S rRNA sequencing, Enterococcus durans (03), Lactobacillus paracasei (03), Lactobacillus plantarum (04), Leuconostoc pseudomesenteroides (01), Saccharomyces cerevisiae (04), Kluyveromyces marxianus (01), Candida tropicalis (01), Pichia kudriavzevii (01), Clavispora lusitaniae (02), Rhodotorula mucilaginosa (01) and, Cyberlindnera fabianii (01). Several microorganisms with potential technological interest are housed in fermented foods from Burkina Faso. These microorganisms are responsible for the fermentation of food through their enzymatic activity, leading to production of fermented food with desirable organoleptic characteristics, improved food safety, the enrichment of nutrients and the promotion of health of consumers.

Fermented Foods, Biodiversity, Bacillus, Lactic Acid Bacteria, Yeast, Rep-PCR