Potential of spontaneous microbial fermentation isolates to improve fermentation and cup quality of wet processed Arabica coffee (coffea arabica)

Abstract

Spontaneous wet processing of coffee currently practiced in Uganda is constrained by long processing times, losses, and inferior quality coffees. Starter cultures are nowadays used to control fermentation of foods. This study evaluated the predominant yeasts and bacteria in the spontaneous fermentation of Arabica coffee (Coffea arabica) from Bugisu and their potential use as starter cultures in the wet fermentation of coffee. A total of 21 samples of the fermenting mass of Arabica coffee (100 ml each) were used for isolation of predominant yeasts and bacteria during spontaneous fermentation. The isolates were grouped by cell morphology and biochemical features and then subjected to polymerase reaction (PCR) for confirmation of species. Genomic DNA of the organisms was extracted and the variable region 3 of 5.8S and 16S rRNA genes for yeast and bacteria respectively were amplified PCR using universal primers ITS1 and ITS4, and P16S and M26S, respectively. Representative isolates from each PCR profile were identified by sequencing using Sanger sequencing and the closest known relatives of the sequences obtained were retrieved from the National Centre for Biotechnology Information data base using a Basic Local Alignment Search Tool (BLAST). The predominant microorganisms were enriched and their effects on the fermentation process were determined. Controlled fermentation of pulped Arabica coffee (100 kg) was carried out. Physicochemical changes namely pectin, total soluble sugars, viscosity, hydrogen potential and titratable acidity were monitored in the fermenting mass using standard AOAC and ISO methods. Coffee beans from the controlled fermentation experiments were roasted at 210oC for 10 min, to medium dark roast profile and evaluated for the cup quality using the Specialty Coffee Association (SCA) cupping protocol. The yeasts Kazachstania exigua and Pichia kudriavzevii, and the bacteria Leuconostoc mesenteroides and Paenibacillus campinasensi were the predominant spp. in the in the spontaneous fermentation of C. arabica in Bugisu sub region. Mixed cultures performed better than single cultures in promoting fermentation.