Microbial diversity and biochemical profiles during spontaneous fine-aroma cocoa fermentation in Northern Peru

Spontaneous fermentation is a key stage in cocoa processing, during which the main flavor and aroma precursor compounds are formed as a result of microbial activity. This study provides the first integrated characterization of microbial diversity and associated biochemical properties during the spontaneous fermentation of fine-aroma cocoa in the Amazonas region of northern Peru. Using culture-dependent methods combined with DNA barcoding, a dynamic community of bacteria, yeasts, and filamentous fungi was identified, with a total of 79 microbial species detected across 144 h of fermentation. Microbial diversity was highest during the early stages of the process (12–48 h), with Shannon index values ranging from 3.02 to 3.08; it gradually declined as temperature increased from 26 to 55 °C and pH decreased from 4.79 to 3.59. Biochemical characterization based on carbohydrate assimilation, ethanol tolerance, and pectinolytic activity allowed the identification of a select group of native microorganisms with high potential for use as starter cultures. Overall, these results provide a scientific basis for the development of locally adapted starter cultures aimed at improving the efficiency, consistency, and quality of the fermentation process in fine-aroma cocoa and chocolate production.