Fructophilic fermentation of honeys from five different neotropical stingless bee species is determined by species-specific differences in lactic acid bacteria

Stingless bee honey (SBH) is a unique fermented food product with growing economic and nutritional relevance in tropical and subtropical regions. Although SBH harbors a fructophilic microbiota, key aspects of microbes/matrix association, including the composition of lactic acid bacteria (LAB) and their chemical contribution, remain largely unknown. Here, we characterised the abundance (by plate count) and diversity (by 16S rRNA sequencing) of LAB isolates from SBHs collected throughout the year from five species ( Tetragonisca fiebrigi , Scaptotrigona aff. postica , Melipona quadrifasciata quadrifasciata , M. torrida, and Tetragona clavipes ) and linked these communities to the honey´s chemical profile using GC-MS. SBH from S. aff. postica, M. quadrifasciata quadrifasciata , and M. torrida exhibited high LAB counts (6 7 log CFU/g) and were dominated by obligate fructophilic Nicoliella strains. This high Nicoliella abundance correlated with key fermentation metabolites, including mannitol, 3-phenyllactic acid, and indole-3-lactic acid. In contrast, honey from Tetragonisca fiebrigi exhibited lower counts ( ca. 4 log CFU/g), but greater diversity, featuring the genera Fructobacillus , Leuconostoc , and Lactococcus genera, and the absence of Nicoliella spp. and its associated metabolites. No LAB was isolated from Tetragona clavipes . LAB abundance correlates inversely with pH ( p < 0.05), supporting their role in fermentation processes. Our results provide the first detailed evidence establishing Nicoliella spp. as key contributors to SBH fermentation and metabolite profile. Furthermore, they revealed an overlooked LAB diversity. These findings are key to developing SBH quality standards, as they demonstrate the high LAB load and support the optimisation of chemical diversity associated with this spontaneously fermented food. • An overlooked FLAB diversity thrives in Neotropical stingless bee honeys (SBH). • Phylogenetic analysis revealed undescribed Nicoliella and Fructobacillus diversity. • Nicoliella spp. are key drivers of fructohilic fermentation in specific honeys. • FLAB metabolites underpin the health-promoting potential of fermented SBH. • Current regulations neglect the critical role of pH and the benign bacterial load of SBH.