Deep microbial community profiling along the fermentation process of pulque, a biocultural resource of Mexico

The biggest non-tree perennial plant species endemic to Mexico were called metl in the Nahua culture; during colonial times, renamed with the Antillean word maguey. Carl von Linné finally renamed them as Agave, a Greek-Latin root word meaning admirable. Since pre-Columbian times, one of the major products obtained from some Agave species is the fermented beverage called pulque or octli. This beverage represents an ancient biotechnological development obtained by the natural fermentation of mead from such plants. Pulque played a central role in Mexican pre-Columbian cultures, while in recent times, there has been a renewed interest in it, due to its high content in nutrients and probiotics. In this study, we used massive sequencing of the 16S rRNA gene and the ribosomal internal transcribed spacer (ITS) to profile the pulque microbiome. We identified 2,855 bacteria operational taxonomic units (OTUs) and 1,494 fungi species in the pulque fermentation. Our results provide the most diverse catalog of microbes during pulque production reported so far. These findings allowed us to identify previously unidentified and core microbes resilient during pulque production, with the potential to be used as fermentation stage biomarkers. We confirmed previous reports of pulque microbes and discovered new ones like the bacteria Sphingomonas and Weisella. Among fungi we found that Saccharomyces cerevisiae was second to Candida zemplina in the studied pulque samples.