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

Abstract

Our approach allowed the identification of a broader microbial diversity in Pulque • We increased 4.4 times bacteria genera and 40 times fungal species detected in mead. • Newly reported bacteria genera and fungal species associated to Pulque fermentationAbstract Some of the biggest non-three plants endemic to Mexico were called metl in the Nahua culture. During colonial times they were renamed with the antillan word maguey . This was changed again by Carl von Linné who called them Agave (a greco-latin voice for admirable). For several Mexican prehispanic cultures, Agave species were not only considered as crops, but also part of their biocultural resources and cosmovision. Among the major products obtained from some Agave spp since pre-hispanic times is the alcoholic beverage called pulque or octli . This beverage represents a precolumbian biotechnological development obtained by the natural fermentation of the mead ( aguamiel ) from such plants. The pulque played a central role in mexican prehispanic cultures, mainly the Mexica and the Tolteca, where it was considered as sacred. For modern Mexicans, pulque is still part of their heritage and, in recent times, there has been a renewed interest in this ancient beverage, due to its high content in nutrients such as essential amino acids. We focus this study in the microbial diversity involved in pulque fermentation process, specially because it is still produced using classic antique technologies,.In this work, we report the microbiome of pulque fermentation stages, using massive sequencing of the 16S rRNA gene and the internal transcribed spacer (ITS) for describing bacterial and fungal diversity and dynamics along pulque production. In this study, we are providing the most diverse catalogue of microbes during pulque production with 57 identified bacterial genus and 94 fungal species, these findings allowed us to identify core microbes resilient during pulque production which point to be potential biomarkers exclusive to each fermentation stage.

Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing

“…Although aguamiel has been a suspected reservoir of Z. mobilis, isolation and detection have remained elusive 17,21,24,25,47 . For instance, Z. mobilis was not detected in aguamiel from Agave atrovirens and Agave salmiana across four seasons using 16S rDNA sequencing and denaturing gradient gel electrophoresis 24 , or from aguamiel from three different locations in Hidalgo State using highthroughput 16S rDNA amplicon sequencing 25 . However, Z. mobilis was identified from aguamiel using selective media, though without validation of species identity with 16S rDNA sequencing 12 .…”

“…1, 2). Importantly, these genera have been found in high abundance in aguamiel and pulque [23][24][25]48 . Temporal shifts in microbial composition during fermentation are consistent with most traditionally fermented foods and beverages 4,10 .…”

“…The thermotolerant yeast K. marxianus was also present at ≥ 0.1% during all stages of fermentation. K. marxianus has been previously identified from aguamiel and pulque 18,25,56,57 , as well as from agave used to ferment other traditionally distilled beverages 15 , and can ferment a more diverse and complex set of substrates than Saccharomyces species [58][59][60][61] . The observation that Saccahromyces species were not significantly correlated with ethanol production, but K. marxianus was, may suggest unequal roles for yeasts in alcohol production during pulque fermentation.…”

“…Studies focused on the microbial diversity of pulque have used traditional culture-based approaches 14,15,23 , and more recently, high-throughput 16S/ITS rDNA metagenomics sequencing 24,25 . However, whole-genome shotgun metagenomic sequencing has not been applied to study the microbial and metabolic diversity of pulque fermentation.…”