Microbial ecology of cassava beer with indigenous inoculum

Background/Question/Methods Cassava beer, chicha, is consumed daily by indigenous Shuar populations living in the Ecuadorian Amazon. A dietary staple, fermentation of cassava tuber (Manihot escuelenta) improves nutritional quality and flavor relative to the raw plant while extending shelf life in a tropical climate. Chicha is a potential source of inoculum for the microbiome (host-associated microbes) of the Shuar people.  Brew-mistresses of each house prepare the beverage by boiling the roots and mashing into a paste while masticating several pieces before adding them to the mash as it cools. The saliva-inoculated mash is fermented for two days and consumed gradually. This process repeats every 1-2 weeks. This research tests the hypothesis that 1) microbial communities are more similar between a brew-mistress and her fermented culture relative to the ferment of her neighbor, and 2) intra-community ferment microbial communities are more closely related to each other relative to a ferment in a neighboring village. This prediction is founded on the island biogeography model of community assembly, where the saliva and chicha of the brew-mistresses represent distinct island habitats. Three fermented chicha samples were collected from eight households in two neighboring villages in the province Morona-Santiago, Ecuador. Three saliva samples were collected from respective brew-mistresses.

Results/Conclusions Microbial DNA was extracted and amplified with bacterial specific 16S primers adapted for high-throughput Illumina sequencing. Yeast from serial dilutions of chicha were grown on 2% maltose-agar culture media and quantified after 3 days at 30°C, (average 700CFU/mL) and genomic DNA extracted for further analysis. All samples are within a 4.0-4.5pH range, indicating maturity of ferment culture. To model the metacommunity ecology of chicha and saliva at the household and village level, I will identify community composition and calculate metrics of community similarity between island habitats.  Transfer of saliva microbes to the chicha during brewing and chicha microbes to the mouth during consumption, creates an opportunity for cyclical interactions between the two habitat types. The brew-mistress and her unique ferment can be visualized as habitats with a “short distance” due to high frequency of dispersal events relative to the “long distance” or less frequent interaction with ferments of her neighbor. Quantifying this relationship through microbial community similarity can lead to improved understanding of spatial and temporal dynamics between the human microbiome and a dispersal-linked environmental habitat. This research applies island biogeography to model metacommunity ecology and explain patterns of genetic overlap in distinct microbial habitats.