Microbial Ecology Survey of Bacteria, Lactic Acid Bacteria, and Fungi in Fermented and Non-fermented Ready-to-Eat Food and Drink

Introduction: In fermented foods, starter cultures are added or natural populations are encouraged to grow; while in other foods microbes are present and are only considered problematic if they grow and spoil the food, produce toxins, or are inherently pathogenic to consumers. With the advent of next generation sequencing (NGS), it is now possible to determine the total microbiota of foods without having to culture specific bacteria on selective agar.

Purpose: NGS of marker genes for total bacteria, lactic acid bacteria, and fungi was performed to determine the variety of microbes present in fermented and non-fermented food types across different manufacturers.

Methods: DNA was extracted from samples of fermented cottage cheese, kombucha, and sour ales, as well as non-fermented guacamole and hummus. Samples were obtained from three manufacturers per type of food. PCR was performed with 16S V4 primers for total bacteria, 16S primers selective for lactic acid bacteria, and fungal ITS primers using the Fluidigm Access Array technology. Illumina sequencing was performed on pooled amplicons and sequence analyses were performed using QIIME v 1.9.

Results: Most sequences obtained for hummus and guacamole were chloroplast and mitochondrial sequences from the plants, herbs, and spices in the foods. Lactococcus lactis was predominant in cottage cheese, while Lactobacillus species and Pediococcus damnosus were present in sour ales. Brettanomyces bruxellensis was the predominant yeast in two of the three breweries, while the majority in the other was Saccharomyces cerevisiae. The greatest diversity and variability within and between manufacturers was found in the kombucha samples for bacterial, LAB, and fungal sequences.

Significance: Microbial ecology was distinct by food type, with the predominant microbes in fermented foods being those of starter cultures, both bacterial and fungal. Further work is needed to determine whether lower chloroplast levels in non-fermented plant-based foods could be an early indicator of spoilage.