Looking at microbes in a natural pickle

Very little is known about the microbiomes involved in making pickles, sauerkraut and other fermented vegetables by natural fermentation where no starter microbial cultures or other media are used.

Now, University of Massachusetts Amherst food scientists have mapped and characterised microbial populations in a vegetable fermentation facility and report that its microbiome was distinct between production and fermentation areas and that the raw vegetables themselves were the main source of fermentation-related microbes in production areas rather than handling or other environmental sources.

Real Pickles is a worker-owned cooperative in Greenfield, Massachusetts, and makes pickles, sauerkraut and other fermented vegetables the old-fashioned way — by natural fermentation.

Company founder Dan Rosenberg said, “It’s fascinating to learn about the influence of fresh vegetables in establishing our facility’s microbiome and suggests that our use of organic vegetables is important to contributing a diverse microbial community to support fermentation. It raises interesting questions about how we can further improve our production practices to be producing fermented and probiotic foods of the highest quality. We’re excited to participate in research that improves understanding of fermented food production and nutrition.”

A state-of-the-art approach, using high-throughput sequencing and genomics, was used to identify the microbial species present instead of culturing the microbes. This allowed the team to quickly identify more microbes than conventional methods, to estimate their relative numbers, predict their likely function and determine the flow of microbes into and within the facility.

The researchers report that Leuconostoc and Lactobacillaceae dominated all surfaces where spontaneous fermentation occurs. Also, they found that “wall, floor, ceiling and barrel surfaces host unique microbial signatures”.