Reassessment of the succession of lactic acid bacteria in commercial cucumber fermentations and physiological and genomic features associated with their dominance

Authors: Perez Diaz, Ilenys; Hayes, Janet; MEDINA-PRADAS, EDUARDO - Instituto De La Grasa; ANEKELLA, KARTHEEK - North Carolina State University; DAUGHTRY, KATHERINE - North Carolina State University; DIECK, SUSAN - North Carolina State University; LEVI, MEREDITH - North Carolina State University; PRICE, ROBERT - North Carolina State University; BUTZ, NATASHA - University Of North Carolina; LU, ZHONGJING - Kennesaw State University; AZCARTE-PERIL, M. ANDREA - University Of North Carolina

Submitted to: Food Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2016
Publication Date: 5/1/2017
Publication URL: https://handle.nal.usda.gov/10113/5598350
Citation: Perez Diaz, I.M., Hayes, J.S., Medina-Pradas, E., Anekella, K., Daughtry, K.V., Dieck, S., Levi, M., Price, R., Butz, N., Lu, Z., Azcarte-Peril, M. 2017. Reassessment of the succession of lactic acid bacteria in commercial cucumber fermentations and physiological and genomic features associated with their dominance. Food Microbiology. 63:217-227. https://doi.org/10.1016/j.fm.2016.11.025.
DOI: https://doi.org/10.1016/j.fm.2016.11.025

Interpretive Summary: A re-assessment of the microbial population present in natural and modern cucumber fermentations was conducted to gain a more detail and in-depth understanding of the pickling process as it is used today. Emphasis was given to those microbes previously known to exist in cucumber fermentations and those that are closely related. A total of eight commercial cucumber fermentation tanks were included in the study. It was learned that the dominant microbes in such fermentations are, in order of prevalence, Lactobacillus pentosus, Lb. plantarum, Lb. brevis, Weissella, Pediococcus ethanolidurans, Leuconostoc and Lactococcus. Lb. namurensis, Bacillus sp., Lb. buchneri, Lb. paracollinoides, Lb. zymae and Streptococcus parasanguinis. These microbes were detected well after the bulk of the sugars was converted to lactic acid. Observations obtained from the genome sequences corresponding to the microbes found in commercial fermentations suggest that Lb. pentosus and Lb. plantarum have unique genome features that allow them to better compete in cucumber fermentations.

Technical Abstract: A compositional re-assessment of the microbiota present in commercial cucumber fermentation using culture independent and dependent methods was conducted, with emphasis on lactic acid bacteria (LAB). Two commercial cucumber fermentation tanks were monitored by measuring pH, dissolved oxygen and temperature, and used as sources of samples for microbial plating, genomic DNA extraction and measurement of organic acids and carbohydrates by HPLC. Six additional commercial tanks were included to identify the dominant microorganisms using molecular methods. A comparative analysis of the publically available genome sequences corresponding to the LAB found in cucumber fermentations was completed to gain an understanding of genomic features possibly enabling dominance. Analyses of the microbiota suggest Lactobacillales prevail in cucumber fermentations, including in order of prevalence Lactobacillus pentosus, Lb. plantarum, Lb. brevis, Weissella spp., Pediococcus ethanolidurans, Leuconostoc spp. and Lactococcus spp. It was observed that Lb. pentosus and Lb. plantarum have comparatively larger genomes, higher gene counts, uniquely distribute the ribosomal clusters across the genome as opposed to close to the origin of replication, and possess more predicted amino acids prototrophies and selected biosynthesis related genes. It is theorized that Lb. pentosus and Lb. plantarum dominance in cucumber fermentations is the result of their genetic make-up.