title: Reassessment of the succession of lactic acid bacteria in commercial cucumber fermentations and physiological and genomic features associated with their dominance.
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.
authors.affiliation: USDA-Agriculture Research Service, SAA, Food Science Research Unit, 322 Schaub Hall-NCSU, Raleigh, NC, 27695, USA. Electronic address: Ilenys.Perez-Diaz@ars.usda.gov.
authors.forename: I M
authors.initials: IM
authors.lastname: Pérez-Díaz
authors.affiliation: USDA-Agriculture Research Service, SAA, Food Science Research Unit, 322 Schaub Hall-NCSU, Raleigh, NC, 27695, USA.
authors.forename: J
authors.initials: J
authors.lastname: Hayes
authors.affiliation: Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA; Department of Food Biotechnology, Instituto de la Grasa, (CSIC), Universitary Campus Pablo de Olavide, Building 46, Seville, 41013, Spain.
authors.forename: E
authors.initials: E
authors.lastname: Medina
authors.affiliation: Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: K
authors.initials: K
authors.lastname: Anekella
authors.affiliation: Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: K
authors.initials: K
authors.lastname: Daughtry
authors.affiliation: Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: S
authors.initials: S
authors.lastname: Dieck
authors.affiliation: Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: M
authors.initials: M
authors.lastname: Levi
authors.affiliation: Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: R
authors.initials: R
authors.lastname: Price
authors.affiliation: Microbiome Core Facility, Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
authors.forename: N
authors.initials: N
authors.lastname: Butz
authors.affiliation: Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, 30144, USA.
authors.forename: Z
authors.initials: Z
authors.lastname: Lu
authors.affiliation: Microbiome Core Facility, Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
authors.forename: M A
authors.initials: MA
authors.lastname: Azcarate-Peril
mesh_terms: D018553:Cucumis sativus / Q000382:microbiology*; D004269:DNA, Bacterial; D005285:Fermentation; D005516:Food Microbiology; D023281:Genomics; D007218:Industrial Microbiology; D056546:Lactobacillales / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology*; D017045:Lactococcus / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D007934:Leuconostoc / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D064307:Microbiota / Q000235:genetics / Q000502:physiology; D010376:Pediococcus / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial
keywords: Cucumber fermentation; Dominance; Genome comparative analysis; Lactobacillus pentosus; Lactobacillus plantarum; Microbiota