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Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl

Published on Feb 1, 2019in Food Microbiology 4.09
· DOI :10.1016/j.fm.2018.08.003
Ilenys M. Pérez-Díaz10
Estimated H-index: 10
(NCSU: North Carolina State University),
Janet S. Hayes (NCSU: North Carolina State University)+ 5 AuthorsMaria Andrea Azcarate-Peril4
Estimated H-index: 4
(UNC: University of North Carolina at Chapel Hill)
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Abstract
Abstract Limited documentation of the cucumber fermentation microbiome has impeded the understanding of the role of microbes on the quality of finished products. We characterized the microbiome of fresh and fermented cucumber samples using culture dependent and independent techniques, with an emphasis on the non-lactic acid bacteria (non-LAB) population. Insubstantial microbiome variations were observed among fresh cucumber types with Rhizobium (31.04%), Pseudomonas (14.08%) , Pantoea (9.25%), Stenotrophomonas (6.83%), and Acinetobacter (6.5%) prevailing. The relative abundance of LAB remained below 0.4% and 4.0% on fresh cucumbers and day 3 of the fermentations brined with 6% sodium chloride, respectively. Fermentation cover brine samples collected on day 1 harbored Pseudomonas , Pantoea , Stenotrophomonas , Acinetobacter , Comamonas , Wautersiella , Microbacterium , Flavobacterium , Ochrobactrum and the Enterobacteriaceae , Citrobacter , Enterobacter and Kluyvera . Plate counts for presumptive Klebsiella and Pseudomonas from fermentation cover brine samples reached 2.80 ± 0.36 and 2.78 ± 0.83 log of CFU/mL, respectively, in 30% and 60% of the nine tanks scrutinized with selective media. Both genera were found in cover brine samples with pH values at 4.04 ± 0.15. We aim at elucidating whether the low relative abundance of non-LAB in commercial cucumber fermentations, in particular Pseudomonas and Enterobacteriaceae , impacts the quality of fermented cucumbers.
  • References (36)
  • Citations (1)
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References36
Newest
Published on Sep 1, 2017in Foodborne Pathogens and Disease 2.00
FiedlerGregor1
Estimated H-index: 1
,
KabischJan1
Estimated H-index: 1
+ 4 AuthorsFranzCharles M.A.P.1
Estimated H-index: 1
Abstract Two hundred fresh produce samples (cucumber, carrots, herbs, leaf lettuce, and ready-to-eat mixed salad leaves) were obtained from retail in northern Germany in 2015. These were investigated for microbial contamination and the presence of foodborne pathogens, including Listeria monocytogenes, Salmonella serovars, presumptive Bacillus (B.) cereus, and Shiga toxin–producing Escherichia coli using culture-dependent (enrichment, plating on selective media) and -independent (real-time polyme...
Published on Aug 1, 2017in Molecular Nutrition & Food Research 4.65
Lauren C. Blekkenhorst7
Estimated H-index: 7
(UWA: University of Western Australia),
Richard Prince58
Estimated H-index: 58
(UWA: University of Western Australia)
+ 7 AuthorsCatherine P. Bondonno15
Estimated H-index: 15
(ECU: Edith Cowan University)
cope Nitrate from vegetables improves vascular health with short term intake. Whether this translates into improved long term health outcomes has yet to be investigated. To enable reliable analysis of nitrate intake from food records there is a strong need for a comprehensive nitrate content of vegetables database. Methods and results A systematic literature search (1980-2016) was performed using Medline, Agricola and CAB abstracts databases. The nitrate content of vegetables database contains 4...
Published on May 1, 2017in Food Microbiology 4.09
Ilenys M. Pérez-Díaz3
Estimated H-index: 3
(ARS: Agricultural Research Service),
Janet Hayes5
Estimated H-index: 5
(ARS: Agricultural Research Service)
+ 8 AuthorsZ. Lu8
Estimated H-index: 8
(KSU: Kennesaw State University)
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...
Published on Dec 1, 2016in Journal of Microbiology 2.32
Shin Ae Lee4
Estimated H-index: 4
(RDA: Rural Development Administration),
Ji-Young Park1
Estimated H-index: 1
(RDA: Rural Development Administration)
+ 5 AuthorsHang-Yeon Weon28
Estimated H-index: 28
(RDA: Rural Development Administration)
The microbiome in the rhizosphere–the region surrounding plant roots–plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culture-dependent approach, two culture media (Reasoner’s 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria...
Published on Oct 18, 2016in PeerJ 2.35
Torbjørn Rognes28
Estimated H-index: 28
(University of Oslo),
Tomas Flouri9
Estimated H-index: 9
(Heidelberg Institute for Theoretical Studies)
+ 2 AuthorsFrédéric Mahé18
Estimated H-index: 18
(TUK: Kaiserslautern University of Technology)
Background: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods: When searching nucleotide sequences, VSEAR...
Published on Sep 26, 2016in PLOS ONE 2.78
Andrea Ottesen15
Estimated H-index: 15
(CFSAN: Center for Food Safety and Applied Nutrition),
S. Gorham3
Estimated H-index: 3
(CFSAN: Center for Food Safety and Applied Nutrition)
+ 6 AuthorsJames Robert White1
Estimated H-index: 1
(CFSAN: Center for Food Safety and Applied Nutrition)
An important data gap in our understanding of the phyllosphere surrounds the origin of the many microbes described as phyllosphere communities. Most sampling in phyllosphere research has focused on the collection of microbiota without the use of a control, so the opportunity to determine which taxa are actually driven by the biology and physiology of plants as opposed to introduced by environmental forces has yet to be fully realized. To address this data gap, we used plastic plants as inanimate...
Published on Jan 1, 2016in Journal of Food Science 2.08
Eduardo Medina3
Estimated H-index: 3
(NCSU: North Carolina State University),
Ilenys M. Pérez-Díaz3
Estimated H-index: 3
(ARS: Agricultural Research Service)
+ 4 AuthorsMaria Andrea Azcarate-Peril4
Estimated H-index: 4
(UNC: University of North Carolina at Chapel Hill)
Fermented cucumber spoilage (FCS) characterized by rising pH and the appearance of manure- and cheese-like aromas is a challenge of significant economical impact for the pickling industry. Previous culture-based studies identified the yeasts Pichia manshurica and Issatchenkia occidentalis, 4 Gram-positive bacteria, Lactobacillus buchneri, Lactobacillus parrafaraginis, Clostridium sp., and Propionibacterium and 1 Gram-negative genus, Pectinatus, as relevant in various stages of FCS given their ab...
Published on Feb 1, 2015in Journal of Dairy Science 3.08
T.M. Scatamburlo2
Estimated H-index: 2
(UFV: Universidade Federal de Viçosa),
Anderson Keizo Yamazi7
Estimated H-index: 7
(UFV: Universidade Federal de Viçosa)
+ 2 AuthorsLuís Augusto Nero20
Estimated H-index: 20
(UFV: Universidade Federal de Viçosa)
Abstract Pseudomonas spp. are usually associated with spoilage microflora of dairy products due to their proteolytic potential. This is of particular concern for protein-based products, such as goat milk cheeses and fermented milks. Therefore, the goal of the present study was to characterize the proteolytic activity of Pseudomonas spp. isolated from goat milk. Goat milk samples (n = 61) were obtained directly from bulk tanks on dairy goat farms (n = 12), and subjected to a modified Internationa...
Published on Aug 1, 2014in Bioinformatics 4.53
Anthony Bolger10
Estimated H-index: 10
(MPG: Max Planck Society),
Marc Lohse20
Estimated H-index: 20
(MPG: Max Planck Society),
Bjoern Usadel15
Estimated H-index: 15
(MPG: Max Planck Society)
Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks...
Published on Jan 1, 2014in Nucleic Acids Research 11.15
Pelin Yilmaz16
Estimated H-index: 16
(MPG: Max Planck Society),
Laura Wegener Parfrey27
Estimated H-index: 27
(UBC: University of British Columbia)
+ 7 AuthorsFrank-Oliver Glckner57
Estimated H-index: 57
(MPG: Max Planck Society)
SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in t...
Cited By1
Newest
Published on Sep 1, 2019in International Journal of Food Microbiology 4.01
Eugenio Parente30
Estimated H-index: 30
,
Francesca De Filippis20
Estimated H-index: 20
(University of Naples Federico II)
+ 2 AuthorsTeresa Zotta20
Estimated H-index: 20
Abstract We present a new version of FoodMicrobionet, a database for the exploration of food bacterial communities. The database, available as an app built with the Shiny package of R, includes data from 44 studies and 2234 samples (food or food environment), covering dairy, meat, fruit and vegetables, cereal based and ready-to-eat foods. The interactive interface allows exploration of data, access to external resources (on line versions of the studies, sequence data on SRA, taxonomic databases)...
Xiaolin Ao4
Estimated H-index: 4
(Sichuan Agricultural University),
Junling Yan (Sichuan Agricultural University)+ -3 AuthorsLi He5
Estimated H-index: 5
(Sichuan Agricultural University)