Characterization of cucumber fermentation spoilage bacteria by enrichment culture and 16S rDNA cloning

Microbial and Biochemical Profile of Different Types of Greek Table Olives

Analysis of table olives microbiome using next-generation sequencing has enriched the available information about the microbial community composition of this popular fermented food. In this study, 16S and 18S rRNA sequencing was performed on table olives of five Greek popular cultivars, Halkidikis, Thassou, Kalamon, Amfissis, and Konservolia, fermented either by Greek style (in brine or salt-drying) or by Spanish style, in order to evaluate their microbial communities. Moreover, analytical methods were used to evaluate their biochemical properties. The prevailing bacterial species of all olives belonged to Lactobacillaceae, Leuconostocaceae, and Erwiniaceae families, while the most abundant yeasts were of the Pichiaceae family. Principal coordinates analysis showed a clustering of samples cured by salt-drying and of samples stored in brine, regardless of their cultivar. The biochemical evaluation of total phenol content, antioxidant activity, hydroxytyrosol, oleuropein, oleocanthal, and oleacein showed that salt-dried olives had low amounts of hydroxytyrosol, while Spanish-style green olives had the highest amounts of oleocanthal. All the other values exhibited various patterns, implying that more than one factor affects the biochemical identity of the final product. The protocols applied in this study can provide useful insights for the final product, both for the producers and the consumers.

Industrial Processing of Algerian Table Olive Cultivars Elaborated as Spanish Style

Olives from the Sigoise, Verdale, and Sevillana cultivars were elaborated as Spanish-style table olives by four Algerian factories, and the quality and food safety of the industrial table olives have been studied by the analysis of physicochemical and microbiological parameters. Differences were observed between the treatments carried out by the different factories throughout the manufacturing process, especially during the washing stage, but no significant differences were found between the analyzed samples for the concentration of sugars and polyphenols. The final pH values reached at the end of fermentation ranged between 5.04 and 4.27, and the titratable acidity was above 0.4% for all samples. Lactic and acetic acids were produced in mean concentrations of 0.68% and 0.21% as a result of lactic acid bacteria (LAB) and yeast metabolism, respectively. However, the presence of butyric, isobutyric, and propionic acids was also detected, and was related to the growth of undesirable spoilage microorganisms, responsible for secondary fermentations. The high-throughput sequencing of bacterial DNA suggested the dominance of LAB species belonging to genera Lactiplantibacillus, Leuconostoc, Pediococcus, Oenococcus, or Enterococcus. The Enterobacteriaceae family was detected during the first days of brining and in only one sample after 120 days of fermentation. Other spoilage microorganisms were found, such as Lentilactobacillus buchneri or the Pectinatus and Acetobacter genera, capable of consuming lactic acid and these played an essential role in the onset of spoilage. The Clostridium and Enterobacter genera, producers of butyric and propionic acids, were responsible for the malodorous fermentation present in the industrial samples that were analyzed. The study concluded that the safety of the table olives analyzed was compromised by the presence of undesirable microorganisms and microbial stability was not guaranteed. The elaboration process can be improved by reducing the washing steps and the time should be reduced to avoid the loss of fermentable matter, with the goal of reaching a pH < 4.0 after the fermentation and preventing the possibility of the growth of spoilage microorganisms and foodborne pathogens.

Pectinatus spp. - Unpleasant and recurrent brewing spoilage bacteria

Traditionally, beer has been recognised as a beverage with high microbiological stability because of the hostile growth environment posed by beer and increasing attention being paid to brewery hygiene. However, the microbiological risk has increased in recent years because of technological advances toward reducing oxygen in beers, besides the increase in novel beer styles production, such as non-pasteurised, flash pasteurised, cold sterilised, mid-strength, and alcoholic-free beer, that are more prone to spoilage bacteria. Moreover, using innovative beer ingredients like fruits and vegetables is an added cause of microbial spoilage. To maintain quality and good brand image, beer spoilage microorganisms are a critical concern for breweries worldwide. Pectinatus and Megasphaera are Gram-negative bacteria mostly found in improper brewing environments, leading to consumer complaints and financial losses. Because of the lack of compiled scientific knowledge on Pectinatus spoilage ability, this review provides a comprehensive overview of the occurrence, survival mechanisms, and the factors affecting beer spoilage Pectinatus species in the brewing process.

Bacteriophages Infecting Gram-Negative Bacteria in a Commercial Cucumber Fermentation

Cucumber fermentations are one of the most important vegetable fermentations in the United States. The fermentation is usually driven by lactic acid bacteria (LAB) indigenous to fresh cucumbers. But LAB are greatly outnumbered by many Gram-negative bacteria on fresh cucumbers, which may influence the growth of LAB and the incidence of bloater defect (hollow cavities formed inside fermented cucumbers) leading to serious economic loss to the pickle industry. Rapid elimination of Gram-negative bacteria is crucial to the dominance of LAB and the reduction of bloater defect in the fermentation. Various factors can affect the viability of Gram-negative bacteria in cucumber fermentation. Bacteriophages (phages) may be one of such factors. This study explored the abundance, diversity, and functional role of phages infecting Gram-negative bacteria in a commercial cucumber fermentation. Cover brine samples were taken from a commercial fermentation tank over a 30-day period. On day 1 and day 3 of the fermentation, 39 Gram-negative bacteria and 26 independent phages were isolated. Nearly 67% of Gram-negative bacterial isolates were susceptible to phage infection. Phage hosts include Enterobacter, Citrobacter, Escherichia, Pantoea, Serratia, Leclercia, Providencia, and Pseudomonas species. About 88% of the isolated phages infected the members in the family Enterobacteriaceae and 58% of phages infected Enterobacter species. Eight phages with unique host ranges were characterized. These phages belong to the Myoviridae, Siphoviridae, or Podoviridae family and showed distinct protein profiles and DNA fingerprints. The infectivity of a phage against Enterobacter cancerogenus was evaluated in cucumber juice as a model system. The phage infection at the multiplicity of infection 1 or 100 resulted in a 5-log reduction in cell concentration within 3 h and rapidly eliminated its host. This study revealed the abundance and variety of phages infecting Gram-negative bacteria, particularly Enterobacteriaceae, in the commercial cucumber fermentation, suggesting that phages may play an important role in the elimination of Gram-negative bacteria, thereby facilitating the dominance of LAB and minimizing bloater defect. To our knowledge, this is the first report on the ecology of phages infecting Gram-negative bacteria in commercial cucumber fermentations.

Comparative genetic and physiological characterisation of Pectinatus species reveals shared tolerance to beer-associated stressors but halotolerance specific to pickle-associated strains

Obligate anaerobic bacteria from the genus Pectinatus have been known to cause beer spoilage for over 40 years. Whole genome sequencing was performed on eleven beer spoilage strains (nine Pectinatus frisingensis, one Pectinatus cerevisiiphilus and one Pectinatus haikarae isolate), as well as two pickle spoilage species (Pectinatus brassicae MB591 and Pectinatus sottacetonis MB620) and the tolerance of all species to a range of environmental conditions was tested. Exploration of metabolic pathways for carbohydrates, amino acids and vitamins showed little difference between beer spoilage- and pickle spoilage-associated strains. However, genes for certain carbohydrate- and sulphur-containing amino acid-associated enzymes were only present in the beer spoilage group and genes for specific transporters and regulatory genes were uniquely found in the pickle spoilage group. Transporters for compatible solutes, only present in pickle-associated strains, likely explain their experimentally observed higher halotolerance compared to the beer spoilers. Genes involved in biofilm formation and ATP Binding Cassette (ABC) transporters potentially capable of exporting hop-derived antimicrobial compounds were found in all strains. All species grew in the presence of alcohol up to 5% alcohol by volume (ABV) and hops extract up to 80 ppm of iso-α-acids. Therefore, the species isolated from pickle processes may pose novel hazards in brewing.

Microbiota and Metabolite Profiling of Spoiled Spanish-Style Green Table Olives

The aim of the present study was to assess the malodorous spoilages of Spanish-style green table olives through microbial and metabolite composition using current measuring techniques (e.g., high-throughput DNA sequencing, headspace solid-phase microextraction combined with gas chromatography-mass spectrometry). Under different alkaline and washing conditions, the spoilage fermentations were reproduced with Gordal and Manzanilla olive cultivars using a low salt concentration (71 g L⁻¹ NaCl) in the initial brine. The degradation of lactic acid and significant increases in volatile fatty acids and phenols were found in all the spoiled samples in comparison with the unspoiled control samples. According to high-throughput DNA sequencing, Cardiobacteriaceae and Ruminococcus were the dominant bacteria in the spoiled samples. PLS regression and Pearson’s correlation coefficient analyses revealed positive and negative correlations among microbial communities, metabolites, and sensory spoilage descriptors. Notably, the “zapatera” descriptor was significantly associated with Propionibacterium, which was positively correlated with acetic acid, propionic acid, succinic acid, and methyl propanoate; while the “butyric” descriptor exhibited a significant positive relationship with the genus Ruminococcus, which gave an almost significant correlation with propionic and butyric acids.

Phenotypic and genotypic diversity of Lactobacillus buchneri strains isolated from spoiled, fermented cucumber

Lactobacillus buchneri is a Gram-positive, obligate heterofermentative, facultative anaerobe commonly affiliated with spoilage of food products. Notably, L. buchneri is able to metabolize lactic acid into acetic acid and 1,2-propanediol. Although beneficial to the silage industry, this metabolic capability is detrimental to preservation of cucumbers by fermentation. The objective of this study was to characterize isolates of L. buchneri purified from both industrial and experimental fermented cucumber after the onset of secondary fermentation. Genotypic and phenotypic characterization included 16S rRNA sequencing, DiversiLab® rep-PCR, colony morphology, API 50 CH carbohydrate analysis, and ability to degrade lactic acid in modified MRS and fermented cucumber media. Distinct groups of isolates were identified with differing colony morphologies that varied in color (translucent white to opaque yellow), diameter (1 mm-11 mm), and shape (umbonate, flat, circular or irregular). Growth rates in MRS revealed strain differences, and a wide spectrum of carbon source utilization was observed. Some strains were able to ferment as many as 21 of 49 tested carbon sources, including inulin, fucose, gentiobiose, lactose, mannitol, potassium ketogluconate, saccharose, raffinose, galactose, and xylose, while others metabolized as few as eight carbohydrates as the sole source of carbon. All isolates degraded lactic acid in both fermented cucumber medium and modified MRS, but exhibited differences in the rate and extent of lactate degradation. Isolates clustered into eight distinct groups based on rep-PCR fingerprints with 20 of 36 of the isolates exhibiting >97% similarity. Although isolated from similar environmental niches, significant phenotypic and genotypic diversity was found among the L. buchneri cultures. A collection of unique L. buchneri strains was identified and characterized, providing the basis for further analysis of metabolic and genomic capabilities of this species to enable control of lactic acid degradation in fermented plant materials.

Consecutive Outbreaks of Enterotoxigenic Escherichia coli O6 in Schools in South Korea Caused by Contamination of Fermented Vegetable Kimchi

BACKGROUND

Two outbreaks of gastroenteritis occurred in South Korea, affecting a middle school in the Jeollanam-do province in 2013 (Outbreak 1) and 10 schools in the Incheon province in 2014 (Outbreak 2). We investigated the outbreaks to identify the pathogen and mode of transmission.

METHODS

A retrospective cohort study was conducted in the Outbreak 1; and case-control studies were performed for the Outbreak 2. Samples from students, environments, and preserved food items were collected and pulsed-field gel electrophoresis (PFGE) was conducted to identify strains of pathogen.

RESULTS

We identified 167 and 1022 students who met the case definition (≥3 loose stools in any 24-h period) in the Outbreaks 1 and 2, respectively. The consumption of cabbage kimchi and young radish kimchi were significantly associated with the illness. Adjusted odds ratios of kimchi were 2.62-11.74. In the Outbreak 1, cabbage kimchi was made and consumed in the school restaurant and in the Outbreak 2, young radish kimchi was supplied by food company X and distributed to all the 10 schools in the Incheon province. Enterotoxigenic Escherichia coli (ETEC) O6 was isolated from fecal samples in 375 cases (33.9%) and from kimchi samples. PFGE patterns of the outbreak strains isolated from cases and food were indistinguishable in each outbreak.

CONCLUSION

The suspected food vehicle in these two consecutive outbreaks was kimchi contaminated with ETEC O6. We recommend continued monitoring and stricter sanitation requirements for the food supply process in Korea, especially in relation to kimchi.

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods

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 ability to metabolize lactic acid. It was the objective of this study to augment the current knowledge of FCS using culture-independent methods to microbiologically characterize commercial spoilage samples. Ion Torrent data and 16S rRNA cloning library analyses of samples collected from commercial fermentation tanks confirmed the presence of L. rapi and L. buchneri and revealed the presence of additional species involved in the development of FCS such as Lactobacillus namurensis, Lactobacillus acetotolerans, Lactobacillus panis, Acetobacter peroxydans, Acetobacter aceti, and Acetobacter pasteurianus at pH below 3.4. The culture-independent analyses also revealed the presence of species of Veillonella and Dialister in spoilage samples with pH above 4.0 and confirmed the presence of Pectinatus spp. during lactic acid degradation at the higher pH. Acetobacter spp. were successfully isolated from commercial samples collected from tanks subjected to air purging by plating on Mannitol Yeast Peptone agar. In contrast, Lactobacillus spp. were primarily identified in samples of FCS collected from tanks not subjected to air purging for more than 4 mo. Thus, it is speculated that oxygen availability may be a determining factor in the initiation of spoilage and the leading microbiota.

Presence of toxic microbial metabolites in table olives

Table olives have an enormous importance in the diet and culture of many Mediterranean countries. Albeit there are different ways to produce this fermented vegetable, brining/salting, fermentation, and acidification are common practices for all of them. Preservation methods such as pasteurization or sterilization are frequently used to guarantee the stability and safety of fermented olives. However, final products are not always subjected to a heat treatment. Thus, microbiota is not always removed and appropriate levels of acidity and salt must be obtained before commercialization. Despite the physicochemical conditions not being favorable for the growth of foodborne pathogens, some illness outbreaks have been reported in the literature. Street markets, inappropriate manipulation and storage conditions were the origin of many of the samples in which foodborne pathogens or their metabolites were detected. Many authors have also studied the survival of pathogens in different styles of table olive elaboration, finding in general that olive environment is not appropriate for their presence. Inhibitory compounds such as polyphenols, low availability of nutrients, high salt content, low pH levels, bacteriocins, or the addition of preservatives act as hurdles against undesirable microorganisms, which contribute to obtaining a safe and good quality product.

Phenotypic and genotypic identification of lactic acid bacteria isolated from traditional pickles of the Çubuk region in Turkey

A total of 152 lactic acid bacteria (LAB) were isolated from pickles produced in the Ankara-Çubuk region. These isolates were clustered into eight groups on the basis of their phenotypic characteristics including cell morphology, CO2 production from glucose, growth at 10 and 45 °C, growth in 6.5 % NaCl, and growth at pH 9.6. API 50 CH carbohydrate fermentation test, 16S ribosomal RNA (rRNA) sequence analysis, and sodium dodecyl sulfate-acrylamide gel electrophoresis (SDS-PAGE) whole-cell protein profile analysis were also performed for precise identification of the isolates at the species level. Molecular identification revealed that the most prevalent LAB species involved in pickle fermentation were Pediococcus ethanolidurans (46 isolates, 30.3 %), Lactobacillus brevis (37 isolates, 24.3 %), Lactobacillus plantarum (37 isolates, 24.3 %), and Lactobacillus buchneri (15 isolates, 9.9 %). Other LAB were found in minor frequencies such as Pediococcus parvulus (8 isolates, 5.3 %), Lactobacillus namurensis (6 isolates, 3.9 %), Lactobacillus diolivorans (1 isolate, 0.7 %), Lactobacillus parabrevis (1 isolate, 0.7 %), and Enterococcus casseliflavus (1 isolate, 0.7 %). When results of phenotypic and genotypic identification methods were compared, differences in the species distribution of LAB associated with pickles were defined between the API and the 16S rRNA sequencing. The API 50 CHL test coincided with the 16S rRNA results in 71 out of the 152 tested isolates, indicating that API gave unreliable identification results. A clear correlation could not be found between the results of whole-cell SDS profiles and 16S rRNA sequencing. Therefore, molecular characterization by 16S rRNA sequencing was considered to be the most reliable method for identifying isolates. The results presented in this work provide insight in to the LAB population associated with traditional Çubuk pickles and constitute a LAB strain resource for further studies involving the development of starter cultures.