Microbial dynamics and biodiversity in table olive fermentation: culture-dependent and -independent approaches

Impact of lactic acid bacteria inoculation on fungal diversity during Spanish-style green table olive fermentations

This study delved into the evolution of fungal population during the fermentation of Spanish-style green table olives (Manzanilla cultivar), determining the influence of different factors such as fermentation matrix (brine or fruit) or the use of a lactic acid bacteria inoculum, on its distribution. The samples (n = 24) were directly obtained from industrial fermentation vessels with approximately 10.000 kg of fruits and 6.000 L of brines. Our findings showcased a synchronized uptick in lactic acid bacteria counts alongside fungi proliferation. Metataxonomic analysis of the Internal Transcribed Spacer (ITS) region unearthed noteworthy disparities across different fermentation time points (0, 24, and 83 days). Statistical analysis pinpointed two Amplicon Sequence Variants (ASV), Candida and Aureobasidium, as accountable for the observed variances among the different fermentation time samples. Notably, Candida exhibited a marked increase during 83 days of fermentation, opposite to Aureobasidium, which demonstrated a decline. Fungal biodiversity was slightly higher in brines than in fruits, whilst no effect of inoculation was noticed. At the onset of fermentation, prominently detected genera were also Mycosphaerella (19.82 %) and Apohysomyces (16.31 %), hitherto unreported in the context of table olive processing. However, their prevalence dwindled to nearly negligible levels from 24th day fermentation onwards (<2 %). On the contrary, they were replaced by the fermentative yeasts Saccharomyces and Isstachenkia. Results obtained in this work will be useful for designing new strategies for better control of table olive fermentations.

Monitoring the yeasts ecology and volatiles profile throughout the spontaneous fermentation of Taggiasca cv. table olives through culture-dependent and independent methods

Taggiasca table olives are typical of Liguria, a Northwestern Italian region, produced with a spontaneous fermentation carried out by placing the raw drupes directly into brine with a salt concentration of 8-12 % w/v. Such concentrations limit the development of unwanted microbes and favor the growth of yeasts. This process usually lasts up to 8 months. Yeasts are found throughout the entire fermentation process and they are mainly involved in the production of volatile organic compounds, which strongly impact the quality of the final product. The aim of this study was to evaluate the dynamics of autochthonous yeasts in brines and olives in a spontaneous process with no lye pre-treatment or addition of acids in the fermenting brine with 10 % NaCl (w/v) in two batches during 2021 harvest. Three hundred seventy-three yeast colonies were isolated, characterized by rep-PCR and identified by the D1/D2 region of the 26S rRNA gene sequencing. Mycobiota was also studied by 26S rRNA gene metataxonomics, while metabolome was assessed through GC-MS analysis. Traditional culture-dependent methods showed the dominance of Candida diddensiae, Wickerhamomyces anomalus, Pichia membranifaciens and Aureobasidium pullulans, with differences in species distribution between batches, sampling time and type of sample (olives/brines). Amplicon-based sequencing confirmed the dominance of W. anomalus in batch 1 throughout the entire fermentation, while Cyteromyces nyonsensis and Aureobasidium spp. were most abundant in the fermentation in batch 2. Volatilome results were analyzed and correlated to the mycobiota data, confirming differences between fermentation stages. Given the high appreciation for this traditional food, this study helps elucidate the mycobiota associated to Taggiasca cv. table olives and its relationship with the quality of the final product.

Enhancing the quality and safety of Nocellara del Belice green table olives produced using the Castelvetrano method

The Castelvetrano method is the most widely used among the various table olive processing styles in Sicily. After debittering, the product is stored at low temperatures to prevent the growth of undesirable microorganisms. In an effort to enhance the production process, yeast isolates underwent genotypic characterization and technological screening. The screening process identified two yeast strains Candida norvegica OC10 and Candida boidinii LC1, which can grow at low temperatures and tolerate high pH values (up to 10) and salinity [10% (w/v)]. During the monitoring period, the inoculated trials showed limited presence of spoilage/pathogenic microorganisms. Additionally, the yeasts limited oxidative phenomena and softening of the drupes. The organic compounds detected were higher in the inoculated trials than in the control, and cold storage induced aromatic decay, which was less pronounced in the trial inoculated with C. norvegica. Sensory analysis revealed that the inoculated trials scored higher in sweetness, hardness and crispness.

Determination of Bacterial Community Structure of Table Olive via Metagenomic Approach in Şarköy

One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy, Tekirdağ-Türkiye using next generation sequencing and 16S metagenomic analysis. Samples were studied as non-pre-enriched (n : 10) and after pre-enrichment (n : 10) to compare the effects of the enrichment process on the bacterial diversity. In non-pre-enriched, the most common genus found was Sphingomonas, followed by Altererythrobacter and Lysobacter. The most common phylum found was Proteobacteria, followed by Bacteroidota and Actinobacteria. In pre-enriched, Bacillus was the most commonly detected genus, followed by Pantoea and Staphylococcus. The most frequently found phylum was Firmicutes, followed by Proteobacteria and Cyanobacteria. This study is the first study for Şarköy, which is the only table olive production place in the Tekirdağ region due to its microclimate feature. Further studies are needed in more table olive samples from different geographical areas to confirm and develop current findings.

The Rising Role of Omics and Meta-Omics in Table Olive Research

Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives' intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives' microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology.

In Silico Evidence of the Multifunctional Features of Lactiplantibacillus pentosus LPG1, a Natural Fermenting Agent Isolated from Table Olive Biofilms

In recent years, there has been a growing interest in obtaining probiotic bacteria from plant origins. This is the case of Lactiplantibacillus pentosus LPG1, a lactic acid bacterial strain isolated from table olive biofilms with proven multifunctional features. In this work, we have sequenced and closed the complete genome of L. pentosus LPG1 using both Illumina and PacBio technologies. Our intention is to carry out a comprehensive bioinformatics analysis and whole-genome annotation for a further complete evaluation of the safety and functionality of this microorganism. The chromosomic genome had a size of 3,619,252 bp, with a GC (Guanine-Citosine) content of 46.34%. L. pentosus LPG1 also had two plasmids, designated as pl1LPG1 and pl2LPG1, with lengths of 72,578 and 8713 bp (base pair), respectively. Genome annotation revealed that the sequenced genome consisted of 3345 coding genes and 89 non-coding sequences (73 tRNA and 16 rRNA genes). Taxonomy was confirmed by Average Nucleotide Identity analysis, which grouped L. pentosus LPG1 with other sequenced L. pentosus genomes. Moreover, the pan-genome analysis showed that L. pentosus LPG1 was closely related to the L. pentosus strains IG8, IG9, IG11, and IG12, all of which were isolated from table olive biofilms. Resistome analysis reported the absence of antibiotic resistance genes, whilst PathogenFinder tool classified the strain as a non-human pathogen. Finally, in silico analysis of L. pentosus LPG1 showed that many of its previously reported technological and probiotic phenotypes corresponded with the presence of functional genes. In light of these results, we can conclude that L. pentosus LPG1 is a safe microorganism and a potential human probiotic with a plant origin and application as a starter culture for vegetable fermentations.

Exploring the Core Microbiota of Four Different Traditional Fermented Beverages from the Colombian Andes

Fermentation is an ancient process used to prepare and preserve food. Currently, fermented beverages are part of the culture of people living in the Colombian Andean Region, and they are a vital part of their cosmology and ancestral vision. Chicha, Forcha, Champús, and Masato are some of the most common Colombian Andes region’s traditional fermented beverages. These drinks come from the fermentation of maize (Zea maize), but other cereals such as wheat or rye, could be used. The fermentation is carried out by a set of bacteria and yeasts that provide characteristic organoleptic properties of each beverage. In this work, the information collected from the metagenomics analyses by sequencing ITS 1-4 (Internal Transcriber Spacer) and the 16S ribosomal gene for fungi and the V3-V4 region of the rDNA for bacteria allowed us to identify the diversity present in these autochthonous fermented beverages made with maize. The sequencing analysis showed the presence of 39 bacterial and 20 fungal genera. In addition, we determined that only nine genera of bacteria and two genera of fungi affect the organoleptic properties of smell, colour, and flavour, given the production of compounds such as lactic acid, alcohol, and phenols, highlighting the critical role of these microorganisms. Our findings provide new insights into the core microbiota of these beverages, represented by Lactobacillus fermentum, Acetobacter pasteurianus, and Saccharomyces cerevisiae.

Effect of Salt Addition and Fermentation Time on Phenolics, Microbial Dynamics, Volatile Organic Compounds, and Sensory Properties of the PDO Table Olives of Gaeta (Italy)

'Oliva di Gaeta' is almost certainly the most important and well-known PDO denomination for table olives in Italy. Their production is based on a specific two-stage trade preparation called the 'Itrana' method. In this work, we investigated how variations in the duration of the initial water fermentation (i.e., 15 and 30 days) and the salt concentration (i.e., 6% and 8% NaCl) influence the chemical features, microbial dynamics, polyphenols, volatile organic compounds, and sensory features of 'Oliva di Gaeta'. The time of the addition of salt did not affect the final concentration in the brine, but a longer initial water fermentation (before salt addition) led to lower pH values. The bacterial count constantly increased until the salt addition (i.e., either 15 or 30 days), while the yeast population peaked on day 30. Generally, the two different salt concentrations did not affect the count of microorganisms at the end of fermentation, with the only exception being a higher lactic acid bacteria count for the treatment with 6% salt added at 30 days. At commercial maturity, the crucial bitter tastant oleuropein was not completely removed from the drupes, and differences in salt concentration and the length of the first-stage water fermentation did not influence its content at the end of olive curing. Richer volatile profiles of olives were detected with higher-salt treatments, while the combination of low salt and early saline treatment provided a more distinct profile. Longer initial water fermentation caused a small increase in some phenolic compounds (e.g., iso-verbascoside, verbascoside, and hydroxytyrosol-glucoside). A panel test indicated that salt application at 30 days resulted in a more "Sour" and "Bitter" taste, irrespective of the salt concentration. The low salt concentration coupled with the late saline treatment resulted in more "Fruity" notes, probably due to the higher production of esters by lactobacilli. The slightly bitter perception of the olives was consistent with the partial removal of oleuropein. Our work revealed the characteristics of the 'Itrana' method and that the variation in salt concentration and its time of application changes parameters ranging from the microbial dynamics to the sensory profile. Specifically, our data indicate that 6% NaCl coupled with a longer initial water fermentation is the most different condition: it is less effective in blocking microbial growth but, at the same time, is more potent in altering the nutritional (e.g., polyphenols) and sensorial qualities (e.g., bitterness and fruitiness) of 'Oliva di Gaeta'.

Fermentation of cv. Kalamata Natural Black Olives with Potential Multifunctional Yeast Starters

The purpose of this study was to explore the inoculated fermentation of cv. Kalamata natural black olives using selected strains of yeast cultures with multifunctional potential. For this purpose, five yeast starters belonging to Candida boidinii (four starters) and Saccharomyces cerevisiae (one starter), previously isolated from table olive fermentation of the same variety and screened for their technological characteristics and probiotic potential, were inoculated in brines at the beginning of fermentation. Microbial populations (lactic acid bacteria, yeasts, and Enterobacteriaceae), pH, titratable acidity, organic acids, and ethanol were monitored during fermentation for a period of 5 months. At the same time, the survival of each starter was assessed by culture-dependent molecular identification at the beginning (0 days), middle (75 days), and final stages (150 days) of fermentation in the brines and olives (at the end of the process only). The results revealed the coexistence of yeasts and lactic acid bacteria (LAB) throughout fermentation in most processes and also the absence of Enterobacteriaceae after the first 20 days of brining. The population of yeasts remained 2 log cycles below LAB counts, except for in the inoculated treatment with C. boidinii Y28, where the yeast starter prevailed from day 60 until the end of the fermentation, as well as in the inoculated treatment with C. boidinii Y30, where no LAB could be detected in the brines after 38 days. At the end of the process, LAB ranged between 4.6 and 6.8 log₁₀ CFU/mL, while yeasts were close to 5.0 log₁₀ CFU/mL, except for the inoculated fermentation with C. boidinii Y27 and spontaneous fermentation (control), in which the yeast counts were close to 3.5 log₁₀ CFU/mL. At the end of fermentation, the recovery percentage of C. boidinii Y27 was 50% in the brines and 45% in the olives. C. boidinii Y28 and S. cerevisiae Y34 could be recovered at 25% and 5% in the brine, respectively, whereas neither starter could be detected in the olives. For C. boidinii Y30, the recovery percentage was 25% in the brine and 10% in the olives. Finally, C. boidinii Y31 could not be detected in the brines and survived at a low percentage (10%) in the olives.

Growth of ɣ-Proteobacteria in Low Salt Cucumber Fermentation Is Prevented by Lactobacilli and the Cover Brine Ingredients

This study investigated the ability of ɣ-proteobacteria, indigenous to fresh cucumber, to grow in the expressed fruit juice (CJM) and fermentation. It was hypothesized that fresh cucumbers can support prolific growth of ɣ-proteobacteria but that the cover brine composition and acid production by the competing lactobacilli in the fermentation of the fruit act as inhibitory agents. The ɣ-proteobacteria proliferated in CJM with an average maximum growth rate (μmax) of 0.3895 ± 0.0929 and doubling time (Td) of 1.885 ± 0.465/h. A significant difference was found between the ɣ-proteobacteria μmax and Td relative to Lactiplantibacillus pentosus LA0445 (0.2319 ± 0.019; 2.89/h) and Levilactobacillus brevis 7.2.43 (0.221 ± 0.015; 3.35/h) but not Lactiplantibacillus plantarum 3.2.8 (0.412 ± 0.119; 1.87/h). While inoculation level insignificantly altered the μmax and Td of the bacteria tested; it impacted the length of lag and stationary phases for the lactobacilli. Unlike the lactobacilli, the ɣ-proteobacteria were inhibited in CJM supplemented with a low salt fermentation cover brine containing calcium chloride, acetic acid and potassium sorbate. The ɣ-proteobacteria, P. agglomerans, was unable to proliferate in cucumber fermentations brined with calcium chloride at a pH of 6.0 ± 0.1 and the population of Enterobacteriaceae was outcompeted by the lactobacilli within 36 h. Together these observations demonstrate that the prolific growth of ɣ-proteobacteria in CJM is not replicated in cucumber fermentation. While the ɣ-proteobacteria growth rate is faster that most lactobacilli in CJM, their growth in cucumber fermentation is prevented by the cover brine and the acid produced by the indigenous lactobacilli. Thus, the lactobacilli indigenous to cucumber and cover brine composition influence the safety and quality of fermented cucumbers. IMPORTANCE While the abundance of specific ɣ-proteobacteria species varies among vegetable type, several harbor Enterobacteriaceae and Pseudomonadaceae that benefit the plant system. It is documented that such bacterial populations decrease in density early in vegetable fermentations. Consequently, it is assumed that they do not contribute to the quality of finished products. This study explored the viability of ɣ-proteobacteria in CJM, used as a model system, CJM supplemented with fermentation cover brine and cucumber fermentation, which are characterized by an extremely acidic endpoint pH (3.23 ± 0.17; n = 391). The data presented demonstrates that fresh cucumbers provide the nutrients needed by ɣ-proteobacteria to proliferate and reduce pH to 4.47 ± 0.12. However, ɣ-proteobacteria are unable to proliferate in cucumber fermentation. Control of ɣ-proteobacteria in fermentations depends on the cover brine constituents and the indigenous competing lactobacilli. This knowledge is of importance when developing guidelines for the safe fermentation of vegetables, particularly with low salt.

Current Status, Recent Advances, and Main Challenges on Table Olive Fermentation: The Present Meets the Future

Table olives are among the most well-known fermented foods, being a vital part of the Mediterranean pyramid diet. They constitute a noteworthy economic factor for the producing countries since both their production and consumption are exponentially increasing year by year, worldwide. Despite its significance, olive’s processing is still craft based, not changed since antiquity, leading to the production of an unstable final product with potential risk concerns, especially related to deterioration. However, based on industrial needs and market demands for reproducible, safe, and healthy products, the modernization of olive fermentation processing is the most important challenge of the current decade. In this sense, the reduction of sodium content and more importantly the use of suitable starter cultures, exhibiting both technological and potential probiotic features, to drive the process may extremely contribute to this need. Prior, to achieve in this effort, the full understanding of table olive microbial ecology during fermentation, including an in-depth determination of microbiota presence and/or dominance and its functionality (genes responsible for metabolite production) that shape the sensorial characteristics of the final product, is a pre-requisite. The advent of meta-omics technology could provide a thorough study of this complex ecosystem, opening in parallel new insights in the field, such as the concept of microbial terroir. Herein, we provide an updated overview in the field of olive fermentation, pointing out some important challenges/perspectives that could be the key to the olive sector’s advancement and modernization.

Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing

Fermented fruits and vegetables play an important role in safeguarding food security world-wide. Recently, robust sequencing-based microbial community analysis platforms have improved microbial safety assessment. This study aimed to examine the composition of bacteria and evaluate the bacterial safety of fermented fruit products using high-throughput 16S-rRNA metagenomic analysis. The operational taxonomic unit-based taxonomic classification of DNA sequences revealed 53 bacterial genera. However, the amplicon sequencing variant (ASV)-based clustering revealed 43 classifiable bacterial genera. Taxonomic classifications revealed that the abundance of Sphingomonas, which was the predominant genus in the majority of tested samples, was more than 85–90% among the total identified bacterial community in most samples. Among these identified genera, 13 low abundance genera were potential opportunistic pathogens, including Acinetobacter, Bacillus, Staphylococcus, Clostridium, Klebsiella, Mycobacterium, Ochrobactrum, Chryseobacterium, Stenotrophomonas, and Streptococcus. Of these 13 genera, 13 major opportunistic pathogenic species were validated using polymerase chain reaction. The pathogens were not detected in the samples of different stages and the final products of fermentation, except in one sample from the first stage of fermentation in which S. aureus was detected. This finding was consistent with that of ASV-based taxonomic classification according to which S. aureus was detected only in the sample from the first stage of fermentation. However, S. aureus was not significantly correlated with the human disease pathways. These results indicated that fermentation is a reliable and safe process as pathogenic bacteria were not detected in the fermentation products. The hybrid method reported in this study can be used simultaneously to evaluate the bacterial diversity, their functional predictions and safety assessment of novel fermentation products. Additionally, this hybrid method does not involve the random detection of pathogens, which can markedly decrease the time of detection and food safety verification. Furthermore, this hybrid method can be used for the quality control of products and the identification of external contamination.

Application of mixed starter culture for table olive production

The fermentation of olives is usually carried out spontaneously by natural microbiota. Spontaneous fermentation has some disadvantages, such as the formation of defects in the end product due to the activities of undesirable microorganisms. The use of starter cultures could be a promising option to provide a more controlled fermentation environment and to reduce the risk of spoilage. Mixed starter culture use (generally selected Lactobacillus strains with or without yeasts) could reduce pH in a shorter time, producing a higher amount of lactic acid and enhancing microbial safety compared to fermentation with starter cultures containing single species or natural fermentation. Their use could also enhance the organoleptical properties of table olives. Particularly the use of yeast (such as strains of W. anomolus, S. cerevisiae) in the fermentation of olives, in combination or sequentially with lactic acid bacteria could result in an increase in volatile compounds and a more aromatic final product.

Microbiota profiling and screening of the lipase active halotolerant yeasts of the olive brine

Searching for novel enzymes that could be active in organic solvents has become an area of interest in recent years. Olive brine naturally provides a suitable environment for the survival of halophilic and acidophilic microorganisms and the resulting genome is thought to be a gene source for determining the halophilic and acidophilic proteins that are active in a non-aqueous organic solvent medium, and so it has been used in several biotechnological and industrial applications. In this study, microbial analysis of natural, cracked green olive brine from the southern region of Turkey has been made by next-generation sequencing of the brine metagenome for the first time in the literature. The number of reads assigned to fungal operational taxonomic units was the highest percentage (73.04%) with the dominant representation of Ascomycota phylum (99% of fungi). Bacterial OTU was 3.56% of the reads and Proteobacteria phylum was 65% of the reads. The lipase production capacity of the yeasts that were grown on the media containing elevated concentrations of NaCl (1-3 M) was determined on a Rhodamine B-including medium. Molecular identification of the selected yeasts was performed and 90% of sequenced yeasts had a high level of similarity with Candida diddensiae, whereas 10% showed similarity to Candida boidinii. The hydrolytic lipase activities using olive oil were analyzed and both yeasts showed cell-bound lipase activity at pH 3.0.

Evaluating the Cytometric Detection and Enumeration of the Wine Bacterium, Oenococcus oeni

Flow cytometry is a high-throughput tool for determining microbial abundance in a range of medical, environmental, and food-related samples. For wine, determining the abundance of Saccharomyces cerevisiae is well-defined and reliable. However, for the most common wine bacterium, Oenococcus oeni, using flow cytometry to determine cell concentration poses some challenges. O. oeni most often occurs in doublets or chains of varying lengths that can be greater than seven cells. This wine bacterium is also small, at 0.2-0.6 μm and may exhibit a range of morphologies including binary fission and aggregated complexes. This work demonstrates a straightforward approach to determining the suitability of flow cytometry for the chain-forming bacteria, O. oeni, and considerations when using flow cytometry for the enumeration of small microorganisms (<0.5 μm). © 2020 International Society for Advancement of Cytometry.

Effects of Different Stress Parameters on Growth and on Oleuropein-Degrading Abilities of Lactiplantibacillus plantarum Strains Selected as Tailored Starter Cultures for Naturally Table Olives

The use of β-glucosidase positive strains, as tailored-starter cultures for table olives fermentation, is a useful biotechnological tool applied to accelerate the debittering process. Nowadays, strains belonging to Lactiplantibacillus plantarum species are selected for their high versatility and tolerance to stress conditions. The present study investigated the effect of different stress factors (pH, temperature and NaCl) on growth and on oleuropein-degrading abilities of selected L. plantarum strains. In addition, the presence of the beta-glucosidase gene was investigated by applying a PCR based approach. Results revealed that, overall, the performances of the tested strains appeared to be robust toward the different stressors. However, the temperature of 16 °C significantly affected the growth performance of the strains both singularly and in combination with other stressing factors since it prolongs the latency phase and reduces the maximum growth rate of strains. Similarly, the oleuropein degradation was mainly affected by the low temperature, especially in presence of low salt content. Despite all strains displayed the ability to reduce the oleuropein content, the beta-glucosidase gene was detected in five out of the nine selected strains, demonstrating that the ability to hydrolyze the oleuropein is not closely related to the presence of beta-glucosidase. Data of the present study suggest that is extremely important to test the technological performances of strains at process conditions in order to achieve a good selection of tailored starter cultures for table olives.

Microbial Diversity of Fermented Greek Table Olives of Halkidiki and Konservolia Varieties from Different Regions as Revealed by Metagenomic Analysis

Current information from conventional microbiological methods on the microbial diversity of table olives is insufficient. Next-generation sequencing (NGS) technologies allow comprehensive analysis of their microbial community, providing microbial identity of table olive varieties and their designation of origin. The purpose of this study was to evaluate the bacterial and yeast diversity of fermented olives of two main Greek varieties collected from different regions-green olives, cv. Halkidiki, from Kavala and Halkidiki and black olives, cv. Konservolia, from Magnesia and Fthiotida-via conventional microbiological methods and NGS. Total viable counts (TVC), lactic acid bacteria (LAB), yeast and molds, and Enterobacteriaceae were enumerated. Microbial genomic DNA was directly extracted from the olives' surface and subjected to NGS for the identification of bacteria and yeast communities. Lactobacillaceae was the most abundant family in all samples. In relation to yeast diversity, Phaffomycetaceae was the most abundant yeast family in Konservolia olives from the Magnesia region, while Pichiaceae dominated the yeast microbiota in Konservolia olives from Fthiotida and in Halkidiki olives from both regions. Further analysis of the data employing multivariate analysis allowed for the first time the discrimination of cv. Konservolia and cv. Halkidiki table olives according to their geographical origin.

FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation

Table olives are considered the most widespread fermented food in the Mediterranean area and their consumption is expanding all over the world. This fermented vegetable can be considered as a natural functional food thanks to their high nutritional value and high content of bioactive compounds that contribute to the health and well-being of consumers. The presence of bioactive compounds is strongly influenced by a complex microbial consortium, traditionally exploited through culture-dependent approaches. Recently, the rapid spread of omics technologies has represented an important challenge to better understand the function, the adaptation and the exploitation of microbial diversity in different complex ecosystems, such as table olives. This review provides an overview of the potentiality of omics technologies to in depth investigate the microbial composition and the metabolic processes that drive the table olives fermentation, affecting both sensorial profile and safety properties of the final product. Finally, the review points out the role of omics approaches to raise at higher sophisticated level the investigations on microbial, gene, protein, and metabolite, with huge potential for the integration of table olives composition with functional assessments.

A Review on Adventitious Lactic Acid Bacteria from Table Olives

Spontaneous fermentation constitutes the basis of the chief natural method of processing of table olives, where autochthonous strains of lactic acid bacteria (LAB) play a dominant role. A thorough literature search has unfolded 197 reports worldwide, published in the last two decades, that indicate an increasing interest in table olive-borne LAB, especially in Mediterranean countries. This review attempted to extract extra information from such a large body of work, namely, in terms of correlations between LAB strains isolated, manufacture processes, olive types, and geographical regions. Spain produces mostly green olives by Spanish-style treatment, whereas Italy and Greece produce mainly green and black olives, respectively, by both natural and Spanish-style. More than 40 species belonging to nine genera of LAB have been described; the genus most often cited is Lactobacillus, with L. plantarum and L. pentosus as most frequent species—irrespective of country, processing method, or olive type. Certain LAB species are typically associated with cultivar, e.g., Lactobacillus parafarraginis with Spanish Manzanilla, or L. paraplantarum with Greek Kalamata and Conservolea, Portuguese Galega, and Italian Tonda di Cagliari. Despite the potential of native LAB to serve as starter cultures, extensive research and development efforts are still needed before this becomes a commercial reality in table olive fermentation.

Evolution of Bacterial Communities, Physicochemical Changes and Sensorial Attributes of Natural Whole and Cracked Picual Table Olives During Spontaneous and Inoculated Fermentation

Table olives are one of the most well-known traditionally fermented products, and their global consumption is exponentially increasing. In direct brining, table olives are produced spontaneously, without any debittering pre-treatment. Up to date, fermentation process remains empirical and inconstant, as it is affected by the physicochemical attributes of the fruit, tree and fruit management of pro and post-harvest. In the present study, whole and cracked Picual table olives were fermented at industrial scale for 120 days, using three distinct methods (natural fermentation, inoculation with lactic acid bacteria (LAB) at a 7 or a 10% NaCl concentration). Microbial, physicochemical and sensorial alterations monitored during the whole process, and several differences were observed between treatments. Results indicated that in all treatments, the dominant microflora were LAB. Yeasts also detected in noteworthy populations, especially in non-inoculated samples. However, LAB population was significantly higher in inoculated compared to non-inoculated samples. Microbial profiles identified by metagenomic approach showed meaningful differences between spontaneous and inoculated treatments. As a result, the profound dominance of starter culture had a severe effect on olives fermentation, resulting in lower pH and higher acidification, which was mainly caused by the higher levels of lactic acid produced. Furthermore, the elimination of Enterobacteriaceae was shortened, even at lower salt concentration. Although no effect observed concerning the quantitated organoleptic parameters such as color and texture, significantly higher levels in terms of antioxidant capacity were recorded in inoculated samples. At the same time, the degradation time of oleuropein was shortened, leading to the production of higher levels of hydroxytyrosol. Based on this evidence, the establishment of starter culture driven Picual olives fermentation is strongly recommended. It is crucial to mention that the inoculated treatment with reducing sodium content was highly appreciated by the sensory panel, enhancing the hypothesis that the production of Picual table olives at reduced NaCl levels is achievable.

Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis

Kalamata natural black olives are one of the most economically important Greek varieties. The microbial ecology of table olives is highly influenced by the co-existence of bacteria and yeasts/fungi, as well as the physicochemical parameters throughout the fermentation. Therefore, the aim of this study was the identification of bacterial and yeast/fungal microbiota of both olives and brines obtained from 29 cv. Kalamata olive samples industrially fermented in the two main producing geographical regions of Greece, namely Aitoloakarnania and Messinia/Lakonia. The potential microbial biogeography association between certain taxa and geographical area was also assessed. The dominant bacterial family identified in olive and brine samples from both regions was Lactobacillaceae, presenting, however, higher average abundances in the samples from Aitoloakarnania compared to Messinia/Lakonia. At the genus level, Lactobacillus, Celerinatantimonas, Propionibacterium and Pseudomonas were the most abundant. In addition, the yeasts/fungal communities were less diverse compared to those of bacteria, with Pichiaceae being the dominant family and Pichia, Ogataea, and Saccharomyces being the most abundant genera. To the best of our knowledge, this is the first report on the microbiota of both olives and brines of cv. Kalamata black olives fermented on an industrial scale between two geographical regions of Greece using metagenomics analysis.

Effect of different inoculation strategies of selected yeast and LAB cultures on Conservolea and Kalamàta table olives considering phenol content, texture, and sensory attributes

BACKGROUND

The effects were studied of different inoculation strategies for selected starters -yeasts and lactic acid bacteria (LAB) - used for the fermentation process of two Greek olive cultivars, Conservolea and Kalamàta. The LAB strains applied were Leuconostoc mesenteroides K T5-1 and L. plantarum A 135-5; the selected yeast strains were S. cerevisiae KI 30-16 and Debaryomyces hansenii A 15-44 for Kalamàta and Conservolea olives, respectively.

RESULTS

Table olive fermentation processes were monitored by performing microbiological analyses, and by monitoring changes in pH, titratable acidity and salinity, sugar consumption, and the evolution of volatile compounds. Structural modifications occurring in phenolic compounds of brine were investigated during the fermentation using liquid chromatography / diode array detection / electrospray ion trap tandem mass spectrometry (LC/DAD/ESI-MSⁿ ) and quantified by high-performance liquid chromatography (HPLC) using a diode array detector. Phenolic compounds in processed Kalamàta olive brines consisted of phenolic acids, verbascoside, caffeoyl-6-secologanoside, comselogoside, and the dialdehydic form of decarboxymethylelenolic acid linked to hydroxytyrosol, whereas oleoside and oleoside 11-methyl ester were identified only in Conservolea olive brines.

CONCLUSION

Volatile profile and sensory evaluation revealed that the 'MIX' (co-inoculum of yeast and LAB strain) inoculation strategy led to the most aromatic and acceptable Kalamàta olives. For the Conservolea table olives, the 'YL' treatment gave the most aromatic and the overall most acceptable product. © 2019 Society of Chemical Industry.

Microbial biogeography of Spanish-style green olive fermentations in the province of Seville, Spain

The aim of this study is to examine the biogeography of the microbial communities associated to the Spanish-style green olive fermentations in the province of Seville (Andalucía, south-western Spain). Also, to understand how microorganisms colonize and persist in non-sterile food fermentations across a specific table olive producing area, i.e. a specific "agroecosystem". The microbial diversity, bacteria and yeast, in 30 ten-ton fermenters of three different fermentations yards (patios) along the olive fermentation was studied. A total of 951 microbial isolates were obtained which were clustered according to their RAPD profile. A total of 376 distinct genotypes were identified, belonging to 57 different microbial species, 41 bacterial and 16 yeast species. Up to 16 bacterial species had not been described before in table olives. Only the species Lactobacillus pentosus showed a ubiquitous presence in all 30 fermenters. Pediococcus parvulus, Lactobacillus collinoides/paracollinoides, Lactobacillus coryniformis, Lactobacillus plantarum, Pichia manshurica and Candida thaimueangensis were found in every patio. Cosmopolitan strains, up to 15, were shared by the three patios and belonged to the species L. pentosus (12 strains), P. parvulus (1), L. collinoides/paracollinoides (1) and P. manshurica (1). To expand our biodiversity analyses to the "regional" level, we have compared our results with those obtained from two previously studied patios of similar characteristics and in the same geographical area. PERMANOVA analysis of the microbial community composition revealed significant differences among different patios in their structure at every fermentation stage. In contrast, SIMPER analyses showed that, as fermentation progressed, the overall dissimilarities among patios were reduced. Discriminant species were identified for each fermentation stage. Among these, L. pentosus and P. parvulus were "eu-constant" species, while L. collinides/paracollinoides and Marinilactibacillus psychrotolerans group were "constant" species that could be considered microbial key taxa based on the occurrence stability index. The characteristic and, presumably, well adapted microbiota associated to the Spanish-style olive fermentations at the specific geographic area described here is a valuable natural resource which should be preserved conveniently. To our knowledge, this is the first study on the microbial biogeography of table olive fermentations, both at the species and strain levels.

Technologies and Trends to Improve Table Olive Quality and Safety

Table olives are the most widely consumed fermented food in the Mediterranean countries. Peculiar processing technologies are used to process olives, which are aimed at the debittering of the fruits and improvement of their sensory characteristics, ensuring safety of consumption at the same time. Processors demand for novel techniques to improve industrial performances, while consumers' attention for natural and healthy foods has increased in recent years. From field to table, new techniques have been developed to decrease microbial load of potential spoilage microorganisms, improve fermentation kinetics and ensure safety of consumption of the packed products. This review article depicts current technologies and recent advances in the processing technology of table olives. Attention has been paid on pre processing technologies, some of which are still under-researched, expecially physical techniques, such ad ionizing radiations, ultrasounds and electrolyzed water solutions, which are interesting also to ensure pesticide decontamination. The selections and use of starter cultures have been extensively reviewed, particularly the characterization of Lactic Acid Bacteria and Yeasts to fasten and safely drive the fermentation process. The selection and use of probiotic strains to address the request for functional foods has been reported, along with salt reduction strategies to address health concerns, associated with table olives consumption. In this respect, probiotics enriched table olives and strategies to reduce sodium intake are the main topics discussed. New processing technologies and post packaging interventions to extend the shelf life are illustrated, and main findings in modified atmosphere packaging, high pressure processing and biopreservaton applied to table olive, are reported and discussed.

Evolution of Yeast Consortia during the Fermentation of Kalamata Natural Black Olives upon Two Initial Acidification Treatments

The objective of this study was to elucidate the yeast consortia structure and dynamics during Greek-style processing of Kalamata natural black olives in different brine solutions. Olives were subjected to spontaneous fermentation in 7% (w/v) NaCl brine solution (control treatment) or brine acidified with (a) 0.5% (v/v) vinegar, and (b) 0.1% (v/v) lactic acid at the onset of fermentation. Changes in microbial counts, pH, acidity, organic acids, sugars, and alcohols were analyzed for a period of 187 days. Yeast consortia diversity was evaluated at days 4, 34, 90, 140, and 187 of fermentation. A total of 260 isolates were characterized at sub-species level by rep-PCR genomic fingerprinting with the oligo-nucleotide primer (GTG)5. The characterization of yeast isolates at species level was performed by sequencing of the D1/D2 domain of 26S rRNA gene. Results showed that yeasts dominated the process presenting a relatively broad range of biodiversity composed of 11 genera and 21 species. No lactic acid bacteria (LAB) or Enterobacteriaceae could be enumerated after 20 and 10 days of fermentation, respectively. The dominant yeast species at the beginning were Aureobasidium pullulans for control and vinegar acidification treatments, and Candida naeodendra for lactic acid treatment. Between 34 and 140 days the dominant species were Candida boidinii, Candida molendinolei and Saccharomyces cerevisiae. In the end of fermentation the dominant species in all processes were C. boidinii and C. molendinolei, followed by Pichia manshurica and S. cerevisiae in lactic acid acidification treatment, P. manshurica in vinegar acidification treatment, and Pichia membranifaciens in control fermentation.

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism

The butyrogenic capability of Lactobacillus (L.) plantarum is highly dependent on the substrate type and so far not assigned to any specific metabolic pathway. Accordingly, we compared three genomes of L. plantarum that showed a strain-specific capability to produce butyric acid in human cells growth media. Based on the genomic analysis, butyric acid production was attributed to the complementary activities of a medium-chain thioesterase and the fatty acid synthase of type two (FASII). However, the genomic islands of discrepancy observed between butyrogenic L. plantarum strains (S2T10D, S11T3E) and the non-butyrogenic strain O2T60C do not encompass genes of FASII, but several cassettes of genes related to sugar metabolism, bacteriocins, prophages and surface proteins. Interestingly, single amino acid substitutions predicted from SNPs analysis have highlighted deleterious mutations in key genes of glutamine metabolism in L. plantarum O2T60C, which corroborated well with the metabolic deficiency suffered by O2T60C in high-glutamine growth media and its consequent incapability to produce butyrate. In parallel, the increase of glutamine content induced the production of butyric acid by L. plantarum S2T10D. The present study reveals a previously undescribed metabolic route for butyric acid production in L. plantarum, and a potential involvement of the glutamine uptake in its regulation.

Effects of Exogenous Yeast and Bacteria on the Microbial Population Dynamics and Outcomes of Olive Fermentations

Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be improved by the deliberate addition of starter culture microbes that accelerate or beneficially modify product outcomes, the impact of either of those microbial additions on community dynamics within the fermentations is not well understood at strain-specific or global scales. Herein, we show how exogenous spoilage yeast or starter lactic acid bacteria confer very different effects on microbial numbers and diversity in olive fermentations. Introduced microbes have long-lasting consequences and result in changes that are apparent even when levels of those inoculants and their major enzymatic activities decline. This work has direct implications for understanding bacterial and fungal invasions of microbial habitats resulting in pivotal changes to community structure and function.

In this study, we examined Sicilian-style green olive fermentations upon the addition of Saccharomyces cerevisiae UCDFST 09-448 and/or Pichia kudriazevii UCDFST09-427 or the lactic acid bacteria (LAB) Lactobacillus plantarum AJ11R and Leuconostoc pseudomesenteroides BGM3R. Olives containing S. cerevisiae UCDFST 09-448, a strain able to hydrolyze pectin, but not P. kudriazevii UCDFST 09-427, a nonpectinolytic strain, exhibited excessive tissue damage within 4 weeks. DNA sequencing of fungal internal transcribed spacer (ITS) regions and comparisons to a yeast-specific ITS sequence database remarkably showed that neither S. cerevisiae UCDFST 09-448 nor P. kudriazevii UCDFST 09-427 resulted in significant changes to yeast species diversity. Instead, Candida boidinii constituted the majority (>90%) of the total yeast present, independent of whether S. cerevisiae or P. kudriazevii was added. By comparison, Lactobacillus species were enriched in olives inoculated with potential starter LAB L. plantarum AJ11R and L. pseudomesenteroides BGM3R according to community 16S rRNA gene sequence analysis. The bacterial diversity of those olives was significantly reduced and resembled control fermentations incubated for a longer period of time. Importantly, microbial populations were highly dynamic at the strain level, as indicated by the large variations in AJ11R and BGM3R cell numbers over time and reductions in the numbers of yeast isolates expressing polygalacturonase activity. These findings show the distinct effects of exogenous spoilage and starter microbes on indigenous communities in plant-based food fermentations that result in very different impacts on product quality.

IMPORTANCE Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be improved by the deliberate addition of starter culture microbes that accelerate or beneficially modify product outcomes, the impact of either of those microbial additions on community dynamics within the fermentations is not well understood at strain-specific or global scales. Herein, we show how exogenous spoilage yeast or starter lactic acid bacteria confer very different effects on microbial numbers and diversity in olive fermentations. Introduced microbes have long-lasting consequences and result in changes that are apparent even when levels of those inoculants and their major enzymatic activities decline. This work has direct implications for understanding bacterial and fungal invasions of microbial habitats resulting in pivotal changes to community structure and function.

Living together in biofilms: the microbial cell factory and its biotechnological implications

In nature, bacteria alternate between two modes of growth: a unicellular life phase, in which the cells are free-swimming (planktonic), and a multicellular life phase, in which the cells are sessile and live in a biofilm, that can be defined as surface-associated microbial heterogeneous structures comprising different populations of microorganisms surrounded by a self-produced matrix that allows their attachment to inert or organic surfaces. While a unicellular life phase allows for bacterial dispersion and the colonization of new environments, biofilms allow sessile cells to live in a coordinated, more permanent manner that favors their proliferation. In this alternating cycle, bacteria accomplish two physiological transitions via differential gene expression: (i) from planktonic cells to sessile cells within a biofilm, and (ii) from sessile to detached, newly planktonic cells. Many of the innate characteristics of biofilm bacteria are of biotechnological interest, such as the synthesis of valuable compounds (e.g., surfactants, ethanol) and the enhancement/processing of certain foods (e.g., table olives). Understanding the ecology of biofilm formation will allow the design of systems that will facilitate making products of interest and improve their yields.

RT-PCR-DGGE Analysis to Elucidate the Dominant Bacterial Species of Industrial Spanish-Style Green Table Olive Fermentations

This paper describes the dominant bacterial species metabolically active through the industrial production of Spanish-style Manzanilla and Gordal olives. For this purpose, samples (brines and fruits) obtained at 0, 15, and 90 fermentation days were analyzed by a culture-independent approach to determine viable cells by reverse transcription of RNA and further PCR-DGGE analysis, detecting at least 7 different species. Vibrio vulnificus, Lactobacillus plantarum group, and Lactobacillus parafarraginis were present in samples from both cultivars; Lactobacillus sanfranciscensis and Halolactobacillus halophilus were detected only in Gordal samples, while Staphylococcus sp. was exclusively found at the onset of Manzanilla fermentations. Physicochemical data showed a typical fermentation profile while scanning electron microscopy confirmed the in situ biofilm formation on the olive epidermis. Different Bacillus, Staphylococcus, and Enterococcus species, not detected during the fermentation process, were also found in the solid marine salt used by the industry for preparation of brines. Elucidation of these non-lactic acid bacteria species role during fermentation is then an appealingly challenge, particularly regarding safety issues.

Effect of green Spanish-style Manzanilla packaging conditions on the prevalence of the putative probiotic bacteria Lactobacillus pentosus TOMC-LAB2

This work focuses on the persistence of the putative probiotic bacteria Lactobacillus pentosus TOMC‐LAB2 on green Spanish‐style Manzanilla olives according to different packaging conditions and storage temperatures. The lactic acid bacteria population decreased with time but the highest survival counts (and lowest yeasts) at the end of storage (8 months) were observed in plastic pouches under nitrogen atmosphere and glass jars with brine stored at 20°C. Molecular techniques showed a 100% presence of the putative probiotic bacteria in biofilms adhered to olive epidermis, while it was absent in PPB (plastic pouches with brine) and in olives stored at 7°C. No changes in NaCl, pH or combined acidity were observed during the storage except for a slight increase in titratable acidity at 20°C. The color of the fruits was stable but degraded at 20°C for olives in plastic pouches with brine.

Microbial bioinformatics for food safety and production

In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.