Use of metabarcoding and source tracking to identify desirable or spoilage autochthonous microorganism sources during black olive fermentations

Advancing biomonitoring of eDNA studies with the Anaconda R package: Integrating soil and One Health perspectives in the face of evolving traditional agriculture practices

Soil health and One Health are global concerns, necessitating the development of refined indicators for effective monitoring. In response, we present the Anaconda R Package, a novel tool designed to enhance the analysis of eDNA data for biomonitoring purposes. Employing a combination of different approaches, this package allows for a comprehensive investigation of species abundance and community composition under diverse conditions. This study applied the Anaconda package to examine the impact of two types of duration fire-fallow cropping systems, using natural forests as a reference, on soil fungal and bacterial communities in Maré Island (New Caledonia). Condition-specific taxa were identified, particularly pathogenic fungi and bacteria, demonstrating the importance of long-term fallowing efforts. Notably, this package also revealed the potential contributions of beneficial soil microbes, including saprophytes and plant-endophyte fungi, in suppressing soil-borne pathogens. Over-represented microbial ASVs associated with both plant and animal pathogens, including those of potential concern for human health, were identified. This underscores the importance of maintaining intrinsic balance for effective disease suppression. Importantly, the advanced analytical and statistical methods offered by this package should be harnessed to comprehensively investigate the effects of agricultural practice changes on soil health within the One Health framework. Looking ahead, the application of this method extends beyond the realm of One Health, offering valuable insights into various ecological scenarios. Its versatility holds promise for elucidating complex interactions and dynamics within ecosystems. By leveraging this tool, researchers can explore the broader implications of agricultural practice modifications, facilitating informed decisions and sustainable environmental management.

Innovative omics strategies in fermented fruits and vegetables: Unveiling nutritional profiles, microbial diversity, and future prospects

Fermented fruits and vegetables (FFVs) are not only rich in essential nutrients but also contain distinctive flavors, prebiotics, and metabolites. Although omics techniques have gained widespread recognition as an analytical strategy for FFVs, its application still encounters several challenges due to the intricacies of biological systems. This review systematically summarizes the advances, obstacles and prospects of genomics, transcriptomics, proteomics, metabolomics, and multi-omics strategies in FFVs. It is evident that beyond traditional applications, such as the exploration of microbial diversity, protein expression, and metabolic pathways, omics techniques exhibit innovative potential in deciphering stress response mechanisms and uncovering spoilage microorganisms. The adoption of multi-omics strategies is paramount to acquire a multidimensional network fusion, thereby mitigating the limitations of single omics strategies. Although substantial progress has been made, this review underscores the necessity for a comprehensive repository of omics data and the establishment of universal databases to ensure precision in predictions. Furthermore, multidisciplinary integration with other physical or biochemical approaches is imperative, as it enriches our comprehension of this intricate process.

Effect of the cleaning and disinfection methods on the hygienic conditions of fermentation tanks of table olives (Olea europaea L.) Negrinha de Freixo cultivar

This study aimed to evaluate and identify the microbial community attached to the surfaces of fermenter tanks used in table olive Negrinha de Freixo cultivar processing through molecular analysis and verify if the cleaning/disinfection was done correctly. Four fermentation tanks previously used in table olive processing were sampled at three different inside areas: upper, middle, and lower. Before sampling, four cleaning/disinfection methods were applied to the tanks, including (i) pressurised water; (ii) a disinfectant product used to clean bowls (Vasiloxe); (iii) 10% sodium hydroxide solution (caustic soda liquid); and (iv) a disinfectant product used by the wine industry (Hosbit). For each sample collected, mesophilic aerobic bacteria, yeast and moulds (YMC), lactic acid bacteria (LAB), as well as total coliforms (TC) and Pseudomonas aeruginosa were evaluated. The results showed significant differences between the different cleaning/disinfection methods applied. The fermenter sanitised with only pressurised water showed a greater abundance of microorganisms than the others. Mesophilic aerobic bacteria were the predominant population, with counts ranging between 2.63 and 5.56 log10 CFU/100 cm2, followed by the moulds (3.11-5.03 log10 CFU/100 cm2) and yeasts (2.42-5.12 log10 CFU/100 cm2). High diversity of microbial communities was observed between the different fermenter tanks. The most abundant species belonged to Aureobasidium, Bacillaceae, Cladosporium, and Rhodotorula genera. LAB, TC, and P. aeruginosa were not detected. This study hopes to improve hygienic conditions and increase the quality assurance and safety of the final product.

Tasting of traditional Polish fermented cucumbers: Microbiology, morpho-textural features, and volatilome

In the present study, naturally fermented and unpasteurized cucumbers (Cucumis sativus L.) collected from 4 producers located in different regions of Poland were studied. The fermented cucumbers were characterized by significant nutritional features in terms of polyphenols content and antioxidant activity. Microbiological analyses revealed active bacterial populations of lactococci, thermophilic cocci, lactobacilli, and coagulase-negative cocci. The microbiological characterization of cucumber and brine samples through metataxonomic analysis allowed the dominant species to be detected, being Lactococcus and Streptococcus in cucumbers, and Lactiplantibacillus, Leuconostoc, Pediococcus, Secundilactobacillus, and Lentilactobacillus in brine. The isolation activity offered a clear picture of the main active lactic acid bacteria at the end of fermentation, being Pediococcus parvulus and Lactiplantibacillus plantarum group. All the studied isolates showed a good attitude in fermenting a cucumber-based broth, thus suggesting their potential application as starter or adjunct cultures for guided cucumber fermentation. Moreover, for the same isolates, strong aminopeptidase activity (due to leucine arylamidase and valine arylamidase) was observed, with potential effect on the definition of the final sensory traits of the product. Only a few isolates showed the ability to produce exopolysaccharides in synthetic medium. Of note, the presence of the hdcA gene in some Pediococcus ethanolidurans isolates also confirmed the need for a thorough characterization of starter candidates to avoid undesired adverse effects on consumer's health. No isolate showed the production of bacteriocins against Listeria innocua used as surrogate for Listeria monocytogenes. Based on the results of Headspace Solid-Phase Microextraction-Gas Chromatography/Mass Spectrometry analysis, a rich and complex volatilome, composed by more than 80 VOCs, was recognized and characterized. In more detail, the detected compounds belonged to 9 main classes, being oxygenated terpenes, alcohols, terpenes, ketones, acids, aldehydes, esters, sulfur, and sesquiterpenes.

Nanopore-Sequencing Metabarcoding for Identification of Phytopathogenic and Endophytic Fungi in Olive (Olea europaea) Twigs

Metabarcoding approaches for the identification of plant disease pathogens and characterization of plant microbial populations constitute a rapidly evolving research field. Fungal plant diseases are of major phytopathological concern; thus, the development of metabarcoding approaches for the detection of phytopathogenic fungi is becoming increasingly imperative in the context of plant disease prognosis. We developed a multiplex metabarcoding method for the identification of fungal phytopathogens and endophytes in olive young shoots, using the MinION sequencing platform (Oxford Nanopore Technologies). Selected fungal-specific primers were used to amplify three different genomic DNA loci (ITS, beta-tubulin, and 28S LSU) originating from olive twigs. A multiplex metabarcoding approach was initially evaluated using healthy olive twigs, and further assessed with naturally infected olive twig samples. Bioinformatic analysis of basecalled reads was carried out using MinKNOW, BLAST+ and R programming, and results were also evaluated using the BugSeq cloud platform. Data analysis highlighted the approaches based on ITS and their combination with beta-tubulin as the most informative ones according to diversity estimations. Subsequent implementation of the method on symptomatic samples identified major olive pathogens and endophytes including genera such as Cladosporium, Didymosphaeria, Paraconiothyrium, Penicillium, Phoma, Verticillium, and others.

Microbial trace investigation throughout the entire chicken supply chain based on metagenomic high-throughput sequencing

As poultry possesses a high risk of contamination by various pathogens and has repeatedly been linked to foodborne outbreaks, ensuring microbiological safety throughout the chicken production chain is essential. In this study, bacterial communities in chickens and associated environments (n = 72), including feces, floors, gloves, and worktables, were trace investigated from the broiler farm, slaughterhouse, meat processing plant, and the market by amplicon sequencing of the V4 region of the 16S rRNA. The bacterial composition in live chickens along the production chain significantly changed across the stages, with distinct microbiota noted at each step. Pseudomonas, Shewanella, Acinetobacter, and Psychrobacter were dominant in the final products. Staphylococcus was abundant in live birds originally (36.83 %) but dramatically decreased after slaughter (3.07 %, 0.06 %, and 0.42 % in slaughtered, processed, and market carcasses, respectively), which may be attributed to defeathering. The proportion of Enterobacteriaceae, Acinetobacter, and Pseudomonas increased from 0.95 %, 0.03 %, and 0.04 % before slaughter to 13.57 %, 34.19 %, and 21.90 %, respectively, after slaughter, highlighting the importance of hygiene management in the succeeding steps. Diversity analysis revealed the possibility of bacterial transmission between samples from the processing plant and the market. Source tracking was performed to identify microbial contamination routes in the chicken microbiome; the major bacterial sources in the final products were the samples from the processing plant (such as processed carcasses, gloves, and worktables), accounting for 93.53 % of the total microbial sources. These results suggest that in-depth knowledge of microbial transmission between chickens and their surroundings can facilitate a precise understanding of microbiological concerns across the poultry production system and help establish safety management measures for the poultry industry.

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.

Metagenomics Approaches for Improving Food Safety: A Review

ABSTRACT

Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology.

HIGHLIGHTS