Microbial diversity in pitted sweet cherries (Prunus avium L.) as affected by High-Hydrostatic Pressure treatment

Microbiome-based classification models for fresh produce safety and quality evaluation

Small sample sizes and loss of sequencing reads during the microbiome data preprocessing can limit the statistical power of differentiating fresh produce phenotypes and prevent the detection of important bacterial species associated with produce contamination or quality reduction. Here, we explored a machine learning-based k-mer hash analysis strategy to identify DNA signatures predictive of produce safety (PS) and produce quality (PQ) and compared it against the amplicon sequence variant (ASV) strategy that uses a typical denoising step and ASV-based taxonomy strategy. Random forest-based classifiers for PS and PQ using 7-mer hash data sets had significantly higher classification accuracy than those using the ASV data sets. We also demonstrated that the proposed combination of integrating multiple data sets and leveraging a 7-mer hash strategy leads to better classification performance for PS and PQ compared to the ASV method but presents lower PS classification accuracy compared to the feature-selected ASV-based taxonomy strategy. Due to the current limitation of generating taxonomy using the 7-mer hash strategy, the ASV-based taxonomy strategy with remarkably less computing time and memory usage is more efficient for PS and PQ classification and applicable for important taxa identification. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing data sets for the application of machine learning in the area of microbial safety and quality of food.

IMPORTANCE

Identification of generalizable indicators for produce safety (PS) and produce quality (PQ) improves the detection of produce contamination and quality decline. However, effective sequencing read loss during microbiome data preprocessing and the limited sample size of individual studies restrain statistical power to identify important features contributing to differentiating PS and PQ phenotypes. We applied machine learning-based models using individual and integrated k-mer hash and amplicon sequence variant (ASV) data sets for PS and PQ classification and evaluated their classification performance and found that random forest (RF)-based models using integrated 7-mer hash data sets achieved significantly higher PS and PQ classification accuracy. Due to the limitation of taxonomic analysis for the 7-mer hash, we also developed RF-based models using feature-selected ASV-based taxonomic data sets, which performed better PS classification than those using the integrated 7-mer hash data set. The RF feature selection method identified 480 PS indicators and 263 PQ indicators with a positive contribution to the PS and PQ classification.

Conventional and non-conventional disinfection methods to prevent microbial contamination in minimally processed fruits and vegetables

Pandemic COVID-19 warned the importance of preparing the immune system to prevent diseases. Therefore, consuming fresh fruits and vegetables is essential for a healthy and balanced diet due to their diverse compositions of vitamins, minerals, fiber, and bioactive compounds. However, these fresh products grew close to manure and irrigation water and are harvested with equipment or by hand, representing a high risk of microbial, physical, and chemical contamination. The handling of fruits and vegetables exposed them to various wet surfaces of equipment and utensils, an ideal environment for biofilm formation and a potential risk for microbial contamination and foodborne illnesses. In this sense, this review presents an overview of the main problems associated with microbial contamination and the several chemicals, physical, and biological disinfection methods concerning their ability to avoid food contamination. This work has discussed using chemical products such as chlorine compounds, peroxyacetic acid, and quaternary ammonium compounds. Moreover, newer techniques including ozone, electrolyzed water, ultraviolet light, ultrasound, high hydrostatic pressure, cold plasma technology, and microbial surfactants have also been illustrated here. Finally, future trends in disinfection with a sustainable approach such as combined methods were also described. Therefore, the fruit and vegetable industries can be informed about their main microbial risks to establish optimal and efficient procedures to ensure food safety.

An overview of the nutritional value, health properties, and future challenges of Chinese bayberry

Chinese bayberry (CB) is among the most popular and valuable fruits in China owing to its attractive color and unique sweet/sour taste. Recent studies have highlighted the nutritional value and health-related benefits of CB. CB has special biological characteristics of evergreen, special aroma, dioecious, nodulation, nitrogen fixation. Moreover, the fruits, leaves, and bark of CB plants harbor a number of bioactive compounds including proanthocyanidins, flavonoids, vitamin C, phenolic acids, and anthocyanins that have been linked to the anti-cancer, anti-oxidant, anti-inflammatory, anti-obesity, anti-diabetic, and neuroprotective properties and to the treatment of cardiovascular and cerebrovascular diseases. The CB fruits have been used to produce a range of products: beverages, foods, and washing supplies. Future CB-related product development is thus expected to further leverage the health-promoting potential of this valuable ecological resource. The present review provides an overview of the botanical characteristics, processing, nutritional value, health-related properties, and applications of CB in order to provide a foundation for further research and development.

The Bacterial and Fungi Microbiota of Soy Sauce-Supplied Lactic Acid Bacteria Treated with High-Pressure Process

Background: Soy sauce is applied as a seasoning in daily life in East Asia. High amounts of salt in soy sauce can inhibit microbial growth in its production and preservation. However, the elevated salt content in food might increase the health risk. Low salt fermentation is rarely used in soil sauce production because of the potential harmful lactic acid bacteria growth. Therefore, dilution after high salt fermentation is commonly used to reduce the salt concentration. Methods: This study aims to treat the low salt fermented soy sauce with a high hydrostatic pressure process (HPP) to eliminate the harmful bacteria and to analyze the microbial community change compared with that in traditional high salt fermentation. Results: The results showed that the bacterial diversity was increased in low-salt and high-pressure (LS-HP)-treated soy sauce, though the bacterial abundance was decreased. Relative abundance in high-salt (HS), low-salt (LS), and LS-HP-treated soy sauce showed specific bacterial strains in the LS-HP group. Similarly, the fungal diversity was also increased in LS-HP-fermented soy sauce and the detected OTUs were increased. The fungi sensitive to salinity and pressure were indicated in our results. Conclusions: The present study suggests the enhanced bacterial and fungal diversity and different microbial community in HS, LS, and LS-HP-treated soy sauce, as well as the availability of LS and HPP treatment on soy sauce production.

Mycobiota in the Carposphere of Sour and Sweet Cherries and Antagonistic Features of Potential Biocontrol Yeasts

Sour cherries (Prunus cerasus L.) and sweet cherries (P. avium L.) are economically important fruits with high potential in the food industry and medicine. In this study, we analyzed fungal communities associated with the carposphere of sour and sweet cherries that were freshly harvested from private plantations and purchased in a food store. Following DNA isolation, a DNA fragment of the ITS2 rRNA gene region of each sample was individually amplified and subjected to high-throughput NGS sequencing. Analysis of 168,933 high-quality reads showed the presence of 690 fungal taxa. Investigation of microbial ASVs diversity revealed plant-dependent and postharvest handling-affected fungal assemblages. Among the microorganisms inhabiting tested berries, potentially beneficial or pathogenic fungi were documented. Numerous cultivable yeasts were isolated from the surface of tested berries and characterized by their antagonistic activity. Some of the isolates, identified as Aureobasidium pullulans, Metschnikowia fructicola, and M. pulcherrima, displayed pronounced activity against potential fungal pathogens and showed attractiveness for disease control.

Hot air treatment reduces postharvest decay in Chinese bayberries during storage by affecting fungal community composition

Chinese bayberry fruit were treated with hot air (HA) at 48 ℃ for 3 h and then stored at 4 ℃ for 15 d. Changes in fungal communities were analyzed by high-throughput sequencing (HTS), and decay and fruit quality were monitored during storage. The results showed that HA treatment effectively maintains fruit quality and the richness and diversity of fungal communities. Heat treatment inhibited decay development and reduced the growth of fungi in the genera Botryotinia spp., Davidiella spp., Hanseniaspora spp., and Candida spp. Canonical correspondence analysis further revealed that Botryotinia spp. and Davidiella spp. were positively correlated with fruit decay and weight loss. FUNGuild analysis demonstrated that HA-treated bayberries had a lower relative abundance within the plant pathogen guild, but higher relative abundance within the endophyte guild. The results suggest that HA treatment reduces pathogens by favoring the increase of endophytes, providing new insight into the decay development and quality changes during the storage of postharvest Chinese bayberries.

Impact of High-Hydrostatic Pressure Treatments Applied Singly or in Combination with Moderate Heat on the Microbial Load, Antimicrobial Resistance, and Bacterial Diversity of Guacamole

Guacamole is an avocado sauce highly appreciated for its pleasant taste and nutritional value. The present study addressed the impact of high-hydrostatic pressure (HP) treatments on the product safety and bacterial diversity. Four HP treatments, 5 min each, were applied: (A) 450 megapascals (MPa) at 22 °C; (B) 450 MPa at 50 °C; (C) 600 MPa at 22 °C; (D) 600 MPa at 50 °C. Controls and treated samples were refrigerated stored for 50 days. The residual surviving fraction was lowest for the 600 MPa treatment at 50 °C. Bacterial growth on media supplemented with antibiotics (cefotaxime and imipenem) or the biocide benzalkonium chloride was detected only from control samples but not from HP-treated samples. High throughput sequencing analysis indicated that the bacterial diversity of control samples was dominated by members of Fam. Enterobacteriaceae, but it changed to a lactic acid microbiota during storage. HP-treated samples showed reduced relative abundances of Enterobacteriaceae and lactic acid bacteria and higher abundances of Pantoea, Ralstonia and Methylobacterium. Results from the study indicate that HP treatments of guacamole at 50 °C show higher microbial inactivation compared to 22 °C. However, all treatments reduced the levels of Enterobacteriaceae and penem-tolerant bacteria and provided product stability against acidification by lactic acid bacteria.

DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables

The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.