Bacterial microbiota composition of fermented fruit and vegetable juices (jiaosu) analyzed by single-molecule, real-time (SMRT) sequencing

Determination of oxyphenisatine and its total ester derivatives content in fermented green plum by ultra performance liquid chromatography-tandem mass spectrometry

Illegal additives such as oxyphenisatine and its esters are prevalent in the slimming food industry, necessitating a robust analytical method for their detection. This study presents a novel UPLC-MS/MS method for the rapid and accurate quantification of total oxyphenisatine levels in fermented green plum, following hydrolysis of its esters. An efficient ultrasonic extraction with a methanol and 0.1 mol/L NaOH mixture (5:5, v/v) was optimised to hydrolyse esters to oxyphenisatine within 18 min. Chromatographic separation was conducted on a C18 column (Waters Acquity UPLC BEH, 2.1 × 100 mm, 1.7 μm) with a mobile phase of 5 mmol/L ammonium acetate and acetonitrile under gradient elution at a flow rate of 0.3 mL/min. The method demonstrated linearity (r2 > 0.999) over 0.1-500 µg/L, with a LOD of 10 µg/kg and LOQ of 30 µg/kg. Quantitative analysis employed positive ion multi-response monitoring and external standardisation, achieving recoveries of 92.4-97.0% and RSDs of 2.9-4.1%. Application to ten real samples gave a 90% detection rate, with measured values closely aligning with theoretical predictions (-11.3 to 13.2% relative difference) and oxyphenisatine content ranging from 159 µg/kg to 452 mg/kg. This UPLC-MS/MS method provides a reliable and efficient tool for monitoring the presence of oxyphenisatine and its derivatives in the context of food safety.

Impact of DNA extraction, PCR amplification, sequencing, and bioinformatic analysis on food-associated mock communities using PacBio long-read amplicon sequencing

BACKGROUND

Long-read 16S rRNA gene amplicon sequencing has a high potential for characterizing food-associated microbiomes. The advantage results from sequencing the full-length (1,500 bp) gene, enabling taxonomic resolution at species level. Here we present a benchmarking study using mock communities representative of milking machine biofilms and raw meat, revealing challenges relevant to food-associated habitats. These were varying species abundances, reliable intra-genus differentiation of species, and detection of novel species with < 98.7% sequence identity to type strains. By using mock communities at different levels of preparation - as mixed whole cells, mixed extracted DNA, and mixed PCR products - we systematically investigated the influence of DNA extraction using two different kits, PCR amplification of 16S rRNA genes, sequencing, and bioinformatics analysis including reference database and gene copy number normalization on bacterial composition and alpha diversity.

RESULTS

We demonstrated that PacBio ccs-reads allowed for correct taxonomic assignment of all species present within the mock communities using a custom Refseq database. However, choice of percent identity values for taxonomic assignment had a strong influence on identification and processing of reads from novel species. PCR amplification of 16S rRNA genes produced the strongest bias on the observed community composition, while sequencing alone reproduced the preset composition well. The PCR bias can in part be attributed to differences in mol% G + C content of 16S rRNA genes resulting in preferred amplification of low mol% G + C-containing taxa.

CONCLUSIONS

This study underlines the importance of benchmarking studies with mock communities representing the habitat of interest to evaluate the methodology prior to analyzing real samples of unknown composition. It demonstrates the advantage of long-read sequencing over short-read sequencing, as species level identification enables in-depth characterization of the habitat. One benefit is improved risk assessment by enabling differentiation between pathogenic and apathogenic species of the same genus.

The indigenous microbial diversity involved in the spontaneous fermentation of red dragon fruit (Hylocereus polyrhizus) identified by means of molecular tools

Red dragon fruit (RDF) is well-known for its high nutritional content, especially the red pigment betacyanins that possess high antioxidant activity. Natural fermentation is an ancient yet outstanding technique that relies on the autochthonous microbiota from fruits and vegetables surfaces to preserve and improve the nutritional values and quality of the food product. The present study was to evaluate and identify the indigenous microbial community (bacteria and fungi) that are involved in the natural fermentation of RDF. Results revealed a total of twenty bacterial pure cultures and nine fungal pure cultures were successfully isolated from fermented red dragon fruit drink (FRDFD). For the first time, the PCR amplification of 16S rRNA and ITS regions and sequence analysis suggested nine genera of bacteria and three genera of fungi (Aureobasidium pullulans, Clavispora opuntiae, and Talaromyces aurantiacus) present in the FRDFD. Four dominant (≥10 % isolates) bacteria species identified from FRDFD were Klebsiella pneumonia, Brevibacillus parabrevis, Bacillus tequilensis and Bacillus subtilis. The carbohydrate fermentation test showed that all the indigenous microbes identified were able to serve as useful starter culture by fermenting sucrose and glucose, thereby producing acid to lower the pH of FRDFD to around pH 4 for better betacyanins stability. The present study provides a more comprehensive understanding of the indigenous microbial community that serves as the starter culture in the fermentation of RDF. Besides, this study provides a useful guide for future research to be conducted on studying the rare bacterial strains (such as B. tequilensis) identified from the FRDFD for their potential bioactivities and applications in medical treatment and functional foods industries.

Microbial Community Variations and Bioconversion Improvements during Soybean-Based Fermentation by Kefir Grains

Soybeans possess unexpected flavors and are difficult to be absorbed by the gastrointestinal tract. Kefir grain fermentation provides diverse strains and bioactive compounds, which may enhance flavor and bioaccessibility. Third-generation sequencing was applied to analyze the microbial diversity in milk and soybean kefir grains in this study. In both types of kefir grains, the most common bacterial genus was Lactobacillus, and their fungal communities were dominated by Kazachstania. Lactobacillus kefiranofaciens was the most abundant species in kefir grains, while Lactobacillus kefiri showed a higher proportion in soybean kefir grains. In addition, the quantification of free amino acids and volatile flavor compounds in soybean solution and soybean kefir have shown the increased content of glutamic acid and a decreased amount of unpleasant beany flavor compounds, demonstrating that the nutritive value and sensory properties of soybean can be improved by kefir grain fermentation. Finally, the bioconversion of isoflavones during fermentation and in vitro digestion was evaluated, suggesting that fermentation is beneficial for aglycone formation and absorption. To conclude, kefir fermentation is proposed to change the microbial structure of kefir grains, promote the nutritional value of soybean-based fermented products, and provide possible solutions for the development of soybean products.

Optimization of the Quality of Chestnut Rose Jiaosu Compound Beverage Based on Probiotic Strains and Fermentation Technology

Chestnut rose is an endemic plant in Guizhou Province, China, also known as seedless prickly pear, rich in mineral elements, vitamin C, and flavonoids. With chestnut rose as the main raw material, with grapes, apples, and other fruits as auxiliary ingredients, through the technical process of deastringency, sterilization, fermentation, blending, and other technical processes to obtain the composite beverage, known as a chestnut rose jiaosu compound beverage, it is hereinafter referred to as CRJCB. The CRJCB fermented from chestnut rose juice is nutritious and has a variety of health effects, and the flavor is unique, with good color, aroma, and taste, which is a new type of beverage. However, at present, the fermentation related technology of CRJCB is not perfect, resulting in its low quality, which seriously restricts the industrialization development of CRJCB. In order to improve the quality of the jiaosu compound beverage, probiotics such as Lactobacillus delbrueckii subsp. Bulgaricus, Lactobacillus casei, Lactobacillus royale (Lactobacillus reuteri), Lactobacillus acidophilus, and Streptococcus thermophilus, etc., were used. The chestnut rose as the main raw material was used for the fermentation, and grapes, apples, and sugar were used as auxiliary materials to carry out the research on the fermentation of single or mixed probiotics. The key fermentation processes affecting the quality of the jiaosu, such as juice preparation, deastringency of chestnut rose juice, fermentation temperature and time, sugar addition, and taste mixing of the jiaosu, were optimized. The optimized ratio, fermentation process parameters, and strains of probiotics of compound beverage with chestnut rose jiaosu, with high quality, were obtained. The experimental results showed that the SOD enzyme activity value was 167.7 U·ml−1, the vitamin C content was 1154.5 mg/100 mL, the soluble solids content was 5.80%, and the nitrite content was 89.8 mg/kg in the compound beverage with chestnut rose jiaosu, obtained by using the optimized ratio and fermentation process parameters proposed in this paper. The development and utilization of chestnut rose resources provide a new idea and is of great significance in promoting the development of the chestnut rose industry.

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.

Chinese bayberry Jiaosu fermentation – changes of mycobiota composition and antioxidant properties

The aim of the study was to investigate the dynamic changes of mycobiota community, and the resultant effects on the antioxidant properties during the Chinese bayberry Jiaosu fermentation. The structure and composition of mycobiota during the Chinese bayberry Jiaosu fermentation were significantly changed (p < 0.001) and clearly clustered into two distinct phases (Phase 1: Day 5–20; Phase 2: Day 30–60, p < 0.001). From Phase 1 to Phase 2, the dominant fungi gradually changed from Saccharomycetales fam Incertae sedis to Saccharomyces cerevisiae. The antioxidative properties (total polyphenols, 1,1-diphenyl-2-picrylhydrazyl [DPPH], superoxide and 2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulphonate) [ABTS] radical scavenging) of Chinese bayberry Jiaosu were significantly increased by 250.4, 73.9, 25.3 and 40.0% respectively (p < 0.001). Co-occurrence network analysis revealed that Saccharomyces cerevisiae contributed to the increase of antioxidative properties in the Chinese bayberry Jiaosu fermentation. Our research indicates that fermentation into Chinese bayberry Jiaosu is an effective and new method for high-valued utilization of Chinese bayberry.