Identification of the Dominant Microbial Species of Spoiled Crisp Grass Carp ( Ctenopharyngodon idellus C. et V.) and Grass Carp ( Ctenopharyngodon idellus) Fillets during Cold Storage by Culture-Independent 16S rDNA Sequence Analysis

Dynamic changes in microbiota during fermentation of bamboo shoots under varying conditions in Guangxi, China

Introduction

The traditional fermentation process for bamboo shoots is long, complex, and yields a product with a non-uniform flavor. To address these issues, we determined the effects of using different parts of the bamboo shoot, different types of fermentation water, water-sealing or not, different types and initial concentrations of organic acids, and different lactobacillus inocula on microbial succession during the fermentation of bamboo shoots. 16S rRNA sequencing was performed using Illumina II high-throughput technology. Species abundance, α-, and β-diversity indices, and linear discriminant analysis effect size (LEfSe) analysis revealed that all detected microorganisms were members of the phyla Firmicutes, Cyanobacteria, and Proteobacteria, of which Firmicutes were dominant.

Methods

The effects of these variables on microbial succession were evaluated through 16S rRNA sequencing using Illumina II high-throughput technology. Species abundance, α- and β-diversity indices, and linear discriminant analysis effect size (LEfSe) analysis were used to identify and analyze the microbial community.

Results

The microbial community was dominated by the phyla Firmicutes, Cyanobacteria, and Proteobacteria, with Firmicutes being the most abundant. The relative abundance of Firmicutes was higher in water-sealed treatment groups than in non-sealed groups. Different organic acids selected specific microbial taxa, and the growth of acid-sensitive Lactococcus and Weissella was inhibited throughout fermentation. Different initial concentrations of organic acids selected biomarker taxa, such as Sphingomonas, which has the ability to degrade organic pollutants. When tap water was used as the fermentation broth, Acinetobacter became the dominant genus but inhibited the production of flavor compounds. Streptococcus thermophilus and Lactobacillus bulgaricus, derived from animal sources, had no significant effect on fermentation. Inoculation with a five-in-one lactic acid bacteria fermentation agent significantly increased the abundance of Clostridium sensu stricto 1, reaching a level 46.6 times that reported in the literature.

Discussion

This study shows that various factors, including water-sealing, organic acids, and microbial inoculation, have significant effects on microbial succession and the flavor profile of fermented bamboo shoots. These findings suggest that optimizing these parameters can improve the consistency and flavor quality of the product.

Integrated 4D label-free proteomics and data mining to elucidate the effects of thermal processing on crisp grass carp protein profiles

The crisp grass carp (CGC; Ctenopharyngodon idellus C. et V.), known for its unique texture and flavour, is a culinary delicacy whose quality is significantly influenced by thermal processing. This study employed 4D label-free proteomics and data mining techniques to investigate the proteomic changes in CGC muscle tissue induced by various heating temperatures. CGC samples were subjected to a series of heat treatments at increasing temperatures from 20 °C to 90 °C. Proteins were extracted, digested, and analysed using high-resolution mass spectrometry. The proteomic data were then subjected to extensive bioinformatics analysis, including GO and KEGG pathway enrichment. We identified a total of 1085 proteins, 516 of which were shared across all the temperature treatments, indicating a core proteome responsible for CGC textural properties. Differential expression analysis revealed temperature-dependent changes, with significant alterations observed at 90 °C, suggesting denaturation or aggregation of proteins at higher temperatures. Functional enrichment analysis indicated that proteins involved in amino acid metabolism, glutathione metabolism, and nucleotide metabolism were particularly affected by heat. Textural analysis correlated these proteomic changes with alterations in CGC quality attributes, pinpointing 70 °C as the optimum temperature for maintaining the desired texture. A strong positive correlation between specific upregulated proteins was identified, such as the tubulin alpha chain and collagen alpha-1(IV) chain, and the improved textural properties of CGC during thermal processing, suggesting their potential as the potential biomarkers. This study offers a comprehensive proteomic view of the thermal stability and functionality of CGC proteins, delivering invaluable insights for both the culinary processing and scientific management of CGC. Our findings not only deepen the understanding of the molecular mechanisms underpinning the textural alterations in CGC during thermal processing but also furnish practical insights for the aquaculture industry. These insights could be leveraged to optimize cooking techniques, thereby enhancing the quality and consumer appeal of CGC products.

Dynamic changes of the bacterial communities in roast chicken stored under normal and modified atmosphere packaging

This study systematically investigated the dynamic changes in bacterial communities in roast chicken in normal and modified atmosphere packaging (MAP). The samples were stored under normal atmosphere and 40%/60% CO₂ /N₂ MAP conditions for 28 days at 4 °C. Changes in the number and type of microorganisms in roast chicken during storage were defined via cultural and 16S rDNA sequencing techniques. More Bacteroides, Chryseobacterium, Lactobacillus, and Acinetobacter than other bacteria were initially found in roast chicken. With normal packaging, Pseudomonas rapidly multiplied and became the main spoilage organism in roast chicken after 7 days, with a relative abundance of >90% of the entire bacterial flora. With MAP, due to the high salt content, Halomonas became the main spoilage organism in roast chicken by the middle of the storage period (14 days). Between days 21 and 28 of storage, Pseudomonas gradually became the main spoilage organism in roast chicken, but its relative abundance was much lower in MAP than in normal packaging, followed by Lachnospiraceae (NK4A136 group) and Altererythrobacter. Our research shows that the microbes in roast chicken mainly originated from the processing environment and operators. The combination of MAP with a low storage temperature could effectively improve the quality and safety of roast chicken meat. PRACTICAL APPLICATIONS: This research showed the dynamic changes in the bacterial community of roast chicken stored under normal and modified atmosphere packaging (MAP). Microorganisms in roast chicken are mainly obtained from the processing environment and operators. Combining MAP with storage at low temperatures can effectively improve the quality and safety of roast chicken.

Effects of temperature on paocai bacterial succession revealed by culture-dependent and culture-independent methods

Paocai is a widely consumed Chinese traditional fermented vegetable product. To understand the effect of temperature on paocai fermentation flora, the bacterial community structure of paocai fermented at 10 °C, 15 °C, 25 °C and 35 °C was analyzed by culture-dependent and culture-independent methods. The results showed that increasing the fermentation temperature in a certain range is beneficial for rapid paocai acid production and shortening of the maturity period. Illumina Miseq sequencing was performed on 56 samples at different fermentation process temperatures using a culture-independent method. A total of 1,964,231 high-quality reads of 16S rRNA V3-V4 regions were obtained, and they were divided into 405 operational taxonomic units (OTUs) and identified as 213 bacterial genera. The bacterial diversity decreased with the progression of fermentation, and some spoiled samples had an increased diversity. The culture-independent method found that at 10 °C, Lactococcus appeared at the start of fermentation, Leuconostoc and Weissella appeared in the middle of fermentation, and Lactobacillus and Leuconostoc dominated fermentation in the late stage. At 15 °C, Lactococcus started fermentation, Leuconostoc appeared in the middle stage, and Lactobacillus was dominant in the late stage. At 25 °C, Lactococcus started fermentation, Weissella and Lactobacillus appeared in the middle stage, and Lactobacillus dominated fermentation in the late stage. Finally, at 35 °C, Lactococcus, Weissella, and Lactobacillus started fermentation, Weissella and Lactobacillus appeared in the middle stage, and Lactobacillus dominated fermentation in the late stage. A total of 647 strains of bacteria were isolated by culture-dependent methods and were divided into 12 genera and 19 species by randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) and 16S ribosomal RNA gene (rDNA) sequencing technology. More types of bacteria were isolated in the early stage of fermentation. At 10 °C, Lactococcus lactis began fermentation, and Lactobacillus brevis and Leuconostoc mesenteroides dominated acid production in the middle and late stages of paocai fermentation. At 15 °C, L. lactis initiates fermentation, while Lactobacillus plantarum dominates the acid fermentation of paocai. At 25 °C and 35 °C, there were a large number of Enterobacteriaceae bacteria in the start-up fermentation stage, and L. plantarum was dominant after 1-2 days of fermentation. Redundancy analysis (RDA) found that the lower the temperature, the more bacterial species that are produced, and the higher the temperature and the longer the time, the more obvious are the effects of L. plantarum on paocai. The results of dominant bacteria studied by culture-dependent and culture-independent methods are similar. The results indicate that most of the dominant microorganisms in the paocai fermentation system are culturable. This discovery can provide data and physical support for modernization and regulation of different types of paocai production.