Analysis of microbiota in Hainan Yucha during fermentation by 16S rRNA gene high‐throughput sequencing

Fermented fish and fermented fish-based products, an ever-growing source of microbial diversity: A literature review

Fermented fish and fermented fish-based products are part of the diet of many countries all over the world. Their popularity is not only due to the unique flavor, the distinct texture, and the good nutritional quality, but also to the easiness of the production process, that is commonly based on empirical traditional methods. Fish fermentation techniques ususally rely on the combination of some key steps, including salting, addition of spices or additives, and maintenance of anaerobic conditions, thus selecting for the multiplication of some pro-technological microorganisms. The objective of the present review was to provide an overview of the current knowledge of the microbial communities occurring in fermented fish and fish-based products. Specific information was collected from scientific publications published from 2000 to 2022 with the aim of generating a comprehensive database. The production of fermented fish and fish-based foods was mostly localized in West African countries, Northern European countries, and Southeast Asian countries. Based on the available literature, the microbial composition of fermented fish and fish-based products was delineated by using viable counting combined with identification of isolates, and culture-independent techniques. The data obtained from viable counting highlighted the occurrence of microbial groups usually associated with food fermentation, namely lactic acid bacteria, staphylococci, Bacillus spp., and yeasts. The identification of isolates combined with culture-independent methods showed that the fermentative process of fish-based products was generally guided by lactobacilli (Lactiplantibacillus plantarum, Latilactobacillus sakei, and Latilactobacillus curvatus) or Tetragenococcus spp. depending on the salt concentration. Among lactic acid bacteria populations, Lactococcus spp., Pediococcus spp., Leuconostoc spp., Weissella spp., Enterococcus spp., Streptococcus spp., and Vagococcus spp. were frequently identified. Staphylococcus spp. and Bacillus spp. confirmed a great adaptation to fermented fish-based products. Other noteworthy bacterial taxa included Micrococcus spp., Pseudomonas spp., Psychrobacter spp., Halanaerobium spp., and Halomonas spp. Among human pathogenic bacteria, the occurrence of Clostridium spp. and Vibrio spp. was documented. As for yeast populations, the predominance of Candida spp., Debaryomyces spp., and Saccharomyces spp. was evidenced. The present literature review could serve as comprehensive database for the scientific community, and as a reference for the food industry in order to formulate tailored starter or adjunctive cultures for product improvement.

Metagenomics assembled genome scale analysis revealed the microbial diversity and genetic polymorphism of Lactiplantibacillus plantarum in traditional fermented foods of Hainan, China

Exploring the microbiome in fermented foods and their effects on food quality and sustainability is beneficial to provide data support for understanding how they affects human physiology. Here, metagenomic sequencing and metagenomic assembled genomes (MAGs) were applied to appraise the microbial diversity of fermented Yucha (FYC) and fermented vegetables (FVE). The antibiotic resistance genes (ARGs) enrichment and genetic polymorphism of Lactiplantibacillus plantarum in fermented foods of different regions were compared. The results showed that Lactiplantibacillus plantarum was the dominant species in FYC, while Lactiplantibacillus fermentum in FVE occupied the dominant position. From 32 high-quality MAGs, the central differential Lactic acid bacteria were higher in FVE. By comparing the Lactiplantibacillus plantarum MAGs in Hainan and Other regions, we found that the total Single Nucleotide Polymorphisms of Lactiplantibacillus plantarum in Hainan were significantly higher than other areas. Six non-synonymous mutations were included in the primary differential mutation, especially TrkA family potassium uptake protein and MerR family transcriptional regulator, which may be related to the hypersaline environment and highest ARGs enrichment in Hainan. This research provides valuable insight into our understanding of the microbiome of fermented food. Meanwhile, the analysis of Lactiplantibacillus plantarum genetic polymorphism based on MAGs helps us understand this strain's evolutionary history.

Microbial community changes induced by Pediococcus pentosaceus improve the physicochemical properties and safety in fermented tilapia sausage

Amine-negative lactic acid bacteria can prevent excess biogenic amines from accumulating in sausage. In this study, the amine-negative Pediococcus pentosaceus 30-7 and 30-15 with good fermentation properties and biogenic amine removal ability were isolated for tilapia sausage production. P. pentosaceus 30-7 improved the physical characteristics such as gel strength and hardness in tilapia sausage, while P. pentosaceus 30-15 significantly enhanced the contents of umami and sweet free amino acids. The microbial metabolic network revealed that the dominant microbial community in the fermentation process including Pediococcus and Lactococcus contributed to the physicochemical formation of sausage. The significant decrease of biogenic amine contents after addition of P. pentosaceus strains mainly resulted from their ability to remove biogenic amines and to inhibit the growth of amine-producing Enterobacter, Citrobacter, and Streptococcus. This study provides an effective method for directionally improving the physicochemical properties and safety in fermented tilapia sausage.

Novel insight into physicochemical and flavor formation in naturally fermented tilapia sausage based on microbial metabolic network

The quality and flavor formation in fermented fish sausages are based on the complex metabolism of microbial community. In this study, the dynamic changes of physicochemical characteristics, volatile compounds, and microbial communities in the naturally fermented tilapia sausage were studied during the fermentation process. The main physical indexes (gel strength, whiteness, and hardness), dominant flavor free amino acids (glycine, alanine, and glutamic acid) and characteristic volatile flavor compounds (hexanal, heptanal, octanal, benzaldehyde, (E)-2-octenal, 4-ethylbenzaldehyde, (E)-2-heptenal, (E,E)-2,4-decadienal, 1-octen-3-ol, 2-pentylfuran, and 2-ethyl-furan) were significantly enhanced after fermentation, and were positively correlated with Lactococcus, Pediococcus, Enterococcus, and Lactobacillus. The microbial metabolic network showed that Lactococcus, Pediococcus, and Enterococcus played a significant role in the formation of physicochemical and flavor characteristics, while the accumulation of biogenic amines might result from the metabolism of Enterococcus, Enterobacter, and Citrobacter. Isolation of lactic acid bacteria in Lactococcus and Pediococcus might be suitable to improve the fermented tilapia sausage. Microbial metabolic network has revealed the physicochemical and flavor formation of tilapia sausage and can provide guidance for future research on screening of starters.

Analysis of the Microbial Diversity and Characteristics of Fermented Blueberry Beverages from Different Regions

In this study, high-throughput sequencing methods were used to analyze the composition and diversity of the microbial communities of three different traditional fermented blueberry beverages (Jiaosu A, Jiaosu B, and Jiaosu C) produced in three different regions. Lactic acid bacteria and yeast counts, total soluble solids, total titration acid, total phenols, total flavonoids, total anthocyanin, superoxide dismutase, and antioxidant activity were analyzed in all samples. The results showed that at the phylum level, the bacteria in all samples were predominantly Firmicutes and Proteobacteria, while the majority of fungus belonged to Ascomycota. At the genus level, Lactobacillus, Gluconobacter, and Acetobacter were the dominant bacteria, and Dekkera and Issatchenkia were the dominant fungi. Our data show that the lactic acid bacteria counts in Jiaosu A were the lowest of the three products, in the range of 4.31–10.9 log CFU/mL, while yeast counts ranged from 6.71 to 7.35 log CFU/mL. The antioxidant activities of Jiaosu C were greater than those of Jiaosu A and Jiaosu B, and Spearman correlation analysis showed that the relative abundance of Lactobacillus and Dekkera was significantly positively correlated with total phenolics, total anthocyanin, total flavonoids, and antioxidant index.