Analysis of bacterial community structure in Saba-Narezushi (Narezushi of Mackerel) by 16S rRNA gene clone library

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.

Characterization of the bacterial community structure in traditional Gifu ayu-narezushi (fermented sweetfish)

In this study, we aimed to elucidate the bacterial biota of ayu-nazushi, which is a fermented salted fish dish made in Gifu City, Japan. In traditional Gifu ayu-nazushi, Lactobacillaceae (mainly Latilactobacillus sakei) was the most dominant family, followed by Enterobacteriaceae. Moreover, fermentation bacteria in ayu-nazushi came from the salted fish, and the bacterial biota in the ayu-nazushi transferred as the fermentation process progressed. In the early stage of fermentation, Leuconostoc mesenteroides was main species, and then in the late stage, L. sakei became predominant. We also observed that when non-salted fish was used for the manufacture of ayu-nazushi, Aeromonas veronii, which is a pathogen for humans, was observed in significant quantities. These results indicate that L. sakei and L. mesenteroides were influential lactic acid bacteria for the fermentation of Gifu ayu-narezushi, and that salting treatment of the fish is an indispensable step in the manufacturing process in order to suppress the growth of Aeromonas species.

Transition and regulation mechanism of bacterial biota in Kishu saba-narezushi (mackerel narezushi) during its fermentation step

The transition of the bacterial biota of Kishu saba-narezushi (mackerel-narezushi) in the Hidaka region of Wakayama prefecture, Japan, was analyzed using amplicon sequencing based on the V3-V4 variable region of the 16S rRNA gene. In the non-fermented sample (0 day), the major genus with the highest abundance ratio was Staphylococcus. In the early stage (fermentation for 2 days), however, the genus Lactococcus became a dominant species, and in the later stage (fermentation for 5 days), the abundance ratio of the genus Lactobacillus increased significantly. Lactococcus lactis strains isolated from the narezushi samples had the ability to suppress the growth of not only Staphylococcus genera but also Lactobacillus. Moreover, the isolates produced a bacteriocin, which was identified as nisin Z. On the basis of these results, it is concluded that L. lactis plays an important role in preparing the fermentation conditions of Kishu saba-narezushi in the early stage by suppressing unwanted microorganisms using lactic acid and nisin Z.

Performance and functional microbial communities of denitrification process of a novel MFC-granular sludge coupling system

The performance, microbial communities and functional gene metabolism of the novel microbial fuel cell (MFC)-granular sludge coupling system was investigated. The results showed that COD and nitrogen removal can be up to 1.3-2.0 kg COD/L, 20-30 mg NO2--N/L, and 60-70 mg NO3--N/L, respectively. Proteobacteria, Chloroflexi, and Firmicutes were the dominant bacterial phyla, and the denitrification process was mainly consisted of the dominant denitrifying bacteria: Thauera (26.21%) and Pseudomonas (14.79%) in the first compartment, combining with denitrifying anaerobic methane oxidation bacteria: NC10 phylum of 0.072% (the first compartment) and 0.089% (the fourth compartment), Candidatus Methylomirabilis oxyfera of 0.044% (the first compartment) and 0.048% (the fourth compartment). According to functional gene classification for Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, metabolism was the main cluster for the whole sequence in the KEGG (7.17-11.41%), indicating that the dominant metabolic pathway played an important role in the degradation of pollutants.

Advantages and limitations of potential methods for the analysis of bacteria in milk: a review

Contamination concerns in the dairy industry are motivated by outbreaks of disease in humans and the inability of thermal processes to eliminate bacteria completely in processed products. HACCP principles are an important tool used in the food industry to identify and control potential food safety hazards in order to meet customer demands and regulatory requirements. Milk testing is of importance to the milk industry regarding quality assurance and monitoring of processed products by researchers, manufacturers and regulatory agencies. Due to the availability of numerous methods used for analysing the microbial quality of milk in literature and differences in priorities of stakeholders, it is sometimes confusing to choose an appropriate method for a particular analysis. The objective of this paper is to review the advantages and disadvantages of selected techniques that can be used in the analysis of bacteria in milk. SSC, HRMA, REP, and RAPD are the top four techniques which are quick and cost-effective and possess adequate discriminatory power for the detection and profiling of bacteria. The following conclusions were arrived at during this review: HRMA, REP and RFLP are the techniques with the most reproducible results, and the techniques with the most discriminatory power are AFLP, PFGE and Raman Spectroscopy.

Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals

Mesophilic and psychrotrophic organism viable counts, as well as high-throughput 16S rRNA gene-based pyrosequencing, were performed with the aim of elucidating the origin of psychrotrophic lactic acid bacteria (LAB) in a ready-to-eat (RTE) meal manufacturing plant. The microbial counts of the products at the end of the shelf life were greatly underestimated when mesophilic incubation was implemented due to overlooked, psychrotrophic members of the LAB. Pseudomonas spp., Enterobacteriaceae, Streptococcaceae, and Lactobacillus spp. constituted the most widespread operational taxonomic units (OTUs), whereas Leuconostoc gelidum was detected as a minor member of the indigenous microbiota of the food ingredients and microbial community of the processing environment, albeit it colonized samples at almost every sampling point on the premises. However, L. gelidum became the most predominant microbe at the end of the shelf life. The ability of L. gelidum to outgrow notorious, spoilage-related taxa like Pseudomonas, Brochothrix, and Lactobacillus underpins its high growth dynamics and severe spoilage character under refrigeration temperatures. The use of predicted metagenomes was useful for observation of putative gene repertoires in the samples analyzed in this study. The end products grouped in clusters characterized by gene profiles related to carbohydrate depletion presumably associated with a fast energy yield, a finding which is consistent with the fastidious nature of highly competitive LAB that dominated at the end of the shelf life. The present study showcases the detrimental impact of contamination with psychrotrophic LAB on the shelf life of packaged and cold-stored foodstuffs and the long-term quality implications for production batches once resident microbiota are established in the processing environment.

Effect of ripening stage on the development of the microbial community during spontaneous fermentation of green tomatoes

BACKGROUND

Spontaneous fermentation of plant-derived material is mainly performed on a small scale, with the exception of fermented olives, cucumbers, sauerkraut and kimchi, which have met worldwide commercial significance.

RESULTS

This study of spontaneous fermentation of green tomatoes at different stages of ripening revealed a significant effect on the growth kinetics of lactic acid bacteria and the final pH value. Leuconostoc mesenteroides dominated spontaneous fermentation when the initial pH value ranged from 3.8 to 4.8 whereas at higher pH values (4.9-5.4) it co-dominated with Leu. citreum and Lactobacillus casei. Application of RAPD-PCR and rep-PCR allowed differentiation at sub-species level, suggesting a microbial succession at that level accompanying the respective at species level.

CONCLUSION

Ripening stage affected the development of the micro-ecosystem through the growth of lactic acid bacteria and concomitant pH value reduction; however, the outcome of the fermentation was only marginally different.

Microbial successions and metabolite changes during fermentation of salted shrimp (saeu-jeot) with different salt concentrations

To investigate the effects of salt concentration on saeu-jeot (salted shrimp) fermentation, four sets of saeu-jeot samples with 20%, 24%, 28%, and 32% salt concentrations were prepared, and the pH, bacterial and archaeal abundances, bacterial communities, and metabolites were monitored during the entire fermentation period. Quantitative PCR showed that Bacteria were much more abundant than Archaea in all saeu-jeot samples, suggesting that bacterial populations play more important roles than archaeal populations even in highly salted samples. Community analysis indicated that Vibrio, Photobacterium, Psychrobacter, Pseudoalteromonas, and Enterovibrio were identified as the initially dominant genera, and the bacterial successions were significantly different depending on the salt concentration. During the early fermentation period, Salinivibrio predominated in the 20% salted samples, whereas Staphylococcus, Halomonas, and Salimicrobium predominated in the 24% salted samples; eventually, Halanaerobium predominated in the 20% and 24% salted samples. The initially dominant genera gradually decreased as the fermentation progressed in the 28% and 32% salted samples, and eventually Salimicrobium became predominant in the 28% salted samples. However, the initially dominant genera still remained until the end of fermentation in the 32% salted samples. Metabolite analysis showed that the amino acid profile and the initial glycerol increase were similar in all saeu-jeot samples regardless of the salt concentration. After 30–80 days of fermentation, the levels of acetate, butyrate, and methylamines in the 20% and 24% salted samples increased with the growth of Halanaerobium, even though the amino acid concentrations steadily increased until approximately 80–107 days of fermentation. This study suggests that a range of 24–28% salt concentration in saeu-jeot fermentation is appropriate for the production of safe and tasty saeu-jeot.

Microbial community structure at different fermentation stages of kutajarista, a herbal formulation

Kutajarista is an Ayurvedic fermented herbal formulation prescribed for gastrointestinal disorders. This herbal formulation undergoes a gradual fermentative process and takes around 2 months for production. In this study, microbial composition at initial stages of fermentation of Kutajarista was assessed by culture independent 16S rRNA gene clone library approach. Physicochemical changes were also compared at these stages of fermentation. High performance liquid chromatography-mass spectrometry analysis showed that Gallic acid, Ellagic acid, and its derivatives were the major chemical constituents recovered in this process. At 0 day of fermentation, Lactobacillus sp., Acinetobacter sp., Alcaligenes sp., and Methylobacterium sp. were recovered, but were not detected at 8 day of fermentation. Initially, microbial diversity increased after 8 days of fermentation with 11 operational taxonomic units (OTUs), which further decreased to 3 OTUs at 30 day of fermentation. Aeromonas sp., Pseudomonas sp., and Klebsiella sp. dominated till 30 day of fermentation. Predominance of γ- Proteobacteria and presence of gallolyl derivatives at the saturation stage of fermentation implies tannin degrading potential of these microbes. This is the first study to highlight the microbial role in an Ayurvedic herbal product fermentation.