Genome-Resolved Metaproteomic Analysis of Microbiota and Metabolic Pathways Involved in Taste Formation During Chinese Traditional Fish Sauce (Yu-lu) Fermentation

Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases

In metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large is critical for the peptide identification step. Therefore, the availability of well-curated reference databases and tools for custom database construction is essential to enhance the performance of metaproteomics analyses. In this review, we first provide an overview of metaproteomics by presenting a concise historical background, outlining a typical experimental and bioinformatics workflow, emphasizing the crucial step of constructing a protein sequence database for metaproteomics. We then delve into the current tools available for building such databases, highlighting their individual approaches, utility, and advantages and limitations. Next, we examine existing protein sequence databases, detailing their scope and relevance in metaproteomics research. Then, we provide practical recommendations for constructing protein sequence databases for metaproteomics, along with an overview of the current challenges in this area. We conclude with a discussion of anticipated advancements, emerging trends, and future directions in the construction of protein sequence databases for metaproteomics.

Salt-Reduced Fish Sauce Produced under Pressurized Carbon Dioxide Treatment Using Sardinops melanostictus, Trachurus japonicus, Konosirus punctatus, Odontamblyopus lacepedii, Their Collective Mixture, and Unused Fish Mixture

Fish sauce is produced at high salt concentrations (>20%) to inhibit the growth of harmful microorganisms. The salt-reduced fish sauce (10% salt) was prepared under pressurized CO2 (pCO2) conditions at 30 °C and 5 MPa for 3 months (FSCO2), from Sardinops melanostictus, Odontamblyopus lacepedii, Trachurus japonicus, Konosirus punctatus, and their collective mixture, as well as unused fish mixture obtained from the Ariake Sea in Japan. FSCO2 exhibited significantly better microbial quality and free amino acid content, lighter color, standardized odor (dashi-like odor), and umami richness qualities compared to fish sauces prepared using the conventional method (FScon) (20% salt), as previously demonstrated, after a fermentation period of 2 months. Bacterial flora analysis implied that the standardization of odor and umami richness may not be the result of specific microbial metabolism. Even when using previously unused fish, it was possible to produce FSCO2 equivalent to that produced by conventional sardines and other fish. These results indicate that the quality of fish sauce can be improved. The flavor of FSCO2 became similar regardless of the type of fish and fermentation period using pCO2 during fermentation, leading to the effective utilization of unutilized fish as a resource for high-quality salt-reduced fish sauce.

Metagenomic analysis and biodiversity of bacteria in traditional fermented fish or Budu from West Sumatera, Indonesia

Objective

This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province, Indonesia, as well as provide basic information about Budu quality.

Materials and methods

To obtain the bacterial microbial composition, deoxyribonucleic acid extraction was carried out using amplicon-sequencing of the 16S-rRNA gene in the V3-V4 region from two types of Budu and carried out in duplicate.

Results

Budu prepared with fresh (Pariaman) or frozen (Pasaman) fish was dominated by Firmicutes (78.455%-92.37%) and Proteobacteria (6.477%-7.23%) phyla. The total microbial species in Budu from Pariaman were higher (227 species) than in Pasaman (153 species). The bacterial species found are Lentibacillus kimchi (1.878%-2.21%), Staphylococcus cohnii (0.597%-0.70%), Peptostreptococcus russeli (0.00%-0.002%), Clostridium disporicum (0.073%-0.09%), Clostridium novyi (0.00%-0.01%), Nioella sediminis (0.00%-0.001%), and Shewanella baltica (0.00%-0.003%). Lentibacillus kimchi, S. cohnii, and C. disporicum are found in both Budu. Nioella sediminis and S. baltica are found in Budu Pariaman. Peptostreptococcus russeli and C. novyi were found in Budu Pasaman.

Conclusion

Metagenomic analysis of Budu from different fish, Pariaman (fresh fish) and Pasaman (frozen fish) showed that the biodiversity of bacteria was barely different. Both Budu found lactic acid bacteria from the Enterococcaceae family, genus Vagococcus, and pathogenic bacteria, such as S. cohnii, P. russeli, C. disporicum, and S. baltica. The discovery of various species of pathogenic bacteria indicates that development is still needed in the Budu production process to improve Budu quality.

Transforming the fermented fish landscape: Microbiota enable novel, safe, flavorful, and healthy products for modern consumers

Regular consumption of fish promotes sustainable health while reducing negative environmental impacts. Fermentation has long been used for preserving perishable foods, including fish. Fermented fish products are popular consumer foods of historical and cultural significance owing to their abundant essential nutrients and distinct flavor. This review discusses the recent scientific progress on fermented fish, especially the involved flavor formation processes, microbial metabolic activities, and interconnected biochemical pathways (e.g., enzymatic/non-enzymatic reactions associated with lipids, proteins, and their interactions). The multiple roles of fermentation in preservation of fish, development of desirable flavors, and production of health-promoting nutrients and bioactive substances are also discussed. Finally, prospects for further studies on fermented fish are proposed, including the need of monitoring microorganisms, along with the precise control of a fermentation process to transform the traditional fermented fish to novel, flavorful, healthy, and affordable products for modern consumers. Microbial-enabled innovative fermented fish products that consider both flavor and health benefits are expected to become a significant segment in global food markets. The integration of multi-omics technologies, biotechnology-based approaches (including synthetic biology and metabolic engineering) and sensory and consumer sciences, is crucial for technological innovations related to fermented fish. The findings of this review will provide guidance on future development of new or improved fermented fish products through regulating microbial metabolic processes and enzymatic activities.