Relative abundance of halophilic archaea and bacteria in diverse salt-fermented fish products

Halophilic lactic acid bacteria - Play a vital role in the fermented food industry

Halophilic lactic acid bacteria have been widely found in various high-salt fermented foods. The distribution of these species in salt-fermented foods contributes significantly to the development of the product's flavor. Besides, these bacteria also have the ability to biosynthesize bioactive components which potentially apply to different areas. In this review, insights into the metabolic properties, salt stress responses, and potential applications of these bacteria have been have been elucidated. The purpose of this review highlights the important role of halophilic lactic acid bacteria in improving the quality and safety of salt-fermented products and explores the potential application of these bacteria.

Human associated Archaea: a neglected microbiome worth investigating

The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.

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.

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.

Characterization of the archaeal community in foods: The neglected part of the food microbiota

Despite the large number of studies conducted on archaea associated with extreme environments, the archaeal community composition in food products is still poorly known. Here, we investigated a new insight into exploring the archaeal community in several food matrices, with a particular focus on determining whether living archaea were present. A total of 71 samples of milk, cheese and its derived brine, honey, hamburger, clam, and trout were analyzed by high-throughput 16S rRNA sequencing. Archaea were detected in all the samples, ranging from 0.62 % of microbial communities in trout to 37.71 % in brine. Methanogens dominated 47.28 % of the archaeal communities, except for brine, which was dominated by halophilic taxa affiliated with the genus Haloquadratum (52.45 %). Clams were found to be a food with high richness and diversity of archaea and were targeted for culturing living archaea under different incubation time and temperature conditions. A subset of 16 communities derived from culture-dependent and culture-independent communities were assessed. Among the homogenates and living archaeal communities, the predominant taxa were distributed in the genera Nitrosopumilus (47.61 %) and Halorussus (78.78 %), respectively. A comparison of the 28 total taxa obtained by culture-dependent and culture-independent methods enabled their categorization into different groups, including detectable (8 out of 28), cultivable (8 out of 28), and detectable-cultivable (12 out of 28) taxa. Furthermore, using the culture method, the majority (14 out of 20) of living taxa grew at lower temperatures of 22 and 4 °C during long-term incubation, and few taxa (2 out of 20) were found at 37 °C during the initial days of incubation. Our results demonstrated the distribution of archaea in all analyzed food matrices, which opens new perspectives to expand our knowledge on archaea in foods and their beneficial and detrimental effects.

Bacterial Diversity of Sun-Dried Spanish Mackerel in Dalian and Application of Lactobacillus plantarum X23 as a Biopreservative

ABSTRACT

Sun-dried Spanish mackerel is a common food in Dalian and made by adding salt and sun drying, which has special physical, chemical, and microbiological properties. In this study, the physicochemical properties and microbial composition of commercially available sun-dried Spanish mackerel in Dalian were assessed, and some Lactobacillus strains were screened as a biopreservative for sun-dried Spanish mackerel preparation. The results showed that the total volatile base nitrogen content in the traditional sun-dried Spanish mackerel samples from Dalian was within 30 mg/100 g, the histamine content was 7 to 17 mg/kg, and the dominant bacteria at the genus level were Lactobacillus, Psychrobacter, and Ralstonia. A strain with biopreservative potential was isolated from a sun-dried Spanish mackerel sample, identified as L. plantarum species by 16S rDNA sequencing, and assigned as L. plantarum X23. Fresh Spanish mackerel flesh was treated with 16% brine and L. plantarum X23 at a dose of 107 CFU/mL and then dried in the sun. The sun-dried Spanish mackerel flesh treated with 16% brine and L. plantarum X23 showed a decreased histamine and acid value, increased free amino acid content, and a higher sensory score compared with the sun-dried Spanish mackerel without L. plantarum X23 treatment (P < 0.05). In conclusion, the sun-dried Spanish mackerel purchased from the supermarkets in Dalian were safely edible, and L. plantarum X23 can significantly reduce the content of histamine and putrescine in self-made, low-salt, sun-dried Spanish mackerel and has potential as a biopreservative for sun-dried Spanish mackerel preparation.

HIGHLIGHTS

"Ethno-microbiology" of ethnic Indian fermented foods and alcoholic beverages

The concept of "ethno-microbiology" is to understand the indigenous knowledge of the Indian people for production of culturally and organoleptically acceptable fermented foods by natural fermentation. About 1000 types of common, uncommon, rare, exotic and artisan fermented foods and beverages are prepared and consumed in different geographical regions by multi-ethnic communities in India. Indian fermented foods are mostly acidic and some are alkaline, along with various types of alcoholic beverages. A colossal diversity of microorganisms comprising bacteria mostly belongs to phylum Firmicutes, filamentous moulds and enzyme- and alcohol-producing yeasts under phyla Ascomycota and Mucoromycota, and few bacteriophages and archaea have been reported from Indian fermented foods. Some microorganisms associated with fermented foods have functionalities and health promoting benefits. "Ethno-microbiology" of ethnic Indian people has exhibited the proper utilisation of substrates either singly or in combination such as fermented cereal-legume mixture (idli, dosa and dhokla) in South and West India, sticky fermented soybean food (kinema and related foods), fermented perishable leafy vegetable (gundruk and related foods), fermented bamboo shoots (soibum and related foods) and fermented fish (ngari and others) in North East India, and fermented meat and sausage-like products in the Indian Himalayas, fermented coconut beverage (toddy) in coastal regions, and various types of naturally fermented milk products (dahi and related products) in different regions of India. This review has also highlighted the "ethno-microbiology" knowledge of the people involving the consortia of essential microorganisms in traditionally prepared amylolytic starters for production of cereal-based alcoholic beverages. The novelty of this review is the interpretation of ethno-microbiological knowledge innovated by ethnic Indian people on the use of beneficial microorganisms for food fermentation to obtain the desired fermented food products for consumption.

Beyond Archaea: The Table Salt Bacteriome

Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.

Diversity of beneficial microorganisms and their functionalities in community-specific ethnic fermented foods of the Eastern Himalayas

The Eastern Himalayan regions of India, Nepal and Bhutan have more than 200 varieties of unsurpassed ethnic fermented foods and alcoholic beverages, which are lesser known outside the world. However, these ethnic foods are region- and community-specific, unique and some are exotic and rare, which include fermented vegetables, bamboo shoots, soybeans, cereals, milk (cow and yak), meats, fishes, and cereal-based alcoholic beverages and drinks. Ethnic communities living in the Eastern Himalayas have invented the indigenous knowledge of utilization of unseen microorganisms present in and around the environment for preservation and fermentation of perishable plant or animal substrates to obtain organoleptically desirable and culturally acceptable ethnic fermented food and alcoholic beverages. Some ethnic fermented products and traditionally prepared dry starters for production of alcoholic beverages of North Eastern states of India and Nepal were scientifically studied and reported till date, and however, limited publications are available on microbiological and nutritional aspects of ethnic fermented foods of Bhutan except on few products. Most of the beneficial microorganisms isolated from some ethnic fermented foods of the EH are listed in microbial food cultures (MFC) safe inventory. This study is aimed to review the updates on the beneficial importance of abundant microbiota and health-promoting benefits and functionalities of some ethnic fermented foods of the Eastern Himalayan regions of North East India, Nepal and Bhutan.

The relationship between flavor formation, lipid metabolism, and microorganisms in fermented fish products

Traditional fermented fish products are favored due to their unique flavors. The fermentation process of fish is accompanied by the formation of flavor substances through a complex metabolic reaction of microorganisms, especially lipolysis and lipid oxidation. However, it is difficult to precisely control the reaction of microorganisms during the fermentation process in modern industrial production, and fermented fish products have lost their traditional characteristic flavors. The purpose of this review is to summarize the different kinds of fermented fish, core microorganisms in it, and flavor formation mechanisms, providing guidance for industrial cultural starters. Future research on the flavor formation mechanism is necessary to confirm the relationship between flavor formation, lipid metabolism, and microorganisms to ensure stable flavor and safety, and to elucidate the mechanism directly toward industrial application.

Role of lactic acid bacteria in flavor development in traditional Chinese fermented foods: A review

Traditional Chinese fermented foods are favored by consumers due to their unique flavor, texture and nutritional values. A large number of microorganisms participate in the process of fermentation, especially lactic acid bacteria (LAB), which are present in almost all fermented foods and contribute to flavor development. The formation process of flavor is complex and involves the biochemical conversion of various food components. It is very important to fully understand the conversion process to direct the flavor formation in foods. A comprehensive link between the LAB community and the flavor formation in traditional Chinese fermented foods is reviewed. The main mechanisms involved in the flavor formation dominated by LAB are carbohydrate metabolism, proteolysis and amino acid catabolism, and lipolysis and fatty acid metabolism. This review highlights some useful novel approaches for flavor enhancement, including the application of functional starter cultures and metabolic engineering, which may provide significant advances toward improving the flavor of fermented foods for a promising market.

High-throughput sequence analysis of bacterial communities and their predictive functionalities in traditionally preserved fish products of Sikkim, India

Traditionally preserved fish products viz. suka ko maccha, a smoked fish product, sidra and sukuti, sun-dried fish products are commonly consumed in Sikkim state in India. Bacterial communities in these fish products were analysed by high-throughput sequence (HTS) method supported by bioinformatics tool. Metataxonomic of the overall bacterial communities in samples revealed the abundance of phylum Firmicutes followed by Proteobacteria. Psychrobacter was abundant genus in all traditionally preserved fish products of Sikkim, followed by Bacillus, Staphylococcus, Serratia, Clostridium, Enterobacter, Pseudomonas, Rummeliibacillus, Enterococcus, Photobacterium, Myroides, Peptostreptococcus, Plesiomonas and Achromobacter. Product-wise distribution showed that Bacillus was abundant in suka ko maacha and sidra samples, whereas Psychrobacter was abundant in sukuti samples. Unique genus to each product was observed on the basis of analysis of shared operational-taxonomic-unit (OTU) contents, Alpha diversity indices showed significantly differences among the samples, and also showed maximum coverage as per Good's coverage (0.99). Beta diversity showed clustering of bacterial compositions between suka ko maacha and sidra, whereas sukuti showed scattering pattern among the other samples, indicating a diverse population in suka ko maacha and sidra samples. Non-parametric analysis of abundant genera and predictive functionalities showed the complex bacterial inter-dependencies with predictive functionalities mostly in metabolism (79.88%).