Next-generation sequencing reveals predominant bacterial communities during fermentation of Thai fish sauce in large manufacturing plants

Ohshima, Chihiro; Takahashi, Hiroki; Insang, Supasit; Phraephaisarn, Chirapiphat; Techaruvichit, Punnida; Khumthong, Rabuesak; Haraguchi, Hiroyuki; Lopetcharat, Kannapon; Keeratipibul, Suwimon

doi:10.1016/j.lwt.2019.108375

Cited by 34 publications

(13 citation statements)

References 39 publications

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“…Regarding bacterial communities, the genus Lactobacillus was highly influential (VIP > 2.2) for the differentiation of olive samples from the area of Aitoloakarnania (Figure S8). These observations highlight the influence of the microclimate conditions on the microbiota of, not only fermented olives [40], but also of other food commodities as well [69,70].…”

Section: Discussionmentioning

confidence: 67%

Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis

et al. 2020

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Kalamata natural black olives are one of the most economically important Greek varieties. The microbial ecology of table olives is highly influenced by the co-existence of bacteria and yeasts/fungi, as well as the physicochemical parameters throughout the fermentation. Therefore, the aim of this study was the identification of bacterial and yeast/fungal microbiota of both olives and brines obtained from 29 cv. Kalamata olive samples industrially fermented in the two main producing geographical regions of Greece, namely Aitoloakarnania and Messinia/Lakonia. The potential microbial biogeography association between certain taxa and geographical area was also assessed. The dominant bacterial family identified in olive and brine samples from both regions was Lactobacillaceae, presenting, however, higher average abundances in the samples from Aitoloakarnania compared to Messinia/Lakonia. At the genus level, Lactobacillus, Celerinatantimonas, Propionibacterium and Pseudomonas were the most abundant. In addition, the yeasts/fungal communities were less diverse compared to those of bacteria, with Pichiaceae being the dominant family and Pichia, Ogataea, and Saccharomyces being the most abundant genera. To the best of our knowledge, this is the first report on the microbiota of both olives and brines of cv. Kalamata black olives fermented on an industrial scale between two geographical regions of Greece using metagenomics analysis.

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Section: Discussionmentioning

confidence: 67%

Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis

et al. 2020

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“…At the phylum level, there were 386 and 133 proteins derived from Firmicutes and Proteobacteria, accounting for 68 and 25% of the total protein, respectively. Ohshima et al ( 22 ) have researched predominant bacterial communities of Thai fish sauce based on next-generation sequencing and demonstrated that Proteobacteria is the predominant bacterial phylum in the middle and late fermentation phases ( 22 ). Proteobacteria constitute the main microbial flora present in shrimp paste ( 23 ) and soybean paste ( 7 ); thus, Proteobacteria may play a key role in the quality characteristics of fermented foods.…”

Section: Resultsmentioning

confidence: 99%

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

Wang

et al. 2022

Front. Nutr.

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Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervision and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previously developed metagenomic database. The abundance of most identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. These proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation revealed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis. This study demonstrated the approaches to identify microbiota functions and metabolic pathways, thereby providing a theoretical basis for taste formation mechanisms during traditional fish sauce fermentation.

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“…Considering this, processed food can be seen as a habitat for halophiles provided that the salt levels are high (Lee, 2013). Indeed halophiles are found in fermented seafood (Das et al, 2020), cheeses (Kothe et al, 2020), sauces (Sagdic et al, 2017;Ohshima et al, 2019), green table olives (Randazzo et al, 2017), and pickles (Stoll et al, 2020). Some halophilic and halotolerant microorganisms can be established in the human gut microbiome, and the gut halophilic microbiota is considered to be linked to some chronic diseases (Seck et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Beyond Archaea: The Table Salt Bacteriome

et al. 2021

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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.

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Next-generation sequencing reveals predominant bacterial communities during fermentation of Thai fish sauce in large manufacturing plants

Cited by 34 publications

References 39 publications

Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis

Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis

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

Beyond Archaea: The Table Salt Bacteriome

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