Lentibacillus lipolyticus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi)

Bacterial community structure, predicted metabolic activities, and formation of volatile compounds attributed to Malaysian fish sauce flavour

The fermentation of Malaysian fish sauce (budu) varies from one to twelve months depending on the producer, resulting in inconsistent quality. The microbiota, their predicted metabolic pathways and volatile metabolites profiles were determined at different stages of budu fermentation. Budu fermented for 1 and 3 months were characterized by the presence of Gram negative Enterobacterales, Gammaproteobacteria, and Fusobacteriaceae, which continuously decrease in abundance over fermentation time. The metabolic pathways prediction grouped 1- and 3- month budu in a cluster enriched with degradation reactions. 6-month budu were dominated by Halanaerobium and Staphylococcus, while the 12-month were dominated by Lentibacillus, Bacilli, and Halomonas. Biosynthesis-type predicted pathways involving protein and lipid derivatives were enriched in 6- and 12-month fermented budu, accumulating 2,6-dimethylpyrazine, methyl 2-ethyldecanoate, 2-phenylacetaldehyde, 3-methylbutanal, and 3-methylbutanoic acid. These compounds may indicate budu maturity and quality. This result may assist as a reference for quality control and fermentation monitoring.

Factors affecting bacterial community dynamics and volatile metabolite profiles of Thai traditional salt fermented fish

Bacterial diversity of the Thai traditional salt fermented fish with roasted rice bran (Pla-ra) was investigated using classical and molecular approaches. Bacterial population of Pla-ra ranged from 10²-10⁶ in solid-state (SSF) and 10⁶-10⁹ CFU/g in submerged (SMF) fermentation types. Halanaerobium spp. and Lentibacillus spp. were the main genera particularly detected when rRNA analysis was applied. Tetragenococcus halophillus were dominant during the final stage in sea salt-recipe samples while Bacillus spp. were found in those rock salt recipes. In contrast, cultural plating demonstrated that Bacillus spp., generally B. amyloliquefaciens, were the dominant genera. In addition, B. pumilus, B. autrophaeus, B.subtilis and B. velezensis shown some relations with rock salt-recipe samples. The main volatile metabolites in all samples were butanoic acid and its derivatives. Key factors affected bacterial profiles and volatile compounds of salt fermented fish were type of salt, addition of roasted rice bran, and fermenting conditions.

Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand

An aerobic, Gram-stain-positive, endospore-forming, rod-shaped and moderately halophilic strain SKP4-6^T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6^T belonged to the genus Halobacillus and was most closely related to Halobacillus salinus JCM 11546^T (98.6 %), Halobacillus locisalis KCTC 3788^T (98.6 %) and Halobacillus yeomjeoni KCTC 3957^T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6^T and its related species were 18.2-19.3 % and 69.84-84.51 %, respectively, which were lower than the threshold recommended for species delineation. The strain grew optimally at 30-40 °C, at pH 7.0 and with 10-15 % (w/v) NaCl. It contained l-Orn-d-Asp in the cell wall peptidoglycan. The DNA G+C content was 44.8 mol%. The major fatty acids were iso-C_15 : 0, anteiso-C_15 : 0 and anteiso-C_17 : 0. The predominant isoprenoid quinone was MK-7. Phosphatidylglycerol and diphosphatidylglycerol were present as major polar lipids. Based on this polyphasic approach, digital DNA-DNA relatedness and ANI values, strain SKP4-6^T represents a novel species of the genus Halobacillus, for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6^T (=JCM 32624^T=TISTR 2595^T).

The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools

Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.

Accumulation of Ectoines By Halophilic Bacteria Isolated from Fermented Shrimp Paste: An Adaptation Mechanism to Salinity, Temperature, and pH Stress

Shrimp paste is a traditional fermented food produced by many Asian countries. Bacteria play important roles in the shrimp paste fermentation process. In order to survive under the low water activity (A_w) conditions caused by the high salt concentration, the bacteria need to employ a special adaptation strategy. This study found that most halophilic bacteria isolated from shrimp paste accumulated ectoines (ectoine and hydroxyectoine) as protective osmotic agents. Five isolated bacteria, including three high ectoine producers and two high hydroxyectoine producers, were selected for further study. Based on their morphological and biochemical characteristics and 16S rRNA gene sequences, the five strains were classified into three genera: Salinivibrio (strains M7 and M316), Salimicrobium (strains M31 and M69), and Vibrio (strain M92). The accumulation of ectoines by Salimicrobium species is reported here for the first time. The effects of salinity, incubation temperature, and initial pH on the growth rate and accumulation of ectoines by the five strains were investigated. The results revealed that the bacterial growth rate was inhibited while the accumulation of ectoines by the five selected strains was triggered by an increase in the external salinity, incubation temperature, or initial pH. In addition, a high concentration of ectoine only (21.2 wt%) was produced by strain M316 at the optimum salinity and temperature, and under pressure of a high initial pH value. To the best of our knowledge, this is the first report demonstrating that the production of ectoines by bacterial strains can be enhanced by increasing the pH of the culture medium to induce pH stress. This finding suggests a new ectoine producer and fermentation strategy that may help to improve the production of ectoines in the future.

Fish sauce fermentation using Marinococcus halotolerans SPQ isolate as a starter culture

A total of 344 halophilic bacteria were isolated from fish fermentation broths, solar salt crystals, seawater, and muds from ponds of salt pans in Vietnam and subjected to aroma evaluation using fish broth containing 29 ~ 30% (w/v) NaCl. One isolate from a salt crystal with the highest aroma score was selected, identified by using 16S rDNA sequence, and named Marinococcus halotolerans SPQ. The GC-MS results of the fish broth fermented by M. halotolerans SPQ revealed elevated concentrations of several aroma compounds such as ethyl alcohol, 1-propanol, 1-butyl alcohol, 1-amyl alcohol, and methionol. During the validation tests for M. halotolerans SPQ, using 2 kg of anchovy fish in 30% (w/v) NaCl at pH 5.78, the total and amino nitrogen values in the broth increased over time from 15.2 g/L at the beginning to 26.3 g/L at 6th month, with these values being comparable to those of the control. The ammoniacal nitrogen value (2.52 g/L) in the inoculated broth at 6th month was slightly higher than that (2.21 g/L) of control. The histamine content of the fish broth inoculated with M. halotolerans SPQ after 6 months was 110.12 mg/L, less than the maximum permitted safety limit of 200 mg/L, indicating it to be safe. Physical parameters, such as the total, amino, ammoniacal nitrogens, and histamine content of fish broth fermented by M. halotolerans MPQ met the standards for Vietnamese fish sauces. Two important umami amino acids, aspartic and glutamic acid, were seen to significantly increase, by 23.5% and 35.1%, respectively, even in the extremely harsh fermentation conditions posed by 30% (w/v) NaCl. The color, odor, and taste of the fish sauce fermented by M. halotolerans SPQ elicited the highest preference score accorded by the panelists. Taken together, M. halotolerans SPQ is a promising starter culture strain for fish sauce fermentation.

Lentibacillus saliphilus. sp. nov., a moderately halophilic bacterium isolated from a saltern in Korea

A novel moderately halophilic bacterial strain, designated YIM 93176^T, was isolated from a saltern in Korea and subjected to a polyphasic taxonomic study. This isolate YIM 93176^T was observed to grow in the presence of 0-22% (w/v) NaCl and at pH 6.0-10.0 and 10-45 °C; optimum growth was observed with 5-10% (w/v) NaCl and at pH 7.0-9.0 and 28-37 °C. Based on 16S rRNA gene sequences analysis, the nearest relatives were Lentibacillus alimentarius M2024^T (96.5% similarity), followed by Virgibacillus carmonensis LMG 20964^T (96.0%) and the other type strains of the family Bacillaceae, but phylogenetic analysis indicated that strain YIM 93176^T belonged to the cluster comprising type species of the genus Lentibacillus. Genome sequencing of strain YIM 93176^T revealed a genome size of 3.2 Mb and a DNA G + C content of 40.5 mol%. The major fatty acids were anteiso-C_15:0 (40.7%) and iso-C_15:0 (26.4%), while the predominant respiratory quinone was menaquinone 7. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. These genotypic and chemotaxonomic characteristics supported affiliation of strain YIM 93176^T to the genus Lentibacillus. In addition, phenotypic characteristics could distinguish strain YIM 93176^T from its closely related species in genus Lentibacillus. Based on the cumulative evidences from the polyphasic taxonomic study, strain YIM 93176^T represents a novel species of the genus Lentibacillus, for which name Lentibacillus saliphilus sp. nov. (type strain YIM 93176^T = CCTCC AB 208139^T = DSM 21375^T) is proposed.

Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food

Two bacterial strains designated NKC220-2^T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic, oxidaseand catalase-positive, rod-shaped, spore-forming, non-motile, and halophilic bacteria. Both strains grew without NaCl, unlike type species in the genus Lentibacillus. The optimal pH for growth was 8.0, higher than that of the type species in the genus Lentibacillus, although growth was observed at pH 5.5-9.0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the two strains (99.3-99.9% similarity) are grouped within the genus Lentibacillus and most closely related to Lentibacillus juripiscarius IS40-3^T (97.4-97.6% similarity) isolated from fish sauce in Thailand. OrthoANI value between two novel strains and Lentibacillus lipolyticus SSKP1-9^T (79.5-79.6% similarity) was far lower than the species demarcation threshold. Comparative genomic analysis displayed differences between the two strains as well as among other strains belonging to Lentibacillus. Furthermore, each isolate had strain-specific groups of orthologous genes based on pangenome analysis. Genomic G + C contents of strains NKC-220-2^T and NKC851-2 were 41.9 and 42.2 mol%, respectively. The strains contained meso-diaminopimelic acid in their cell walls, and the major menaquinone was menaquinone-7. Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified glycolipid, aminophospholipid, and phospholipid were the major polar lipid components of both strains. The major cellular fatty acids of the strains were anteiso-C_15:0 and anteiso-C_17:0. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic features, strains NKC220-2^T and NKC851-2 represent novel species of the genus Lentibacillus, for which the name Lentibacillus cibarius sp. nov. is proposed. The type strain is NKC220-2^T (= KACC 21232^T = JCM 33390^T).