Brevibacterium koreense sp. nov., a moderately halophilic bacterium isolated from jogae-jeotgal, a Korean fermented seafood

A novel Gram-stain-positive, non-spore-forming, non-motile and rod-shaped bacterium, designated strain CBA3109T, was isolated from jogae-jeotgal (fermented clam), a traditional Korean fermented seafood. Strain CBA3109T showed growth at 10-30 °C (optimum, 25 °C) and pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-15% (w/v) NaCl (optimum, 5%). Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain CBA3109T belonged to the genus Brevibacterium, with the highest similarities to Brevibacterium aurantiacum NCDO 739T (98.26%) and B. antiquum VKM Ac-2118T (98.14%). Strain CBA3109T contained MK-8(H2) as the major menaquinone. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major fatty acids (>10%) were anteiso-C15 :  0 and anteiso-C17 :  0. The main polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity and digital DNA-DNA hybridization values between strain CBA3109T and the closest species were 86.2-87.0% and 31.1-33.0 %, respectively. The DNA G+C content of strain CBA3109T was 62.7%. Based on the morphological, phylogenetic, chemotaxonomic and genotypic data, strain CBA3109T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium koreense sp. nov. is proposed. The type strain is CBA3109T (= KACC 23387T = DSM 117564T).

Whole-Genome Sequencing of Peribacillus frigoritolerans Strain d21.2 Isolated in the Republic of Dagestan, Russia

Pesticide-free agriculture is a fundamental pillar of environmentally friendly agriculture. To this end, there is an active search for new bacterial strains capable of synthesizing secondary metabolites and toxins that protect crops from pathogens and pests. In this study, we isolated a novel strain d21.2 of Peribacillus frigoritolerans from a soil sample collected in the Republic of Dagestan, Russia. Leveraging several bioinformatic approaches on Illumina-based whole-genome assembly, we revealed that the strain harbors certain insecticidal loci (coding for putative homologs of Bmp and Vpa) and also contains multiple BGCs (biosynthetic gene clusters), including paeninodin, koranimine, schizokinen, and fengycin. In total, 21 BGCs were predicted as synthesizing metabolites with bactericidal and/or fungicidal effects. Importantly, by applying a re-scaffolding pipeline, we managed to robustly predict MGEs (mobile genetic elements) associated with BGCs, implying high genetic plasticity. In addition, the d21.2's genome was free from genes encoding for enteric toxins, implying its safety in use. A comparison with available genomes of the Peribacillus frigoritolerans strain revealed that the strain described here contains more functionally important loci than other members of the species. Therefore, strain d21.2 holds potential for use in agriculture due to the probable manifestation of bactericidal, fungicidal, growth-stimulating, and other useful properties. The assembled genome is available in the NCBI GeneBank under ASM4106054v1.

Brevibacterium litoralis sp. nov., a cellulose-degrading strain isolated from marine surface sediment

A Gram stain-positive, non-spore-forming, non-motile, short-rod actinomyces strain GXQ1321T was isolated from maritime surface sediments in Beihai (21° 41' 21.65″ N, 109° 05' 76.56″ E), Guangxi Zhuang Autonomous Region, and a number of categorization studies were performed. Following a period of 72 h of incubation at a temperature of 30 °C within a modified actinomycete culture medium, the colony was light-yellow, circular, smooth, central bulge, convex, opaque, with a 1.2-2.3 mm diameter. Strain GXQ1321T had the ability to degrade cellulose. Chemotaxonomic studies revealed that the major methylnaphthoquinones in strain GXQ1321T was MK-8(H2). The most prevalent cellular fatty acids were anteiso-C19:0, anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The whole-cell sugars of the strain GXQ1321T were identified rhamnose, xylose and glucose. Meso-diaminopimelic acid was found in the peptidoglycan hydrolysate, and the polar lipids were identified as diphosphatidylglycerol, three phosphoglycolipid, phosphatidylglycerol and two unknown glycolipid. This strain had 69.6% DNA G+C content. Strain GXQ1321T is classified as Brevibacterium based on its 16S rRNA gene sequence. It is closely related to Brevibacterium samyangense SST-8 T (96.8%) and Brevibacterium rongguiense 5221 T (96.3%). The average nucleotide identity (ANI) values of GXQ1321T and the above two type strains were 73.9-77.1%, and the digital DNA-DNA hybridisation (dDDH) values were 15.3-21.1%. Based on the phylogenetic, chemotaxonomic and physiological data, strain GXQ1321T was considered to be a novel species of the genus Brevibacterium, named Brevibacterium litoralis sp. nov, with the type strain GXQ1321T (= MCCC 1K08964T = KCTC 59167 T).

Complete Genome Sequence of Brevibacterium frigoritolerans Ant232, Isolated from Antarctic Snow

We report the complete and circularized genome sequences of Brevibacterium frigoritolerans Ant232, generated using a combination of Illumina and PacBio platforms. The high-quality complete genome consists of a circular 5,586,945-bp chromosome and a 305,498-bp plasmid, with G+C contents of 40.66% and 36.8%, respectively.

Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments

During a study of the marine actinobacterial biodiversity, a large number of Brevibacterium strains were isolated. Of these, five that have relatively low 16S rRNA gene similarity (98.5-99.3%) with validly published Brevibacterium species, were chosen to determine taxonomic positions. On the basis of 16S rRNA gene sequence analysis and BOX-PCR fingerprinting, strains o2^T, YB235^T, and WO024^T were selected as representative strains. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly differentiated the three strains from each other and from their closest relatives, with values ranging from 82.8% to 91.5% for ANI and from 26.7% to 46.5% for dDDH that below the threshold for species delineation. Strains YB235^T, WO024^T, and o2^T all exhibited strong and efficient decolorization activity in congo red (CR) dyes, moderate decolorization activity in toluidine blue (TB) dyes and poor decolorization in reactive blue (RB) dyes. Genes coding for peroxidases and laccases were identified and accounted for these strains' ability to effectively oxidize a variety of dyes with different chemical structures. Mining of the whole genome for secondary metabolite biosynthesis gene clusters revealed the presence of gene clusters encoding for bacteriocin, ectoine, NRPS, siderophore, T3PKS, terpene, and thiopeptide. Based on the phylogenetic, genotypic and phenotypic data, strains o2^T, YB235^T and WO024^T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2^T = JCM 33844^T = MCCC 1A09961^T), Brevibacterium pigmenatum sp. nov. (type strain YB235^T = JCM 33843^T = MCCC 1A09842^T) and Brevibacterium atlanticum sp. nov. (type strain WO024^T = JCM 33846^T = MCCC 1A16743^T) are proposed.

Brevibacterium renqingii sp. nov., isolated from the Daqu of Baijiu

Two bacterial strains, designated REN4^T and REN4-1, were isolated from daqu sample collected from baijiu factory located in Shanxi, China. The two strains shared highly similar 16S rRNA gene sequences (99.67% identities) and formed a monophyletic clade within the Brevibacterium 16S rRNA gene tree, showing 97.56-97.85% 16S rRNA gene sequence identities with type strains Brevibacterium permense VKM Ac-2280 ^T, Brevibacterium sediminis FXJ8.269 ^T, Brevibacterium oceani BBH7^T and Brevibacterium epidermidis NCIMB 702286 ^T. They contained MK-8(H₂) as the most predominant menaquinone, antesio-C_15:0, antesio-C_17:0, Iso-C_16:0 and Iso-C_17:0 as the major cellular fatty acids, DPG (diphosphatidylglycerol), PG (phosphatidylglycerol), PGL (phosphatidylglycerollipids), and PL (phospholipids) as the main polar lipids. The genomic DNA G + C content of strains REN4 and REN4-1 were 64.35, 65.82 mol%. Moreover, the low DNA-DNA relatedness values, physiological and biochemical characteristics, and taxonomic analysis allowed the differentiation of strains REN4^T and REN4-1 from the other recognized species of the genus Brevibacterium. Therefore, strain REN4^T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium renqingii sp. nov. is proposed, with the type strain REN4^T (= JCM 33953 T = KCTC 49366 ^T).

Analysis of the complete genome sequence of Brevibacterium frigoritolerans ZB201705 isolated from drought- and salt-stressed rhizosphere soil of maize

Purpose

To analyze the complete genome sequence of the Brevibacterium frigoritolerans ZB201705, a Brevibacterium strain was isolated from the maize rhizosphere in drought- and salt-stressed soil, and the activity of the strain under simulated drought and high salt conditions was assessed.

Methods

We used a combination of the PacBio RS and Illumina sequencing platforms to obtain the complete genome sequence of B. frigoritolerans ZB201705.

Results

The genome consists of 5,475,560 bp in a linear chromosome with no gaps, 4,391 protein-coding sequences, 39 ribosomal RNAs, and 81 transfer RNAs. The genome analysis revealed many putative gene clusters involved in defense mechanisms. In addition, an activity analysis of the strain under high-salt and simulated drought conditions helped clarify its potential tolerance to these abiotic stresses.

Conclusions

Our data revealed the complete genome sequence of the new isolated strain, and showed that it produces many proteins involved in drought and salt stress responses, suggesting that B. frigoritolerans ZB201705 may be a potential factor to increase crop yield under abiotic stresses. The information provided here on the genome of B. frigoritolerans ZB201705 provides valuable insight into rhizobacteria-mediated plant salt and drought tolerance and rhizobacteria-based solutions for agriculture under abiotic stress.

Halophilic & halotolerant prokaryotes in humans

Halophilic prokaryotes are described as microorganisms living in hypersaline environments. Here, we list the halotolerant and halophilic bacteria which have been isolated in humans. Of the 52 halophilic prokaryotes, 32 (61.54%) were moderately halophilic, 17 (32.69%) were slightly halophilic and three (5.76%) were extremely halophilic prokaryotes. At the phylum level, 29 (54.72%) belong to Firmicutes, 15 (28.84%) to Proteobacteria, four (7.69%) to Actinobacteria, three (5.78%) to Euryarchaeota and one (1.92%) belongs to Bacteroidetes. Halophilic prokaryotes are rarely pathogenic: of these 52 halophilic prokaryotes only two (3.92%) species were classified in Risk Group 2 (Vibrio cholerae, Vibrio parahaemolyticus) and one (1.96%), species in Risk Group 3 (Bacillus anthracis).

Description of Mycobacterium chelonae subsp. bovis subsp. nov., isolated from cattle (Bos taurus coreanae), emended description of Mycobacterium chelonae and creation of Mycobacterium chelonae subsp. chelonae subsp. nov

Three rapidly growing mycobacterial strains, QIA-37T, QIA-40 and QIA-41, were isolated from the lymph nodes of three separate Korean native cattle, Hanwoo (Bos taurus coreanae). These strains were previously shown to be phylogenetically distinct but closely related to Mycobacterium chelonae ATCC 35752T by taxonomic approaches targeting three genes (16S rRNA, hsp6 and rpoB) and were further characterized using a polyphasic approach in this study. The 16S rRNA gene sequences of all three strains showed 99.7 % sequence similarity with that of the M. chelonae type strain. A multilocus sequence typing analysis targeting 10 housekeeping genes, including hsp65 and rpoB, revealed a phylogenetic cluster of these strains with M. chelonae. DNA-DNA hybridization values of 78.2 % between QIA-37T and M. chelonae indicated that it belongs to M. chelonae but is a novel subspecies distinct from M. chelonae. Phylogenetic analysis based on whole-genome sequences revealed a 95.44±0.06 % average nucleotide identity (ANI) value with M. chelonae, slightly higher than the 95.0 % ANI criterion for determining a novel species. In addition, distinct phenotypic characteristics such as positive growth at 37 °C, at which temperature M. chelonae does not grow, further support the taxonomic status of these strains as representatives of a novel subspecies of M. chelonae. Therefore, we propose an emended description of Mycobacterium chelonae, and descriptions of M. chelonae subsp. chelonae subsp. nov. and M. chelonae subsp. bovis subsp. nov. are presented; strains ATCC 35752T(=CCUG 47445T=CIP 104535T=DSM 43804T=JCM 6388T=NCTC 946T) and QIA-37T (=KCTC 39630T=JCM 30986T) are the type strains of the two novel subspecies.

Mycobacterium paraintracellulare sp. nov., for the genotype INT-1 of Mycobacterium intracellulare

Three mycobacterial strains, isolated from independent Korean patients with pulmonary infections, belonging to the Mycobacterium intracellulare genotype 1 (INT-1) were characterized using a polyphasic approach. The sequences of the 16S rRNA gene and internal transcribed spacer 1 (ITS1) of the INT-1 strains were identical to those of Mycobacterium intracellulare ATCC 13950T. However, multilocus sequence typing (MLST) analysis targeting five housekeeping genes (hsp65, rpoB, argG, gnd and pgm) revealed the phylogenetic separation of these strains from M. intracellulare ATCC 13950T. DNA-DNA hybridization values of >70 % confirmed that the three isolates belong to the same species, while the values of <70 % between one of them and the type strains of M. intracellulare and Mycobacterium chimaera confirmed their belonging to a distinct species. In addition, phenotypic characteristics such as positive growth on MacConkey agar and in acidic broth culture, unique matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS profiles of lipids, and unique mycolic acids profiles further supported the taxonomic status of these strains as representatives of a novel species of the Mycobacterium avium complex named Mycobacterium paraintracellulare. The type strain is MOTT64T (=KCTC 29084T=JCM 30622T).

Weissella jogaejeotgali sp. nov., isolated from jogae jeotgal, a traditional Korean fermented seafood

Strain FOL01T was isolated from traditionally fermented Korean jogae jeotgal (fermented clams). Phylogenetic sequence analysis of the 16S rRNA gene from FOL01T revealed that it is closely related to Weissella thailandensis FS61-1T and Weissella paramesenteroides ATCC 33313T with 99.39 % and 98.50 % 16S rRNA gene sequence similarities, respectively. API and VITEK analyses showed that strain FOL01T could be separated from its nearest phylogenetic relatives with respect to carbohydrate fermentation and antibiotic resistance. Subsequent amplified rRNA gene restriction analysis of 16S rRNA genes and HaeIII-restriction enzyme profiling of genomic DNAs revealed different band patterns. In addition, DNA-DNA hybridization of genomic DNAs showed 63.9 % relatedness. Analysis of the composition of cellular fatty acids confirmed that strain FOL01T differs from its close relatives and supports the proposal to assign this organism to a novel species of the genus Weissella. Based on these results, strain FOL01T could be classified as a novel species of the genus Weissella, for which the name Weissella jogaejeotgali sp. nov. is proposed. The type strain is FOL01T ( = KCCM 43128T = JCM 30589T).

Garicola koreensis gen. nov., sp. nov., isolated from saeu-jeot, traditional Korean fermented shrimp

A novel Gram-staining-positive, non-endospore-forming, aerobic bacterium, designated strain SJ5-4T, was isolated from seau-jeot, a traditional food that is made by fermentation of highly salted [approximately 25 % (w/v)] shrimp in Korea. Cells were moderately halophilic, non-motile cocci or short rods that showed catalase- and oxidase-positive reactions. Growth of strain SJ5-4T was observed at 15–40 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 6.5–7.0) and in the presence of 1–17 % (w/v) NaCl (optimum, 6 %). The major cellular fatty acids of strain SJ5-4T were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid, three glycolipids and an unidentified lipid were detected as the polar lipids. Strain SJ5-4T belonged to the exceptionally small group of strains within the order Micrococcales that show a peptidoglycan cross-linked according to the A-type but containing 2,4-diaminobutyric acid. The G+C content of the genomic DNA was 61.8 mol%. MK-7, MK-8 and MK-9 were detected as the isoprenoid quinones. Strain SJ5-4T was most closely related to members of the genus Nesterenkonia, with 16S rRNA gene sequence similarities of 93.1–94.8 %. However, phylogenetic inference based on 16S rRNA gene sequences showed that strain SJ5-4T formed a phyletic lineage distinct from members of the genus Nesterenkonia within the family Micrococcaceae . On the basis of its phenotypic and molecular features, strain SJ5-4T represents a novel genus and species of the family Micrococcaceae , for which the name Garicola koreensis gen. nov., sp. nov. is proposed. The type strain of Garicola koreensis is SJ5-4T ( = KACC 16909T = JCM 18572T = DSM 28238T).

Salimicrobium jeotgali sp. nov., isolated from salted, fermented seafood

A Gram-staining-positive, aerobic, motile bacterium, designated strain MJ3(T), was isolated from myeolchi-jeot (anchovy jeotgal), a traditional fermented seafood in South Korea. Cells were non-endospore-forming cocci showing catalase- and oxidase-positive reactions. Growth of strain MJ3(T) was observed at 15-45 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 1-24% (w/v) NaCl (optimum, 10% NaCl). Phylogenetic inference based on 16S rRNA gene sequences showed that strain MJ3(T) formed a tight phyletic lineage with members of the genus Salimicrobium. Strain MJ3(T) was related most closely to Salimicrobium salexigens 29CMI(T), Salimicrobium album DSM 20748(T), Salimicrobium flavidum ISL-25(T), Salimicrobium luteum BY-5(T) and Salimicrobium halophilum DSM 4771(T), with similarities of 98.8%, 98.7%, 98.6%, 98.4% and 98.3%, respectively. However, the DNA-DNA relatedness values between strain MJ3(T) (KF732837) and S. salexigens DSM 22782(T), S. album DSM 20748(T), S. flavidum DSM 23127(T), S. luteum KCTC 3989(T) and S. halophilum JCM 12305(T) were 60 ± 5.4%, 58.5 ± 6.5%, 43.6 ± 5.5%, 37.2 ± 5.8% and 16.7 ± 0.2%, respectively. Chemotaxonomic data (sole isoprenoid quinone, MK-7; major cell-wall type, meso-diaminopimelic acid; major cellular fatty acids, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0; major polar lipids, phosphatidylglycerol and diphosphatidylglycerol; DNA G+C content, 46.3 mol%) also supported the affiliation of strain MJ3(T) with the genus Salimicrobium. Therefore, strain MJ3(T) represents a novel species of the genus Salimicrobium, for which the name Salimicrobium jeotgali sp. nov. is proposed. The type strain is MJ3(T) ( = KACC 16972(T) = JCM 19758(T)).

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.