Lentibacillus halophilus sp. nov., from fish sauce in Thailand

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).

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

A Gram-stain-positive, aerobic, spore-forming, moderately halophilic bacterium, SSKP1-9^T, was isolated from traditional salted shrimp paste (Ka-pi) produced in Samut Sakhon Province, Thailand. This strain grew optimally at 37-40 °C, pH 7.0 and in the presence of 8-16 % (w/v) NaCl. The 16S rRNA gene sequence similarity values between strain SSKP1-9^T and Lentibacillus juripiscarius TISTR 1535^T and Lentibacillus halophilus TISTR 1549^T were 98.7 and 97.2 %, respectively. Based on 16S rRNA gene sequence similarity, strain SSKP1-9^T represents a distinct novel species, as shown by phenotypic traits, DNA-DNA hybridization and average nucleotide identity values. In addition, the whole-cell protein profile confirmed the novelty of the taxon. The genomic DNA G+C content was 44.6 mol%. The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, four unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis support that strain SSKP1-9^T represents a novel species of Lentibacillus, for which the name Lentibacilluslipolyticus sp. nov. is proposed. The type strain is SSKP1-9^T (=JCM 32625^T=TISTR 2597^T).

The extremely halophilic archaeon Halobacterium salinarum ETD5 from the solar saltern of Sfax (Tunisia) produces multiple halocins

The extremely halophilic archaeon Halobacterium salinarum strain ETD5 was previously isolated from the solar saltern of Sfax (Tunisia) and shown to encode and express halocin S8. The Hbt. salinarum ETD5 culture supernatant was shown here to exhibit high antimicrobial activity against several halophilic archaea and bacteria of different genera, showing a cross-domain inhibition. The antimicrobial activity was destroyed by proteases, thus pointing to halocins. A bioguided purification procedure was applied using two chromatography steps and antimicrobial assays directed against Halorubrum chaoviator ETR14. In-gel screening assay showed the presence of two antimicrobial bands of approximately 8 and 14 kDa, for which characterization was investigated by N-terminal sequencing and mass spectrometry. The full-length form of halocin S8 that contains 81 amino acids and differs from the 36 amino acid short-length halocin S8 previously described from an uncharacterized haloarchaeon S8a, was identified in the 8 kDa halocin band. A novel halocin that we termed halocin S14 was found in the 14 kDa band. It exhibits amino acid sequence identities with the N-terminally truncated region of the archaeal Mn-superoxide dismutase. These results show that Hbt. salinarum ETD5 produces multiple halocins, a feature that had not been described until now in the domain Archaea.

Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi

A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)).

Evolution in the Bacillaceae

The family Bacillaceae constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the Bacillaceae , the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.

Identification of moderately halophilic bacteria from Thai fermented fish ( pla-ra ) and proposal of Virgibacillus siamensis sp. nov

Forty-one isolates of moderately halophilic bacteria were isolated from fermented fish (pla-ra) in Thailand. On the basis of their phenotypic and chemotaxonomic characteristics, DNA-DNA relatedness and 16S rRNA gene sequences analyses, they were divided into six groups. The isolates in Group I to V were Gram-positive rod-shaped bacteria. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and menaquinone with seven isoprene units (MK-7). An isolate in Group VI was a Gram-negative rod-shaped bacterium. The DNA G+C contents of tested strains ranged from 36.5-63 mol%. Ten strains (Group I) were identified as Virgibacillus dokdonensis, 13 isolates (Group II) as V. halodenitrificans, 14 isolates (Group III) as V. marismortui, 1 isolate (Group IV) as Virgibacillus sp., 2 isolates (Group V) as Bacillus vietnamnensis, and 1 isolate (Group VI) as Chromohalobacter salexigens. Isolate MS3-4 in Group IV was closely related to V. carmonensis KCTC 3819(T) (95.9%). This strain contained anteiso-C(15:0) (55.8%) and anteiso-C(17:0) (17.7%) as major cellular fatty acids and had phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid as polar lipids. The DNA G+C content of MS3-4 was 38.0 mol%. The strain from Group IV is proposed as Virgibacillus siamensis sp. nov. and MS3-4(T) is the type strain (JCM 15395(T) =PCU 312(T) =TISTR 1957(T)).

Lentibacillus jeotgali sp. nov., a halophilic bacterium isolated from traditional Korean fermented seafood

A novel, Gram-positive, non-motile, endospore-forming and moderately halophilic bacterium, strain GrbiT, was isolated from a traditional Korean fermented seafood. The organism grew optimally in the presence of 10–15 % NaCl, at 37 °C and pH 8.0. The peptidoglycan of the cell wall consisted of meso-diaminopimelic acid, and the predominant menaquinone was MK-7. The major fatty acids of strain GrbiT were iso-C16 : 0 (36.4 %), anteiso-C15 : 0 (30.3 %) and iso-C14 : 0 (18.2 %). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C content was 42.5 mol%. Strain GrbiT was most closely related to the type strain Lentibacillus kapialis JCM 12580T, with which it shared 97.5 % 16S rRNA gene sequence similarity. The DNA–DNA hybridization value between strains GrbiT and L. kapialis JCM 12580T was 8 %. Based on phenotypic, genotypic and phylogenetic data, strain GrbiT should be classified as a novel species within the genus Lentibacillus, for which the name Lentibacillus jeotgali sp. nov. is proposed. The type strain is GrbiT (=KCTC 13300T=JCM 15795T).

Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov., isolated from salt in Thai fish sauce

Two red-pigmented, strictly aerobic, pleomorphic rod-shaped and extremely halophilic archaea, designated strains HST01-2R(T) and HST03(T), were isolated from salt in a fish sauce sample from Thailand. The novel strains grew optimally at 37 °C, pH 7.0, and in the presence of 20-25 % (w/v) NaCl. The DNA G+C contents of the isolates were 61.6-62.2&emsp14;mol%. Phylogenetic analysis based on a comparison of 16S rRNA gene sequences revealed that strains HST01-2R(T) and HST03(T) were placed in the radiation of species of the genus Haloarcula. The chemotaxonomic properties of the two strains, i.e. the presence of MK-8 and MK-8(H(2)) as the major menaquinone components and C(20)C(20) derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a triglycosyl diether as major polar lipids, supported the assignment of the two strains to the genus Haloarcula. Nevertheless, several phenotypic features and the low DNA-DNA relatedness between the two strains and related species of the genus Haloarcula (13.4-46.9 %) enabled the strains to be distinguished from each other and from recognized species. Therefore, strains HST01-2R(T) and HST03(T) represent two novel species in the genus Haloarcula, for which the names Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov. are proposed, respectively. The type strains are HST01-2R(T) (=BCC 40029(T)=JCM 15759(T)=PCU 313(T)) and HST03(T) (=BCC 40030(T)=JCM 15760(T)=PCU 314(T)).

Lentibacillus persicus sp. nov., a moderately halophilic species isolated from a saline lake

A Gram-staining-positive, moderately halophilic bacterium, designated strain Amb31(T), was isolated from water of the hypersaline lake Aran-Bidgol in Iran and characterized taxonomically using a polyphasic approach. Cells were rods, motile and able to produce ellipsoidal endospores at a central position in swollen sporangia. Strain Amb31(T) was facultatively anaerobic and catalase- and oxidase-positive. The strain grew in a complex medium supplemented with 3-25 % (w/v) NaCl (optimum 7.5-10 %). Optimal growth was at 30-35 degrees C and pH 7.5. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain Amb31(T) belonged to the genus Lentibacillus; it exhibited 16S rRNA gene sequence similarity values of 96.8 and 96.4 % to Lentibacillus salicampi SF-20(T) and Lentibacillus salinarum AHS-1(T), respectively, and values of 95.9-94.7 % to the type strains of other recognized species of Lentibacillus. The cell-wall peptidoglycan of strain Amb31(T) was based on meso-diaminopimelic acid and MK-7 was the respiratory isoprenoid quinone. The major fatty acids were anteiso-C(15 : 0) (44.7 %), iso-C(16 : 0) (21.4 %) and anteiso-C(17 : 0) (15.9 %) and the polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, five phospholipids and a glycolipid. The DNA G+C content was 44.1 mol%. All these features confirmed the placement of strain Amb31(T) within the genus Lentibacillus and the strain could be clearly differentiated from strains of the other species of Lentibacillus on the basis of several phenotypic, genotypic and chemotaxonomic features. DNA-DNA relatedness with the type strain of the most closely related strain, L. salicampi DSM 16425(T), was 28 %. Therefore, strain Amb31(T) represents a novel species of the genus Lentibacillus, for which the name Lentibacillus persicus sp. nov. is proposed. The type strain is Amb31(T) (=CCM 7683(T) =CECT 7524(T) =DSM 22530(T) =LMG 25304(T)).

Gracilibacillus thailandensis sp. nov., from fermented fish (pla-ra)

A novel strain, designated TP2-8(T), was isolated from fermented fish (pla-ra) in Thailand. It stained Gram-positive and the cells were aerobic, endospore-forming rods. The strain grew at pH 6-8 (optimum pH 7), 15-55 degrees C (optimum 37 degrees C) and 1-22 % (w/v) NaCl (optimum 5-10 %). It contained meso-diaminopimelic in the cell-wall peptidoglycan. MK-7 and cellular fatty acids anteiso-C(15 : 0), iso-C(15 : 0) and anteiso-C(17 : 0) were major components. Polar lipids diphosphatidylglycerol and phosphatidylglycerol and unidentified lipids were detected. The DNA G+C content was 37.6 mol%. Comparison of the 16S rRNA gene sequence of strain TP2-8(T) with those of other members of the family Bacillaceae indicated that it was a member of the genus Gracilibacillus (94.9-99.2 % sequence similarity) and was closely related to Gracilibacillus saliphilus YIM 91119(T) (99.2 % similarity), G. lacisalsi BH312(T) (98.6 %), G. orientalis XH-63(T) (97.7 %), 'G. quinghaiensis' YIM C229 (97.7 %) and G. boraciitolerans T-16X(T) (97.2 %). Strain TP2-8(T) showed low DNA-DNA relatedness (< or = 49%) to G. saliphilus YIM 91119(T), G. lacisalsi DSM 19029(T), G. orientalis CCM 7326(T), 'G. quinghaiensis' DSM 17858 and G. boraciitolerans JCM 21714(T). On the basis of the physiological and biochemical characteristics and molecular data presented, strain TP2-8(T) is proposed to represent a novel species, Gracilibacillus thailandensis sp. nov. (type strain TP2-8(T) =JCM 15569(T) =PCU 304(T) =TISTR 1881(T)).

Salinivibrio siamensis sp. nov., from fermented fish (pla-ra) in Thailand

A Gram-negative, facultatively anaerobic, moderately halophilic bacterium, strain ND1-1(T), was isolated from fermented fish (pla-ra) in Thailand. The cells were curved rods, motile and non-endospore-forming. The novel strain grew optimally at 37 degrees C, at pH 8 and in the presence of 9-10 % (w/v) NaCl. The predominant respiratory lipoquinone was Q-8. The major cellular fatty acids were C(16 : 0) and C(12 : 0). Polar lipid analysis revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 49.0 mol%. Comparative 16S rRNA gene sequence analyses indicated that strain ND1-1(T) was closely related to Salinivibrio costicola, which comprises three subspecies, and Salinivibrio proteolyticus with gene sequence similarities of 98.3-98.6 %. Strain ND1-1(T) showed low levels of DNA-DNA relatedness with S. costicola subsp. costicola JCM 15095(T) (33.2 %), S. costicola subsp. alcaliphilus DSM 16359(T) (38.4 %), S. costicola subsp. vallismortis JCM 15096(T) (59.7 %), and S. proteolyticus AF-2004(T) (42.1 %). On the basis of the physiological and biochemical characteristics and the molecular data presented, strain ND1-1(T) should be classified as a novel species of the genus Salinivibrio for which the name Salinivibrio siamensis sp. nov. is proposed. The type strain is ND1-1(T) (=JCM 14472(T)=PCU 301(T)=TISTR 1810(T)).

Halococcus thailandensis sp. nov., from fish sauce in Thailand

Fifteen strains of red-pigmented, strictly aerobic, coccoid, extremely halophilic archaea were isolated from fish sauce (nam-pla) produced in Thailand. They grew optimally at 37 °C, pH 6–8 and in the presence of 20–30 % (w/v) NaCl. The DNA G+C contents of the isolates were 60.0–61.8 mol%. They had MK-8(H2) as a major menaquinone component and C20C20 and C20C25 derivatives of phosphatidylglycerol, phosphatidylglycerol methylphosphate and a sulfated glycolipid, S-DGA-1, as major polar lipid components. 16S rRNA gene sequence comparisons revealed that a representative strain, HDB5-2T, was affiliated with Halococcus dombrowskii JCM 12289T, Halococcus qingdaonensis JCM 13587T and Halococcus morrhuae JCM 8876T (levels of similarity of 98.2–98.7 %). Based on data from DNA–DNA hybridization experiments, the 15 strains represented a single species, showing hybridization values of >78.9 % to representative strain HDB5-2T, but were unrelated to either Halococcus dombrowskii JCM 12289T or Halococcus morrhuae JCM 8876T, with levels of relatedness of <50 %. Moreover, a comparison of phenotypic properties discriminated these new isolates from recognized species of the genus Halococcus. The 15 strains are thus considered to represent a novel species of the genus Halococcus, for which the name Halococcus thailandensis sp. nov. is proposed. The type strain is HDB5-2T (=BCC 20213T =JCM 13552T =PCU 278T).

Piscibacillus salipiscarius gen. nov., sp. nov., a moderately halophilic bacterium from fermented fish (pla-ra) in Thailand

A Gram-positive, spore-forming and moderately halophilic bacterium was isolated from fermented fish (pla-ra) in Thailand. Cells of the isolate, RBU1-1T, were strictly aerobic, motile rods and contained meso-diaminopimelic acid in the cell-wall peptidoglycan. Menaquinone with seven isoprene units (MK-7) was the predominant quinone. This isolate grew at 15–48 °C, pH 5–9 and in 2–30 % NaCl (optimally 10–20 %). The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Polar lipid analysis revealed the presence of phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 36.7 mol%. 16S rRNA gene sequence analysis revealed that strain RBU1-1T was a member of the family Bacillaceae, and belonged to a cluster with Filobacillus and Tenuibacillus; strain RBU1-1T showed 16S rRNA gene sequence similarities of 96.0–96.9 % to members of these two genera. Strain RBU1-1T could also be differentiated from members of the genera Filobacillus and Tenuibacillus based on certain phenotypic characteristics such as cell-wall composition, mode of flagellation and growth pH range. Therefore, strain RBU1-1T is considered to represent a novel species in a new genus in the family Bacillaceae, for which the name Piscibacillus salipiscarius gen. nov., sp. nov. is proposed. The type strain of Piscibacillus salipiscarius is RBU1-1T (=JCM 13188T=PCU 270T=TISTR 1571T).

Lentibacillus halodurans sp. nov., a moderately halophilic bacterium isolated from a salt lake in Xin-Jiang, China

A Gram-positive, rod-shaped, spore-forming and moderately halophilic bacterium (strain 8-1T) was isolated from a sediment sample of a neutral salt lake in Xin-Jiang, China. The strain grew optimally at 30 °C, pH 7.0–7.5 and 8–12 % (w/v) NaCl. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The predominant isoprenoid quinone was MK-7 and the cell-wall peptidoglycan contained meso-diaminopimelic acid. Phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids were found to be the major polar lipid components. The genomic DNA G+C content was 43.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain 8-1T was closely related to Lentibacillus salarius KCTC 3911T (98.0 % sequence similarity) and other recognized species within the genus Lentibacillus (94.5–95.9 %). The level of DNA–DNA relatedness between strain 8-1T and L. salarius KCTC 3911T was 40 %. Based on the phenotypic and genotypic data presented, strain 8-1T is considered to represent a novel species of the genus Lentibacillus, for which the name Lentibacillus halodurans sp. nov. is proposed. The type strain is 8-1T (=CGMCC 1.3702T=DSM 18342T).

Lentibacillus kapialis sp. nov., from fermented shrimp paste in Thailand

Two strains of strictly aerobic, moderately halophilic Gram-positive rods were isolated from fermented shrimp paste (‘ka-pi’) produced in Thailand. They produced a red pigment and grew optimally in the presence of 5–30 % NaCl. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C15 : 0. Phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids were found to be the major polar lipid components. The DNA G+C content was 41.2–41.6 mol%. Comparative 16S rRNA gene sequence analyses showed that strain PN7-6T was most closely related to Lentibacillus salarius KCTC 3911T with 96.5 % sequence similarity. On the basis of phenotypic and molecular properties, the two isolates represent a novel species of the genus Lentibacillus, for which the name Lentibacillus kapialis sp. nov. is proposed. The type strain is PN7-6T (=JCM 12580T=PCU 259T=TISTR 1551T).