Brachybacterium subflavum sp. nov., a novel actinobacterium isolated from the foregut of grass carp.

A novel actinobacterium, designated CFH 10395T, was isolated from the foregut of grass carp (Ctenopharyngodon idella), which had been fed with ginseng extract supplement. The taxonomic position was investigated by a polyphasic approach. Cells of CFH 10395T were Gram-staining-positive, aerobic, ovoid-shaped, non-spore-forming and non-motile. On the basis of the results of 16S rRNA gene sequence analysis, CFH 10395T was most closely related to Brachybacterium endophyticum KCTC 49087T, Brachybacterium squillarum JCM 16464T and Brachybacterium paraconglomeratum JCM 17781T (97.85%, 97.51 and 97.29% similarity, respectively). CFH 10395T grew at 4-37 °C, pH 5.0-9.0 and in the presence of up to 10.0 % NaCl (w/v). The dominant menaquinone was MK-7. The whole-cell sugars were rhamnose, glucose, mannose and galactose. meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The genome size was 3.99 Mbp with a DNA G+C content of 71.9 mol%. On the basis of the results of phylogenetic analysis, physiological properties, chemotaxonomic characteristics, low average nucleotide identity (ANI) and digital DDH (dDDH) results [ANI calculated using MUMmer (ANIm) <87 %, ANI calculated using blast (ANIb) <83 % and dDDH <23 %], it is concluded that CFH 10395T represents a novel species of the genus Brachybacterium, for which the name Brachybacterium subflavum sp. nov., is proposed. The type strain is CFH 10395T (=CGMCC 1.13804T=KCTC 49235T).

Brevibacillus migulae sp. nov., isolated from a Yellow River sediment sample.

Strain CFH S0501T, a novel Gram-stain-positive, aerobic, rod-shaped, endospore-forming and motile micro-organism with peritrichous flagella, was isolated from a sediment sample collected from the Yellow River in Henan Province, PR China. Optimum growth was observed at 28 °C, pH 7.0 and without NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain belonged to the genus Brevibacillus and was closely related to Brevibacillus centrosporus DSM 8445T and Brevibacillus ginsengisoli Gsoil 3088T (with 96.8 and 96.7 % sequence similarity, respectively). The predominant menaquinone was MK-7. Major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unidentified phospholipids and an unidentified polar lipid. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid. The genome size was 5.26 Mbp with a G+C content of 49.7 mol%. The average nucleotide identity (ANI) and in silico DNA-DNAhybridization (DDH) values between CFH S0501T and the other species of the genus Brevibacillus were found to be low (ANIm <86.11 %, ANIb <70.30 % and DDH <25.00 %). Based on physiological properties, chemotaxonomic characteristics and low ANI and DDH results, strain CFH S0501T is considered to represent a novel species, for which the name Brevibacillus migulae sp. nov. is proposed. The type strain is CFH S0501T (=DSM 29940T=BCRC 80809T).

Isoptericola halalbus sp. nov., a halotolerant actinobacterium isolated from saline lake sediment.

A novel Gram-stain-positive bacterium, designated CFH 91151T, was isolated from sediment collected from a saline lake in Yuncheng, Shanxi Province, PR China. Cells of strain CFH 91151T were rod-or v-shaped, aerobic, non-motile, non-spore-forming and halotolerant. Results of 16S rRNA gene sequence analysis revealed that strain CFH 91151T was closely related to Isoptericola variabilis MX5T and Isoptericola nanjingensis H17T (98.7 and 98.4% sequence similarity, respectively). The strain grew at 4-45 °C, pH 5.0-9.0 and with 0-14.0 % (w/v) NaCl. Cells were positive for catalase, nitrate was not used and H2S was not produced. Major cellular fatty acids were anteiso-C15 : 0 (62.76 %), anteiso-C17 : 0 (12.09 %) and iso-C15 : 0 (9.46 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids and three unidentified glycolipids. The menaquinone was MK-9 (H4). The genome size was 4.10 Mbp with a G+C content of 72.4 mol%. The average amino acid identity (ANI) and in silico DNA-DNA hybridization (DDH) values between CFH 91151T and the other species of the genus Isoptericola were found to be low (ANIm <87.19 %, ANIb <84.38 % and DDH <29.30 %). Based on physiological properties, chemotaxonomic characteristics and low ANI and DDH results, strain CFH 91151T is considered to represent a novel species, for which the name Isoptericola halalbus sp. nov. is proposed. The type strain is CFH 91151T (=DSM 105976T=KCTC 49061T).

Halomonas lactosivorans sp. nov., isolated from salt-lake sediment.

A bacteria strain, designated CFH 90008T, was isolated from a salt lake sediment sample collected from Yuncheng city, Shanxi Province, PR China. Strain CFH 90008T was Gram-stain-negative, strictly aerobic, motile with lateral flagella and rod-shaped. Colonies were yellow, circular and smooth. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CFH 90008T belonged to the genus Halomonas, showing highest sequence similarity to Halomonas daqingensis DQD2-30T (98.6 %), Halomonas saliphila LCB169T (98.5 %), Halomonas desiderata FB2T (98.1 %) and Halomonas kenyensis AIR-2T (98.0 %). Good growth was observed at 10-50 °C, pH 6.0-9.0 and with NaCl concentration from 1.0 to 12.0 % (w/v). The predominant quinone was Q9. The major fatty acid (>10 %) was C18 : 1 ω7c, C16 : 0 and C16 : 1 ω7c. The genome of strain CFH 90008T was 4.36 Mbp with a genomic DNA G+C content of 66.7 mol%. Based on low average nucleotide identity and DNA-DNAhybridization results, chemotaxonomic characteristics, and differential physiological properties, strain CFH 90008T could not be classified into any recognized species of the genus Halomonas. Therefore, a new species, for which the name Halomonas lactosivorans sp. nov. is proposed. The type strain is CFH 90008T (=DSM 103220T=KCTC 52281T).

Amycolatopsis nivea sp. nov., isolated from a Yellow River sample.

A novel actinobacterium, designated strain CFH S0261T, was isolated from a sediment sample of the Yellow River. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of strain CFH S0261T were Gram-reaction-positive, aerobic, non-motile. Growth occurs at 15-37 °C, pH 6.0-8.0 and with 0-9.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CFH S0261T was a member of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain CFH S0261T is most closely related to the type strains of Amycolatopsis niigatensis LC11T (98.95 %), Amycolatopsis echigonensis LC2T (98.81 %) and Amycolatopsis albidoflavus IMSNU 22139T (98.73 %). The whole-genome of CFH S0261T showed a G+C content of 69.5 mol%. The ANI values and in silico DDH values between CFH S0261T and the other species of the genus Amycolatopsis were found to be low (ANIb <90.61 % and DDH <53.40 %). The cell wall diamino acid in the peptidoglycan of strain CFH S0261T was meso-diaminopimelic acid and the whole-cell hydrolysate comprised arabinose, galactose, glucose, rhamnose and ribose. The predominant menaquinone was MK-9(H4). The major cellular fatty acids were C16 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and four unidentified glycolipids. On the basis of phenotypic, genotypic and phylogenetic data, strain CFH S0261T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis nivea sp. nov. is proposed. The type strain is CFH S0261T (=KCTC 39515T =CCTCC AA 2014028T).

Thermus thermamylovorans sp. nov., isolated from a hot spring.

A novel thermophilic bacterium, designated CFH 72773T was isolated from the enrichment of a Jinze hot spring sample which was collected from Dientan town, Tengchong county, Yunnan province, south-western PR China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and non-sporulating. The taxonomic position of the strain was investigated by using a polyphasic approach. Growth occurred at 37-75 °C, pH 6.0-8.0 and with 0-2.0 % (w/v) NaCl. Comparison of the 16S rRNA gene sequences indicated the strain represented a member of the genus Thermus and showed close relationships to the type strains Thermus caliditerrae YIM 77925T (96.3 % similarity) and Thermus igniterrae RF-4T (96.2 % similarity). The whole genome of CFH 72773T consisted of 2.25 Mbp and the DNA G+C content was 69.5 mol%. A total of 2262 genes, including a variety of enzymes for chemolithotrophy and anerobic respiration, were predicted. The strain had a unique negative oxidase activity and could hydrolyze starch at high temperature. Furthermore, various genes related to methane, sulfur, fumarate and nitrate metabolism were found, all these indicated that it is worth studying the novel strain. The predominant menaquinone is MK-8. The predominant cellular fatty acids included iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. The major polar lipids were comprised of aminophospholipid, glycolipid and two phospholipids. On the basis of low ANI values, different phenotypic and chemotaxonomic characters and phylogenetic analysis, we made a proposal that strain CFH 72773T represents a novel member of the genus Thermus, for which the name Thermus thermamylovorans sp. nov. is proposed. The type strain is CFH 72773T (=CCTCC AB2018244T=KCTC 43129T).

Paracoccus luteus sp. nov., isolated from the intestine of grass carp.

A novel Gram-negative bacterium, designated CFH 10530T, was isolated from the intestine of grass carp. The sample was collected from the aquaculture training base at the College of Fisheries, Henan Normal University, Xinxiang, PR China. Cells of strain CFH 10530T were coccoid, ovoid or short-rod-shaped, aerobic, non-spore-forming and non-motile. 16S rRNA gene sequence analysis demonstrated that strain CFH 10530T was closely related to Paracoccus endophyticus SYSUP0003T (97.7 % sequence similarity), Paracoccus halophilus HN-182T (96.5 %) and Paracoccus panacisoli DCY94T (96.1 %). The strain grew optimally at 25-28 °C, at pH 7.0 and with 0-2 % (w/v) NaCl. Cells were positive for catalase and oxidase, nitrate was reduced and H2S was not produced. The isoprenoid quinone was Q-10. Major cellular fatty acids were summed feature 8, C18 : 0 and C18 : 03-OH. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid and five unidentified polar lipids. The genome size was 3 331 229 bp with a G+C content of 69.6 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between CFH 10530T and the other species of the genus Paracoccus were found to be below the recommended levels for species delineation (ANIm <85, ANIb <80 and dDDH <24 %). Based on its physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain CFH 10530T is considered to represent a novel species for which the name Paracoccus luteus sp. nov., is proposed. The type strain is CFH 10530T (=KCTC 62919T=CGMCC 1.16597T).

Azospirillum thermophilum sp. nov., isolated from a hot spring.

A novel Gram-staining negative, aerobic, motile by flagellum, rod-shaped bacterium, designated CFH 70021T was isolated from a hot spring soil sample collected from Tengchong, Yunnan province, PR China. Growth of CFH 70021T occurred at 15-50 °C (optimum 50 °C), pH 5.0-7.0 (optimum pH 7.0) and with 0-3.0 % (w/v) NaCl (optimum 0 %, w/v). The genome of CFH 70021T consisted of four complete circular chromosomes and five plasmids, the genomic DNA G+C content was 69.3 mol%. Comparison of the 16S rRNA gene sequences indicated that CFH 70021T represented a member of the genus Azospirillum and showed close relationship with the type strains of Azospirillum agricola CC-HIH038T (97.8 %), Azospirillum rugosum IMMIB AFH-6T (97.6 %), Azospirillum doebereinerae GSF71T (97.6 %), Azospirillum thiophilum DSM 21654T (97.4 %) and Azospirillum picis IMMIB TAR-3T (97.2 %). The polar lipids of CFH 70021T contained diphosphatidylglycerol, phosphatidylmehtylethanolamine, phosphatidylglycerol, phosphatidylcholine, two aminolipids and an unidentified phospholipid. The predominant cellular fatty acids (>10 %) included C19:0cyclo ω8c (11.4 %), C16 : 0 (27.6 %) and summed feature 8 (C18:1ω7c/C18:1ω6c, 40.9 %). The major isoprenoid quinone was Q-10. On the basis of the low ANIb result (<78 %) and different phenotypic and chemotaxonomic characters, we conclude that strain CFH 70021T represents a novel member of the genus Azospirillum, for which the name Azospirillum thermophilum sp. nov. is proposed. The type strain is CFH 70021T (=KCTC 62259T= CCTCC AB2018121T).

Nocardia yunnanensis sp. nov., an actinomycete isolated from a soil sample.

A novel actinomycete strain, designated CFH S0054T, was isolated from a soil sample collected from Xiaokongshan in Tengchong, Yunnan Province, in south-west PR China. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain CFH S0054T belonged to the genus Nocardia. Based on the results of 16S rRNA gene sequence analysis, strain CFH S0054T was most closely related to Nocardia concava IFM 0354T (98.3 %), Nocardia inohanensis NBRC 100128T (97.9 %), Nocardia otitidiscaviarum NBRC 14405T (97.9 %) and Nocardia heshunensis CFH S0067T (97.8 %). Strain CFH S0054T contained C16 : 0, C18 : 1 ω9c, C18 : 0 10-methyl (TBSA) and summed feature 3 as major cellular fatty acids and MK-8 (H4ω-cycl) as the major respiratory quinone. The polar lipid profile included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and unknown phospholipids. The cell wall contained meso-diaminopimelic acid, and the whole-cell hydrolysates were arabinose, galactose, glucose, fructose, ribose and mannose. The genome of strain CFH S0054T was 7.9 Mbp with a G+C content of 68.4 mol%, the average nucleotide identity (ANI) values between strain CFH S0054T and N. concava IFM0354T were low (ANIm<87.7 % and ANIb=84.1 %). On the basis of phylogenetic, physiological and chemotaxonomic data, strain CFHS0054T is considered to represent a novel species of the genus Nocardia, for which the name Nocardiayunnanensis sp. nov. is proposed, The type strain is CFH S0054T (DSM 46763T=JCM 30082T).

Microbacterium ureisolvens sp. nov., isolated from a Yellow River sample.

A Gram-stain positive, aerobic, non-motile and short-rod-shaped strain, CFH S00084T, was isolated from a sediment sample of the Yellow River in Henan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CFH S00084T clustered within members of Microbacterium and was most closely related to the type strains Microbacterium yannicii JCM 18959T and Microbacterium arthrosphaerae DSM 22421T (98.97 % and 98.36 % similarity, respectively). The strain grew optimally at 25-37 °C, at pH 7.0 and in 0-3 % (w/v) NaCl. The major whole-cell sugars were rhamnose and glucose. The cell-wall peptidoglycan mainly contained glycine, alanine and ornithine. The menaquinones of strain CFH S00084T were MK-13, MK-12 and MK-11. The major fatty acids detected were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The genome of strain CFH S00084T was 4.03 Mbp with a G+C content of 70.5 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between CFH S00084T and the other species of the genus Microbacterium were found to be low (ANIm <85 %, ANIb <75 % and dDDH <24 %). The phylogenomic analysis provided evidence for clear phylogenetic divergence between strain CFH S00084T and its closely related type strains. On the basis of the differential physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain CFH S00084T is considered to represent a novel species for which the name Microbacteriumureisolvens sp. nov. is proposed. The type strain is CFH S00084T (=KCTC 39802T=DSM 103157T).

Paracoccus halotolerans sp. nov., isolated from a salt lake.

A novel Gram-stain-negative, aerobic, non-motile, coccus-shaped bacterium, designated CFH 90064T, was isolated from a salt lake sediment sample collected from Yuncheng city, Shanxi province, PR China. 16S rRNA gene sequence comparisons and phylogenetic analyses showed that the strain belonged to the genus Paracoccus and clustered with Paracoccus zeaxanthinifaciens R-1512T (98.2 % similarity), Paracoccus homiensis DD-R11T (97.6 % similarity) and Paracoccus fistulariae 22-5T (96.5 % similarity), respectively. Growth of strain CFH 90064T was observed at 10-37 °C, pH 6.0-9.0 and with NaCl concentrations of up to 6.0 % (w/v). Strain CFH 90064T contained Q-10 as the only isoprenoid quinone, and the major fatty acid was C18 : 1ω7c. Polar lipids of strain CFH 90064T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified glycolipid, an unidentified aminolipid and an unidentified phospholipid. The genome of strain CFH 90008T was 3.75 Mbp with a DNA G+C content of 65.1 %. Based on the phylogenetic analyses, low average nucleotide identity results, chemotaxonomic characteristics and differential physiological properties, strain CFH 90064T could not be classified into any recognized species of the genus Paracoccus, suggesting that this strain represents a novel species, for which the name Paracoccushalotolerans sp. nov. is proposed. The type strain is CFH 90064T (=CCTCC AB 2016131T=DSM 103234T).

Paenibacillus esterisolvens sp. nov., isolated from soil.

A Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CFH S0170T, was isolated from a soil sample collected from Catba island in Ha Long Bay, Hai Phong City, Vietnam. Comparison of the 16S rRNA gene sequences showed that strain CFH S0170T belonged to the genus Paenibacillus and showed closest relationship with Paenibacillus vulneris CCUG 53270T (98.1 % similarity). Phylogenetic analysis demonstrated that the novel candidate formed a coherent branch with P. vulneris CCUG 53270T and Paenibacillus yunnanensis YN2T. Furthermore, the novel strain shared 87.2 % rpoB gene sequence similarity with P. vulneris CCUG 53270T. Growth of strain CFH S0170T occurred at 10-40 °C, pH 6.0-8.0 and with 0-2.0 % (w/v) NaCl. Strain CFH S0170T contained mannose, glucose and rhamnose as the major whole-cell sugars. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid, lysine and aspartic acid. The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, glycolipids and phospholipids. The dominant cellular fatty acids included anteiso-C15 : 0 and C15 : 0. The genomic DNA G+C content was 50.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain CFH S0170T is affiliated to the genus Paenibacillus, but could be distinguished from other valid species of this genus. It is concluded that strain CFH S0170T should be considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus esterisolvens sp. nov. is proposed. The type strain is CFH S0170T (=KCTC 33624T=BCRC 80802T).