Amino Acid Identity Values Research Articles

Bifidobacterium favimelis sp. nov., isolated from black comb honey.

A strain of the bacterial genus Bifidobacterium, IMAU50987T, that was isolated from black comb honey from Lianghe County, Dehong Autonomous Prefecture, Yunnan Province, China, could not be accurately identified as a known species using 16S rRNA gene sequencing. In this study, the taxonomic status of strain IMAU50987T was evaluated using whole-genome sequencing combined with phenotypic analyses. Strain IMAU50987T was Gram-positive, non-motile and non-spore-forming. Comparative of 16S rRNA gene sequence similarity analysis indicated that strain IMAU50987T could be attributed to the genus Bifidobacterium and most closely related to the B. mellis Bin7NT (98.5% identity). Comparative sequence analysis of eight housekeeping genes (pyrG, thrS, glnA1, recA, tuf, dnaB, rpoC and xfp) showed that strain IMAU50987T was different from closely related species. Phylogenomic analysis based on the 88 single-copy genes in the phylogenetic tree showed that strain IMAU50987T belonged to the B. asteroides group. The highest average nucleotide identity value for strain IMAU50987T was 77.0% in comparison with B. choladohabitans B14384H11T and B. apis F753-1T. However, the highest digital DNA-DNA hybridization value was 23.1% compared with B. apis F753-1T and B. xylocopae XV2T; the highest average amino acid identity value was 73.2% compared with B. polysaccharolyticum W8117T. These values are below the accepted threshold for novel species boundaries. The draft genome size of strain IMAU50987T was 1.9 Mb, and the DNA G+C content was 63.5%. The major cellular fatty acids of strain IMAU50987T were C16 : 0, C18 : 1 ω9c and Sum in Feature 7 (C19 : 1 ω7c/C19 : 1 ω6c). The cell-wall peptidoglycan was of the A3α l-Lys-Gly type. Based on data from this study, a novel species, Bifidobacterium favimelis sp. nov., is proposed with the type strain IMAU50987T (= GDMCC 1.4189T = JCM 36315T).

Microbispora maris sp. nov., a novel actinobacterium isolated from the gill of the leopard coral grouper (Plectropomus leopardus).

A novel actinomycete, designated strain ZYX-F-249T, was isolated from the gill of a leopard coral grouper in Yongxing Island, Hainan Province, China. Based on 16S rRNA gene sequence analysis, strain ZYX-F-249T belonged to the genus Microbispora, with high similarities to Microbispora rosea ATCC 12950T (98.7 %), Microbispora hainanensis 211020T (98.5 %), Microbispora clausenae CLES2T (98.4 %), Microbispora bryophytorum NEAU-TX2-2T (98.1 %) and Microbispora oryzaeRL4-1ST (98.0 %). Phylogenetic analysis of the 16S rRNA gene sequence of strain ZYX-F-249T showed that the strain formed a stable subclade with Microbispora rosea ATCC 12950T in the genus Microbispora. The cell wall of the novel isolate contained meso-diaminopimelic acid, while whole-cell sugars were madurose, glucose and ribose. The predominant menaquinones were MK-9(H6), MK-9(H4), MK-9(H2) and MK-9(H0). The characteristic phospholipids (PLs) were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol mannoside, glycophospholipids and an unknown PL. The major cellular fatty acids (>10%) were iso-C16 : 0 and iso-C18 : 0. Genome sequencing showed a DNA G+C content of 71.6%. The low average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values demonstrated that strain ZYX-F-249T could be readily distinguished from closely related species. Based on data from these phylogenetic, chemotaxonomic and physiological characteristics, strain ZYX-F-249T represents a novel species of the genus Microbispora, for which the name Microbispora maris sp. nov. is proposed. The type strain is ZYX-F-249T (=CCTCC AA 2023030T =JCM 36778T).

Polyphasic Identification of Rhizomonospora bruguierae gen. nov., sp. nov., Isolated from Mangrove Rhizosphere Soil.

A novel yellowish-white actinobacterial strain, designated as TS60-4CT, was isolated from the rhizosphere soil of the mangrove Bruguiera gymnorhiza (L.) Lam. in Okinawa, Japan, and was subjected to a polyphasic assessment. The strain could grow at 0-3.0% NaCl concentrations (w/v), pH 6.0-10.0, and 20-37°C. The 16S rRNA gene sequences-based phylogeny showed that the novel isolate belongs to the family Micromonosporaceae and that it shared the highest sequence similarity (98.4%) with Micromonospora craniellae LHW63014T. The hydrolysate of cell-wall of strain TS60-4CT contained alanine, glutamic acid, glycine, and meso-A2pm. The acyl type of muramic acid was N-glycolyl. The main (> 10%) fatty acids were anteiso-C17:0 (22.1%), iso-C16:0 (17.8%), iso-C15:0 (14.7%), and anteiso-C15:0 (10.3%) and the predominant menaquinones of the isolate were MK-9(H6) and MK-9(H4). The polar lipids of the isolate were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified aminolipid, and three unidentified lipids. The genome size of strain TS60-4CT was 6.7 Mbp with a DNA G + C content of 72.4%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity value could differentiate strain TS60-4CT from its closely related taxa. The genome of the strain had 22 putative biosynthetic gene clusters for secondary metabolites, indicating a significant potential as a producer of bioactive chemicals. Consequently, the strain is considered to represent a novel genus and a new species of the family Micromonosporaceae, for which the name Rhizomonospora bruguierae gen. nov., sp. nov. is proposed. The type species is R. bruguierae, with the type strain TS60-4CT (= NBRC 107566T = TBRC 2024T).

Comparative genomic analyses of the genus Robertmurraya and proposal of the novel species Robertmurraya mangrovi sp. nov., isolated from mangrove soil.

A Gram-positive, aerobic, motile, rod-shaped bacterial strain, designated 31A1RT, was isolated from the mangrove soil of Xilian village, Zhanjiang, China. Strain 31A1RT thrives at temperatures ranging from 15 to 45°C (optimum at 30°C), pH 6.5-10 (optimum at 8.5), and in the presence of 0-5% (w/v) NaCl (optimum at 1.5%). The strain shares the highest 16S rRNA gene sequence similarity with Robertmurraya crescens (97.24%) and Robertmurraya dakarensis (97.18%). The complete genome of strain 31A1RT spans 4.71 Mbp with a genomic DNA G + C content of 35.9 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain 31A1RT and type strains of other species of the genus Robertmurraya were 71.24-72.11% and 19.90-21.40%, respectively. The amino acid identity values and percentage of conserved proteins ranged from 66.94 to 68.10% and from 58.34 to 61.62%, respectively, aligning with intrageneric cutoff values. The major fatty acids (≥ 5.0%) were iso-C14:0 (5.0%), iso-C15:0 (41.4%), iso-C16:0 (12.6%), C16:1ω7c alcohol (12.2%), and iso-C17:1 ω10c (6.5%). The polar lipids profile was mainly composed of diphosphatidyl glycerol, phosphatidyl glycerol, and phosphatidyl ethanolamine. We also profiled the pan-genome and metabolic features of genomic assemblies of strains belonging to the genus Robertmurraya, which indicated functional capacities and metabolic similarities. Consequently, we propose that strain 31A1RT represents a new species in the genus Robertmurraya, for which the name Robertmurraya mangrovi sp. nov. is proposed, with the type strain being 31A1RT (= GDMCC 1.4378T = JCM 36937T).

Streptomyces yaizuensis sp. nov., a berninamycin C-producing actinomycete isolated from sponge.

While screening for antibiotics in a marine sample, we discovered a berninamycin C-producing actinomycete, designated YSPA8T, isolated from a sponge. A polyphasic approach was used to determine the taxonomic position of the strain. Strain YSPA8T formed sympodially branched aerial mycelia that ultimately segment into chains of spores. Comparative and phylogenetic analyses of the 16S rRNA gene sequence showed that strain YSPA8T were closely related to Streptomyces clavuligerus ATCC 27064T (99.66%), Streptomyces amakusaensis NRRL B-3351T (98.69%), Streptomyces inusitatus NBRC 13601T (98.48%), and 'Streptomyces jumonjinensis' JCM 4947 (98.41%). The phylogenetic tree using the 16S rRNA gene sequences, and both phylogenomic trees suggested that the closest relative of strain YSPA8T was S. clavuligerus ATCC 27064T. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between strain YSPA8T and S. clavuligerus ATCC 27064T were 84.1%, 28.9%, and 82.5%, respectively, which were below the thresholds of 95%, 70%, and 95% for a prokaryotic conspecific assignment. The G + C of the strain YSPA8T was 72.6%. Whole-cell hydrolysates of strain YSPA8T contained LL-diaminopimelic acid. The predominant menaquinones were MK-9(H6) (49%) and MK-9(H8) (48%), and the major fatty acids were C16:0 (26.8%), C16:1 ω7c/ω6c (17.2%), iso-C16:0 (16.0%), and iso-C15:0 (12.5%). The major phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, and other unidentified phospholipids. Based on the phenotypic, phylogenetic, genomic, and chemotaxonomic data, strain YSPA8T represents a novel species of the genus Streptomyces, and the proposed name for this species is Streptomyces yaizuensis sp. nov. The type strain is YSPA8T (=NBRC 115866T = TBRC 17196T).

Polymorphospora lycopeni sp. nov., a lycopene-producing actinomycetes isolated from lakeside soil sample of Baiyangdian.

A novel actinomycetes producing lycopene, designated HBU208002T, was isolated from a lakeside soil sample collected in Baiyangdian, located in Xiong'an New Area of China, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the strain HBU208002T fell within the genus Polymorphospora and was closely related to Polymorphospora rubra JCM 14904T (99.73% identity). However, the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and average amino acid identity (AAI) values between the strain HBU208002T and P. rubra JCM 14904T were 91.78, 44.7 and 91.6%, respectively, which were lower than the ANI (95-96%), DDH (>70%) and AAI (>95%) thresholds of prokaryotic microbial defined species. The predominant fatty acids of the strain HBU208002T were iso-C16:0, C17:1 ω8c. The menaquinones of the strain HBU208002T were MK-8(H8) and MK9(H4), while those of P. rubra JCM 14904T were MK-10(H6), MK-10(H4), MK-9(H6) and MK-9(H4). Meanwhile, some phenotypic characterizations and antibacterial activities distinguished the strain HBU208002T from P. rubra JCM 14904T. The strain HBU208002T exhibited inhibitory effects on Fusarium graminearum, Fusarium verticillioides and Botrytis cinerea, but P. rubra JCM 14904T had no activity. Therefore, the strain HBU208002T should be assigned as representing a novel species of the genus Polymorphospora, for which the name Polymorphospora lycopeni was proposed. The type strain is HBU208002T (=KCTC49833T = GDMCC4.236T).

Aquibaculum sediminis sp. nov., a halotolerant bacteria isolated from salt lake sediment.

An aerobic, Gram-stain negative bacterium was isolated from sediment samples of Barkol salt lake in Hami City, Xinjiang Uygur Autonomous Region, China, with the number EGI_FJ10229T. The strain is ellipse-shaped, oxidase-negative, catalase-positive, and has white, round, smooth, opaque colonies on marine 2216 E agar plate. Growth occurs at 4.0-37.0℃ (optimal:30.0℃), pH 7.0-9.0 (optimal: pH 8.0) and NaCl concentration of 0-8.0% (optimal: 3.0%). Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that the isolated strain should be assigned to the genus Aquibaculum and was most closely related to Aquibaculum arenosum CAU 1616T. Average nucleotide identity (ANI) and Average amino-acid identity (AAI) values between the type species of the genus Aquibaculum and other related type species were lower than the threshold values recommended for bacterial species. The genomic DNA G + C content of EGI_FJ10229T was 65.41%. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylethanolamine and unidentified phospholipid. The major fatty acids (> 5%) were C19:0 cyclo ω8c (42.0%) and C18:1 ω7c (33.78%). The respiratory quinone identified was Q-10. Differential phenotypic and genotypic characteristics of this strain and species of genus Aquibaculum showed that the strain should be classified as representing a new species belonging to this genus, for which the name Aquibaculum sediminis sp. nov. is proposed. The type strain of the proposed novel species is EGI_FJ10229T (= KCTC 8570T = GDMCC 1.4598T).

Paralimibaculum aggregatum gen. nov. sp. nov. and Biformimicrobium ophioploci gen. nov. sp. nov., two novel heterotrophs from brittle star Ophioplocus japonicus.

Two novel Gram-stain-negative, strictly aerobic, halophilic and non-motile bacterial strains, designated NKW23T and NKW57T, were isolated from a brittle star Ophioplocus japonicus collected from a tidal pool in Wakayama, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NKW23T represented a member of the family Paracoccaceae, with Limibaculum halophilum CAU 1123T as its closest relative (94.4% sequence identity). NKW57T was identified as representing a member of the family Microbulbiferaceae, with up to 94.9% sequence identity with its closest relatives. Both strains displayed average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values below the species delimitation threshold against their closest relatives. Additionally, amino acid identity (AAI) values of both strains fell below the genus-defining threshold. Phylogenetic trees based on genome sequences indicated that NKW23T formed a novel lineage, branching deeply prior to the divergence of the genera Limibaculum and Thermohalobaculum, with an evolutionary distance (ED) of 0.31-0.32, indicative of genus-level differentiation. NKW57T similarly formed a distinct lineage separate from the species of the genus Microbulbifer. The major respiratory quinones of NKW23T and NKW57T were ubiquinone-10 (Q-10) and Q-8, respectively. The genomic DNA G+C contents of NKW23T and NKW57T were 71.4 and 58.8%, respectively. On the basis of the physiological and phylogenetic characteristics, it was proposed that these strains should be classified as novel species representing two novel genera: Paralimibaculum aggregatum gen. nov., sp. nov., with strain NKW23T (=JCM 36220T=KCTC 8062T) as the type strain, and Biformimicrobium ophioploci gen. nov., sp. nov., with strain NKW57T (=JCM 36221T=KCTC 8063T) as the type strain.

Microbulbifer spongiae sp. nov., isolated from marine sponge Diacarnus erythraeanus.

A novel bacterium, designated as MI-GT, was isolated from marine sponge Diacarnus erythraeanus. Cells of strain MI-GT are Gram-stain-negative, aerobic, and rod or coccoid-ovoid in shape. MI-GT is able to grow at 10-40 °C (optimum, 28 °C), with 1.0-8.0% (w/v) NaCl (optimum, 4.0%), and at pH 5.5-9.0 (optimum, pH 8.0). The 16S rRNA gene sequence of strain MI-GT shows 98.35, 97.32 and 97.25% similarity to those of Microbulbifer variabilis Ni-2088T, Microbulbifer maritimus TF-17T and Microbulbifer echini AM134T, respectively. Phylogenetic analysis also exhibits that strain MI-GT falls within a clade comprising members of the genus Microbulbifer (class Gammaproteobacteria). The genome size of strain MI-GT is 4478124 bp with a G+C content of 54.51 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MI-GT and other type strains are 71.61-76.44% (ANIb), 83.27-84.36% (ANIm) and 13.4-18.7% (dDDH), respectively. These values are significantly lower than the recommended threshold values for bacterial species delineation. Percentage of conserved proteins and average amino acid identity values among the genomes of strain MI-GT and other closely related species are 52.04-59.13% and 67.47-77.21%, respectively. The major cellular fatty acids of MI-GT are composed of summed feature 8 (C18 : 1 ω7c or C18 : 1 ω6c), iso-C11 : 0 3-OH, iso-C15 : 0, C16 : 0, and summed feature 9 (C17 : 1 iso ω9c or C16 : 0 10-methyl). The polar lipids of MI-GT mainly consist of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and two glycolipids. The major respiratory quinone is Q-8. Based on differential phenotypic and phylogenetic data, strain MI-GT is considered to represent a novel species of genus Microbulbifer, for which the name Microbulbifer spongiae sp. nov. is proposed. The type strain is MI-GT (=MCCC 1K07826T=KCTC 8081T).

Pseudohoeflea coraliihabitans sp. nov., a poly-β-hydroxybutyrate-producing, halotolerant bacterium isolated from coral sediment in the Dapeng peninsula (Guangdong, China).

A Gram-stain-negative, strictly aerobic, motile, flagellated, rod-shaped, halotolerant, and poly-β-hydroxyalkanoate-producing bacterium, designated DP4N28-3T, was isolated from offshore sediment surrounding hard coral in the Dapeng peninsula (Guangdong, PR China). Growth occurred at 15-35 °C (optimal at 30 °C), pH 6.0-9.5 (optimal at 6.0-7.0), and 0.0-30.0 % NaCl concentration (w/v, optimal at 0.0-2.0 %), showing halotolerance. Phylogeny based on 16S rRNA gene sequences, five housekeeping genes, and genome sequences identified Pseudohoeflea suaedae DSM 23348T (98.1 %, 16S rRNA gene sequence similarity) as the most related species to strain DP4N28-3T. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between strain DP4N28-3T and P. suaedae DSM 23348T were all below the threshold of species demarcation. Major phenotypic differences were the flagella type and the limited sources of single carbon utilization by strain DP4N28-3T, which only included acetic acid, acetoacetic acid, d-glucuronic acid, and glucuronamide. Strain DP4N28-3T harboured the class I poly-β-hydroxyalkanoate synthase gene (phaC) and produced poly-β-hydroxybutyrate. The fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c, 49.4 %) and C16 : 0 (13.4 %). The major cellular polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, and sulfoquinovosyl diacylglycerol. The respiratory quinone was Q-10. The results of the phylogenetic, genomic, phenotypic, and chemotaxonomic analysis indicated that the isolated strain represents the type strain of a novel species. Based on these results, strain DP4N28-3T (=MCCC 1K05639T=KCTC 82803T) is proposed as the type strain of the novel species Pseudohoeflea coraliihabitans sp. nov.

Ideonella margarita sp. nov., Ideonella lacteola sp. nov., Pseudaquabacterium inlustre sp. nov. and Pseudaquabacterium rugosum sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the family Sphaerotilaceae.

Four Gram-stain-negative, aerobic, rod-shaped and motile strains (LYT19WT, DXS22WT, DXS29WT and BYS139WT) were isolated from streams in China. All four strains showed highest 16S rRNA gene sequence similarities to the species of genus Ideonella. The calculated average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values among strains LYT19WT, DXS22WT, DXS29WT, BYS139WT and other closely related strains were less than 79.5, 22.5 and 74.0%, respectively, indicating that each of the four strains should represent an independent novel species. The further reconstructed phylogenomic tree showed that strains LYT19WT and DXS29WT clustered closely with Ideonella strains, but strains DXS22WT and BYS139WT formed an independent clade with Aquabacterium terrae and Aquabacterium pictum. Comparing with other Aquabacterium species, A. terrae and A. pictum harboured distinct physiological and genetic characteristics, so it was reasonable to propose a novel genus Pseudaquabacterium to accommodate A. terrae, A. pictum, DXS22WT and BYS139WT. The major fatty acids of the four strains contained C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and one unidentified aminophospholipid. Combining above descriptions, strains LYT19WT and DXS29WT should represent two novel species of the genus Ideonella, for which the names Ideonella margarita sp. nov. (type strain LYT19WT=GDMCC 1.3205T=KCTC 92545T) and Ideonella lacteola sp. nov. (type strain DXS29WT=GDMCC 1.3207T=KCTC 92547T) are proposed, respectively. Strains DXS22WT and BYS139WT should represent two novel species of the new genus Pseudaquabacterium, for which the names Pseudaquabacterium inlustre sp. nov. (type strain DXS22WT=GDMCC 1.3206T=KCTC 92546T) and Pseudaquabacterium rugosum sp. nov. (type strain BYS139WT=GDMCC 1.3208T=KCTC 92548T) are proposed, respectively.

Peteryoungia algae sp. nov. isolated from seaweeds of Gouqi Island, China, and its unique genetic features among Peteryoungia strains.

A Gram-stain-negative, light khaki, strictly aerobic, rod-shaped, motile via multiple flagella, and catalase- and oxidase-positive bacterium, designated as SSM4.3T, was isolated from the seaweed of Gouqi Island in the East China Sea. The novel isolate grows at 0-5.0% NaCl concentrations (w/v) (optimum 1%), pH 5.0-9.0 (optimum pH 7.0), and 15-37°C (optimum 30°C). The 16S rRNA gene sequences-based phylogeny indicates that the novel marine isolate belongs to the family Rhizobiaceae and that it shared the greatest sequence similarity (98.9%) with Peteryoungia rhizophila CGMCC 1.15691T. This classification was also supported by phylogenetic analysis using core genes. The predominant fatty acids (≥ 10%) of the strain were identified as C18:1 ω7c/C18:1 ω6c. Q-10 was identified as the major isoprenoid quinone, with trace levels of Q-9 present. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The complete genome size of strain SSM4.3T is 4.39Mb with a DNA G+C content of 61.3%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between the genomes of strain SSM4.3T and its closely related representatives were 74.80-86.93%, 20.00-32.30%, and 70.30-91.52%, respectively. Phylogenetic analysis, grounded on the core genes, reveals the evolutionary relationship between SSM4.3T and other Peteryoungia strains. Pan-genomics analysis of 8 previously classified Peteryoungia species and SSM4.3T revealed their unique genetic features and functions. Overall, strain SSM4.3T was considered to be a new species of the Peteryoungia genus; the name Peteryoungia algae sp. nov. has been proposed, with type strain SSM4.3T (= LMG 32561 = MCCC 1K07170).

Gilvirhabdus luticola gen. nov., sp. nov., a mesophilic and halophilic bacterium isolated from tidal flat sediment.

Two novel bacteria, MJ-SS3T and MJ-SS4, were isolated from tidal flat sediment sampled in Gochang, Republic of Korea. The isolates were Gram-stain-negative, aerobic, non-motile, rod-shaped, yellow-coloured, oxidase-positive, and catalase-positive. Strains MJ-SS3T and MJ-SS4 grew at 20-37 °C (optimum, 30 °C), at pH 6-8 (optimum, pH 7.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 2.0 % NaCl). Strains MJ-SS3T and MJ-SS4 showed 99.9 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on genome and 16S rRNA gene sequences indicated that strains MJ-SS3T and MJ-SS4 were affiliated with the family Flavobacteriaceae and most closely related to Formosa maritima 1494T (95.3 %), Hanstruepera flava NBU2984T (95.2 %), Yeosuana marina JLT21T (95.2 %), Meridianimaribacter flavus NH57NT (95.1 %), and Geojedonia litorea YCS-16T (95.1 %). The major respiratory quinone was menaquinone-6. The major identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and amino lipids. The major cellular fatty acids of strain MJ-SS3T were iso-C15 : 1 G (24.6 %), iso-C15 : 0 (21.6 %), and iso-C17 : 0 3-OH (15.8 %). The genome length of strain MJ-SS3T is 3.1 Mbp (DNA G+C content, 32.5 mol%) and it has 2822 coding and 59 tRNA genes. The average amino acid identity and average nucleotide identity values, as well as biochemical, phylogenetic, and physiological characteristics, strongly supported the genotypic and phenotypic differentiation of strains MJ-SS3T and MJ-SS4 from other members of the family Flavobacteriaceae. Hence, strains MJ-SS3T and MJ-SS4 are considered to represent a novel species of a new genus in the family Flavobacteriaceae, for which the Gilvirhabdus luticola gen. nov., sp. nov. is proposed. The type strain is MJ-SS3T (=KCTC 102114T=KEMB 20189T=JCM 36595T), with reference strain MJ-SS4 (=KCTC 102115=KEMB 20190).

Genome-based reclassification of Kineococcus aureolus Xu et al. 2017 as a later heterotypic synonym of Kineococcus terrestris Xu et al. 2017.

We aimed to elucidate the relationship between Kineococcus terrestris and Kineococcus aureolus through whole-genome-based analysis. The genome-derived 16S rRNA gene sequences of K. terrestris KCTC 39738T and K. aureolus KCTC 39739T shared a 100% similarity. Phylogenetic trees based on 16S rRNA gene and whole-genome sequences revealed that K. terrestris KCTC 39738T and K. aureolus KCTC 39739T formed a robust clade, indicating a close relationship between them. Genomic comparison showed that the two strains shared 99.1% average nucleotide identity, 92.0% digital DNA-DNA hybridization and 98.9% average amino acid identity values, all of which exceeded the recommended threshold values for species classification. Most phenotypic characteristics between the two species were almost identical. Based on the above evidence, we propose the reclassification of Kineococcus aureolus Xu et al. 2017 as a later heterotypic synonym of Kineococcus terrestris Xu et al. 2017. Since these two species were proposed in the same article, the principle of priority does not apply. Our proposal is supported by the fact that the nomenclatural authorities first described Kineococcus terrestris.

Actinomycetospora aeridis sp. nov., Actinomycetospora flava sp. nov. and Actinomycetospora aurantiaca sp. nov., endophytic actinobacteria isolated from wild orchid (Aerides multiflora Roxb).

Three novel mycelium-forming actinobacteria, designated OC33-EN06T, OC33-EN07T, and OC33-EN08T, were isolated from wild orchid (Aerides multiflora Roxb), collected from a hill evergreen forest in Northern Thailand. Strains OC33-EN06T and OC33-EN07T showed the highest 16S rRNA gene similarity with Actinomycetospora lutea TT00-04T, 99.17 and 99.45%, respectively. Strain OC33-EN08T showed high similarity with four species, namely 'Actinomycetospora termitidis Odt1-22T' (99.37%), Actinomycetospora chiangmaiensis DSM 45062T (99.02%), Actinomycetospora corticicola 014-5T (99.02%), and Actinomycetospora soli SF1T (98.81%). Comparative genome analysis of OC33-EN06T, OC33-EN07T, and OC33-EN08T with the closely related type strains showed that average nucleotide identity (ANI) based on blast, ANI based on MUMmer, and average amino acid identity values were less than 95% and the digital DNA-DNA hybridization values were less than 70%, all below the thresholds for species demarcation. The digital G+C content of OC33-EN06T, OC33-EN07T, and OC33-EN08T were 74.5, 74, and 74 mol%, respectively. These three strains developed bud-like chains of non-motile cylindrical spores with a smooth surface. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained ribose, arabinose, and galactose. The predominant menaquinone was MK-8(H4). The phospholipid profile included phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylinositol. Based on comparative analysis of genotypic, phenotypic and chemotaxonomic data, strains OC33-EN06T (=TBRC 18349T=NBRC 116543T), OC33-EN07T (=TBRC 18350T=NBRC 116544T), and OC33-EN08T (=TBRC 18318T=NBRC 116542T) represent the type strains of three novel species of the genus Actinomycetospora for which the names Actinomycetospora aeridis sp. nov., Actinomycetospora flava sp. nov., and Actinomycetospora aurantiaca sp. nov., are proposed.

Desertibaculum subflavum gen. nov., sp. nov., a novel member of the family Sneathiellaceae isolated from the Kumtag Desert soil.

A novel rod-shaped bacterium, designated as strain SYSU D60015T that formed yellowish colonies was isolated from a sandy soil collected from the Kumtag Desert in Xinjiang, China. Cells were Gram-stain-negative, oxidase-positive, catalase-negative and motile with a single polar flagellum. Growth optimum occurred between 28 and 37°C, pH 7.0 and with 0-0.5% (W/V) NaCl. The predominant cellular fatty acids (> 5%) were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C19:0 cyclo ω8c, C18:1 ω7c 11-methyl and C16:0. The polar lipid profile contained one phosphatidylethanolamine, one diphosphatidylglycerol, one phosphatidylglycerol, one unidentified phospholipid, three unidentified aminolipids, two unidentified aminophospholipids and seven unidentified lipids. The only respiratory quinone was ubiquinone-10. Based on 16S rRNA gene sequence phylogenetic analysis, strain SYSU D60015T was found to form a distinct linage within the family Sneathiellaceae, and had 16S rRNA gene sequence similarities of 90.8% to Taonella mepensis H1T, and 90.2% to Ferrovibrio denitrificans S3T. The genome of SYSU D60015T was 5.66 Mb in size with 68.2% of DNA G + C content. The low digital DNA-DNA hybridization (dDDH, 18.0%), average nucleotide identity (ANI, 77.5%) and amino acid identity (AAI, 56.0%) values between SYSU D60015T and Ferrovibrio terrae K5T indicated that SYSU D60015T might represent a distinct genus. Based on the phylogenetic, phenotypic, chemotaxonomic and genomic data, we propose Desertibaculum subflavum gen. nov., sp. nov. as a novel species of a new genus within the family Sneathiellaceae. The type strain is SYSU D60015T (= NBRC 112952T = CGMCC 1.16256T).

Winogradskyella pelagia sp. nov., isolated from coastal sediment.

An orange-pigmented, Gram-stain-negative, strictly aerobic, non-flagellated and rod-shaped bacterium, designated strain DF17T, was isolated from coastal sediment collected from Jingzi Wharf, Weihai, PR China. The optimal growth conditions were determined to be at 30 °C, pH 7.5, and in 3 % (w/v) NaCl. According to phylogenetic analysis of the 16S rRNA gene sequence, strain DF17T showed the highest sequence similarity of 96.9 % to Winogradskyella aquimaris KCTC 23502T. The DNA G+C content was 35.8 mol%, and the major fatty acids were iso-C15 : 1 G, iso-C15 : 0, and iso-C17 : 0 3-OH. The major polar lipids were two aminoglycolipids, one phosphatidylethanolamine and four unidentified lipids. The predominant respiratory quinone was menaquinone-6 (MK-6). The average nucleotide identity, digital DNA-DNA hybridization, and amino acid identity values between strain DF17T and other Winogradskyella species were below the species delineation thresholds of 69.35-72.95 %, 16.9-19.6 % and 71.25-78.93 %, respectively. On the basis of its phenotypic, genetic and physiological characteristics, strain DF17T is suggested to represent a novel species of the genus Winogradskyella, for which the name Winogradskyella pelagia sp. nov. is proposed. The type strain is DF17T (MCCC 1H00456T=KCTC 82421T).

Cognatishimia coralii sp. nov., a marine bacterium isolated from seawater surrounding corals.

Coral reefs are declining due to the rising seawater temperature. Bacteria within and surrounding corals play key roles in maintaining the homeostasis of the coral holobiont. Research on coral-related bacteria could provide benefits for coral reef restoration. During the isolation of coral-associated bacteria, a Gram-stain-negative, motile bacterium (D5M38T) was isolated from seawater surrounding corals in Daya Bay, Shenzhen, PR China. Phylogenetic analysis revealed that strain D5M38T represents a novel species in the genus Cognatishimia. The temperature range for strain D5M38T growth was 10-40 °C, and the optimum temperature was 37 °C. The salinity range for the growth of this isolate was from 0 to 4.0 %, with an optimal salinity level of 0.5 %. The pH range necessary for strain D5M38T growth was between pH 5.0 and 9.0, with an optimal pH being 7.5. The predominant fatty acid was summed feature 8 (65.0 %). The major respiratory quinone was Q-10. The DNA G+C content was 56.8 %. The genome size was 3.88 Mb. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain D5M38T and its two closest neighbours, Cognatishimia activa LMG 29900T and Cognatishimia maritima KCTC 23347T, were 73.2/73.6%, 73.2/73.6% and 19.7/19.5%, respectively. Strain D5M38T was clearly distinct from its closest neighbours C. activa LMG 29900T and C. maritima KCTC 23347T, with 16S rRNA gene sequence similarity values of 97.5 and 97.3 %, respectively. The phylogenetic analysis, along with the ANI, AAI, and dDDH values, demonstrated that strain D5M38T is a member of the genus Cognatishimia, and is distinct from the other two recognized species within this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain D5M38T. Thus, strain D5M38T is considered to be classified as representing a novel species in the genus Cognatishimia, for which the name Cognatishimia coralii sp. nov. is proposed. The type strain is D5M38T (=MCCC 1K08692T=KCTC 8160T).

Neisseria leonii sp. nov., isolated from the nose, lung, and liver of rabbits.

A taxogenomic study of three strains (3986T, 51.81, and JF 2415) isolated from rabbits between 1972 and 2000 led to the description of a new Neisseria species. The highest sequence similarity of the 16S rRNA gene was found to Neisseria animalis NCTC 10212T (96.7 %). The 16S rRNA gene similarity above 99 % and average nucleotide identity (ANI) values above 96 % among the strains, indicated that they belong to the same species. At the same time, the strains shared ANI values below 81 % and dDDH values below 24 % with all described Neisseria species. In the bac120 gene phylogenetic tree, the three strains clustered near Neisseria elongata and Neisseria bacilliformis in the Neisseria clade. However, the Neisseria clade is not monophyletic, and includes the type strains of Morococcus cerebrosus, Bergeriella denitrificans, Kingella potus, Uruburuella suis, and Uruburuella testudinis. Neisseria shayeganii clustered outside the clade with members of the genus Eikenella. Amino acid identity (AAI) values were calculated, and a threshold of 71 % was used to circumscribe the genus Neisseria. According to this proposed AAI threshold, strains 3986T, 51.81, and JF 2415 were placed within the genus Neisseria. The cells of the three strains were Gram-stain-negative diplococcobacilli and non-motile. Optimal growth on trypticase soy agar occurred at 37 °C and pH 8.5 in aerobic conditions. Notably, all strains exhibited indole production in the API-NH test, which is atypical for Neisseria and the family Neisseriaceae. The strains exhibited a common set of 68 peaks in their MALDI-TOF MS profiles, facilitating the swift and accurate identification of this species. Based on genotypic and phenotypic data, it is proposed that strains 3986T, 51.81, and JF 2415 represent a novel species within the genus Neisseria, for which the name Neisseria leonii sp. nov. is proposed (type strain 3986T=R726T=CIP 109994T=LMG 32907T).

Aquibaculum arenosum gen. nov., sp. nov., a novel member of the family Rhodovibrionaceae, isolated from sea sand.

A Gram-negative, non-motile, and creamy-white coloured bacterium, designated CAU 1616T, was isolated from sea sand collected at Ayajin Beach, Goseong-gun, Republic of Korea. The bacterium was found to grow optimally at 37 °C, pH 8.0-8.5, and with 1-5 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain CAU 1616T within the order Rhodospirillales. The highest 16S rRNA gene sequence similarity was to Fodinicurvata fenggangensis YIM D812T (94.1 %), Fodinicurvata sediminis YIM D82T (93.7 %), Fodinicurvata halophila BA45ALT (93.6 %) and Algihabitans albus HHTR 118T (92.3 %). Comparing strain CAU 1616T with closely related species (Fodinicurvata fenggangensis YIM D812T and Fodinicurvata sediminis YIM D82T), the average nucleotide identity based on blast+ values were 69.7-69.8 %, the average amino acid identity values were 61.3-61.4 %, and the digital DNA-DNA hybridization values were 18.4-18.5 %. The assembled draft genome of strain CAU 1616T had 29 contigs with an N50 value of 385.8 kbp, a total length of 3 490 371 bp, and a DNA G+C content of 65.1 mol%. The predominant cellular fatty acids were C18 : 1 2-OH, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The major respiratory quinone was Q-10. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1616T represents a novel genus in the family Rhodovibrionaceae, for which the name Aquibaculum arenosum gen. nov., sp. nov. is proposed. The type strain is CAU 1616T (=KCTC 82428T=MCCC 1K06089T).