16S rRNA Gene Sequence Similarity Research Articles

Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter

Three Gram-stain-negative, aerobic, short rod-shaped and motile strains (FXH3WT, SHGZ20W and SMYT11WT) were isolated from freshwater environments in China. Comparisons based on the 16S rRNA gene sequences indicated that strains FXH3WT and SHGZ20W showed the highest 16S rRNA gene sequence similarity of about 99.6% to ‘Luteimonas cellulosilyticus’ MIC 1.5, and strain SMYT11WT showed the highest 16S rRNA gene sequence similarity of 99.8% to Luteimonas fraxinea D4P002T, respectively. Observing the phylogenetic trees reconstructed based on the 16S rRNA gene sequences, the species of genera Luteimonas and Lysobacter were not monophyletic and often mixed together. The further reconstructed phylogenomic tree and Genome Taxonomy Database also showed that the species of both genera were polyphyletic, implying that the current taxonomic status of the species of both genera was questionable. The calculated OrthoANIu, digital DNA–DNA hybridization and average amino acid sequence identity (AAI) values supported that strains FXH3WT and SHGZ20W should belong to the same novel species and strain SMYT11WT should also represent an independent novel species. Combining the AAI values and phylogenomic analyses, the species of genera Luteimonas and Lysobacter should be reassigned to 12 genera (Luteimonas, Lysobacter, Cognatiluteimonas, Noviluteimonas, Pseudoluteimonas, Solilutibacter, Agrilutibacter, Cognatilysobacter, Marilutibacter, Novilysobacter, Montanilutibacter and Aerolutibacter). The AAI values 69.5–76.0% were also proposed as the Lysobacteraceae-specific thresholds for genus delineation. Strain SMYT11WT should represent a novel species of the genus Luteimonas, for which the name Luteimonas flava sp. nov. (type strains SMYT11WT=GDMCC 1.4275T=KCTC 8304T) is proposed. Strains FXH3WT and SHGZ20W should represent a novel species of a new genus Aquilutibacter rugosus gen. nov., sp. nov. The type strain of the type species is FXH3WT (=GDMCC 1.4096T=KCTC 8154T).

Roseovarius phycicola sp. nov. and Roseovarius rhodophyticola sp. nov., isolated from marine red algae.

Two Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacteria, designated as strains S88T and W115T, exhibiting catalase- and oxidase-positive reactions, were isolated from marine red algae in South Korea. Strain S88T exhibited growth at 20-30 °C, pH 6.0-9.0 and 2.0-5.0% (w/v) NaCl, while strain W115T grew at 20-30 °C, pH 7.0-9.0 and 2.0-5.0% (w/v) NaCl. Strain S88T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C16 : 0 2-OH as major fatty acids (>5%), with major polar lipids being phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and two unidentified lipids. Strain W115T contained summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0 as major fatty acids (>5%), with major polar lipids including phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and unidentified lipids. Ubiquinone-10 was the sole respiratory quinone in both strains, and the genomic DNA G+C contents were 57.0% for strain S88T and 56.5% for strain W115T. Despite 99.86% 16S rRNA gene sequence similarity, strains S88T and W115T shared 88.8% average nucleotide identity (ANI) and 36.8% digital DNA-DNA hybridization (dDDH) value, indicating different species. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences, respectively, revealed that strains S88T and W115T formed a phylogenetic lineage within the genus Roseovarius. ANI and dDDH values of both strains with other type strains were less than 73.7 and 20.3%, respectively, confirming that they represent novel species. Based on phenotypic, chemotaxonomic and molecular characteristics, strains S88T and W115T represent two novel species of the genus Roseovarius, for which the names Roseovarius phycicola sp. nov. (S88T =KACC 23423T =JCM 36647T) and Roseovarius rhodophyticola sp. nov. (W115T =KACC 23690T =JCM 36651T) are proposed, respectively.

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).

Pseudomonas huanghezhanensis sp. nov. and Pseudomonas fjordensis sp. nov., two novel species isolated from seawater of Arctic Kongsfjorden in the Ny-Ålesund area, Svalbard.

Two Gram-stain-negative bacterial strains, BSw22131T and DMSP-1T, were isolated from seawater of Arctic Kongsfjorden in the Ny-Ålesund area, Svalbard. Strains BSw22131T and DMSP-1T were within the genus Pseudomonas and presented 98.1 and 99.8% 16S rRNA gene sequence similarity to Pseudomonas piscicola P50T and Pseudomonas paracarnis V5/DAB/2/5T, respectively. However, the results of multilocus sequence analysis (concatenated 16S rRNA, gyrB, rpoB and rpoD gene sequences) and whole-genome sequence analysis indicated that BSw22131T and DMSP-1T were most closely related to Pseudomonas petrae P2653T and Pseudomonas lactis DSM 29167T, respectively. The genome G+C contents of strains BSw22131T and DMSP-1T were 58.2 and 60.0%, respectively. The two isolates presented digital DNA-DNA hybridization and average nucleotide identity values of less than 70 and 96%, respectively, with type strain genomes of their close relatives. BSw22131T contained summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c), C16 : 0 and summed feature 8 (C18 : 1 ω6c/C18 : 1 ω7c) as the major cellular fatty acids, whereas DMSP-1T contained an additional C17 : 0-cyclo as the major fatty acid. The major quinones of both strains were Q-9 (57.5-77.2%) and Q-8 (22.8-37.2%), and their major cellular polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. BSw22131T could be differentiated from its related species by positive ornithine decarboxylase, esterase (C8) and l-rhamnose and d-fructose-6-PO4 utilization, whereas DMSP-1T could be differentiated by positive acid phosphatase but negative p-hydroxyphenylacetic acid utilization. The two strains were negative for the reduction of nitrates but contained genes related to dimethylsulfoniopropionate catabolism. The results of the polyphasic taxonomy analysis revealed that strains BSw22131T and DMSP-1T represent two novel species of the genus Pseudomonas, for which the names Pseudomonas huanghezhanensis sp. nov. (type strain BSw22131T = CCTCC AB 2019135T = JCM 36635T = DSM 117336T) and Pseudomonas fjordensis sp. nov. (type strain DMSP-1T = CCTCC AB 2019124T = JCM 36636T = DSM 117337T) are proposed.

Antioxidant Activity and Suppression of Intracellular Radical Generation of Streptomyces Strains and Genome Analysis of Strain ET3-23

Actinomycetes, predominantly found in soil, represent a remarkable source of natural products. The natural antioxidants obtained from them have been employed for human infectious diseases. In particular, Streptomyces strains serve as significant sources of natural antioxidants with demonstrated health benefits. The in vitro antioxidant activity and the inhibition of intracellular radical generation by crude extracts from various Streptomyces strains were evaluated and the genome sequence of selected strains was analyzed. Strains CT2-10, NE1-12, and ET3-23 showed 16S rRNA gene sequence similarity to Streptomyces capoamus JCM 4734T (98.94%), Streptomyces nigra 452T (99.78%), and Streptomyces morookaense LMG 20074T (99.49%), respectively. The genome analysis of strain ET3-23 had 106 contigs, with a total length of 8121874 bp and an average G+C content of 71.46%. Ethyl acetate extracts of strains CT2-10, ET3-23, and NE1-12 exhibited, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activity with IC50 555.9 µg/mL, 66.5 µg/mL, and 463.3 µg/mL and showed NO scavenging activity, except for CT2-10. Strain NE1-12 significantly inhibited ROS production induced by hydrogen peroxide on macrophage cells, while strains NE1-12 and CT2-10 inhibited NO production induced by lipopolysaccharides with IC50 82.4 µg/mL and 2.3 µg/mL, respectively. These findings suggest their ability to modulate NO production which is crucial in inflammatory responses and tissue injury. The antioxidant activities of Streptomyces strains indicate their potential as valuable sources of bioactive natural products and effective antioxidant agents, warranting further investigation for therapeutic applications.

Paracoccus spongiarum sp. nov., isolated from the marine sponge, Phakellia elegans.

A facultative anaerobic Gram-negative bacterium, designated as strain 2205BS29-5T, was isolated from a marine sponge, Phakellia elegans, in Beomseom on Jeju Island, Republic of Korea, and taxonomically characterized. The cells were catalase and oxidase positive, non-motile, coccoid-rod shaped and capable of poly-β-hydroxybutyrate production. Growth was observed at 10-37 °C (optimum, 25 °C) and pH 5.0-8.0 (optimum, pH 7.0), and in the presence of 0-9% NaCl (w/v) (optimum, 3.0-4.0%). The major cellular fatty acids and respiratory quinone were identified as summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) and Q-10, respectively. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, four phosphoglycolipids, two unidentified amino lipids and eight unidentified lipids. The DNA G+C content was 67.8%. Strain 2205BS29-5T was most closely represented by Paracoccus amoyensis 11-3T and P. caeni MJ17T with 97.8 and 97.5% 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA genes and whole-genome sequences showed that strain 2205BS29-5T was affiliated with the genus Paracoccus. Genomic analysis showed that strain 2205BS29-5T could synthesize vitamin B family (folate and cobalamin) and ectoine. The average nucleotide identity and digital DNA-DNA hybridization values between strain 2205BS29-5T and P. amoyensis 11-3T were 77.1% and 18.8%, respectively, and with P. caeni MJ17T were 78.4 and 21.2%, respectively. Based on phylogenetic, chemotaxonomic and genome relatedness analyses, strain 2205BS29-5T represents a novel species of the genus Paracoccus, for which the name Paracoccus spongiarum sp. nov. is proposed. The type strain is 2205BS29-5T (=LMG 33062T =KACC 23240T).

Roseobacter sinensis sp. nov., a marine bacterium capable to synthesize arachidonic acid.

Strain WL0113T was isolated from surface seawater of the coast of Lianyungang, Jiangsu province, PR China. Strain WL0113T shared highest 16S rRNA gene sequence similarity with Roseobacter insulae YSTF-M11T (98.8%), followed by R. cerasinus AI77T (98.8%), R. ponti MM-7T (98.0%). Strain WL0113T was Gram-stain-negative, cream, aerobic, non-motile and coccoid- to oval-shaped, and able to grow at pH 6.5-9.0 (optimum, pH 7.0-8.0), at 10-37°C (optimum, 28°C) and in the presence of 1-5% (w/v; optimum, 2.5%) NaCl. Ubiquinone-10 was detected as dominant. The main fatty acids (> 5%) of the strain WL0113T were C16:0, iso-C17:0 3OH, C20:4ω6,9,12,15c (arachidonic acid), and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The major polar lipids include phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, glycophospholipid, unknown aminolipid, unknown phospholipid, and two unknown polar lipids. The ANI and dDDH values between strain WL0113T and Roseobacter cerasinus were 80.4% and 23.0%, respectively. The genomic DNA G + C content of strain WL0113T was 63.1%. Based on these data, it is proposed that strain WL0113T represent novel species of the genus Roseobacter, for which the name Roseobacter sinensis sp. nov. is proposed. The type strain is WL0113T (= GDMCC 1.3082T = JCM 35567T).

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).

Leuconostoc koreense sp. nov., isolated from kimchi, a fermented vegetable.

The novel strain CBA3628T was isolated from kimchi, a Korean fermented vegetable. CBA3628T is a cocci-shaped, Gram-stain-positive, catalase- and oxidase-negative and facultatively anaerobic bacterium. The results of phylogenetic analysis based on 16S rRNA gene sequencing indicated that CBA3628T represented a member of the genus Leuconostoc of the family Leuconostocaceae. CBA3628T has a circular chromosomal genome and three plasmids of 1 864 558 bp (37% DNA G+C content), containing 1,887 genes, 1,762 predicted protein-coding genes, 4 complete rRNA loci and 70 tRNA genes. The cells were non-haemolytic, non-motile and non-spore forming. The optimal growth of CBA3628T occurred at 30 °C, pH 6.0 and with 0-2% (w/v) NaCl. The major polar lipids of CBA3628T were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids (>10%) of CBA3628T were C16 : 0, C20 : 0 and C19 : 0 cyclo ω8c. CBA3628T contained A3α-type peptidoglycans. CBA3628T was most closely related to Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293T, L. mesenteroides subsp. dextranicum DSM 20484T and L. suionicum DSM 20241T with 99.52% 16S rRNA gene sequence similarity. However, the average nucleotide identities of 91.9%, 91.7% and 91.1% and the digital DNA-DNA hybridisation values of 45.6%, 45.4% and 45.4% indicated that the novel isolate represented a distinct species. Phylogenetic analyses of both the 16S rRNA gene and genome sequences revealed that CBA3628T formed a distinct phylogenetic lineage within the genus Leuconostoc and was most closely related to Leuconostoc litchii MB7T. The ANI and dDDH values between CBA3628T and L. litchii MB7T were 84.9 and 22.8%, respectively. Functional genes belonging to COG categories E, J and K were enriched in the genome of CBA3628T (>7.9%). On the basis of its physiological, chemotaxonomic, phylogenetic and genomic properties, strain CBA3628T represents a novel species from the genus Leuconostoc, for which we propose the name Leuconostoc koreense sp. nov., with the type strain CBA3628T (= KACC 23049T = DSM 116836T).

Sorlinia euscelidii gen. nov., sp. nov., a novel acetic acid bacterium isolated from the leafhopper Euscelidius variegatus (Hemiptera: Cicadellidae).

Acetic acid bacteria - belonging to the Acetobacteraceae family - are found in the gut of many sugar-feeding insects. In this study, six strains have been isolated from the hemipteran leafhopper Euscelidius variegatus. While they exhibit high 16S rRNA gene sequence similarities to uncultured members of the Acetobacteraceae family, they could not be unequivocally assigned to any particular type species. Considering the clonality of the six isolates, the EV16PT strain was used as a representative of this group of isolates. The genome sequence of EV16PT is composed of a 2.388 Mbp chromosome, with a DNA G+C content of 57 mol%. Phylogenetic analyses based on the 16S rRNA gene sequence and whole-genome multilocus sequence analysis indicate that EV16PT forms a monophyletic clade with the uncultivated endosymbiont of Diaphorina citri, the Candidatus Kirkpatrickella diaphorinae. Such a phylogenetic clade is positioned between those of Asaia-Swaminathania and Kozakia. The genomic distance metrics based on gene and protein sequences support the proposal that EV16PT is a new species belonging to a yet-undescribed genus. It is a rod-shaped Gram-stain-negative bacterium, strictly aerobic, non-motile, non-spore-forming, showing optimal growth without salt (NaCl) at 30 °C and pH of 6-7. The major quinone is Q10, and the dominant cellular fatty acids (>10%) are C18:l ω7c, C19 : 0 cyclo ω6c, C16 : 0 and C19 : 1 2OH. The polar lipid profile comprises diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine, along with unidentified aminophospholipids, glycophospholipids, aminolipids and lipids. Based on a polyphasic approach, including phylogenetic, phylogenomic, genome relatedness, phenotypic and chemotaxonomic characterisations, EV16PT (= KCTC 8296T, = DSM 117028T) is proposed as a representative of a novel species in a novel genus with the proposed name Sorlinia euscelidii gen. nov., sp. nov., in honour of Prof. Claudia Sorlini, an Italian environmental microbiologist at the University of Milan who inspired the research on microbial diversity, including symbiosis in plants and animals.

Paenibacillus suaedae sp. nov. and Paenibacillus violae sp. nov., isolated from the roots of Suaeda japonica Makino and Viola mandshurica W. Becker with plant growth-promoting potential.

Two novel Gram-positive strains, chi10T and PFR10T, were isolated from the roots of Suaeda japonica Makino and Viola mandshurica W. Becker, respectively. The strains are facultatively aerobic, rod-shaped, motile via peritrichous flagella and endospore-forming. Strains chi10T and PFR10T showed the highest 16S rRNA gene sequence similarity to Paenibacillus alvei DSM 29T (99.0%) and Paenibacillus planticolens LMG 31457T (99.3%). Furthermore, the phylogenetic and phylogenomic analyses demonstrated that strains chi10T and PFR10T were closely related to the genus Paenibacillus. The digital DNA-DNA hybridization (dDDH) values for strains used in the phylogenetic analysis and strain chi10T ranged from 19.6 to 28.4%, while for strain PFR10T, the values ranged from 19.8 to 53.5%, according to the Genome-to-Genome Distance Calculator 3.0, which were all less than 70%. Additionally, the dDDH value between strains chi10T and PFR10T was 22.0%, confirming that they are different species of the genus Paenibacillus. The average nucleotide identity between chi10T and PFR10T and other species of the genus Paenibacillus were 68.4-84.7% and 67.8-93.6%, respectively. In addition, the major polar lipids of chi10T and PFR10T consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acid profile of strain chi10T was iso-C15 : 0 and anteiso-C15 : 0, whereas the major fatty acid profile of strain PFR10T was iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The sole respiratory quinone in strains chi10T and PFR10T was menaquinone-7. Phylogenomic, phenotypic and genome analyses strongly indicated that chi10T and PFR10T could be two novel Paenibacillus species for which the names Paenibacillus suaedae sp. nov. (type strain chi10T = KACC 23258T = TBRC 17803T) and Paenibacillus violae sp. nov. (type strain PFR10T = KACC 23263T = TBRC 17804T) are proposed, respectively.

Isolation and characterization of two new species, Hymenobacter mellowenesis sp. nov. and Hymenobacter aranciens sp. nov., from soil.

Strains M29T and ASUV-10-1T, which are aerobic, non-flagellated, and Gram-stain-negative, were isolated from soil samples collected in Inje (37°57'49.1"N 128°19'53.7"E) and Cheonan City (36°48'47.1"N 127°05'22.4"E), South Korea. Phylogenetic analyses based on rRNA gene sequences revealed that strains M29T and ASUV-10-1T form a distinct branch within the family Hymenobacter (order Cytophagales, class Cytophagia). Strain M29T is most closely related to Hymenobacter rubidus DG7BT with a 16S rRNA gene sequence similarity of 97.05%. Strain ASUV-10-1T shows closest genetic similarity to Hymenobacter frigidus B1789T (96.42%), Hymenobacter jeongseonensis BT683T (95.97%), and Hymenobacter terricola 3F2TT (95.65%). The optimal growth conditions for these strains are pH 7.0, no NaCl, and a temperature of 25°C. The dominant cellular fatty acids identified in these strains are iso-C15:0, anteiso-C15:0, and Summed Feature 3 (C16:1ω 7c / C16:1ω 6c). Both strains predominantly contain MK-7 as the respiratory quinone. The major polar lipids in strains M29T and ASUV-10-1T are phosphatidylethanolamine, aminophospholipid, and aminolipid. Based on biochemical, chemotaxonomic, and phylogenetic data, it is evident that M29T and ASUV-10-1T represent new species within the genus Hymenobacter. The new species were classified based on biochemical and chemotaxonomic characteristics. The taxonomic classification of these species was conducted following the guidelines and protocols outlined in Bergey's Manual of Systematic Bacteriology. We followed the methods for determining physiological and biochemical characteristics, as well as chemotaxonomic markers such as fatty acid profiles, quinone types, and polar lipid compositions. We also compared with the results of carbohydrate utilization and enzyme activities results [Bergey 1994]. Therefore, we propose the names Hymenobacter mellowenesis for strain M29T (= KCTC 102056T = NBRC 116578T) and Hymenobacter aranciens for strain ASUV-10-1T (= KCTC 92969T = NBRC 116575T).

Streptomyces albidocamelliae sp. nov., an endophytic actinomycete isolated from the leaves of Camellia oleifera.

A novel actinobacterium strain, HUAS 14-6T, was isolated from the healthy leaves of Camellia oleifera collected from Changde City, Hunan Province, China. Strain HUAS 14-6T produced tight spiral spore chains consisting of oval or spherical spores with a smooth surface. 16S rRNA gene sequence analysis revealed that strain HUAS 14-6T belonged to the genus Streptomyces and shared highest similarity to Streptomyces bungoensis DSM 41781T (99.72%). Phylogenetic analysis based on 16S rRNA gene sequences indicated strain HUAS 14-6T was in a clade with S. bungoensis DSM 41781T. However, the ANIm and dDDH between strain HUAS 14-6T and S. bungoensis DSM 41781T were 88.16% and 31.2%, respectively, far less than the species-level thresholds. Phylogenetic trees based on the five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that strain HUAS 14-6T formed a separate branch, indicating that this strain could belong to a potential new species. Pairwise MLSA distances between strain HUAS 14-6T and all type strains exhibiting 16S rRNA gene sequence similarities of ≥98.7% to it were much higher than the maximum range of 0.014 recommended for delineating a new Streptomyces species. Based on polyphasic taxonomic study, HUAS 14-6T represents a novel species within the genus Streptomyces for which the name Streptomyces albidocamelliae sp. nov. is proposed. The type strain is HUAS 14-6T (=MCCC 1K08365T=JCM 35920T).

Adlercreutzia wanghongyangiae sp. nov., and Adlercreutzia shanghongiae sp. nov., two new members of the genus Adlercreutzia isolated from plateau pika (Ochotona curzoniae).

Four anaerobic, Gram-stain-positive, non-motile, non-sporulating rod-shaped bacterial strains (R7T, R21, R22 and R25T) were isolated from the intestinal contents of plateau pika (Ochotona curzoniae) collected from the Qinghai-Tibet Plateau, PR China. The four isolates grew at between 25 and 42 °C (optimally at 35-37 °C), and with 0.3-3.3% NaCl (w/v) [optimum, 1.3% (w/v)]. Adding l-arginine to the medium could promote their growth. Strains R7T and R21 were most closely related to Adlercreutzia caecimuris B7T (97.48% 16S rRNA gene sequence similarity). Strains R25T and R22 were most closely related to Adlercreutzia equolifaciens DSM 19450T (98.25% 16S rRNA gene sequence similarity). The genome sequences of R7T and R25T were 2.89 and 2.90 Mb in size with 63.6 and 62.8 mol% DNA G+C contents, respectively. Phylogenetic analysis based on 16S rRNA gene sequences and core genes revealed that R7T and R21 were most closely related to A. caecimuris B7T and Adlercreutzia mucosicola DSM 19490T, whereas R25T and R22 were most closely related to A. equolifaciens DSM 19450T and Adlercreutzia rubneri ResAG-91T. R7T, R25T and the closely related species had average nucleotide identity (ANI) values of 81.9-83.2% as well as digital DNA-DNA hybridisation (dDDH) values between 27.3 and 27.9%, which clearly indicated that they represent two novel species within the genus Adlercreutzia. For R7T and R25T, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the whole cell sugars included galactose, glucose and ribose. On the basis of these results, we propose that strains R7T and R25T represent two novel species of the genus Adlercreutzia, namely Adlercreutzia wanghongyangiae sp. nov. and Adlercreutzia shanghongiae sp. nov., respectively. The type strains are R7T (=GDMCC 1.4459T=KCTC 25860T) and R25T (=GDMCC 1.4458T=KCTC 25861T).

The identification of Finegoldia dalianensis sp. nov., isolated from the pus of the patient with skin abscess and genomic analysis of the strains belonging to Finegoldia genus

ObjectivesTo comprehensively characterize a new species, named Finegoldia dalianensis sp. nov., isolated from the pus of a skin abscess from a patient and genomic analysis of the strains belonging to Finegoldia genus. MethodsStrain LY240594T was definitively characterized through phylogenetic, genomic, and biochemical approach. Extensive genomic comparisons, involving the genome of LY240594T and those of 82 Finegoldia strains from GenBank, were instrumental in revealing genetic relationships within the Finegoldia genus. ResultsStrain LY240594 was initially identified as F. magna based on MALDI-TOF MS analysis, showing 99.7% 16S rRNA gene sequence similarity with the type strain of F. magna CCUG 17636T. However, there were 68.5% similarity with dDDH method and 90.9% similarity by ANI analysis respectively, between LY240594T and the selected type strain, F. magna DSM 20470T.Biochemical differences were also found between two strains. The ANI and genomic analysis of 82 Finegoldia sp. strains and Strain LY240594 revealed that those strains could be categorized into at least three groups using a 95% ANI threshold. ConclusionComprehensive characterization supported the proposal of a new species within the genus Finegoldia, named Finegoldia dalianensis sp. nov. The type strain, LY240594T (=GDMCC 1.4375T =KCTC 25838T), features 1,938 genes and a G+C content of 31.8 mol%. Genomic comparisons and ANI studies elucidated substantial heterogeneity within the Finegoldia genus.

Paracraurococcus lichenis sp. nov., isolated from lichen in Thailand.

A novel bacterium, designated as strain LOR1-02T and isolated from a lichen sample collected from Kham Riang Subdistrict, Kantharawichai District, Maha Sarakham Province, Thailand, underwent thorough investigation utilizing a polyphasic taxonomic approach. Strain LOR1-02T demonstrated growth within a temperature range of 20-42°C (optimal at 30°C), pH range of 5.0-7.5 (optimal at pH 7.0), and tolerance to 4.0% (w/v) NaCl. Phylogenetic analysis revealed its close relation to Paracraurococcus ruber JCM 9931T, with a 16S rRNA gene sequence similarity of 97.16%, placing it within the genus Paracraurococcus. The approximate genome size of strain LOR1-02T was determined to be 8.6Mb, with a G + C content of 70.9mol%. Additionally, ANIb, ANIm, and AAI values between the whole genomes of strain LOR1-02T and type strains were calculated as 82.6-83.4%, 86.1-86.8%, and 81.4-82.2%, respectively, while the dDDH value was determined to be 26.3-28.5% (C.I. 24.0-31.0%). The predominant fatty acids detected were C18:1ω7c and/or C18:1ω6c, C16:0, and C18:12OH. The major ubiquinone identified was Q-10, and the polar lipids included phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, along with unidentified phosphoaminolipid, lipids, and an amino lipid. Based on comprehensive phenotypic, chemotaxonomic, and genotypic characterization, it is concluded that strain LOR1-02T represents a novel species within the genus Paracraurococcus, for which the name Paracraurococcus lichenis sp. nov. is proposed. The type strain designation is LOR1-02T (= JCM 33121T =NBRC 112776T = TISTR 2503T).

Dongia sedimenti sp. nov., isolated from river sediment.

A Gram-stain-negative, non-spore-forming and strictly aerobic bacterial strain, designated R-7T, was isolated from river sediment in Wuxi, Jiangsu, PR China. Cells (1.6-3.8 µm long and 0.6-0.8 µm wide) were slightly curved to straight rods and motile by means of a polar flagellum. The strain grew optimally on Reasoner's 2A medium at 30 °C, pH 7.0 and with 1.0% (w/v) NaCl. Strain R-7T exhibited closest 16S rRNA gene sequence similarities to Dongia mobilis CGMCC 1.7660T (95.4%), D. rigui 04SU4-PT (94.6%) and D. soli D78T (93.8%). The phylogenetic trees based on genomic and 16S rRNA gene sequences showed that strain R-7T was clustered in the genus Dongia. The obtained average nucleotide identity and digital DNA-DNA hybridization values between R-7T and the three type strains of the genus Dongia were 73.4, 72.8 and 72.4% and 19.5, 19.0 and 18.7%, respectively. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, two unidentified aminophospholipids and nine unidentified polar lipids. The major cellular fatty acids (>5% of the total) were cyclo-C19 : 0 ω8c, C16 : 0 and C16 : 0 2-OH. The DNA G+C content was 65.5 mol%. On the basis of the evidence presented in this study, strain R-7T represents a novel species of the genus Dongia, for which the name Dongia sedimenti sp. nov. is proposed, with strain R-7T (=KCTC 8082T=MCCC 1K08805T) as the type strain.

Analysis of genomic and characterization features of Luteolibacter soli sp. nov., isolated from soil.

The strain designated as Y139T is a novel Gram-stain-negative, aerobic, and non-motile bacterium, was isolated from a soil sample in McClain County, Oklahoma, United States. The cells of strain Y139T were a rod-shaped, with the width of 0.4-0.7 and the length of 1.5-2.0 . Growth occurred at 20-37°C (optimum, 30°C), pH 5.5-9.5 (optimum, pH 7.0), and 0-1.0% NaCl (w/v) (optimum, 0%). The polar lipid profiles included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, and an unidentified lipid. The major fatty acids included C16:0, iso-C14:0, and C16:1 ω9c. Menaquinone-9 (MK-9) was recognized as the only respiratory quinone. Strain Y139T showed the highest 16S rRNA gene sequence similarity to Luteolibacter flavescens MCCC 1K03193T (98.3%). Phylogenetic analysis positioned it within the genus Luteolibacter. The draft genome of strain Y139T consisted of 7,106,054 bp, and contained 5,715 open reading frames (ORFs), including 5,656 coding sequences (CDSs) and 59 RNA genes. The genomic DNA G + C content was found to be 62.5%. Comparing strain Y139T with L. flavescens MCCC 1K03193T and Luteolibacter arcticus CCTCC AB 2014275T, the average nucleotide identity (ANI) values were 80.6 and 82.1%, respectively. Following phylogenetic, physiological, biochemical, and chemotaxonomic analyses, a novel species within the genus Luteolibacter, designated as Luteolibacter soli sp. nov., was proposed for strain Y139T, which was also assigned as the type strain (=KCTC 92644T = MCCC 1H01451T). Further analysis of core genes across 9 Luteolibacter species uncovered significant genomic divergence, particularly in those related to cofactor, vitamin, and energy metabolism. Analysis of biogeographic distribution suggested that lake and soil were the main habitats for the genus Luteolibacter. Additionally, the genus Luteolibacter was sensitive to climate warming and precipitation.

Lapidilactobacillus salsurivasis sp. nov., Secundilactobacillus muriivasis sp. nov., and Streptococcus parasalivarius sp. nov., isolated from Traditional Chinese Pickle.

Four Gram-stain-positive bacterial strains (designated 475-2T, 46-6BT, 778-2T and A810-3), isolated from traditional Chinese pickle, were characterized using a polyphasic taxonomic approach. Strain 475-2T was most closely related to the type strain of Lapidilactobacillus achengensis, having 99.9% 16S rRNA gene sequence similarity, 94.1-95.1% average nucleotide identity (ANI) and 57.6% digital DNA-DNA hybridization (dDDH) values. Strain 46-6BT was most closely related to the type strain of Secundilactobacillus similis, having 99.8% 16S rRNA gene sequence similarity, 94.3-94.9% ANI and 58.9-59.2% dDDH values. Strains 778-2T and A810-3 were phylogenetically related to the type strains of Streptococcus salivarius, Streptococcus thermophilus and Streptococcus vestibularis, having 99.7-99.9% 16S rRNA gene sequence similarities, 89.1-94.4% ANI and 39.0-55.5% dDDH values. Based upon the data obtained in the present study, three novel species, Lapidilactobacillus salsurivasis sp. nov., Secundilactobacillus muriivasis sp. nov. and Streptococcus parasalivarius sp. nov., are proposed and the type strains are 475-2T (= JCM 36613T = CCTCC AB 2023258T = LMG 33412T), 46-6BT (= JCM 36612T = CCTCC AB 2023259T = LMG 33411T) and 778-2T (= JCM 36614T = CCTCC AB 2023257T = LMG 33413T), respectively.

Actinomycetota Amycolatopsis nalaikhensis sp. nov. and Amycolatopsis carbonis sp. nov., two novel actinobacteria with antimicrobial activity isolated from a coal mining site in Mongolia.

Two-novel filamentous actinobacteria designated strains 2-2T and 2-15T were isolated from soil of a coal mining site in Mongolia, and their taxonomic positions were determined using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that each of the strains formed a distinct clade within the genus Amycolatopsis. The 16S rRNA gene sequence similarity analysis showed that both strains were mostly related to Amycolatopsis rhabdoformis NCIMB 14900T with 99.0 and 99.4% sequence similarity, respectively. The genome-based comparison indicated that strain 2-2T shared the highest digital DNA-DNA hybridization value of 35.6% and average nucleotide identity value of 86.9% with Amycolatopsis pretoriensis DSM 44654T, and strain 2-15T shared the corresponding values of 36.5 and 87.9% with A. rhabdoformis NCIMB 14900T, all of which being well below the thresholds for species delineation. The chemotaxonomic properties of both strains were typical of the genus Amycolatopsis. In silico prediction of chemotaxonomic markers was also carried out, and the results were consistent with the chemotaxonomic profiles of the genus. Genome mining for secondary metabolite production in strains 2-2T and 2-15T revealed the presence of 29 and 24 biosynthetic gene clusters involved in the production of polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptides, lanthipeptide, terpenes, siderophore, and a number of other unknown type compounds. Both strains showed broad antifungal activity against several filamentous fungi and also antibacterial activity against methicillin-resistant Staphylococcus aureus and Acinetobacter baumannii. The phenotypic, biochemical, and chemotaxonomic properties indicated that both strains could be clearly distinguished from other species of Amycolatopsis, and thus the names Amycolatopsis nalaikhensis sp. nov. (type strain, 2-2T=KCTC 29695T=JCM 30462T) and Amycolatopsis carbonis (type strain, 2-15T=KCTC 39525T=JCM 30563T) are proposed accordingly.