Streptomyces lycopersici sp. nov. and Streptomyces cucumeris sp. nov., two novel actinobacteria isolated from rhizosphere soil with broad-spectrum antifungal activity

Two actinobacterial strains, designated NEAU-383T and NEAU-Y11T, exhibiting antifungal activity, were isolated from the rhizosphere soil of plants in Harbin, Heilongjiang Province, and Guangzhou, Guangdong Province, respectively. Both strains formed short, wrinkled, spiral spore chains on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains NEAU-383T and NEAU-Y11T were most closely related to Streptomyces iranensis HM 35T, Streptomyces rapamycinicus NRRL B-5491T and Streptomyces coffeae CA1R205T. However, digital DNA-DNA hybridization values between the two strains and their close relatives (27.1% between the two strains; 27.5-59.0% for NEAU-383T; 27.0-39.8% for NEAU-Y11T) fell below the 70% species delineation threshold. The genomic G+C contents were 71.0 mol% for NEAU-383T and 70.5 mol% for NEAU-Y11T. Both strains contained glucose and ribose as whole-cell sugars. The predominant menaquinones were MK-9(H6) and MK-9(H8), with NEAU-Y11T additionally containing MK-9(H4). The major fatty acids (>10%) in both strains included iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0, whilst iso-C17 : 0 was also a major component in NEAU-383T. Both strains contained phosphatidylethanolamine and hydroxy-phosphatidylethanolamine as polar lipids. Additionally, NEAU-383T also possessed diphosphatidylglycerol, phosphatidylinositol, an unidentified ninhydride-positive lipid and five unidentified lipids, whereas NEAU-Y11T additionally contained two unidentified ninhydride-positive lipids and five unidentified lipids. Genomic analysis revealed that both strains possess abundant secondary metabolite biosynthesis gene clusters, including those for antibiotics, siderophores, polyketides and terpenoids, along with metabolic pathways associated with environmental adaptation. These findings provide insight into the potent antimicrobial activity exhibited by both strains. Based on genotypic, phenotypic and chemotaxonomic analyses, strains NEAU-383T and NEAU-Y11T represent two novel species within the genus Streptomyces, for which the names Streptomyces lycopersici (type strain NEAU-383T=JCM 36736T=MCCC 1K08878T) and Streptomyces cucumeris (type strain NEAU-Y11T=JCM 36418T=MCCC 1K08681T) are proposed.

Representatives of the Synergistaceae family, taxonomic description and genome sequence of Caenicola nitritireducens gen nov., sp. nov., a novel fermenting and amino-acid degrading bacterium isolated from a municipal anaerobic digester sludge

Members of the phylum Synergistota are important but understudied components of microbial communities during anaerobic digestion. In this study, their diversity was assessed in full-scale anaerobic digester sludge samples from Marrakesh wastewater treatment plant (Morocco), using 16S rRNA gene community profiling, as well as targeted isolation, physiological characterization, and genome sequencing of novel Synergistaceae isolates. The 16S rRNA gene analysis identified 23 operational taxonomic units (OTUs) belonging to the family of Synergistaceae, representing 8.8 % of the total microbial community. 17 of these OTUs belonged to previously uncultured taxa. A dominant OTU19, presumably a new representative of the family of Synergistaceae was isolated in pure culture (strain DS-S4T) and subjected to both culture- and genome-based characterizations. Phylogenetic analysis revealed that strain DZ-S4T was related to Cloacibacillus porcorum CL-84T and Cloacibacillus evryensis 158T but with low sequence similarity of 89.94 % and 88.60 %, respectively. Based on genome relatedness, including Average Nucleotide Identity (ANI) and Amino Acid Identity (AAI), strain DZ-S4T is considered to represent a novel genus for which the name Caenicola gen.nov is proposed. Moreover, several phenotypic and eco-physiological properties differentiated the novel isolate from its related species, indicating that the strain represents a new species for which the name Caenicola nitritireducens sp. nov. is proposed, with strain DZ-S4T (=DSM 104940T = JCM 31897T) being the type strain. Additionally, this study investigates the ecological role of strain DZ-S4T, specifically the protein degradation, the bioconversion of carbohydrates, and the nitrite reduction during anaerobic digestion.

Proposal of Paenibacillus kandeliae sp. nov, Isolataed from Leaf of Kandelia candel

A novel bacterial strain, designated JQZ6Y-1T, was isolated from the leaf of Kandelia candel at Maowei sea Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that strain JQZ6Y-1T formed a stable clade with Paenibacillus wenxiniae DSM 100576T and Paenibacillus hunanensis CGMCC 1.8907T within the genus Paenibacillus. The 16S rRNA gene sequence similarities of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 98.3% and 98.2%, respectively. The average nucleotide identity values of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 77.5% and 80.4%, respectively. The digital DNA-DNA hybridization values of strain JQZ6Y-1T with the related species P. wenxiniae DSM 100576T and P. hunanensis CGMCC 1.8907T were 22.9% and 23.0%, respectively. These values clearly indicated that strain JQZ6Y-1T represented a novel species. The diagnostic diamino acid in the cell-wall peptidoglycan of strain JQZ6Y-1T was meso-diaminopimelic acid, and MK-7 was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids, and one unidentified lipid. The major fatty acids were anteiso-C15:0 and C16:0. Cells of strain JQZ6Y-1T were Gram positive and rod shaped. Optimum growth occurred at pH 7.0, 30 ℃, and with 1-2% (w/v) NaCl. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizations, strain JQZ6Y-1T could be classified as a novel species of the genus Paenibacillus, for which the name Paenibacillus kandeliae sp. nov. is proposed. The type strain is JQZ6Y-1T (=CGMCC 1.18974T = JCM 34547T).

Genome Sequencing of the Antibiotic-Resistant Leucobacter sp. HNU-1 and Its Developmental Toxicity in Caenorhabditis elegans

To date, Leucobacter species have been identified from diverse sources with various ecological and functional roles. However, the genomic features and pathogenic potential of antibiotic-resistant Leucobacter strains remain understudied. Here, we isolated the Leucobacter sp. HNU-1 from tropical Hainan Province, China, and found it can induce diapause in Caenorhabditis elegans following ingestion, while exhibiting no significant effects on the nematode's lifespan, survival rate, locomotion, and intestinal epithelial cells. This bacterium demonstrates resistance to multiple antibiotics, including kanamycin, streptomycin, sulfonamides, and vancomycin. On LB medium, Leucobacter sp. HNU-1 forms yellow, opaque colonies with a smooth, moist surface, regular edges, a convex center, and no surrounding halo, with diameters ranging from 2 to 3 mm. Furthermore, we performed whole-genome sequencing using third-generation high-throughput sequencing technology. De novo assembly revealed a genome size of 3,375,033 bp, with a GC content of 70.37%. A total of 3270 functional genes, accounting for 88.98% of the genome, were annotated, along with six potential CRISPR sequences and other genetic elements. Genomic and bioinformatic analyses further identified antibiotics-related genes. This research provides a theoretical foundation for investigating antibiotic-resistant environmental bacteria in tropical environments and offers new insights into potential therapeutic strategies for microbial infections and host-microbe interactions.

Sedimentitalea sediminis sp. nov., a novel bacterium isolated from marine sediment

Strain HM32M-2 T, an aerobic, catalase-positive, oxidase-positive, and Gram-stain-negative bacterium, was isolated from a sandy sediment sample collected from Qinzhou Gulf in Guangxi Zhuang Autonomous Region, China. Strain HM32M-2 T grew at 15-37 °C (optimum, 30 °C), at pH 5.5-9.5 (optimum, pH 8.5), and with 1.0-12.0% (w/v) NaCl (optimum, 3.0%). Strain HM32M-2 T exhibited the highest 16S rRNA gene sequence similarity with Sedimentitalea nanhaiensis NH52FT (98.4%). Phylogenetic analyses based on 16S rRNA gene sequences and whole-genome sequences showed that strain HM32M-2 T formed a distinct lineage with Sedimentitalea nanhaiensis NH52FT. The draft genome of strain HM32M-2 T was 3.40 Mbp in size and its DNA G + C content was 63.6%. Comparative genome analysis revealed that average nucleotide identity and digital DNA-DNA hybridization among strain HM32M-2 T and other Sedimentitalea species were below cut-off levels of 95-96% and 70%, respectively. Chemotaxonomic analyses indicated that strain HM32M-2 T contained Q-10 as the respiratory quinone, C18:1ω7c as the major cellular fatty acid, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified aminolipid, and one unidentified lipid as the major polar lipids. Strain HM32M-2 T had a typical chemical composition of fatty acids, polar lipids, and quinones for Sedimentitalea species, but could be distinguished from known species of the genus Sedimentitalea. On the basis of the polyphasic evidence, strain HM32M-2 T should be classified as a novel species of the genus Sedimentitalea, for which the name Sedimentitalea sediminis sp. nov. is proposed. The type strain is HM32M-2 T (= MCCC 1K08873T = KCTC 8272 T).

Flavobacterium anseongense sp. nov. and Flavobacterium wongokense sp. nov., isolated from freshwater and freshwater soil in South Korea

Two novel, non-motile, Gram-stain-negative, rod-shaped bacterial strains, designated AS60T and WG47T, were isolated from freshwater in South Korea. To clarify their taxonomic positions, both strains were characterized based on genomic information, including 16S rRNA gene and draft genome sequences. Phylogenetic analyses revealed that both isolates belong to the genus Flavobacterium. Based on 16S rRNA gene sequencing, AS60T clustered with Flavobacterium silvisoli KACC 21178T (96.09%), Flavobacterium cheonhonense KACC 14967T (96.07%) and Flavobacterium sangjuense KACC 17473T (95.96%). Strain WG47T showed the highest similarity to Flavobacterium dankookense KACC 23179T (97.14%), F. cheonhonense KACC 14967T (97.07%) and Flavobacterium chungnamense KACC 14971T (96.71%). The draft genomes of AS60T and WG47T were 3.07 and 3.30 Mb, with G+C contents of 35.6 and 38.9 mol%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were calculated. For AS60T, ANI values compared to F. silvisoli KACC 21178T, F. cheonhonense KACC 14967T and WG47T were 76.67, 79.38 and 76.01%, respectively, with dDDH values of 20, 19.6 and 22.1%. For WG47T, ANI values compared to F. dankookense KACC 23179T and F. cheonhonense KACC 14967T were 75.12 and 74.75%, with dDDH values of 19.9 and 19.2%. Both strains exhibited MK-6 as the predominant respiratory quinone, and their fatty acid profiles included iso-C15:1, iso-C15:0 3OH, iso-C15:1 G, iso-C16:0, iso-C16:0 3OH and iso-C17:0 3OH. Phosphatidylethanolamine was the major polar lipid. Strain WG47T was found to produce flexirubin-type pigments, while AS60T did not. These results, combined with phenotypic and biochemical data, suggest that strains AS60T and WG47T represent two novel species of Flavobacterium, for which the names Flavobacterium anseongense sp. nov. (AS60T=KACC 22413T=LMG 32491T) and Flavobacterium wongokense sp. nov. (WG47T=KACC 22407T=LMG 32500T) are proposed.

Proposal of Paraglaciecola agarilytica (Yong et al. 2007) Shivaji and Reddy 2014 as a later heterotypic synonym of Paraglaciecola chathamensis (Matsuyama et al. 2006) Shivaji and Reddy 2014 and an emended description of Paraglaciecola chathamensis

In this paper, the comparative genome analysis was used to re-evaluate the taxonomic relationship between Paraglaciecola chathamensis and Paraglaciecola agarilytica. The 16S rRNA gene sequence analysis indicated that P. chathamensis S18K6T shared the highest sequence identity with P. agarilytica NO2T (99.9%), Paraglaciecola mesophila KMM 241T (99.2%) and Paraglaciecola polaris LMG 21857T (98.5%). Phylogenetic analysis based on 16S rRNA gene sequences and whole-genome sequences showed that P. chathamensis S18K6T was most closely related to P. agarilytica NO2T. However, the average nucleotide identity and digital DNA-DNA hybridization values among them were greater than the threshold of 95-96% and 70 % for the delineation of prokaryotic genomic species, confirming that they represented the same species. Besides, phenotypic characteristics and chemotaxonomic properties between P. agarilytica KCTC 12755T and P. chathamensis JCM 13645T were almost identical, further verifying this result. Consequently, we propose that P. agarilytica (Yong et al. 2007) Shivaji and Reddy 2014 is a later heterotypic synonym of P. chathamensis (Matsuyama et al. 2006) Shivaji and Reddy 2014.

Predictions to Increase Lasso Peptide Production in the Heterologous Host Streptomyces coelicolor M1152

Production of specialized metabolites are restricted to the metabolic capabilities of the organisms. Genome-scale models (GEM)s are useful to study the whole metabolism and to find metabolic engineering targets to increase the yield of a target compound. In this work we use a modified model of Streptomyces coelicolor M145 to simulate the production of lagmysin A (LP4) and the novel lagmysin B (LP2) lasso peptide, in the heterologous host Streptomyces coelicolor M1152. Overexpression targets were identified using the flux scanning based on enforced objective flux (FSEOF) algorithm and flux variability analysis (FVA), considering growth in minimum and in complex medium. Thirteen reactions were found as candidate metabolic engineering targets for both lasso peptides considering both settings. We propose the overexpression of enzymes of the glycolysis pathway (GAPD, PGK, PGM and ENO) and leucine biosynthesis (IPPS, IPPMIb, IPPMIa, IPMD and OMCDC) to enhance the production of either lagmysin A or B.

Identification of four novel Streptomyces isolated from machair grassland soil using a culture-based bioprospecting strategy: Streptomyces caledonius sp. nov., Streptomyces machairae sp. nov., Streptomyces pratisoli sp. nov. and Streptomyces achmelvichensis sp. nov

A culture-dependent bioprospecting strategy, based on the use of several selective isolation media, revealed the presence of relatively high numbers of streptomycete-like colonies from machair grassland soil, in which carbonate minerals dominate. Representatives were shown to be bioactive in primary and secondary antimicrobial screens conducted through standard plug assays. The comparison of the whole-genome sequences showed that four of the isolates were novel species in the genus Streptomyces, for which the names Streptomyces caledonius sp. nov. (=DSM 118365; =NCIMB 15554), Streptomyces machairae sp. nov. (=DSM 118363; =NCIMB 15553), Streptomyces pratisoli sp. nov. (=DSM 118364; =NCIMB 15555) and Streptomyces achmelvichensis sp. nov. (=NCIMB 15556; =DSM 118366) are proposed. Genomes of the novel strains were found to be rich in biosynthetic gene clusters predicted to encode for diverse, specialized metabolites, notably antibiotics. They also contained stress-related genes that provided an insight into how streptomycetes cope with the prevailing conditions in machair grassland soils. It can be concluded that selective isolation and dereplication of streptomycetes from the unique machair habitat provides a practical way of isolating novel Streptomyces strains for ecological and biotechnological studies.

Taxonomic description of Micromonospora reichwaldensis sp. nov. and its biosynthetic and plant growth-promoting potential

Micromonospora strains proved to be a model organism for drug discovery and plant growth promotion (PGP). Strain DSM 115977 T was subjected to polyphasic taxonomic analysis and genome mining for biosynthetic gene clusters and PGP-associated genes in order to determine its taxonomic rank and assess its biosynthetic potential. The strain was found to form a novel species within the evolutionary radiation of the genus Micromonospora. The strain contained glucose, mannose, xylose, and ribose as whole-cell sugars and the isomer DL-diaminopimelic acid in its peptidoglycan. Strain DSM 115977T had iso-C15:0, iso-C16:0, C17:1cis 9, C17:0, iso-C17:0, and 10-methyl-C17:0 as fatty acid profile (>5%) and MK10-H4 and MK10-H6 as the predominant menaquinones (>10%). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, glycophospholipids, phosphoaminolipid, unidentified lipids, and phospholipids. The genome of the strain had a size of 7.0 Mbp with a DNA G + C content of 73.4%. It formed a well-supported sub-clade with its close phylogenomic neighbor, Micromonospora echinofusca DSM 43913T (98.7%). Digital DNA-DNA hybridization and average nucleotide identity derived from sequence comparisons between the strain and its close phylogenomic neighbors were below the thresholds of 70 and 95-96% for prokaryotic species demarcation, respectively. Based on these findings, strain DSM 115977T (Asg4T = KCTC 59188T) merits to be considered as the type strain of a new species for which the name Micromonospora reichwaldensis sp. nov. is proposed. Genome mining for biosynthetic gene clusters encoding specialized secondary metabolites highlighted its ability to produce potentially novel therapeutic compounds. The strain is rich in plant growth-promoting genes whose predicted products directly and indirectly affect the development and immune system of the plant.

IMPORTANCE

In view of the significant pharmaceutical, biotechnological, and ecological potentials of micromonosporae, it is particularly interesting to enhance the genetic diversity of this genus by focusing on the isolation of novel strain from underexplored habitats, with the promise that novel bacteria will lead to new chemical entities. In this report, modern polyphasic taxonomic study confirmed the assignment of strain DSM 115977T to a novel species for which the name Micromonospora reichwaldensis sp. nov. is proposed. The strain harbors in its genomic sequence several biosynthetic gene clusters for secondary metabolites and genes associated with plant growth-promoting features. The results of this study provide a very useful basis for launching more in-depth research into agriculture and/or drug discovery.

Taklimakanibacter albus sp. nov., an Endophytic Bacterial Species Isolated from the Root of Paris polyphylla var. yunnanensis

A Gram-negative, white-pigment, rod-shaped bacterial strain YIM B02566T was isolated from the root of Paris polyphylla var. yunnanensis in China. Strain YIM B02566T exhibited optimal growth at 28 °C and pH 7.0 on Reasoner's 2A agar without NaCl supplementation. Phylogenetic analyses based on the 16S rRNA gene sequences and the concatenation of 433 single-copy orthologous genes revealed that strain YIM B02566T formed a distinct lineage in the genus Taklimakanibacter. The sequence similarity of the 16S rRNA gene between YIM B02566T and two known species of genus Taklimakanibacter were 99.12% (T. deserti SYSU D60010T) and 99.05% (T. lacteus SYSU D60012T), respectively. The principal fatty acids were C19:0 cyclo ω8c, C16:0, and summed feature 8. Strain YIM B02566T contained UQ-10 as the sole respiratory quinone. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, two unidentified aminolipids, and an unidentified polar lipid. The whole-genome analysis indicated that the genome size was 7.2 Mbp, and the genomic DNA G + C content was 62.9%. The digital DNA-DNA hybridization values between strain YIM B02566T and two Taklimakanibacter species were 24.50% (T. deserti SYSU D60010T) and 25.40% (T. lacteus SYSU D60012T). Meanwhile, the ANI and AAI values between strain YIM B02566T and its closest neighbours are well below the proposed thresholds for species determination. Therefore, based on polyphasic analysis, the isolate represents a novel species, for which the name Taklimakanibacter albus is proposed. The type strain is YIM B02566T (= CGMCC 1.18656T = JCM 34643T).

Comparative genomics reveals genetic diversity and differential metabolic potentials of the species of Arachnia and suggests reclassification of Arachnia propionica E10012 (=NBRC_14587) as novel species

The genus Arachnia, including Arachnia propionica and Arachnia rubra, are part of the normal oral and respiratory microbiota but can act as opportunistic pathogens in humans. This study investigates the functional, phylogenomic and taxonomic characteristics of 10 completely sequenced Arachnia strains, to elucidate their evolutionary relationships and divergence patterns, focusing on genomic variability and functional diversity. Phylogenetic analyses revealed distinct patterns, with Arachnia propionica strains showing significant divergence compared to the conserved Arachnia rubra strains. Notably, E10012 (=NBRC 14587) emerged as a distinct lineage with unique adaptations, while NCTC11666 exhibited a unique phylogenetic position, suggesting subspecies-level classification. Functional analyses highlighted variability among Arachnia propionica strains, with E10012 (=NBRC 14587) showing genes linked to choline metabolism and metal resistance, and NCTC11666 enriched in carbohydrate-active enzymes like GH179. In contrast, Arachnia rubra demonstrated genomic conservation, indicative of evolutionary specialization. This study reveals that strains E10012 (=NBRC 14587) and NCTC11666 displayed unique genomic features and distinct phylogenetic positioning, suggesting their reclassification as potential novel species and subspecies respectively. This underscores the balance between genomic conservation and diversification in Arachnia, reflecting their ecological adaptability and functional roles in the oral microbiome.

Pelomonas baiyunensis sp. nov., Pelomonas candidula sp. nov., Pelomonas dachongensis sp. nov., Pelomonas lactea sp. nov., Pelomonas margarita sp. nov., Pelomonas nitida sp. nov., Pelomonas parva sp. nov. and Roseateles rivi sp. nov., isolated from streams in China

Eight Gram-stain-negative, aerobic and motile strains (BYS78WT, BYS87WT, BYS96WT, BYS180WT, DC23WT, DXS20WT, LKC17WT and LYH14WT) were isolated from streams in China and showed the highest 16S rRNA gene sequence similarities with the species of genus Pelomonas. The calculated average nucleotide identity, digital DNA-DNA hybridization and average amino acid sequence identity values among these eight strains and other closely related strains were less than 89.8, 39.1 and 89.4 %, respectively, indicating that each of the eight strains should represent an independent novel species. The further reconstructed phylogenomic tree showed that seven isolated strains clustered closely with the Pelomonas strains. Only strain BYS180WT clustered with the Roseateles strains. The phylogenomic tree also showed that the taxonomic status of the recently published species (Paucibacter sediminis, Roseateles aquae, 'Roseateles caseinilyticus', 'Roseateles cellulosilyticus', Roseateles subflavus and Roseateles violae) was questionable. 'R. caseinilyticus' and 'R. cellulosilyticus' should be reassigned to the genus Pelomonas as Pelomonas caseinilytica P7T (=KACC 22504T=TBRC 15694T) and Pelomonas cellulosilytica P8T (=KACC 22505T=TBRC 15695T), respectively. P. sediminis, R. aquae, R. subflavus and R. violae should be reassigned to the genus Kinneretia as Kinneretia sediminis, Kinneretia aquae, Kinneretia subflava and Kinneretia violae, respectively. Combining the above descriptions, strains BYS78WT, BYS87WT, BYS96WT, DC23WT, DXS20WT, LKC17WT and LYH14WT should represent seven novel species of the genus Pelomonas, for which the names Pelomonas baiyunensis sp. nov. (type strain BYS87WT=GDMCC 1.4090T=KCTC 8151T), Pelomonas candidula sp. nov. (type strain BYS78WT=GDMCC 1.4089T=KCTC 8152T), Pelomonas dachongensis sp. nov. (type strain DC23WT=GDMCC 1.4087T=KCTC 8148T), Pelomonas lactea sp. nov. (type strain DXS20WT=GDMCC 1.4088T=KCTC 8147T), Pelomonas margarita sp. nov. (type strain LKC17WT=GDMCC 1.4086T=KCTC 8146T), Pelomonas nitida sp. nov. (type strain BYS96WT=GDMCC 1.4091T=KCTC 8150T) and Pelomonas parva sp. nov. (type strain LYH14WT=GDMCC 1.4276T=KCTC 8301T) are proposed, respectively. Strain BYS180WT should represent a novel species of the genus Roseateles, for which the name Roseateles rivi sp. nov. (type strain BYS180WT=GDMCC 1.4098T=KCTC 8149T) is proposed.

Description and genomic characterization of Mesorhizobium marinum sp. nov., a bacterium isolated from sea sediment

Two Gram-stain-negative, aerobic strains, designed ZMM04-4T and ZMM04-5, were isolated from sea sediment collected from Qinzhou Bay, Guangxi Zhuang Automous Region, China. The predominant respiratory quinone was ubiquinone-10. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, aminophospholipid and phospholipid. The predominant fatty acids were C18:1ω7c, C19:0 cyclo ω8c and C16:0. Strain ZMM04-4T shared 99.7 % similarity of 16S rRNA gene sequence with ZMM04-5. The digital DNA-DNA hybridization and average nucleotide identity values between strain ZMM04-4T and ZMM04-5 were 92.9 % and 98.6 %, respectively, indicating that strains ZMM04-4T, ZMM04-5 belong to the same species. Phylogenetic and phylogenomic analysis indicated that strains ZMM04-4T and ZMM04-5 belong to the genus Mesorhizobium and showed the highest sequence similarity to Mesorhizobium qingshengii CGMCC 1.12097T (97.7 %-97.8 % sequence similarity) and Mesorhizobium shangrilense DSM 21850T (97.7 %-97.8 %). The average nucleotide identity and digital DNA-DNA hybridization values between strains ZMM04-4T, ZMM04-5 and their closely related species were within the ranges of 76.5 %-77.2 % and 20.9 %-21.8 %, respectively, indicating that strains ZMM04-4T, ZMM04-5 were novel species. In accordance with phylogenetic and genomic as well as phenotypic and chemotaxonomic characterizations, strains ZMM04-4T and ZMM04-5 should be assigned to the genus Mesorhizobium and indentified as a novel species, for which the name Mesorhizobium marinum sp. nov., is proposed. The type strain is ZMM04-4T (=MCCC 1K08883T = KCTC 8273T).

Niallia tiangongensis sp. nov., isolated from the China Space Station

Understanding the characteristics of microbes during long-term space missions is essential for safeguarding the health of astronauts and maintaining the functionality of spacecraft. In this study, a Gram-positive, aerobic, spore-forming, rod-shaped strain JL1B1071T was isolated from the surface of hardware on the China Space Station. This strain belongs to the genus Niallia, with its closest relative being Niallia circulans ATCC 4513T. The genome of JL1B1071T is 5 166 230 bp in size, with a G+C content of 35.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between JL1B1071T and N. circulans ATCC 4513T are 83.3 and 27.5%, respectively, both below the recommended thresholds for species delineation. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0. The major quinone was menaquinone-7 (MK-7). Notably, strain JL1B1071T demonstrates a unique ability to hydrolyse gelatin, suggesting that it can utilize gelatin as a substrate in nutrient-limited environments. Genomic analysis of JL1B1071T revealed two conserved signature indels in the GAF domain-containing protein and DNA ligase D protein, which are specific to the genus Niallia. Additionally, structural and functional differences in proteins BshB1 and SplA were identified, which may enhance biofilm formation, oxidative stress response and radiation damage repair, thereby aiding its survival in the space environment. Based on phenotypic, physiological and chemotaxonomic characteristics, as well as genome annotation, strain JL1B1071T was considered a novel species within the genus Niallia and is proposed to be named Niallia tiangongensis sp. nov. The type strain is JL1B1071T (=GDMCC 1.4642=KCTC 43715).

Taxonomic description and genome sequence of Anaerorudis cellulosivorans gen. Nov. sp. nov., a novel cellulose- and Xylan-degrading bacterium of the Bacteroidota phylum isolated from a lab-scale methanogenic landfill bioreactor digesting municipal solid waste

Bacteria responsible for the anaerobic decomposition of lignocellulosic waste biomass play key roles in the global carbon cycle and possess enzymes with potential industrial application. Here, a novel anaerobic, thermophilic, non-spore-forming bacterium, strain m5T, was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor digesting anaerobic municipal solid waste. Cells were Gram-stain-negative, catalase-negative, oxidase-negative, rod-shaped, and non-motile. The genomic DNA G + C content was 40.92 mol%. The optimal NaCl concentration, temperature and pH for growth were 0.5-1 g.L-1, 45 °C, and at pH 7.0, respectively. The major fatty acids were C14:0, C16:0, C18:0, C18:1ω9c, and anteisoC15:0. Strain m5T was able to grow in the absence of yeast extract on glucose, fructose, arabinose, cellobiose, galactose, maltose, raffinose, sucrose, lactose, and pyruvate. In the presence of 0.2 % yeast extract, strain m5T grew on wide range of carbohydrates and amino acids, and was able to use complex substrates such cellulose and xylan. Major end products from cellulose and xylan degradation were valerate and propionate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was most closely related to Seramator thermalis SYSU GA16112T (94.42 % 16S rRNA gene sequence identity). Genome-based relatedness as well as both Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) strongly supported that strain m5T belongs to the Dysgonomonadaceae family. Metagenomic analysis of the landfill bioreactor community revealed that the Dysgonomonadaceae family was the most abundant in the constructed bioreactors. Based on its unique genomic features, strain m5T is considered to represent a novel genus, for which the name Anaerorudis is proposed. Moreover, several phenotypic, biochemical, and physiological properties differentiated the novel bacterial strain from related species, indicating that the strain represents a new species for which the name Anaerorudis cellulosivorans sp. nov. is proposed, with strain m5T (= DSM 112743T = ATCC TSD-267T) being the type of strain. This study highlights the biotechnological potential of strain m5T, specifically in the bioconversion of cellulose and xylan, a recalcitrant substrate within lignocellulosic plant biomass, to enhance biogas production.

Kitasatospora camelliae sp. nov., isolated from rhizosphere soil of Camellia oleifera

Strain HUAS MG31T was isolated from the rhizosphere soil of Camellia oleifera collected from Taoyuan County, China. This strain produced white substrate mycelium and hair brown aerial mycelium without diffusible pigment on the Gause's synthetic No. 1 medium. Aerial mycelia differentiated into rectiflexible spore chains consisting of spherical or cylindrical spores with smooth surfaces. Cell wall peptidoglycan of strain HUAS MG31T contained meso-diaminopimelic acid, and whole-cell sugars were galactose and mannose. The menaquinones of strain HUAS MG31T were MK-9(H6), MK-9(H8) and MK-9(H4). The major cellular fatty acids consisted of Summed Feature 9 (iso-C17 : 1 ω9c/10-methyl C16 : 0), iso-C16 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0, Summed Feature 3 (iso H-C16 : 1 /C16 : 1 ω6c) and cyclo C17 : 0. Sequence analysis based on the full-length 16S rRNA gene of strain HUAS MG31T showed that it shared highest sequence similarities to Kitasatospora paranensis HKI 0190T (99.5%) and Kitasatospora terrestris HKI 0186T (99.4%). The phylogenomic tree shows that strain HUAS MG31T forms an independent subclade, indicating that it might belong to a potential novel species. The results from phylogenetic trees based on 16S rRNA gene sequences showed that strain HUAS MG31T was most closely related to K. paranensis HKI 0190T. However, the average nucleotide identity and the digital DNA-DNA hybridization between strain HUAS MG31T and K. paranensis JCM 13005T were 87.0 %/81.2% and 25.8 %, respectively, below the 95%-96% and 70 % threshold that defined a new species. Meanwhile, phenotypic, chemotaxonomic characteristics and MALDI-TOF MS results further confirmed that strain HUAS MG31T was significantly different from K. paranensis JCM 13005T. Therefore, these results reveal that strain HUAS MG31T represents a novel species of the genus Kitasatospora, for which the name Kitasatospora camelliae sp. nov. is proposed. The type strain is HUAS MG31T (=MCCC 1K09225T= JCM 37022T).

Fructilactobacillus frigidiflavus sp. nov., a pigmented species, and Levilactobacillus lettrarii sp. nov., a propionate-producing species isolated from sourdough

The sourdough isolates FUA3702, FUA3912 and FUA3913T, as well as FUA3695T and FUA3914, could not be identified to known species of the Lactobacillaceae. The 16S rRNA gene sequences of FUA3702 and FUA3913, FUA3695 and FUA3914 were>99% identical to Fructilactobacillus sanfranciscensis and Levilactobacillus lanxiensis, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strain FUA3913T when compared to Fl. sanfranciscensis were 83.67 and 26.60%, respectively. In addition, strains FUA3702, FUA3912 and FUA3913T produce different levels of a yellow C30 carotenoid, but pigmentation has not been described in Fl. sanfranciscensis. The ANI and dDDH values of FUA3695T and FUA3914 when compared to Lv. langxiensis were 95.22 and 61.20%, respectively. In addition, FUA3695 and FUA3914 convert lactate to 1,2-propanediol and further to propionate. The conversion of lactate to propionate by a single strain has not been documented for any of the species in the Lactobacillaceae. Based on the genomic and physiological characteristics, we proposed the novel species Fructilactobacillus frigidiflavus sp. nov. FUA3913T (=DSM 118650T=LMG 33758T) and Levilactobacillus lettrarii sp. nov. FUA3695T (=DSM 118651T=LMG 33759T).

Re-evaluation of boundaries of Streptococcus mitis and Streptococcus oralis and demonstration of multiple later synonyms of Streptococcus mitis, Streptococcus oralis and Streptococcus thalassemiae: description of Streptococcus mitis subsp. carlssonii subsp. nov. and emended description of Streptococcus mitis

The commensal species Streptococcus mitis and Streptococcus oralis are genetically diverse to a degree that challenges traditional definitions of species. This causes automatic identification based on DNA sequences or cellular extract profiles problematic. Based on an initial analysis of 266 genomes, we subjected a subset of 100 representative genomes to detailed phylogenetic, pairwise distance and gene pattern analyses. S. mitis and S. oralis constitute a continuum of clones that are genetically unique. To recognize most isolates as separate species is biologically and practically meaningless. We recommend bending the proposed similarity borders to accommodate the biological reality. Accordingly, we conclude that Streptococcus toyakuensis, Streptococcus chosunensis, Streptococcus gwangjuensis, Streptococcus humanilactis and Streptococcus hohhotensis are later heterotypic synonyms of S. mitis. Type strains of effectively but not validly published 'Streptococcus shenyangsis', 'Streptococcus symci' and 'Streptococcus vulneris' belong in S. mitis. Streptococcus parapneumoniae and Streptococcus nakanonensis are later synonyms of Streptococcus thalassemiae. Streptococcus downii is a later synonym of Streptococcus oralis subsp. dentisani, and the type of 'Streptococcus halitosis' belongs in Streptococcus oralis subsp. tigurinus. The genome sequence of the type of the recently proposed 'Streptococcus bouchesdurhonensis' is based on a mixed culture. Phylogenetic results and the pattern of presence/absence of accessory genes support the distinction of two subspecies of S. mitis, i.e. Sreptococcus mitis subsp. mitis subsp. nov. (type strain is NCTC 12261T) and Sreptococcus mitis subsp. carlssonii subsp. nov. (type strain is SK608=CCUG 55085T=LMG 33510T). The special population structure of the Streptococcus mitis-pneumoniae-pseudopneumoniae-thalassemiae complex renders automated classification of isolates based on average nucleotide identity or digital DNA-DNA hybridization values problematic. As an alternative, for initial taxonomic assignment, we present a whole-genome phylogeny-based method that enables phylogenetic comparison of new isolates in the context of a set of 117 well-characterized reference strains assigned to the Mitis/Sanguinis group.

Streptomyces tabacisoli sp. nov, isolated from the rhizosphere soil of Nicotiana tabacum

Strain HUAS MG91T, a novel actinobacterium, was isolated from the rhizosphere soil of Nicotiana tabacum collected from Changde City, China. This strain could form short, rod-shaped spores with a smooth surface and Rectiflexibles spore chains on Gause's synthetic No.1 medium. Comparison of 16S rRNA gene sequences showed that strain HUAS MG91T exhibited the highest similarity to Streptomyces kunmingensis NBRC 14463 T (98.95%). Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that strain HUAS MG91T was closely related to S. kunmingensis NBRC 14463 T. However, the ANIm and dDDH values between them were 87.25% and 28.60%, respectively, lower than the 96.7% ANIm threshold and 70.0% cutoff point used as guideline values for Streptomyces species delineation. On the basis of phenotypic and genotypic differentiation from tested strains, strain HUAS MG91T is proposed to represent a novel species of the genus Streptomyces, named Streptomyces tabacisoli sp. nov. The type strain is HUAS MG91T (=MCCC 1K09288T = JCM 37027 T).

Polyphasic taxonomic description of Streptomyces okerensis sp. nov. and Streptomyces stoeckheimensis sp. nov. and their biotechnological potential

Streptomyces strains DSM 116494T and DSM 116496T were isolated from sediment samples of the River Oker in Braunschweig, Germany, and subjected to a polyphasic taxonomic study and genome mining for specialized secondary metabolites. Phenotypic, genetic and genomic data confirmed the assignment of these strains to the Streptomyces genus. Pairwise 16S rRNA gene sequence similarity values between the strains and validly named Streptomyces species reached 99.5 and 99.7% for strains DSM 116494T and DSM 116496T, respectively. Genome-based phylogeny demonstrated that Streptomyces pilosus and Streptomyces griseoflavus species were the close relatives to strain DSM 116494T, while Streptomyces vinaceus species was the nearest neighbour to strain DSM 116496T. Digital DNA-DNA hybridization and average nucleotide identity comparisons of the genomic sequence of the strains and their close phylogenomic relatives revealed that values were below the determined threshold of 70 and 95-96% for prokaryotic species demarcation, respectively. The strains were distinguished from their close neighbours based on biochemical, chemotaxonomic and enzymatic data. Given these results, the strains merit being affiliated to novel species within the genus Streptomyces, for which the names Streptomyces okerensis sp. nov. (=OG2.3T=DSM 116494T=KCTC 59408T) and Streptomyces stoeckheimensis sp. nov. (=OG3.14T=DSM 116496T=KCTC 59410T) are proposed. Strains DSM 116494T and DSM 116496T harboured several biosynthetic gene clusters encoding potentially novel antimicrobial and anticancer compounds. Crude extracts of strains DSM 116494T and DSM 116496T inhibited the growth of Gram-negative bacteria (Escherichia coli ΔtolC, Proteus vulgaris) and a multi-drug-resistant Gram-positive, Staphylococcus aureus.

Tenuifilum osseticum sp. nov., a novel thermophilic hydrolytic bacterium within the Tenuifilaceae isolated from a North Ossetian thermal spring, and emended description of the genus Tenuifilum

A novel anaerobic moderately thermophilic bacterium, strain 4138-strT, was isolated from a thermal spring of North Ossetia (Russian Federation). Gram-negative cells were non-sporeforming, straight or curved filamentous rods, occasionally forming rosettes. The strain grew at 30-55 °C, pH range of 6.1-8.7, NaCl range of 0-4 %, with an optimum at 50 °C, pH 7.1-7.5 and 0.2-0.4 % NaCl. It was a chemoorganoheterotroph, growing on simple sugars (glucose, maltose, cellobiose, etc.) and carbohydrates (starch, pullulan, laminarin, xylan, lichenan, curdlan, pachyman) or proteinaceous substrates (peptone, tryptone, gelatin, casein). Sulfur was used as electron acceptor. Major products of glucose fermentation were acetate, hydrogen, and carbon dioxide. Major cellular fatty acids were iso-C15:0 and anteiso-C15:0. The quinone was MK-7. The size of the whole genome of strain 4138-strT was 3.275 Mbp; DNA G + C content was 42.1 %. Genome analysis allowed to identify genes encoding carbohydrate-active enzymes and extracellular proteases. In addition, central metabolism and fermentation pathways of strain 4138-strT were reconstructed. According to both phylogenetic analyses, based on 16S rRNA gene sequences and conserved protein sequences, as well as genome-based comparisons, strain 4138-strT formed a species-level lineage within Tenuifilum genus of Tenuifilaceae family (phylum Bacteroidota). Here we propose a novel species Tenuifilum osseticum sp. nov. with type strain 4138-strT(=KCTC 25386T = VKM B-3628T = UQM 41477T).

Streptomyces solicamelliae sp. nov. and Streptomyces solicathayae sp. nov., isolated from the rhizosphere soil of Camellia oleifera and Cathaya argyrophylla

Two novel actinobacteria strains, HUAS MG47T and HUAS YS2T, were isolated from the rhizosphere soil of Camellia oleifera and Cathaya argyrophylla collected from Changde City, Hunan Province, China. These two strains could form rectiflexible spore chains consisting of short cylindrical spores with smooth surfaces, suggesting that they had typical characteristics of the genus Streptomyces. The cell wall peptidoglycan contained ll-diaminopimelic acid as a diagnostic amino acid. The predominant menaquinones were MK-9 (H6), MK-9 (H8) and MK-9 (H4). The genome sizes of HUAS MG47T and HUAS YS2T were 7.35 and 7.88 Mbp with a G+C content of 72.3 and 72.0 mol%, respectively. Phylogenetic analysis based on the 16S rRNA gene and five housekeeping gene sequences (atpD, gyrB, recA, rpoB and trpB) indicated that strains HUAS MG47T and HUAS YS2T formed an evolutionary lineage with Streptomyces tritici CGMCC 4.7393T. However, the values of multilocus sequence analysis evolutionary distance, average nucleotide identity and DNA-DNA hybridization between these two strains and their closely related relatives indicated that they were clearly different from other known Streptomyces species. Consequently, based on the polyphasic taxonomic study, HUAS MG47T and HUAS YS2T represent two novel Streptomyces species for which the names Streptomyces solicamelliae sp. nov. (HUAS MG47T=MCCC 1K09365T=JCM 37293T) and Streptomyces solicathayae sp. nov. (HUAS YS2T=MCCC 1K08940T=JCM 36737T) are proposed, respectively.

A Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species

Bacterial vaginosis (BV) is a prevalent condition associated with an imbalance in the vaginal microbiota, often involving species of Gardnerella . The taxonomic complexity and inconsistent nomenclature of Gardnerella have impeded progress in understanding the role of specific species in health and disease. In this study, we conducted a comprehensive genomic and pangenomic analysis to resolve taxonomic ambiguities and elucidate metabolic and virulence potential across Gardnerella species. We obtained complete, closed genomes for 42 Gardnerella isolates from women with BV and curated publicly available genome sequences (n = 291). Average nucleotide identity (ANI) analysis, digital DNA-DNA hybridization (dDDH), and the cpn60 gene sequences identified nine species and eleven subspecies within Gardnerella , for which we refined species and subspecies boundaries and proposed updated nomenclature. Pangenome analysis revealed species-specific gene clusters linked to metabolic pathways, virulence factors, and niche adaptations, distinguishing species specialized for mucin degradation in the vaginal environment from those potentially adapted to urinary tract colonization. Notably, we identified lineage-specific evolutionary divergence in gene clusters associated with biofilm formation, carbohydrate metabolism, and antimicrobial resistance. We further discovered the first cryptic plasmids naturally present within the Gardnerella genus. Our findings provide a unified framework for Gardnerella taxonomy and nomenclature, and enhance our understanding of species-specific functional capabilities, with implications for Gardnerella research, diagnostics, and targeted therapeutics in BV.

Taxonomic refinement of Bacillus thuringiensis

Bacillus thuringiensis is the most important biological control agent against various agricultural pests. The bacterium taxonomically belongs to the Bacillus cereus group, which also contains human pathogenic species, e.g., Bacillus anthracis. Thus, precise identification and taxonomic delineation of candidate strains for agricultural usage is of high importance in terms of both public health and biosecurity. By October 2023, whole genome sequences (WGS) of 885 bacterial strains were labeled as B. thuringiensis in the NCBI GenBank database. This study investigates the taxonomic authenticity of those strains using DNA similarity indexes, i.e., average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). All strains were compared with the type strain of B. thuringiensis ATCC 10972T. WGS-based phylotaxonomic investigations showed that out of 885 strains 803 strains authentically belonged to B. thuringiensis while 82 strains were mislabeled as B. thuringiensis having dDDH and ANI values less than the acceptable threshold of 70 and 95% respectively, for prokaryotic species definition in comparison with the B. thuringiensis type strain. Among these 82 mislabeled strains, 39 strains need to be reclassified within the B. cereus group in the species B. anthracis (33 strains), Bacillus toyonensis (five strains), and Bacillus mycoides (one strain). Furthermore, four strains were identified as Bacillus tropicus while one strain belonged to each of the species Bacillus licheniformis, Bacillus paranthracis, and Bacillus weidmannii. The remaining 36 strains did not match with any known Bacillus species nor the species of other bacterial genera, thus they could be assigned to hypothetical new species. Results of the present study, on the one hand, pave the way of comprehensive taxonomic refinements within B. thuringiensis species. On the other hand, highlight the role of taxonomic investigations in targeting authentic B. thuringiensis strains for biological control purposes.

Pseudoalteromonas holothuriae sp. nov., isolated from the sea cucumber Holothuria forskali

Two motile bacterial strains, designated as cfHf56-1T and SW 252, were isolated from the coelomic fluid of Holothuria forskali and from the surrounding seawater at the animal sampling site, respectively. The sea cucumber was collected in the Glénan archipelago (Brittany, France). Strains cfHf56-1T and SW 252 were Gram-stain-negative, non-spore-forming and rod-shaped bacteria. Colonies made on marine agar plates were brown in color. The pH and temperature ranges for growth were 7-8 and 18-30 °C, respectively, in marine broth. The major fatty acids were 16 : 1 cis9 and 16 : 0. Phylogenetic analyses evidenced that both strains belong to a novel species in the genus Pseudoalteromonas. The strains were closely related to the type strains of Pseudoalteromonas caenipelagi, Pseudoalteromonas byunsanensis and Pseudoalteromonas amylolytica, with 75-78 % ANI and 19-21 % dDDH values. In this context, cfHf56-1T (= CIP 111854T = CECT 30642T) is considered as the type strain of the novel species for which the name Pseudoalteromonas holothuriae sp. nov. is proposed. The genome of the type strain is characterized by a size of 5.1 Mbp and a G+C content of 40.5%.

Description of Flavobacterium fructosi sp. nov., Flavobacterium xylosi sp. nov. and Flavobacterium zhouii sp. nov., three new members of the genus Flavobacterium

Three novel strains, designated LB3P45T, LS2P90T and ZS1P70T, were isolated from glaciers located on the Tibetan Plateau, PR China. These strains were Gram-stain-negative, aerobic, rod-shaped and yellow or orange coloured. Phylogenetic analysis based on the 16S rRNA gene and genomic sequences indicated that they belong to the genus Flavobacterium. The 16S rRNA gene sequence similarity among the three strains ranged from 97.4 to 98.6%. Strain LB3P45T showed 98.9% and 98.7% similarity to Flavobacterium urumqiense CGMCC 1.9230T and Flavobacterium xinjiangense JCM 11314T, respectively. Strain LS2P90T displayed 99.0% and 98.7% similarity to F. xinjiangense JCM 11314T and F. urumqiense CGMCC 1.9230T. Strain ZS1P70T had the highest sequence similarity with F. xinjiangense JCM 11314T (98.0%) and F. urumqiense CGMCC 1.9230T (97.8%). The average nucleotide identity and digital DNA-DNA hybridization values between these strains and their closest relatives were lower than 93.0% and 47.9%, respectively. All three strains contained summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) as the major fatty acids. Based on phenotypic characteristics, phylogenetic analysis and genotypic data, the three novel species are proposed: Flavobacterium fructosi sp. nov. (LB3P45T=CGMCC 1.11439T=NBRC 114819T), Flavobacterium xylosi sp. nov. (LS2P90T=CGMCC 1.11685T=NBRC 114823T) and Flavobacterium zhouii sp. nov. (ZS1P70T=CGMCC 1.24124T=NBRC 114829T).

Vogesella oryzagri sp. nov., isolated from the rhizosphere of rice and in silico genome mining for the prediction of biosynthetic gene clusters

A Gram-stain-negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-64T, was isolated from the rhizosphere of rice. The colonies were observed to be creamy white-coloured, smooth, spherical and 0.5-1.1 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAHUQ-64T was able to grow at 10-40 °C, at pH 5.0-9.5 and in the presence of 0-2.0% NaCl (w/v). The strain was positive for both catalase and oxidase tests. The strain was positive for hydrolysis of l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Vogesella and is closely related to Vogesella oryzae L3B39T (98.6% sequence similarity) and Vogesella facilis TTM-24T (98.2%). The novel strain MAHUQ-64T has a draft genome size of 3 827 146 bp (22 contigs), annotated with 3612 protein-coding genes, 74 tRNA and 4 rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-64T and its closest member V. oryzae L3B39T were 86.5 and 33.4%, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAHUQ-64T. The genomic DNA G+C content was determined to be 63.4 mol%. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as summed feature 3 (comprising C16  :  1 ω7c and/or C16  :  1 ω6c) and C16  :  0. Based on dDDH, ANI value, genotypic analysis and chemotaxonomic and physiological data, strain MAHUQ-64T represents a novel species within the genus Vogesella, for which the name Vogesella oryzagri sp. nov. is proposed, with MAHUQ-64T (=KACC 22245T=CGMCC 1.19000T) as the type strain.

Tersicoccus mangrovi sp. nov., a novel actinobacterium from mangrove sediment in Semarang city, Indonesia

A Gram-stain-positive, aerobic and non-motile actinobacterium, designated strain MR15.9T, was isolated from sediment collected from a mangrove ecosystem in Semarang city, Indonesia. Strain MR15.9T grew at 4-37 °C (optimum 30 °C), pH 6.0-11.0 (optimum 7.0-8.0), with 0-10% (w/v) NaCl (optimum 0-3%). The genome of strain MR15.9T was 3.67 Mbp with 71.7 mol% G+C content. Phylogenetic analysis based on 16S rRNA gene sequence and genome sequence directed that strain MR15.9T formed a well-supported clade with Tersicoccus solisilvae CGMCC 1.15480T and Tersicoccus phoenicis 1P05MAT and shared the highest similarity to T. solisilvae CGMCC 1.15480T (98.9% sequence similarity) and T. phoenicis 1P05MAT (98.6% sequence similarity). However, the comparative genome analysis between strain MR15.9T and T. solisilvae CGMCC 1.15480T gave average nt identity value of 85.2% and digital DNA-DNA hybridization value of 29.0%, which were below the statistical threshold for the delineation of the species. Chemotaxonomic data showed that the major fatty acids were anteiso-C15:0, anteiso-C17:0 and iso-C16:0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unidentified phospholipids. MK-8(H2) and MK-9(H2) were noted as the predominant respiratory quinones in this strain. The results of polyphasic characterization indicated that strain MR15.9T represents a novel species of the genus Tersicoccus. The name Tersicoccus mangrovi sp. nov. is proposed, with the type strain MR15.9T (=MCCC 1K08875T=KCTC 59105T).

Reclassification of Salisediminibacterium haloalkalitolerans Sultanpuram et al. 2015 as a Later Heterotypic Synonym of Salisediminibacterium halotolerans Jiang et al. 2012

In the present study, the taxonomic position of Salisediminibacterium haloalkalitolerans was evaluated by determining the 16S rRNA gene sequence similarity, genome relatedness, and phylogenetic analyses. The 16S rRNA gene sequences extracted from the genomes of Salisediminibacterium haloalkalitolerans 10nlgT and Salisediminibacterium halotolerans DSM 26530T showed 100% similarity, supporting their classification as the same species. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between S. haloalkalitolerans and S. halotolerans were 97.7 and 80.2%, respectively, above the cutoff value (95-96% ANI; 70% dDDH) for species delineation. S. haloalkalitolerans and S. halotolerans should be classified as the same species because the 16S rRNA gene phylogeny and phylogenomic tree (based on 71 bacterial single-copy genes) showed no genetic divergence between them. Based on the above results and the rule of priority in nomenclature, we propose to reclassify Salisediminibacterium haloalkalitolerans Sultanpuram et al. 2015 as a later heterotypic synonym of Salisediminibacterium halotolerans Jiang et al. 2012.

Corynebacterium mayonis sp. nov. isolated from a human blood culture

A novel Corynebacterium species, strain BD556T, isolated from blood, was identified at Mayo Clinic, Rochester, MN, USA. After failing definitive identification using MALDI-ToF MS and partial 16S rRNA gene sequencing, BD556T was characterized using a polyphasic approach, including phenotypic, biochemical and whole-genome sequencing methods. BD556T was a Gram-positive rod with clubbed ends, facultatively anaerobic, catalase-positive, oxidase-negative and non-motile. Colonies were white, opaque and non-haemolytic with halo-like edges. BD556T grew at 35 °C in room air, with CO2 and under anaerobic conditions. BD556T grew well in 0 and 6% NaCl and weakly in 10% NaCl. The genome size was 2 349 779 bp with a G+C content of 60.39%. Phylogenetic analysis using 16S rRNA gene sequence analysis, average nucleotide identity and digital DNA-DNA hybridization between the genome of BD556T and the closest type strains from the Type Strain Genome Server database yielded separation values well beyond those required for species delineation. Chemotaxonomic analyses of BD556T revealed ribose, arabinose and galactose as whole-cell sugars and an A1γ meso-diaminopimelic acid-direct peptidoglycan type. The major cellular fatty acids were C15 : 0 (21.0%), C16 : 0 (14.8%), C17 : 1 ω9c (26.2%), C17 : 0 (13.3%) and C18 : 1 ω9c (18.3%). Polar lipids included diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids and phospholipids. BD556T also contained mycolic acids (32-36 carbons) typical of corynebacteria. The respiratory quinones were dominated by MK-8(H2) (71.2%) and MK-9(H2) (25.9%), with smaller amounts of MK-7(H2) and MK-10(H2). The results presented support the tenet that BD556T (=TSD 427T=NCTC 15078T) is a novel species for which the name Corynebacterium mayonis sp. nov. is proposed.

Phenylobacterium ferrooxidans sp. nov., isolated from a sub-surface geothermal aquifer in Iceland

A novel bacterial strain, HK31-GT, was isolated from a subsurface geothermal aquifer (Hellisheidi, SW-Iceland) and was characterized using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA gene along with phylogenomic position indicated that the novel strain belongs to the genus Phenylobacterium. Cells are motile Gram-negative thin rods. Physiological characterization showed that strain HK31-GT is a mesophilic bacterium able to grow from 10 to 30 °C, at pH values between 6 and 8 and at NaCl concentrations between 0 and 0.5 %. Optimal growth was observed without sodium chloride at 25 °C and pH 6. Strain HK31-GT is chemoorganoheterotroph and its major saturated fatty acids are C18:1ω7c, C16:1ω6c and C16:0, the predominant quinone is Q-10 and the major polar lipid is phosphatidylglycerol. The new strain also possesses the capacity to use ferrous iron (Fe(II)) as the sole energy source and can also be considered as a chemolithoautotrophic microorganism. The overall genome of strain HK31-GT was estimated to be 4.46 Mbp in size with a DNA G + C content of 67.95 %. Genes involved in iron metabolism were identified, but no genes typically involved in Fe(II)-oxidation were found. According to the overall genome relatedness indices (OGRI) values, six MAGs from groundwater have been assigned to the same species as the new strain HK31-GT. Furthermore, OGRI values between the genome of strain HK31-GT and the genomes of its closest relatives are below the species delineation threshold. Therefore, given the polyphasic approach used, strain HK31-GT represents a novel species of the genus Phenylobacterium, for which the name Phenylobacterium ferrooxidans sp. nov. is proposed. The type strain is HK31-GT (DSM 116432T = UBOCC-M-3429T = LMG 33376T).

Paludibacillus litoralis gen. nov., sp. nov.: a novel species of a novel genus in the family Paracoccaceae, isolated from the sediment of a tidal flat located in Zhoushan, China

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as HZG-20T, was isolated from a tidal flat in Zhoushan, Zhejiang Province, China. The 16S rRNA sequence similarities between strain HZG-20T and Pikeienuella piscinae RR4-56T, Coraliihabitans acroporae NNCM2T, Parvibaculum indicum P31T and Zhengella mangrovi X9-2-2T were 98.9, 91.7, 91.0 and 91.0%, respectively. Colonies of strain HZG-20T were 1.4 mm in diameter, milky white, round, smooth and convex after cultivating on marine agar at 30 °C for 48 h. Cells were catalase and oxidase-negative. Growth occurred at 15-37 ℃ (optimum, 28 ℃), pH 5.0-9.0 (optimum, pH 6.0-8.0) and with 0-8% (w/v) NaCl (optimum, 1-3%). It contained Menaquinone-8 (H2) as the sole respiratory quinone, and C16:0 (11.8-13.6%), C18:1  ω9c (6.8-13.3%) and C15:0 anteiso (10.9-27.7%) as the major cellular fatty acids. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid, one unidentified phosphoglycolipid, two unidentified glycolipids (GL1-GL2) and three unidentified lipids (L1-L3). The genome of strain HZG-20T was 3 835 886 bp in length, comprised 3746 protein-coding genes, with DNA G+C content of 67.1 mol%. The phylogenetic and phylogenomic trees indicated that strain HZG-20T formed an independent and stable clade with P. piscinae RR4-56T. However, the average nucleotide identity, digit DNA-DNA hybridization and average amino acid identity values between strain HZG-20T and P. piscinae RR4-56T, C. acroporae NNCM2T, P. indicum P31T and Z. mangrovi X9-2-2T were 81.6, 71.1, 68.7 and 69.5%; 23.0, 18.5, 17.9 and 17.5%; and 78.2, 56.8, 56.5 and 61.9%, respectively, together with distinct chemotaxonomic features, indicating strain HZG-20T should not be assigned to known genera. As a result, a novel species of a novel genus within the family Paracoccaceae, designated as Paludibacillus litoralis gen. nov., sp. nov., was proposed. The type strain is HZG-20T (MCCC 1K08468T=KCTC 82692T).

Arvimicrobium flavum gen. nov., sp. nov., A Novel Genus in the Family Phyllobacteriaceae Isolated From Forest Soil

During the study of microbial diversity of forest soil in the Republic of Korea, a yellow pigment-producing, Gram-stain-negative, rod-shaped, motile bacterium was isolated and designated as strain 1W2T. This strain grew at temperature of 10-37 °C, at pH of 5.0-9.0, and at NaCl concentration of 0-3.0% (w/v). The 16S rRNA gene sequencing and genome sequencing revealed that strain 1W2T is a member of the family Phyllobacteriaceae but exhibits low similarity with known genera, suggesting that this strain is a new genus within the family. This strain showed the closest similarity to the genera Mesorhizobium (96.6-96.9%), Aminobacter (96.4 -96.6%), Aquamicrobium (96.5-96.7%), and Pseudaminobacter (96.6-96.7%). The nearest relative of 1W2T was Mesorhizobium shangrilense CCBAU 65327 T with the 16S rRNA gene sequence similarity of 96.9%. The genome size was 5,545,526 bp with DNA G + C content of 64.7%. The values of overall genomic relatedness indices between strain 1W2T and the reference members were 20.4-21.3% for digital DNA-DNA hybridization, 74.0-76.6% for average nucleotide identity, and 68.1-61.2% for amino acids identity. Chemotaxonomic profiling revealed that Q-10 was the sole ubiquinone; summed feature 8 (C18:1ω7c and/or C18:1ω6c), iso-C13:0, and C19:0 cyclo ω8c were the predominant fatty acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, and phosphatidylethanolamine were the major polar lipids. Based on these data, strain 1W2T represents a novel species of a new genus in the family Phyllobacteriaceae. Accordingly, we proposed the name Arvimicrobium flavum gen. nov., sp. nov., with the type strain 1W2T (= KCTC 92441 T = NBRC 116019 T).

Identification and characterization of a novel chromosome-encoded aminoglycoside O-nucleotidyltransferase gene, ant(9)-Id, in Providencia sp. TYF-12 isolated from the marine fish intestine

Background

The mechanisms underlying the resistance of the genus Providencia to aminoglycosides are complex, which poses a challenge for the efficient treatment of infectious diseases caused by these pathogens. To help clinicians treat infections more effectively, a more comprehensive understanding of antibiotic resistance mechanisms is urgently needed.

Methods

Plates were streaked to isolate bacteria from the intestinal contents of fish. The standard agar dilution method was used to determine the minimum inhibitory concentrations (MICs) of the antimicrobial agents. Molecular cloning was carried out to study the function of the novel antibiotic inactivation gene ant(9)-Id. The kinetic parameters of ANT(9)-Id were measured by a SpectraMax multifunctional microplate reader. Whole-genome sequencing and bioinformatic analysis were conducted to elucidate the sequence structure and evolutionary relationships of similar genes.

Results

The novel aminoglycoside O-nucleotidyltransferase gene ant(9)-Id was encoded on the chromosome of a species-unclassified isolate designated Providencia sp. TYF-12, which was isolated from the intestine of a marine fish. Among the 11 aminoglycosides tested, ant(9)-Id was resistant to only spectinomycin. The MIC of spectinomycin for the recombinant strain carrying ant(9)-Id (pUCP20-ant(9)-Id/DH5α) increased 64-fold compared with that of the control strain (pUCP20/DH5ɑ). ANT(9)-Id shares the highest amino acid (aa) identity of 46.70% with the known drug resistance enzyme ANT(9)-Ic. Consistent with the MIC results, ANT(9)-Id showed high affinity and catalytic efficiency for spectinomycin, with a K m of 8.94 ± 2.50 μM and a k cat/K m of 26.15 μM-1·s-1. This novel resistance gene and its close homologs are conserved in Providencia strains from various sources, including some of clinical significance. No mobile genetic elements (MGEs) surrounding the ant(9)-Id(-like) genes were identified.

Conclusion

This work revealed and characterized a novel spectinomycin resistance gene, ant(9)-Id, along with its biological features. Identifying novel resistance genes in pathogens can assist in rational medication use and the identification of additional antimicrobial resistance mechanisms in microbial populations.

Genome sequences of Microvirga spp. CF3062 and CF3016 isolated from nodules found on herbarium specimens collected in 2004 and 2015

We present the genomes of two Microvirga isolates isolated from nodules found on Medicago lupulina herbarium specimens at the Marion Ownbey Herbarium at Washington State University. These genomes and others from herbarium specimens offer an unprecedented opportunity to study the bacterial evolution of plant-associated microbes over long time scales.

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).

Cerasicoccus fimbriatus sp. nov., isolated from the mid-ridge of the Southwest Indian Ocean

A Gram-stain-negative bacterium, designated as strain TK19100T, was isolated from the mid-ridge of the Southwest Indian Ocean. Cells of strain TK19100T were strictly aerobic, non-motile and short-rod shaped with fimbriae-like structures around the cell surface. Growth occurred at 15-40 °C, at pH 6.0-9.0 and with 1-10% (w/v) NaCl. Strain TK19100T shared the highest 16S rRNA gene sequence similarity with Cerasicoccus frondis NBRC 105381T of 97.74%, followed by Cerasicoccus arenae KCTC 12870T of 97.69% and Cerasicoccus maritimus NBRC 105382T of 97.40%. The phylogenetic tree based on both 16S rRNA genes and 92 core genes placed strain TK19100T in a new linage within the genus Cerasicoccus. The genome size of strain TK19100T was 5.07 Mb with the DNA G + C content 56.1%. The average nucleotide identity value and the digital DNA-DNA hybridization value of strain TK19100T compared with the closest related species, Cerasicoccus frondis, were 78.39% and 23.70%, respectively. Strain TK19100T encoded a previously unreported combination of GH16 and Carbohydrate Binding Module 96. The major fatty acids of strain TK19100T were C14:0 and C18:1 ω9c. Menaquinone-7 was the sole respiratory quinone. The phenotypic and genotypic characterization analysis indicate that strain TK19100T represents a novel species affiliated to the genus Cerasicoccus, for which the name Cerasicoccus fimbriatus sp. nov. is proposed. The type strain is TK19100T (= CGMCC 1.18957T = NBRC 116189T).

Xenorhabdus bharatensis sp. nov., Xenorhabdus entomophaga sp. nov., Xenorhabdus siamensis sp. nov., and Xenorhabdus thailandensis sp. nov. Isolated from Steinernema Entomopathogenic Nematodes

Four Gram-stain-negative bacterial strains, CS20T, AUT15.5T, XENO-11T, and CCN3.3T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel species within the genus Xenorhabdus (Gammaproteobacteria, Morganellaceae). In this study, we described these new species using whole-genome phylogenomic reconstructions, sequence identity values from core genome sequences, and phenotypic characterization. Phylogenetic reconstructions based on 16S rRNA gene sequences showed that: (i) strain CS20T is closely related to X. stockiae DSM 17904T, (ii) strain AUT15.5T is closely related to X. budapestensis DSM 16342T, (iii) strain XENO-11T is closely related to X. khoisanae DSM 25463T, and (iv) strain CCN3.3T is closely related to X. griffiniae DSM 17911T. The 16S rRNA gene sequence similarity value between strain CS20T and X. stockiae DSM 17904T is 97.8%, between strain AUT15.5T and X. budapestensis DSM 16342T is 98.1%, between strain XENO-11T and X. khoisanae DSM 25463T is 97.8%, and between strain CCN3.3T and X. griffiniae DSM 17911T is 98.6%. Phylogenomic reconstructions using whole-genome sequences showed that: (i) strain CS20T is closely related to X. stockiae DSM 17904T and X. innexi DSM 16336T, (ii) strain AUT15.5T is closely related to X. indica DSM 17382T, (iii) strain XENO-11T is closely related to X. khoisanae DSM 25463T, and (iv) strain CCN3.3T is closely related to X. griffiniae DSM 17911T. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains CS20T, AUT15.5T, XENO-11T, and CCN3.3T and the type strains of their more closely related species are below the 70% and the 95-96% divergence thresholds, respectively, used for prokaryotic species delineation. Hence, we propose the following four new species: Xenorhabdus bharatensis sp. nov. (the type strain is CS20T=CCM 9320T=CCOS 2070T), X. entomophaga sp. nov. (the type strain is XENO-11T=CCM 9389T=CCOS 2111T), X. siamensis sp. nov. (the type strain is AUT15.5T=CCM 9405T=CCOS 2116T), and X. thailandensis sp. nov. (the type strain is CCN3.3T=CCM 9406T=CCOS 2115T). The following biochemical tests may be useful for differentiating the novel species from their more closely related taxa: acetoin production, arginine dihydrolase, citrate utilization, gelatinase, glucose oxidation, indole production, and tryptophan deaminase. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.

A distinct Borrelia clade within the relapsing fever group from cat-infesting Haemaphysalis semermis Neumann 1901 (Acari: Ixodidae)

An undescribed relapsing fever group Borrelia species was detected in a male Haemaphysalis semermis tick infesting a rural cat in an indigenous population in Pahang National Park, Peninsular Malaysia. The 16 S rRNA gene sequence revealed close similarity of this variant to several undescribed Borrelia species and Borrelia theileri, with genetic distances ranging from 0.58 to 0.72%. Furthermore, the flaB, gyrB, and the concatenated 16 S rRNA + flaB + gyrB sequence analyses demonstrated that this variant is distinctly separated from multiple undescribed Borrelia species, Borrelia miyamotoi, and B. theileri, with genetic distances ranging from 3.41 to 7.00%. This study not only reports the first Borrelia found in H. semermis but also suggests that it forms a distinct clade within the relapsing fever group in Peninsular Malaysia.

Campylobacter sputorum subsp. bovis subsp. nov., isolated from cattle, and an emended description of Campylobacter sputorum

Six urease-negative Campylobacter strains were isolated from cattle faeces over a 19-month period from 2009 to 2010. These strains were initially identified as Campylobacter sputorum by 16S rRNA gene and atpA typing. Initial studies characterizing these strains by multilocus sequence typing and genome sequencing further supported their classification as C. sputorum but indicated that these strains form a divergent clade within the species. A polyphasic study was undertaken here to clarify their taxonomic position. Phylogenetic analyses were performed based on 16S rRNA gene sequences and the concatenated sequences of 330 core genes, with the latter analysis also placing the six strains into a clade distinct from the three C. sputorum biovars. Pairwise digital DNA-DNA hybridization values identified these strains as C. sputorum, and the pairwise average nucleotide identity values were consistent with those observed between current Campylobacter subspecies pairs. Standard phenotypic testing was also performed. All strains are microaerobic, anaerobic, motile, Gram-negative and oxidase- and catalase-positive; cells are curved rods or spirals. Strains can be distinguished from the C. sputorum biovars by the presence of alkaline phosphatase activity and triphenyltetrazolium chloride reduction and absence of nitrate reduction. The data presented here show that these strains represent a novel subspecies within C. sputorum, for which the name C. sputorum subsp. bovis subsp. nov. (type strain RM8705T=LMG 32300T=CCUG 75470T) is proposed.

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).

A Novel Strain Burkholderia theae GS2Y Exhibits Strong Biocontrol Potential Against Fungal Diseases in Tea Plants (Camellia sinensis)

BACKGROUND

Tea plants (Camellia sinensis) are widely cultivated cash crops. However, fungal diseases lead to significant reductions in both the yield and quality of tea. Therefore, searching for economical, eco-friendly, and efficient biological control measures is crucial for protecting tea plants from pathogenic fungi.

METHODS

The confrontation assays were performed to identify the antagonistic bacteria against tea pathogenic fungi and evaluate the antifungal activity of these bacteria.

RESULTS

Here, three tea pathogenic fungi were identified: Colletotrichum siamense HT-1, Diaporthe phaseolorum HT-3, and Fusarium fujikuroi HT-4. Notably, D. phaseolorum was the first to be reported in tea plants in China. Some tea pathogenic fungi showed a high relative abundance, suggesting a potential disease risk in tea plantations. Strain GS2Y, isolated from tea rhizosphere soil, exhibited strong antifungal activity against tea pathogenic fungi and represented a novel species within the genus Burkholderia, designated as Burkholderia theae. GS2Y could directly inhibit tea pathogenic fungi by disrupting the cellular structures and protect tea plants from fungal diseases caused by C. siamense HT-1 and D. phaseolorum HT-3.

CONCLUSIONS

B. theae GS2Y might function as a potentially valuable resource for biocontrol agents, laying the foundation for the development of strategies to manage fungal diseases in tea plants.

Photorhabdus viridis sp. nov. Isolated from Heterorhabditis zealandica Entomopathogenic Nematodes

A novel bacterial species, Photorhabdus viridis sp. nov., represented by strain GreenT, isolated from Heterorhabditis zealandica MJ2C entomopathogenic nematodes, is described. Phylogenetic reconstructions using 16S rRNA gene sequences show that strain GreenT is closely related to P. thracensis DSM 15199 T. The 16rRNA gene sequences of these two strains are 98.8% identical. Phylogenetic reconstructions using whole-genome sequences show that strain GreenT is closely related to P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T. Digital DNA-DNA hybridization (dDDH) values between strain GreenT and its three more close relative species, P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T, are 49%, 59%, and 59%, respectively. In addition, average nucleotide identity (ANI) values between GreenT and P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T are 92.4%, 94.4%, and 94.6%, respectively. The novel species also differs in their biochemical capacities from the biochemical capacities of their more closely related taxa. The following biochemical tests may be particularly useful in this context: Arginine dihydrolase, gelatinase, and glucose and mannitol oxidation. Given the clear phylogenetic separation, the sequence divergence values, and the phenotypic differences, we conclude that strain GreenT represents a novel bacterial species, for which we propose the name Photorhabdus viridis sp. nov. with GreenT (= CCM 9407 T = CCOS 2117 T = MJ2CT) as the type strain. Our study contributes to a better understanding of the taxonomy and biodiversity of an important bacterial group with great biotechnological and agricultural potential.

Biotechnological and pharmaceutical potential of twenty-eight novel type strains of Actinomycetes from different environments worldwide

Actinomycetes are a prolific source of bioactive natural compounds many of which are used as antibiotics or other drugs. In this study we investigated the genomic and biochemical diversity of 32 actinobacterial strains that had been deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures decades ago. Genome-based phylogeny and in silico DNA-DNA hybridization supported the assignment of these strains to 26 novel species and two novel subspecies and a reclassification of a Streptomyces species. These results were consistent with the biochemical, enzymatic, and chemotaxonomic features of the strains. Most of the strains showed antimicrobial activities against a range of Gram-positive and Gram-negative bacteria, and against yeast. Genomic analysis revealed the presence of numerous unique biosynthetic gene clusters (BGCs) encoding for potential novel antibiotic and anti-cancer compounds. Strains DSM 41636T and DSM 61640T produced the antibiotic compounds A33853 and SF2768, respectively. Overall, this reflects the significant pharmaceutical and biotechnological potential of the proposed novel type strains and underlines the role of prokaryotic systematics for drug discovery. In order to compensate for the gender gap in naming prokaryotic species, we propose the eponyms for all newly described species to honour female scientists.

Biodiversity of Aspergillus Species and Their Mycotoxin Production Potential in Dry Meat

This study aimed to examine fungi diversity in dried beef meat sold in Ekiti State, characterize the isolated fungi, and determine the aflatoxin-producing ability of the Aspergillus fungi in the samples. Dried beef meat was collected from different markets in Ekiti State and screened for the presence of filamentous fungi using molecular methods. Samples were cultured aseptically on potato dextrose agar (PDA) for fungi isolation, and molecular identification was performed using DNA extraction, Polymerase chain Reaction (PCR), ITS-1/ITS-4 primer pair, and nucleotide sequencing. The results obtained indicated a range of filamentous fungi genera including Aspergillus, Rhizopus, Penicillium, Fusarium, Cladosporium, Alternaria, and other fungi species contaminating the dried meat at (43%), (42%), (3%), (2%), (2%), (1%), and (7%), respectively. High incidences were recorded for Aspergillus flavus, Aspergillus niger, and Aspergillus fumigatus in most of the screened samples. Aspergillus flavus accounted for (24.7%) of all the Aspergillus species isolated with the presence of the gene needed for aflatoxin production. The occurrences of these filamentous fungal species pose a cause for concern, as most of these fungal species are known producers of certain toxic substances. Maximum likelihood phylogenetic analysis showed a high similarity index score, which indicated a good relationship between isolated Aspergillus Species and the closely related strains from GenBank, isolated from different sources and countries. The implication of this study is that consumer health may be at risk through exposure to contaminated dried meat.

Enterovibrio qingdaonensis sp. nov. and Enterovibrio gelatinilyticus sp. nov., two marine bacteria isolated from surface seawater of Qingdao offshore

Two Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped marine bacteria, designated strains ZSDZ35T and ZSDZ42T, were isolated from surface seawater of Qingdao offshore. Phylogenetic analysis of the 16S rRNA genes and whole genome data placed ZSDZ35T and ZSDZ42T within the genus Enterovibrio. Strain ZSDZ35T was most closely related to Enterovibrio nigricans DSM 22720T with 97.55% sequence similarity, whereas ZSDZ42T was most closely related to Enterovibrio calviensis DSM 14347T with 98.97% sequence similarity. Strain ZSDZ35T grew with 0-8% (w/v) NaCl (optimum 4%), at 16-37 °C (optimum 28 °C) and pH 6.0-9.0 (optimum pH 8.0); whereas strain ZSDZ42T grew with 1-7% (w/v) NaCl (5%), at 4-28 °C (8 °C) and pH 6.0-9.0 (pH 7.0). Both strains shared the same major fatty acid components of summed feature 3 (C16:1ω7c or/and C16:1ω6c), summed feature 8 (C18:1ω7c and C18:1ω6c) and C16:0, with different proportions. The DNA G + C contents of strains ZSDZ35T and ZSDZ42T were 47.2% and 46.7%, respectively. Based on the results of polyphasic analyses, ZSDZ35T and ZSDZ42T are considered to represent novel species, for which the names Enterovibrio qingdaonensis sp. nov. (type strain, ZSDZ35T = MCCC 1K06293T = KCTC 82887T) and Enterovibrio gelatinilyticus sp. nov. (type strain, ZSDZ42T = MCCC 1K06294T = KCTC 82886T) are proposed, respectively.

Applying rearrangement distances to enable plasmid epidemiology with pling

Plasmids are a key vector of antibiotic resistance, but the current bioinformatics toolkit is not well suited to tracking them. The rapid structural changes seen in plasmid genomes present considerable challenges to evolutionary and epidemiological analysis. Typical approaches are either low resolution (replicon typing) or use shared k-mer content to define a genetic distance. However, this distance can both overestimate plasmid relatedness by ignoring rearrangements, and underestimate by over-penalizing gene gain/loss. Therefore a model is needed which captures the key components of how plasmid genomes evolve structurally - through gene/block gain or loss, and rearrangement. A secondary requirement is to prevent promiscuous transposable elements (TEs) leading to over-clustering of unrelated plasmids. We choose the 'Double Cut and Join Indel' (DCJ-Indel) model, in which plasmids are studied at a coarse level, as a sequence of signed integers (representing genes or aligned blocks), and the distance between two plasmids is the minimum number of rearrangement events or indels needed to transform one into the other. We show how this gives much more meaningful distances between plasmids. We introduce a software workflow pling (https://github.com/iqbal-lab-org/pling), which uses the DCJ-Indel model, to calculate distances between plasmids and then cluster them. In our approach, we combine containment distances and DCJ-Indel distances to build a TE-aware plasmid network. We demonstrate superior performance and interpretability to other plasmid clustering tools on the 'Russian Doll' dataset and a hospital transmission dataset.

Hydrogenimonas leucolamina sp. nov., a hydrogen- and sulphur-oxidizing mesophilic chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Western Pacific Ocean

A novel mesophilic bacterium, strain SS33T, was isolated from a deep-sea hydrothermal vent chimney at Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean. The cells of strain SS33T were motile short rods with a single polar flagellum. The growth of strain SS33T was observed at the temperature range between 33 and 55 °C (optimum growth at 45 °C), at the pH range between 5.0 and 7.1 (optimum growth at pH 6.0) and in the presence of between 2.0 and 4.5% (w/v) NaCl [optimum growth at 3.5% (w/v)]. Strain SS33T was a facultative anaerobic chemolithoautotroph using molecular hydrogen and elemental sulphur as the sole electron donor. Nitrate, nitrous oxide, sulphate, elemental sulphur and molecular oxygen were capable of serving as the sole electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences placed strain SS33T in the genus Hydrogenimonas belonging to the class Epsilonproteobacteria. The closely related species of strain SS33T were Hydrogenimonas urashimensis SSM-Sur55T (95.96%), Hydrogenimonas thermophila EP1-55-1%T (95.75%) and Hydrogenimonas cancrithermarum ISO32T (95.24%). According to the taxonomic and physiological characteristics, it is proposed that strain SS33T was classified into a novel species of genus Hydrogenimonas, Hydrogenimonas leucolamina sp. nov., with SS33T (=JCM 39184T =KCTC 25253T) as the type strain. Furthermore, the genome comparison of Epsilonproteobacteria revealed that their [NiFe] hydrogenase genes belonging to Group 1b could be divided into two phylogenetic lineages and suggested that the reverse gyrase gene has been lost after division to the genus Hydrogenimonas.

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).