Adlercreutzia faecimuris sp. nov., producing propionate and acetate isolated from mouse feces.

A novel strictly anaerobic bacterium, strain JBNU-10 T, was isolated from BALB/c mouse feces. Cells of the strain JBNU-10 T were Gram-stain positive, non-motile and rod-shaped. Optimum growth occurred at 37℃, with 1% (w/v) NaCl and at pH 7. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain JBNU-10 T belonged to the genus Adlercreutzia and were closely related to Adlercreutzia muris WCA-131-CoC-2 T (95.90%). The genome sequencing of strain JBNU-10 T revealed a genome size of 2,790,983 bp, a DNA G + C content of 69.4 mol%. It contains a total of 2,266 CDSs, 5 rRNA genes and 49 tRNA genes. According to the data obtained strain JBNU-10 T shared ANI value below 77.6- 67.7%, dDDH value below 23.8% with the closely type species. Strain JBNU-10 T possessed iso-C16:0 DMA, C18:1 CIS 9 FAME, and C18:0 DMA as the major fatty acids and had DMMK-6. The major end products of fermentation is propionate and acetate. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain JBNU-10 T represent a novel species of the genus Adlercreutzia. The type strain is JBNU-10 T (= KCTC 25028 T = CCUG 75610 T).

Reclassification of Some Exiguobacterium Species Based on Genome Analysis.

The Exiguobacterium genus comprises Gram-stain-positive and facultatively anaerobic bacteria. Some Exiguobacterium species have previously shown significant high 16S rRNA gene sequence similarities with each other. This study evaluates the taxonomic classification of those Exiguobacterium species through comprehensive genome analysis. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were determined for various Exiguobacterium species pairs. The ANI and dDDH values between Exiguobacterium enclense and Exiguobacterium indicum, Exiguobacterium aquaticum and Exiguobacterium mexicanum, Exiguobacterium soli and Exiguobacterium antarcticum, and Exiguobacterium sibiricum and Exiguobacterium artemiae were above the cut-off level (95-96% for ANI and 70% for dDDH) for species delineation. Based on the findings, we propose to reclassify Exiguobacterium enclense as a later heterotypic synonym of Exiguobacterium indicum, Exiguobacterium aquaticum as a later heterotypic synonym of Exiguobacterium mexicanum, Exiguobacterium soli as a later heterotypic synonym of Exiguobacterium antarcticum and Exiguobacterium sibiricum as a later heterotypic synonym of Exiguobacterium artemiae.

Turicibacter faecis sp. nov., isolated from faeces of heart failure mouse model.

Strain TC023T, a Gram-positive, long, rod-shaped, spore-forming anaerobe, was isolated from the faeces of a heart failure mouse model. The strain formed greyish-white coloured colonies with a convex elevation on brain-heart infusion medium supplemented with 0.1 % sodium taurocholate, incubated at 37 °C for 2 days. Taxonomic analysis based on the 16S rRNA gene sequence showed that TC023T belonged to the genus Turicibacter, and was closely related to Turicibacter bilis MMM721T (97.6 %) and Turicibacter sanguinis MOL361T (97.4 %). The whole genome of the strain has a G+C content of 37.3 mol%. The average nucleotide identity and genome-to-genome distance between TC023T and Turicibacter bilis MMM721T were 77.6 % and 24.3 %, respectively, and those with Turicibacter sanguinis MOL361T were 75.4 % and 24.3 %, respectively. These genotypic, phenotypic, and biochemical analyses indicated that the isolate represents a novel species in the genus Turicibacter, and the name Turicibacter faecis sp. nov. is proposed. The type strain is TC023T (RIMD 2002001T=TSD 372T).

Isolation and characterization of a novel Waltera species and reclassification of Brotolimicola acetigignens Hitch et al. 2022 as Waltera acetigignens comb. nov.

Obligately anaerobic, Gram-stain-negative, wavy rods, strains 17YCFAHCo10, 18YCFAH0.3Co2 and 19YCFAH0.3Co2, were isolated from faecal samples of healthy Japanese people. The three isolates showed the highest 16S rRNA gene sequence similarity to Waltera intestinalis WCA3-601-WT-6HT (99.2-100 %) and Brotolimicola acetigignens f_CXYT (99.2-99.7 %). The 16S rRNA gene sequence analysis showed that the three isolates formed a cluster with W. intestinalis WCA3-601-WT-6HT. Strain 19YCFAH0.3Co2 formed a subcluster with the type strain of W. intestinalis and did not form a cluster with the other two isolates. B. acetigignens f_CXYT also formed a cluster with W. intestinalis WCA3-601-WT-6HT and three isolates. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain 19YCFAH0.3Co2 and W. intestinalis WCA3-601-WT-6HT were higher (72 % dDDH and 97 % ANI) than the cut-off values for species delimitation, indicating that strain 19YCFAH0.3Co2 is W. intestinalis. On the other hand, the dDDH and ANI values between strains 17YCFAHCo10 and 18YCFAH0.3Co2 and the type strain of W. intestinalis were lower (<34 % dDDH and <87 % ANI) than the cut-off values for species delimitation, indicating that these two isolates are different species from W. intestinalis. The percentage of conserved proteins and the average amino acid identity values support the assignment of the isolates to the genus Waltera. Strains 17YCFAHCo10 and 18YCFAH0.3Co2 could be distinguished from W. intestinalis by their inability to ferment melibiose and ribose and lack of activity for ß-glucuronidase. In addition, the dDDH and ANI values between two strains (17YCFAHCo10 and 18YCFAH0.3Co2) and B. acetigignens f_CXYT were higher (>78 % dDDH and >97 % ANI), indicating these two strains and B. acetigignens are the same species. As the genus Waltera has priority, B. acetigignens is transferred to the genus Waltera as Waltera acetigignens comb. nov. The type strain of W. acetigignens is f_CXYT (=JCM 34988T=DSM 107528T).

Pengzhenrongella phosphoraccumulans sp. nov., isolated from high Arctic glacial till, and emended description of the genus Pengzhenrongella.

A yellow pigmented, Gram-stain-positive, motile, facultatively anaerobic and irregular rod-shaped bacteria (strain M0-14T) was isolated from a till sample collected from the foreland of a high Arctic glacier near the settlement of Ny-Ålesund in the Svalbard Archipelago, Norway. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that M0-14T formed a lineage within the family Cellulomonadaceae, suborder Micrococcineae. M0-14T represented a novel member of the genus Pengzhenrongella and had highest 16S rRNA gene sequence similarity to Pengzhenrongella sicca LRZ-2T (97.3 %). Growth occurred at 4-25 °C (optimum 4-18 °C), at pH 6.0-9.0 (optimum pH 7.0), and in the presence of 0-5 % (w/v) NaCl. The predominant menaquinone was MK-9(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The major polar lipids were phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylinositol, one undefined phospholipid and five undefined phosphoglycolipids. The cell-wall diamino acid was l-ornithine whereas rhamnose and mannose were the cell-wall sugars. Polyphosphate particles were found inside the cells of M0-14T. Polyphosphate kinase and polyphosphate-dependent glucokinase genes were detected during genomic sequencing of M0-14. In addition, the complete pstSCAB gene cluster and phnCDE synthesis genes, which are important for the uptake and transport of phosphorus in cells, were annotated in the genomic data. According to the genomic data, M0-14T has a metabolic pathway related to phosphorus accumulation. The DNA G+C content of the genomic DNA was 70.8 %. On the basis of its phylogenetic relationship, phenotypic properties and chemotaxonomic distinctiveness, strain M0-14T represents a novel species of the genus Pengzhenrongella, for which the name Pengzhenrongella phosphoraccumulans sp. nov. is proposed. The type strain is M0-14T (= CCTCC AB 2012967T = NRRL B-59105T).

Azotosporobacter soli gen. nov., sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.

A nitrogen-fixing strain designated SG130T was isolated from paddy soil in Fujian Province, China. Strain SG130T was Gram-staining-negative, rod-shaped, and strictly anaerobic. Strain SG130T showed the highest 16S rRNA gene sequence similarities with the type strains Dendrosporobacter quercicolus DSM 1736T (91.7%), Anaeroarcus burkinensis DSM 6283T (91.0%) and Anaerospora hongkongensis HKU 15T (90.9%). Furthermore, the phylogenetic and phylogenomic analysis also suggested strain SG130T clustered with members of the family Sporomusaceae and was distinguished from other genera within this family. Growth of strain SG130T was observed at 25-45 °C (optimum 30 °C), pH 6.0-9.5 (optimum 7.0) and 0-1% (w/v) NaCl (optimum 0.1%). The quinones were Q-8 and Q-9. The polar lipids were phosphatidylserine (PS), phosphatidylethanolamine (PE), glycolipid (GL), phospholipid (PL) and an unidentified lipid (UL). The major fatty acids (> 10%) were iso-C13:0 3OH (26.6%), iso-C17:1 (15.6%) and iso-C15:1 F (11.4%). The genomic DNA G + C content was 50.7%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T (ANI 68.0% and dDDH 20.3%) were both below the cut-off level for species delineation. The average amino acid identity (AAI) between strain SG130T and the most closely related type strain D. quercicolus DSM 1736T was 63.2%, which was below the cut-off value for bacterial genus delineation (65%). Strain SG130T possessed core genes (nifHDK) involved in nitrogen fixation, and nitrogenase activity (106.38 µmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the above results, strain SG130T is confirmed to represent a novel genus of the family Sporomusaceae, for which the name Azotosporobacter soli gen. nov., sp. nov. is proposed. The type strain is SG130T (= GDMCC 1.3312T = JCM 35641T).

Polyphasic Investigation of Aliiroseovarius salicola sp. nov., Isolated from Seawater.

A novel Gram-stain-negative, strictly aerobic, short-rod-shaped, and chemo-organoheterotrophic bacterium, designated KMU-50T, was isolated from seawater gathered from Dadaepo Harbor in South Korea. The microorganism grew at 0-4.0% NaCl concentrations (w/v), pH 6.0-8.0, and 4-37 °C. The 16S rRNA gene sequence-based phylogenetic tree demonstrated that the strain KMU-50T is a novel member of the family Roseobacteraceae and were greatly related to Aliiroseovarius crassostreae CV919-312T with sequence similarity of 98.3%. C18:1 ω7c was the main fatty acid and ubiquinone-10 was the only isoprenoid quinone. The dominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified phospholipids, an unidentified aminolipid, and an unidentified lipid. The genome size of strain KMU-50T was 3.60 Mbp with a DNA G+C content of 56.0%. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between the genomes of strain KMU-50T and its closely related species were 76.0-81.2% and 62.2-81.5%, respectively. The digital DNA-DNA hybridization (dDDH) value of strain KMU-50T with the strain of A. crassostreae CV919-312T was 25.1%. The genome of the strain KMU-50T showed that it encoded many genes involved in the breakdown of bio-macromolecules, thus showing a high potential as a producer of industrially useful enzymes. Consequently, the strain is described as a new species in the genus Aliiroseovarius, for which the name Aliiroseovarius salicola sp. nov., is proposed with the type strain KMU-50T (= KCCM 90480T = NBRC 115482T).

Genetic Transformation of Cryptococcus Species with Agrobacterium Transfer DNA.

Transformation of foreign DNA into Cryptococcus species is a powerful tool for exploring gene functions in these human pathogens. Agrobacterium tumefaciens-mediated transformation (AtMT) has been used for the stable introduction of exogenous DNA into Cryptococcus for over two decades, being particularly impactful for insertional mutagenesis screens to discover new genes involved in fungal biology. A detailed protocol to conduct this transformation method is provided in the chapter. Scope for modifications and the benefits and disadvantages of using AtMT in Cryptococcus species are also presented.

Mannheimia indoligenes sp. nov., proposed for clade V organisms of Mannheimia.

A set of 25 strains belonging to clade V of Mannheimia mainly isolated from cattle was investigated and is proposed to represent Mannheimia indoligenes sp. nov. The species can be separated from the other validly published species of the genus by pheno- and genotype. Only indole separates M. indoligenes and Mannheimia varigena while two to seven characters separate M. indoligenes from other species of Mannheimia. Thirteen strains belonging to biogroups 6, 7, 8C, 9, 10, 12 and UG5 formed a monophyletic group based on 16S rRNA gene sequence comparisons with 98-100 % similarity. Eight of these strains were further included in the whole genome comparison. Digital DNA-DNA hybridization showed that the similarities between the suggested type strain M14.4T and the other strains of M. indoligenes were 62.9 % or higher. The average nucleotide identity was 95.5 % or higher between M14.4T and the other strains of the species. The rpoB gene sequence similarity was 95-100 % within M. indoligenes. MALDI-TOF allowed a clear separation from other Mannheimia species further supporting classification as a novel species and making it the diagnostic identification tool of choice for M. indoligenes. The type strain is M14.4T (=CCUG 77347T=DSM 116804T) isolated from a cattle tongue in Scotland.

Splendidivirga corallicola gen. nov., sp. nov. and Agaribacillus aureus gen. nov., sp. nov., two bacteria isolated from coral Porites lutea, and proposal of Splendidivirgaceae fam. nov.

The Bacteroidota is one of the dominant bacterial phyla in corals. However, the exact taxa of those coral bacteria under the Bacteroidota are still unclear. Two aerobic, Gram-stain-negative, non-motile rods, designated strains BMA10T and BMA12T, were isolated from stony coral Porites lutea collected from Weizhou Island, PR China. Global alignment of 16S rRNA gene sequences indicated that both strains are closest to species of Fulvivirga with the highest identities being lower than 93 %, and the similarity value between these two strains was 92.3 %. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that these two strains form an monophylogenetic lineage alongside the families Fulvivirgaceae, Reichenbachiellaceae, Roseivirgaceae, Marivirgaceae, Cyclobacteriaceae, and Cesiribacteraceae in the order Cytophagales, phylum Bacteroidota. The genomic DNA G+C contents of BMA10T and BMA12T were 38.4 and 41.9 mol%, respectively. The major polar lipids of BMA10T were phosphatidylethanolamine, unidentified aminophospholipid, four unidentified aminolipids, and five unidentified lipids. While those of BMA12T were phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids. The major cellular fatty acids detected in both isolates were iso-C15 : 0 and C16 : 1 ω5c. Carbohydrate-active enzyme analysis indicated these two strains may utilize coral mucus or chitin. Based on above characteristics, these two strains are suggested to represent two new species in two new genera of a new family in the order Cytophagales, for which the name Splendidivirga corallicola gen. nov., sp. nov., Agaribacillus aureus gen. nov., sp. nov. and Splendidivirgaceae fam. nov. are proposed. The type strain of S. corallicola is BMA10T (=MCCC 1K08300T=KCTC 102045T), and that for A. aureus is BMA12T (=MCCC 1K08309T=KCTC 102046T).

Eubacterium album sp. nov., a butyrate-producing bacterium isolated from faeces of a healthy human.

An oval to rod-shaped, Gram-stain-positive, strictly anaerobic bacterium, designated LFL-14T, was isolated from the faeces of a healthy Chinese woman. Cells of the strain were non-spore-forming, grew optimally at 37 °C (growth range 30-45 °C) and pH 7.0 (growth range 6.0-9.0) under anaerobic conditions in the liquid modified Gifu anaerobic medium (mGAM). The result of 16S rRNA gene-based analysis indicated that LFL-14T shared an identity of 94.7 0% with Eubacterium ventriosum ATCC 27560T, indicating LFL-14T represented a novel taxon. The results of genome-based analysis revealed that the average nucleotide identity (ANI), the digital DNA-DNA hybridisation (dDDH) and average amino acid identity (AAI) between LFL-14T and its phylogenetically closest neighbour, Eubacterium ventriosum ATCC 27560T, were 77.0 %, 24.6 and 70.9 %, respectively, indicating that LFL-14T represents a novel species of the genus Eubacterium. The genome size of LFL-14T was 2.92 Mbp and the DNA G+C content was 33.14 mol%. We analysed the distribution of the genome of LFL-14T in cohorts of healthy individuals, type 2 diabetes patients (T2D) and patients with non-alcoholic fatty liver disease (NAFLD). We found that its abundance was higher in the T2D cohort, but it had a low average abundance of less than 0.2 % in all three cohorts. The percentages of frequency of occurrence in the T2D, healthy and NAFLD cohorts were 48.87 %, 16.72 % and 13.10 % respectively. The major cellular fatty acids of LFL-14T were C16 : 0 (34.4 %), C17 : 0 2-OH (21.4 %) and C14 : 0 (11.7 %). Additionally, the strain contained diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE), as well as unidentified phospholipids and unidentified glycolipids. The glucose fermentation products of LFL-14T were acetate and butyrate. In summary, On the basis of its chemotaxonomic, phenotypic, phylogenetic and phylogenomic properties, strain LFL-14T (= CGMCC 1.18005T = KCTC 25580T) is identified as representing a novel species of the genus Eubacterium, for which the name Eubacterium album sp. nov. is proposed.

Sphingobacterium oryzagri sp. nov., isolated from rice paddy soil.

An aerobic, Gram-stain-negative and short rod-shaped bacterial strain, designated M6-31T, was isolated from rice paddy soil sampled in Miryang, Republic of Korea. Growth was observed at 4-35 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-4 % (w/v) NaCl (optimum, 0 % w/v). Phylogenetic analysis based on 16S rRNA gene sequences grouped strain M6-31T with Sphingobacterium bambusae IBFC2009T, Sphingobacterium griseoflavum SCU-B140T and Sphingobacterium solani MLS-26-JM13-11T in the same clade, with the 16S rRNA gene sequence similarities ranging from 95.8 to 96.6 %. A genome-based phylogenetic tree reconstructed by using all publicly available Sphingobacterium genomes placed strain M6-31T with S. bambusae KACC 22910T, 'Sphingobacterium deserti' ACCC 05744T, S. griseoflavum CGMCC 1.12966T and Sphingobacterium paludis CGMCC 1.12801T. Orthologous average nucleotide identity and digital DNA-DNA hybridization values between strain M6-31T and its closely related strains were lower than 74.6 and 22.0 %, respectively. The respiratory quinone was menaquinone-7, and the major polar lipid was phosphatidylethanolamine. The major fatty acids (>10 %) were C15 : 0 iso, C17 : 0 iso 3OH and summed feature 3. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that strain M6-31T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium oryzagri sp. nov. (type strain M6-31T=KACC 22765T=JCM 35893T) is proposed.

Streptomyces pyxinae sp. nov. and Streptomyces pyxinicus sp. nov. isolated from lichen Pyxine cocoes (Sw.) Nyl.

Two novel actinobacteria, designated as LP05-1T and LP11T, were isolated from the lichen Pyxine cocoes (Sw.) Nyl. collected in Bangkok, Thailand. Genotypic and phenotypic analyses revealed that both strains represented members of the genus Streptomyces. The 16S rRNA gene of LP05-1T showed the highest similarity to the genome of Streptomyces gelaticus (98.41 %), while the 16S rRNA gene of LP11T was most similar to that of Streptomyces cinerochromogenes (98.93 %). The major menaquinones in LP05-1T were MK-9(H8), MK-9(H6), MK-9(H4) and MK-9(H2), and in LP11T, they were MK-9(H8) and MK-9(H6). Both strains exhibited the major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, with LP05-1T also possessing iso-C17 : 0. The polar lipids of LP05-1T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified lipid, while those of LP11T consisted of phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid and an unidentified glycolipid. The digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) values indicated that both strains are distinct from each other with values below 70 and 95 %, respectively. dDDH, ANI by blast (ANIb) and ANI by MUMmer (ANIm) values between LP05-1T and its closely related type strains were 26.07-26.80 %, 81.24-82.01 % and 86.82-86.96 %, respectively, while those for LP11T and its closely related type strains were 30.70-31.70 %, 84.09-85.31 % and 88.02-88.39 %, respectively. The results of the taxonomic investigation, including dDDH and ANI values, indicate that LP05-1T and LP11T are novel type strains of two novel species within the genus Streptomyces. The names proposed are Streptomyces pyxinae sp. nov. for strain LP05-1T (=TBRC 15494T, =NBRC 115434T) and Streptomyces pyxinicus sp. nov. for strain LP11T (=TBRC 15493T, =NBRC 115421T).

Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing.

Whole-genome reconstruction of bacterial pathogens has become an important tool for tracking transmission and antimicrobial resistance gene spread, but highly accurate and complete assemblies have largely only historically been achievable using hybrid long- and short-read sequencing. We previously found the Oxford Nanopore Technologies (ONT) R10.4/kit12 flowcell/chemistry produced improved assemblies over the R9.4.1/kit10 combination, however long-read only assemblies contained more errors compared to Illumina-ONT hybrid assemblies. ONT have since released an R10.4.1/kit14 flowcell/chemistry upgrade and recommended the use of Bovine Serum Albumin (BSA) during library preparation, both of which reportedly increase accuracy and yield. They have also released updated basecallers trained using native bacterial DNA containing methylation sites intended to fix systematic basecalling errors, including common adenosine (A) to guanine (G) and cytosine (C) to thymine (T) substitutions. To evaluate these improvements, we successfully sequenced four bacterial reference strains, namely Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus, and nine genetically diverse E. coli bloodstream infection-associated isolates from different phylogroups and sequence types, both with and without BSA. These sequences were de novo assembled and compared against Illumina-corrected reference genomes. In this small evaluation of 13 isolates we found that nanopore long-read-only R10.4.1/kit 14 assemblies with updated basecallers trained using bacterial methylated DNA produce accurate assemblies with ≥40×depth, sufficient to be cost-effective compared with hybrid ONT/Illumina sequencing in our setting.

Commensalibacter nepenthis sp. nov. and Commensalibacter oyaizuii sp. nov., from fluid in a Nepenthes pitcher cup and a butterfly (Junonia lemonias) in Thailand.

Two novel Gram-negative, aerobic, rod-shaped, non-motile bacteria, strains TBRC 10068T and TBRC 16381T, were isolated from a fluid sample from a close-pitcher cup (Nepenthes gracilis) and an insect sample (Junonia lemonias), respectively. Comparing the 16S rRNA gene sequences with those found in EzBioCloud's publicly available databases revealed that the two strains exhibited a close genetic relationship with Commensalibacter intestini A911T; the calculated sequence similarities were 98.56 and 97.70  %, respectively. The average nucleotide identity and digital DNA-DNA hybridization values of the two Commensalibacter strains, as well as those of their closely related type strains, were found to be lower than the species demarcation threshold of 95 and 70 %, respectively. The phylogenomic analysis of strains TBRC 10068T and TBRC 16381T showed that they belong to the genus Commensalibacter. However, they formed distinct lineages separate from all other strains of Commensalibacter by use of 81 bacterial core genes. In addition, the comparative genomic analysis revealed that the core orthologues of strains TBRC 10068T and TBRC 16381T, compared to the closely related type strains of Commensalibacter species, had distinct genetic profiles. Strain TBRC 10068T contained 163 unique genes, whereas strain TBRC 16381T contained 83. The three Commensalibacter species possessed Q-9 as the primary isoprenoid quinone homologue. The results of a polyphasic taxonomic investigation indicated that strains TBRC 10068T and TBRC 16381T represent two separate new species within the genus Commensalibacter. The species were designated as Commensalibacter nepenthis sp. nov. with the type strain TBRC 10068T (=KCTC 92798T) and Commensalibacter oyaizuii sp. nov. with the type strain TBRC 16381T (=KCTC 92799T).

Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov., isolated from desert soil, and reclassification of Pedobacter xinjiangensis as Desertivirga xinjiangensis comb. nov. and Pedobacter mongoliensis as Paradesertivirga mongoliensis gen.nov., comb. nov.

Two novel bacterial strains, designated as SYSU D00823T and SYSU D00873T, were isolated from sandy soil of the Gurbantunggut Desert in Xinjiang, north-west China. SYSU D00823T and SYSU D00873T shared 99.0 % 16S rRNA gene sequence identity, and were both most closely related to Pedobacter xinjiangensis 12157T with 96.1 % and 96.0 % similarities, respectively. Phylogenetic and phylogenomic analyses revealed that the two isolates and P. xinjiangensis 12157T formed a separate distinct cluster in a stable subclade with the nearby species Pedobacter mongoliensis 1-32T, as well as the genera Pararcticibacter and Arcticibacter. Furthermore, P. mongoliensis 1-32T formed a separate deep-branching lineage and did not form a cluster with members of the genus Pedobacter. The average nucleotide identity and digital DNA-DNA hybridization values between SYSU D00823T and SYSU D00873T and related species were well below the thresholds for species delineation (<81.0 % and <24.0 %, respectively). The genomes of SYSU D00823T and SYSU D00873T were 6.19 and 6.43 Mbp in size with 40.4 % and 40.5 % DNA G+C contents, respectively. The predominant fatty acids (>10 %) of SYSU D00823T and SYSU D00873T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). Menaquinone-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine, glycosphingolipid, aminoglycolipid/glycolipid, aminophospholipid and three or four unidentified polar lipids. These data indicated that strains SYSU D00823T and SYSU D00873T should be assigned to two novel species of a new genus within the family Sphingobacteriaceae, for which the names Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov. are proposed. The type strains are SYSU D00823T (=CGMCC 1.18630T=MCCC 1K04973T=KCTC 82278T) and SYSU D00873T (=CGMCC 1.18629T=MCCC 1K04974T=KCTC 82281T), respectively. Accordingly, the reclassification of P. xinjiangensis as Desertivirga xinjiangensis comb. nov., and P. mongoliensis as Paradesertivirga mongoliensis gen. nov., comb. nov. are also proposed.

Paenarthrobacter aromaticivorans sp. nov., a paraoxon-degrading bacterium isolated from red pepper cultivation soil.

A bacterial strain designated MMS21-TAE1-1T, capable of degrading paraoxon, was isolated from red pepper soil (36° 25' 26.0″ N, 126° 25' 47.0″ E) and subjected to polyphasic taxonomic characterisation. MMS21-TAE1-1T was an aerobic, non-motile and Gram-stain-positive bacterium. MMS21-TAE1-1T showed growth at 10-37 °C (optimum, 30 °C), at pH 4-10 (optimum, pH 7) and in the presence of 0-6 % NaCl (optimum, 0 %). On the basis of the results of 16S rRNA gene sequence analysis, MMS21-TAE1-1T could be assigned to the genus Paenarthrobacter and shared the highest sequence similarities with Paenarthrobacter aurescens NBRC 12136T (99.72 %), then with Paenarthrobacter nitroguajacolicus G2-1T (99.65 %) and Paenarthrobacter ilicis DSM 20138T (99.17 %). However, the results of genome-based comparison using orthologous average nucleotide identity (orthoANI) and digital DNA-DNA hybridisation indicated that MMS21-TAE1-1T could be readily distinguished from all species of the genus with validly published names. The predominant menaquinone of MMS21-TAE1-1T was MK-9(H2). The diagnostic polar lipids were diphosphatidylglycerol and phosphatidylinositol, and unidentified glycolipids were also present. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The chemotaxonomic properties of MMS21-TAE1-1T were generally consistent with those of members of the genus Paenarthrobacter. The genome of MMS21-TAE1-1T contained genes related to degradation of aromatic compounds. It is evident from the results of this study that strain MMS21-TAE1-1T merits recognition as representing a novel species of the genus Paenarthrobacter, for which the name Paenarthrobacter aromaticivorans sp. nov. is proposed. The type strain is MMS21-TAE1-1T (=KCTC 49652T = LMG 32368T).

Phytohabitans maris sp. nov., isolated from marine sediment.

A novel actinobacterium, strain ZYX-F-186T, was isolated from marine sediment sampled on Yongxing Island, Hainan Province, PR China. Based on the results of 16S rRNA gene sequence analysis, strain ZYX-F-186T belongs to the genus Phytohabitans, with high similarity to Phytohabitans kaempferiae KK1-3T (98.3 %), Phytohabitans rumicis K11-0047T (98.1 %), Phytohabitans flavus K09-0627T (98.1 %), Phytohabitans houttuyneae K11-0057T (97.9 %), Phytohabitans suffuscus K07-0523T (97.7 %), and Phytohabitans aurantiacus RD004123T (97.7 %). Phylogenetic analysis of 16S rRNA gene sequences showed that the strain formed a single subclade in the genus Phytohabitans. The novel isolate contained meso-diaminopimelic acid, d-glutamic acid, glycine, d-alanine, and l-lysine in the cell wall. The whole-cell sugars were xylose, arabinose, ribose, and rhamnose. The predominant menaquinones were MK-9(H8), MK-9(H6), and MK-9(H4). The characteristic phospholipids were phosphatidylethanolamine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylglycerol, and an unknown phospholipid. The major fatty acids (>5 %) were iso-C16 : 0, anteiso-C17 : 0, and iso-C18 : 0. Genome sequencing showed a DNA G+C content of 71.9 mol%. Low average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values demonstrated that strain ZYX-F-186T could be readily distinguished from its closely related species. Based on its phylogenetic, chemotaxonomic, and physiological characteristics, strain ZYX-F-186T represents a novel species of the genus Phytohabitans, for which the name Phytohabitans maris sp. nov. is proposed. The type strain is ZYX-F-186T (=CGMCC 4.8025T=CCTCC AA 2023025T=JCM 36507T).

Draconibacterium aestuarii sp.nov., a Glycolipid-Producing Bacterium Isolated from Tidal Flat Sediment and Emended Description of the Genus Draconibacterium.

A facultatively anaerobic, Gram-negative, curved rod-shaped bacterium (4.0-17.0 µm long, 0.6-0.9 µm wide), designated Z1-6T, was obtained from tidal flat sediment collected from YueAo village in Zhoushan, Zhejiang, People's Republic of China. Strain Z1-6T occurred at 15-45 °C (optimum 28-32 °C), pH 6.0-9.0 (optimum 7.0-7.5), and in the presence of 1-5% (w/v) NaCl (optimum 1-2%). The strain contained iso-C15:0 and antesio-C15:0 as the major fatty acids. An unsaturated menaquinone with seven isoprene units (MK-7) was the predominant respiratory quinone. The polar lipids included phosphatidylethanolamine (PE), one aminophospholipid (APL), two phospholipids (PL1 and PL2), three glycolipids (GL1, GL2, and GL3), and two unidentified lipids (L1 and L2). The genomic DNA G+C content of strain Z1-6T was 39.2%, and the genome size was 6.4 Mb. The strain showed the highest average nucleotide identity (ANI) value of 73.5-74.6%, digital DNA-DNA hybridization (dDDH) value of 19.3-20%, average amino acid identity (AAI) value of 72.0-73.1% with the members of genus Draconibacterium. Phylogenetic analysis based on 16S rRNA gene sequences and genome revealed that strain Z1-6T formed a distinct branch in the clade of the genus Draconibacterium. Based on the phenotypic, phylogenetic, chemotaxonomic analyses and genomic data, strain Z1-6T represents a novel species of the genus Draconibacterium, for which the name Draconibacterium aestuarii sp. nov. (The type strain Z1-6T = MCCC 1K07533T = KCTC 92310T) is proposed.

Enterovirga aerilata sp. nov. and Knoellia koreensis sp. nov., isolated from an automobile air conditioning system.

Two strictly aerobic and rod-shaped bacteria, labelled as DB1703T and DB2414ST, were obtained from an automobile air conditioning system. Strain DB1703T was Gram-stain-negative, while strain DB2414ST was Gram-stain-positive. Both strains were catalase-positive and oxidase-negative. Strains DB1703T and DB2414ST were able to grow at 18-42 °C. Strain DB1703T grew within a NaCl range of 0-3 % and a pH range of 6.0-8.0; while strain DB2414ST grew at 0-1 % and pH 6.5-8.5. The phylogenetic and 16S rRNA gene sequence analysis indicated that strains DB1703T and DB2414ST belonged to the genera Enterovirga and Knoellia, respectively. Strain DB1703T showed the closest phylogenetic similarity to Enterovirga rhinocerotis YIM 100770T (94.8 %), whereas strain DB2414ST was most closely related to Knoellia remsis ATCC BAA-1496T (97.7 %). The genome sizes of strains DB1703T and DB2414ST were 4 652 148 and 4 282 418 bp, respectively, with DNA G+C contents of 68.8 and 70.5 mol%, respectively. Chemotaxonomic data showed Q-10 as the sole ubiquinone in DB1703T and ML-8 (H4) in DB2414ST. The predominant cellular fatty acid in DB1703T was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), whereas iso-C16 : 0, C17 : 1 ω8c, and iso-C15 : 0 were dominant in DB2414ST. Overall, the polyphasic taxonomic comparisons showed that strains DB1703T and DB2414ST were distinct from their closest taxa and represent novel species within the genera Enterovirga and Knoellia, respectively. Accordingly, we propose the names Enterovirga aerilata sp. nov., with the type strain DB1703T (=KCTC 72724T=NBRC 114759T), and Knoellia koreensis sp. nov., with the type strain DB2414ST (=KCTC 49355T=NBRC 114620T).