Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique.

In the effort of isolating novel microbial species, the strain PL0132T was isolated from a fallen leaf under fresh water at a stream, which glided when grown on a tap water medium (without nutrients). The strain was determined to be Gram-negative, strictly aerobic, and rod-shaped, which grew optimally at 25 °C, pH 6-7, and the strain tolerates 1% (w/v) NaCl concentration. The complete genome of strain PL0132T comprises one contig with a sequencing depth of 76×, consisting of 8,853,064 base pairs and the genomic DNA G + C content was 46.7% (genome). 16S rRNA gene sequence analysis revealed that strain PL0132T represents a member of the phylum Bacteroidetes and is affiliated with the genus Spirosoma. Based on genomic, phenotypic, and chemotaxonomic characteristics, the strain PL0132T represents a novel species of the genus Spirosoma, for which the name Spirosoma foliorum sp. nov. is proposed (= KCTC 72228 T = InaCC B1447T).

Cellulosimicrobium fucosivorans is a later heterotypic synonym of Cellulosimicrobium composti.

The taxonomic relationship of Cellulosimicrobium fucosivorans SE3T and Cellulosimicrobium composti BIT-GX5T was re-evaluated. The type strains of the two species shared 99.9 % 16S rRNA gene sequence similarity, and whole genome sequence comparisons showed that the two species shared a 86.3 % digital DNA‒DNA hybridization (dDDH) value, a 98.5 % average nucleotide identity (ANI) score and a 98.2 % average amino acid identity (AAI) value. These values were higher than the recommend novel species recognition threshold values of 16S rRNA gene similarity of 98.6 %, dDDH cutoff value of 70 %, and ANI and AAI cutoff values of 95-96 %. In addition, the phylogenetic tree based on the 16S rRNA gene sequences as well as the phylogenomics tree based on whole genomes supported these two strains being closely related. Based on the principle of priority, we propose that Cellulosimicrobium fucosivorans is a later heterotypic synonym of Cellulosimicrobium composti.

Three marine species of the genus Fulvivirga, rich sources of carbohydrate-active enzymes degrading alginate, chitin, laminarin, starch, and xylan.

Bacteroidota is a group of marine polysaccharide degraders, which play a crucial role in the carbon cycle in the marine ecosystems. In this study, three novel gliding strains, designated as SS9-22T, W9P-11T, and SW1-E11T, isolated from algae and decaying wood were proposed to represent three novel species of the genus Fulvivirga. We identified a large number of genes encoding for carbohydrate-active enzymes, which potentially participate in polysaccharide degradation, based on whole genome sequencing. The 16S rRNA sequence similarities among them were 94.4-97.2%, and against existing species in the genus Fulvivirga 93.1-99.8%. The complete genomes of strains SS9-22T, W9P-11T, and SW1-E11T comprised one circular chromosome with size of 6.98, 6.52, and 6.39 Mb, respectively; the GC contents were 41.9%, 39.0%, and 38.1%, respectively. The average nucleotide identity and the digital DNA-DNA hybridization values with members in the genus Fulvivirga including the isolates were in a range of 68.9-85.4% and 17.1-29.7%, respectively, which are low for the proposal of novel species. Genomic mining in three genomes identified hundreds of carbohydrate-active enzymes (CAZymes) covering up to 93 CAZyme families and 58-70 CAZyme gene clusters, exceeding the numbers of genes present in the other species of the genus Fulvivirga. Polysaccharides of alginate, chitin, laminarin, starch, and xylan were degraded in vitro, highlighting that the three strains are rich sources of CAZymes of polysaccharide degraders for biotechnological applications. The phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of three novel species in the genus Fulvivirga, for which the names Fulvivirga ulvae sp. nov. (SS9-22T = KCTC 82072T = GDMCC 1.2804T), Fulvivirga ligni sp. nov. (W9P-11T = KCTC 72992T = GDMCC 1.2803T), and Fulvivirga maritima sp. nov. (SW1-E11T = KCTC 72832T = GDMCC 1.2802T) are proposed.

Investigating the antibacterial mechanism of Ampelopsis cantoniensis extracts against methicillin-resistant Staphylococcus aureus via in vitro and in silico analysis.

Methicillin-resistant Staphylococcus aureus (MRSA) is a critical pathogen responsible for a wide variety of serious infectious diseases in humans. The accelerated phenomena of drug tolerance, drug resistance, and dysbacteriosis provoked by antibiotic misuse are impeding the effectiveness of contemporary antibiotic therapies primarily used to treat this common worldwide pathogen. In this study, the antibacterial activity of 70% ethanol extract and multiple polar solvents of Ampelopsis cantoniensis were measured against the clinical MRSA isolate. The agar diffusion technique was employed to determine the zone of inhibition (ZOI), accompanied by the use of a microdilution series to identify the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). Our results revealed that the ethyl acetate fraction exhibited the most significant antibacterial activity, which was determined to be bacteriostatic based on the MBC/MIC ratio 8. A list of compounds isolated from A. cantoniensis was computationally studied to further investigate the mechanism of action with the bacterial membrane protein PBP2a. The combination of molecular docking and molecular dynamics methods showed that the main compound, dihydromyricetin (DHM), is expected to bind to PBP2a at allosteric site. In addition, DHM was identified as the major compound of ethyl acetate fraction, which accounts for 77.03 ± 2.44% by high performance liquid chromatography (HPLC) analysis. As a concluding remark, our study addressed the antibacterial mechanism and suggested the prioritization of natural products derived from A. cantoniensis as a potential therapy for MRSA.Communicated by Ramaswamy H. Sarma.

Halorubrum salinarum sp. nov., an extremely halophilic archaeon isolated from a saturated brine pond of a saltern.

A novel extremely halophilic archaeon, strain RHB-CT, was isolated from a saturated brine pond of a solar saltern in Bolinao, Pangasinan, Philippines. Colonies were orange-red-pigmented, smooth, convex and round on a solid modified growth medium containing 25 % (w/v) of total salts. Cells of strain RHB-CT on the solid modified growth medium were ovoid-shaped (0.89-2.66 µm long), while the cells in a liquid modified growth medium were rod-shaped (1.53-5.65 µm long and 0.45-1.03 µm wide). The strain was Gram-stain-negative, motile and strictly aerobic. Strain RHB-CT grew with NaCl concentrations ranging from 10 to 30 % (w/v; optimum, 20-25 %), at pH 6.5-8.5 (optimum, pH 7.0-7.5) and at 20-55 °C (optimum, 40-45 °C). Furthermore, the strain grew even in the absence of Mg2+; however, when supplemented with Mg2+, growth was observed optimally at 0.2-0.4 M Mg2+. The 16S rRNA gene phylogeny inferred that the strain is a member of the genus Halorubrum and was related to Halorubrum xinjiangense CGMCC 1.3527T (99.0 %), Halorubrum sodomense DSM 3755T (98.8 %), Halorubrum coriense Ch2T (98.8 %), Halorubrum trapanicum NRC 34021T (98.4 %) and Halorubrum distributum JCM 9100T (98.1 %). The rpoB' gene sequences also showed that strain RHB-CT is related to Hrr. xinjiangense JCM 12388T (97.1 %), Hrr. distributum JCM 9100T (97.1 %), Hrr. coriense JCM 9275T (96.5 %), Hrr. californiense JCM 14715T (96.5 %), Hrr. trapanicum JCM 10477T (96.3%), Hrr. sodomense JCM 8880T (96.2%) and Hrr. tebenquichense DSM 14210T (95.6 %). The DNA G+C content of strain RHB-CT was 68.7 mol% (genome). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain RHB-CT and the closely related species of Halorubrum were below 40 and 90 %, respectively, which are far below the thresholds to delineate a new species. The polar lipids of strain RHB-CT were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and sulfated mannosyl glycosyl diether. Based on dDDH and ANI values, and the significant morphological and physiological differences from known taxa, it is hereby suggested that strain RHB-CT represents a novel species of the genus Halorubrum, for which the name Halorubrum salinarum sp. nov. is proposed. The type strain is RHB-CT (=KCTC 4274T=CMS 2103T).

Lactococcus kimchii sp. nov., a new lactic acid bacterium isolated from kimchi.

A coccus strain designated S-13T was isolated from commercial baechu-kimchi in Korea. Comparison of the 16S rRNA gene sequence indicated that strain S-13T had the highest similarity to Lactococcus taiwanensis 0905C15T (97.9 %), Lactococcus lactis subsp. tructae L105T (97.6 %), Lactococcus lactis subsp. cremoris NCDO 607T (97.5 %), Lactococcus lactis subsp. hordniae NBRC 100931T (97.2 %), and Lactococcus lactis subsp. lactis JCM 5805T (97.2 %). The detailed phylogenetic analyses based on the 16S rRNA, rpoB and recA genes indicated that S-13T was separated from the other species and subspecies in the genus Lactococcus. The DNA-DNA relatedness between S-13T and closely related type strains, such as L. taiwanensis 0905C15T, L. lactis subsp. tructae L105T, L. lactis subsp. cremoris NCDO 607T, L. lactis subsp. hordniae NBRC 100931T, and L. lactis subsp. lactis JCM 5805T was 25.6, 20.4, 25.1, 20.2 and 21.7 %, respectively. The major fatty acids were C16 : 0, cyclo-C19 : 0ω8c and C 14 : 0. The DNA G+C content of S-13T was 39.4 mol%. From the results of the phenotypic characteristics and chemotaxonomic analysis, it was concluded that strain S-13T represents a novel species in the genus Lactococcus for which the name Lactococcus kimchii sp. nov. (=KCTC 21096T=NBRC 113348T) is proposed.