Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

A Gram-positive, moderately halophilic, rod-shaped and facultatively anaerobic strain T66^T, was isolated from the rhizosphere soil of mangrove Acanthus ebracteatus in Guangxi, China. Strain T66^T was observed to grow at 15–40 ℃ (optimum 30 ℃), pH 5–8 (optimum 6–7) and with 2–20% (w/v) NaCl (optimum 6%). The phylogenetic tree of the 16S rRNA gene sequences depicted a cluster of strain T66^T to be closely related to Halobacillus litoralis SL-4 ^T (98.72%), Halobacillus dabanensis D-8 ^T (98.70%) and Halobacillus campisalis ASL-17 ^T (98.66%). The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain T66^T belonged to the genus Halobacillus and formed a separate branch. The digital DNA-DNA hybridisation and average nucleotide identify values between strain T66^T and its related species were 17.80–19.80% and 70.78–73.22%, respectively, which were lower than the threshold recommended for species delineation. The genomic DNA G + C content was 40.9%. The predominant isoprenoid quinone was MK-7, the cell-wall peptidoglycan contained meso-diaminopimelic acid, and the major fatty acids that accounted for more than 10.0% were anteiso-C_15:0 (68.4%) and anteiso-C_17:0 (13.4%). Phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids and an unidentified glycolipid were found in the polar lipid extraction. Strain T66^T could hydrolyse casein and contains several genes (e. g. vanY, vpr, pbpG and elpC) involved in protease. Therefore, strain T66^T is salt-tolerant and produces protease, and it may have development and utilisation value in flavouring agents and food curing. Based on phenotypic, chemotaxonomic data and genotypic characteristics, strain T66^T represents a novel species of the genus Halobacillus, for which the name Halobacillus rhizosphaerae sp. nov. is proposed. The type strain is T66^T (= JCM 36534 ^T = MCCC 1K08701^T).

Mycobacteroides abscessus is a non-tuberculous mycobacteria implicated in causing lung infections. It is difficult to control owing to resistance to antibiotics and disinfectants. This work was aimed at comprehending: the pan-genome architecture, evolutionary dynamics, and functionalities of pan-genome components linked to COGs and KEGG. Around 2802 core genes were present in each strain of the M. abscessus genome. The number of accessory genes ranged from 1615 to 2481. The open pan-genome of M. abscessus was attributed to the accessory genes underlining its adaptability in the host. Phylogenetic analysis revealed cluster-based relationships and highlighted factors shaping variability and adaptive capabilities. Transcription, metabolism, and pathogenic genes were vital for M. abscessus lifestyle. The accessory genes contributed to the diverse metabolic capability. The incidence of a significant portion of secondary metabolite biosynthesis genes provided insights for investigating their biosynthetic gene clusters. Additionally, a high proportion of xenobiotic biodegradation genes highlighted potential metabolic capabilities. In silico screening identified a potential vaccine candidate among hypothetical proteins in COGs. Functional analysis of M. abscessus pan-genome components unveiled factors associated with virulence, pathogenicity, infection establishment, persistence, and resistance. Notable amongst them were: MMPL family transporters, PE-PPE domain-containing proteins, TetR family transcriptional regulators, ABC transporters, Type—I, II, III, VII secretion proteins, DUF domain-containing proteins, cytochrome P450, VapC family toxin, virulence factor Mce family protein, type II toxin-antitoxin system. Overall, these results enhanced understanding of the metabolism, host–pathogen dynamics, pathogenic lifestyle, and adaptations. This will facilitate further investigations for combating infections and designing suitable therapies.

A novel methanotrophic strain 9N^T was isolated from the sludge of a freshwater lake. Cells were aerobic, Gram-stain-negative, non-motile pleomorphic rods with intracytoplasmic membrane systems that appropriate type-II methanotrophs and hemispherical and spherical exocellular formations on the perimeter of the cell wall surface. The novel isolate grows only on methane or methanol as the sole carbon and energy source, at 10–37 °C (optimum 28–30 °C), pH 4.5–9.0 (optimum 7.0–7.5), up to 1% NaCl (optimum 0.3–0.5%). Methanol supported the growth of the strain 9N^T in a wide range of concentrations from 0.05 to 5.0% (v/v) with an optimum of 0.5% (v/v). The major fatty acids were C_18:1ω8c and C_18:1ω7c. Based on 16S rRNA gene sequence phylogenetic analysis, strain 9N^T was closely related to representatives of the genus Methylocystis (96.5–98.3%). The genome of strain 9N^T was 3.34 Mbp in size with 63.5% of G + C content. The average nucleotide identity and digital DNA–DNA hybridization values between strain 9N^T and closely related type strains of genus Methylocystis were 78.0–82.4% and 20.9–24.3%, respectively. The careful genome annotation of the novel strain shows it possessed genes for the detoxification of arsenate and cyanides as well as genes potentially involved in plant growth promotion (such as biosynthesis of indoles, cytokinins, polyhydroxybutyrate, siderophore production, and nitrogen fixation). Based on the phylogenetic, phenotypic, chemotaxonomic and genomic data, we propose Methylocystis borbori sp. nov. as novel species of the genus Methylocystis. The type strain is 9N^T (= VKM B-3616^T = KCTC 92566^T).

This study revisits the taxonomic classification of the genus Nocardiopsis through the application of advanced genome-based methodologies, representing a notable advancement beyond traditional approaches that primarily rely on 16S rRNA gene sequences and phenotypic traits. The advent of Next-Generation Sequencing (NGS) and sophisticated bioinformatic tools has enabled a more precise framework for prokaryotic classification. However, many recognized species still lack complete genome sequences. In this study, we employed overall genome-related indices (OGRI), particularly Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH), to reassess the phylogenetic relationships within the genus. Comparative analyses of complete 16S rRNA sequences demonstrated high genetic similarity between N. umidischolae 66/93 ^T and N. tropica VKMAc-1457 ^T (99.61% similarity), as well as between N. rhodophaea JCM15313^T and N. rosea JCM15314^T (100% identity). The dDDH, ANI%, FastANI%, ANIm, and ANIb values further supported these results, with 73.2%, 96.94%, 96.15%, 97.19%, and 96.74% for the former pair, and 93.6%, 99.13%, 99.97%, 99.98%, and 99.27% for the latter pair, respectively. All values surpassed the species delineation thresholds of 70% for dDDH and 95–96% for ANI. Consequently, we propose reclassifying N. umidischolae as a heterotypic synonym of N. tropica, and N. rosea as a heterotypic synonym of N. rhodophaea, in accordance with the International Code of Nomenclature of Prokaryotes (ICNP).

The two-species microbial cocultures are effective in terms of awakening the cryptic biosynthetic pathways. They may also lead to the improved production of previously discovered molecules. Importantly, only a few outcomes of the cocultures may prove desirable, namely those leading to the formation of useful secondary metabolites. To address this issue, a method allowing for the evaluation of the final outcome of the co-culture process and fine-tune the cocultivation strategy was proposed. The systematic approach was supported by the experimental data from the bioreactor runs with the participation of Aspergillus terreus and Penicillium rubens confronted with Streptomyces rimosus and Streptomyces noursei. Kinetic, morphological and metabolic aspects of dominance were analysed via the newly proposed formula describing the dominance pattern. The suggested method involved the determination of the numerical value representing the dominance level. When it was high (value 1) no useful metabolites were formed apart from those originating from the winning counterpart. But either for the partial dominances or when the winning organism changed within the run or when the competition ended in draw, the number of the secondary metabolites of interest in the broth was the highest. Next, the systematic approach illustrated how the delayed inoculation strategy influenced the level of dominance leading to the change of winning counterpart and the set of metabolites produced. The proposed systematic approach allows for the reliable determination of the level of dominance in the two-species cocultures to seek for the potentially useful substances for future applications.

Asian Seabass (Lates calcarifer) is widely farmed as a sustainable source of protein for countries in the tropical Indo-West Pacific region. However, microbial species of the gut microbiome of healthy Asian Seabass remain largely uncharacterized and uncultured. Here, we analysed the microbial composition along the gastrointestinal tract of a farmed healthy Asian Seabass. We used different cultivation approaches to obtain isolates from the seabass intestinal tract and describe the isolation and characterization of a novel strain, TLL-SE01^T. Analysis of the strain’s 16S rRNA gene indicates that the strain belongs to the family Vibrionaceae with Photobacterium damselae as its closest relative, albeit sharing only 94.8% (aligned region 1553 bp) nucleotide identity. Comparative genomic analysis with all validly published Vibrionaceae species with available genomes revealed average nucleotide identity (ANI) and DNA–DNA hybridisation (DDH) values of around 70% and 24% respectively to strain TLL-SE01^T, which are well below proposed thresholds for species delineation (ANI, 95–96%; DDH, 70%). The alignment fraction and ANI genus demarcation boundaries for all genera in the Vibrionaceae family were determined for which strain TLL-SE01^T is well below the calculated values, indicating that it belongs to a novel genus. Single- and core-gene phylogenetic analysis places strain TLL-SE01^T in a monophyletic clade, further supporting its designation to a novel genus. Phenotypic comparison between strain TLL-SE01^T and its close relatives indicated additional differences, such as growth response at different salt concentrations and different metabolic capabilities. Based on genotypic, phylogenetic and phenotypic differences to other Vibrionaceae species, we propose a novel species in a new genus, Parasalinivibrio latis gen. nov. sp. nov. and strain TLL-SE01^T (= BCRC 81435^T = JCM 36283^T) as the type strain.

Strain WL0113^T was isolated from surface seawater of the coast of Lianyungang, Jiangsu province, PR China. Strain WL0113^T shared highest 16S rRNA gene sequence similarity with Roseobacter insulae YSTF-M11^T (98.8%), followed by R. cerasinus AI77^T (98.8%), R. ponti MM-7 ^T (98.0%). Strain WL0113^T was Gram-stain-negative, cream, aerobic, non-motile and coccoid- to oval-shaped, and able to grow at pH 6.5–9.0 (optimum, pH 7.0–8.0), at 10–37  °C (optimum, 28 °C) and in the presence of 1–5% (w/v; optimum, 2.5%) NaCl. Ubiquinone-10 was detected as dominant. The main fatty acids (> 5%) of the strain WL0113^T were C_16:0, iso-C_17:0 3OH, C_20:4ω6,9,12,15c (arachidonic acid), and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The major polar lipids include phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, glycophospholipid, unknown aminolipid, unknown phospholipid, and two unknown polar lipids. The ANI and dDDH values between strain WL0113^T and Roseobacter cerasinus were 80.4% and 23.0%, respectively. The genomic DNA G + C content of strain WL0113^T was 63.1%. Based on these data, it is proposed that strain WL0113^T represent novel species of the genus Roseobacter, for which the name Roseobacter sinensis sp. nov. is proposed. The type strain is WL0113^T (= GDMCC 1.3082^T = JCM 35567^T).

Soft rot is one of the top ten most dangerous plant pathogens in agricultural production, storage, and transport, and the use of microorganisms and their metabolites to control soft rot is a current research hotspot. In this study, we identified the antimicrobial substance in the metabolite of Paenibacillus polymyxa KH-19, and determined that the antimicrobial substance of this strain was an active protein. The protein was completely precipitated at 40–60% ammonium sulphate saturation and showed good inhibitory effects against seven pathogenic bacteria including Pectobacterium carotovorum BC2 and seven pathogenic fungi including Pyricularia oryzae. The MIC of the protein was 51.563 µg/mL, temperature acid–base UV and light stability insensitive to protease, with high-temperature resistance. The antimicrobial protein was isolated and purified by DEAE-anion exchange column and Sephadex G-75 gel filtration chromatography, and the LC–MS/MS assay identified the protein as lysophosphatidyl esterase with a molecular weight of 25.255 kDa. The purified antimicrobial protein increased the inhibitory effect against P. carotovorum BC2, with the diameter of the circle of inhibition being 26.50 ± 0.915 mm. Bioinformatics analysis showed that the protein has the molecular formula of C₁₁₁₇H₁₇₃₂N₃₁₆O₃₃₈S₅, encodes 224 amino acids, has an aliphatic index of 88.39, and belongs to the category of hydrophilic unstable proteins. The present study is the first report of an active protein with extreme thermoplastic and resistance to P. carotovorum BC2, which provides a reference for the preparation and application of the antimicrobial substances of P. polymyxa KH-19, as well as a theoretical basis for the study of the function of lysophosphodiesterase protein and its use as a microbial preparation.

A Gram-positive, aerobic, motile, rod-shaped bacterial strain, designated 31A1R^T, was isolated from the mangrove soil of Xilian village, Zhanjiang, China. Strain 31A1R^T thrives at temperatures ranging from 15 to 45 °C (optimum at 30 °C), pH 6.5–10 (optimum at 8.5), and in the presence of 0–5% (w/v) NaCl (optimum at 1.5%). The strain shares the highest 16S rRNA gene sequence similarity with Robertmurraya crescens (97.24%) and Robertmurraya dakarensis (97.18%). The complete genome of strain 31A1R^T spans 4.71 Mbp with a genomic DNA G + C content of 35.9 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain 31A1R^T and type strains of other species of the genus Robertmurraya were 71.24–72.11% and 19.90–21.40%, respectively. The amino acid identity values and percentage of conserved proteins ranged from 66.94 to 68.10% and from 58.34 to 61.62%, respectively, aligning with intrageneric cutoff values. The major fatty acids (≥ 5.0%) were iso-C_14:0 (5.0%), iso-C_15:0 (41.4%), iso-C_16:0 (12.6%), C_16:1ω7c alcohol (12.2%), and iso-C_17:1 ω10c (6.5%). The polar lipids profile was mainly composed of diphosphatidyl glycerol, phosphatidyl glycerol, and phosphatidyl ethanolamine. We also profiled the pan-genome and metabolic features of genomic assemblies of strains belonging to the genus Robertmurraya, which indicated functional capacities and metabolic similarities. Consequently, we propose that strain 31A1R^T represents a new species in the genus Robertmurraya, for which the name Robertmurraya mangrovi sp. nov. is proposed, with the type strain being 31A1R^T (= GDMCC 1.4378^T = JCM 36937^T).