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

A novel bacterial symbiont, strain Bradyrhizobium sp. RDT46^T, was previously isolated from root nodules of Retama dasycarpa, a Moroccan endemic legume shrub. Phylogenetic analysis of the 16S rRNA gene placed the strain within the Bradyrhizobium japonicum supergroup, and Multi-Locus Sequence Analysis (MLSA) of four concatenated housekeeping genes (atpD, glnII, gyrB and recA) revealed that strain RDT46^T is 93.91% closely related to B. frederickii CNPSo 3426^T. Phylogenomic analysis of 81 single copy-core gene sequences further confirmed that the type strain B. frederickii is its closest relative. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values were below the species delineation thresholds when compared to the closest type strain, with values of 93.8 and 52.2%, respectively. Genomic analysis revealed the absence of the canonical nod genes, the presence of nitrogen-fixation genes and few type III secretion system related genes. These findings combined with morphophysiological and fatty acid content analyses, as well as the ability of strain RDT46^T to renodulate R. dasycarpa, support the designation of strain RDT46^T as a novel species within the genus Bradyrhizobium, for which we propose the name Bradyrhizobium dasycarpae sp. nov. RDT46^T (=CCMM B1347^T=DSM 120572^T) as type strain.

A Gram-negative, aerobic, non-motile, ovoid bacterium, designated strain MF3-039^T, was isolated from tidal mudflat sediment sampled in Gunsan, Republic of Korea. The strain formed yellow-pigmented colonies on marine agar and was positive for catalase and oxidase. It grew at temperatures ranging from 10 to 37 °C (optimum, 25 °C), pH levels from 6.0 to 9.0 (optimum, 7.0), and 0 to 7.0% (w/v) NaCl (optimum, 2.0%). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain MF3-039^T clustered within the genus Altererythrobacter (family Erythrobacteraceae), with closest sequence similarity to Altererythrobacter insulae KCTC 63421^T (97.9%), Altererythrobacter ishigakiensis ATCC BAA-2084^T (97.9%), Altererythrobacter rubellus NBRC 112769^T (97.2%), and Tsuneonella suprasediminis KCTC 62388^T (97.1%). The draft genome was 2.9 Mbp with a G + C content of 60%. Genomic comparisons indicated average nucleotide identity and digital DNA–DNA hybridisation values below 95% and 70%, respectively, with related Altererythrobacter species. Chemotaxonomic analysis revealed ubiquinone-10 as the primary respiratory quinone, C_17:1 ω6c and summed feature 8 (comprising C_18:1 ω7c/C_18:1 ω6c), and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) as predominant fatty acids, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, a sphingoglycolipid, an unidentified glycolipid, and an unidentified lipid as major polar lipids. The combination of phenotypic, chemotaxonomic, genomic, and phylogenetic features clearly distinguishes strain MF3-039^T from existing genera within the family Erythrobacteraceae. On the basis of these polyphasic analyses, strain MF3-039^T represents a novel genus and species, for which the name Litorerythrobacter xanthomarinus gen. nov., sp. nov. is proposed. The type strain is MF3-039^T (= KEMB 23948^T = KCTC 8705^T = TBRC 19385^T).

A strain designated YIM 98842^T, belonging to the genus Virgibacillus was isolated and characterized from a hypersaline sediment of Aiding Lake in Xinjiang Province, North-west China. The strain was Gram-positive, halophilic, rod-shaped, aerobic and motile, could grow at 10–50 ℃, 0–20% (w/v) NaCl concentrations, pH 6.5–9.5, with optimal growth at 37 ℃, 5–10% (w/v) NaCl and pH 7.5. The lipidomic profile showed diphosphatidylglycerol, phosphatidylglycerol and one undetermined phospholipid as the major polar lipids. The whole cell analysis indicated MK-7 as the predominant menaquinone, meso-diaminopimelic acid with ribose and glucose–NH₃ as the typical whole-cell sugars, anteiso-C_15:0, iso-C_16:0, iso-C_15:0, iso-C_14:0 as the main fatty acids. The genomic DNA G + C content was 40.4 mol%. A phylogenetic analysis based on the 16S rRNA gene of the strain YIM 98842^T with publicly available reference data revealed that the YIM 98842^T belongs to the genus Virgibacillus, with the highest similarity to Virgibacillus kimchii (98.25%) and Virgibacillus salarius SA-Vb1^T (97.04%). The evidence of the phenotypic, chemotaxonomic, and phylogenetic analysis indicated that strain YIM 98842^T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus aidingensis sp. nov. is proposed. The type strain is YIM 98842^T (= CGMCC 1.17259^T = NBRC 114104^T).

The present study investigated the phylogenetic relationships among marine copepod populations in the coastal areas of Tamil Nadu and Pondicherry regions, India. Two molecular markers-a nuclear 18S rRNA gene and a mitochondrial COI gene-were evaluated for their accuracy and taxonomic resolution in classifying species within the subclass Copepoda. Phylogenetic analyses were performed on 21 copepod isolates, comprising 12 sequences derived from 18S rRNA and 9 from the COI gene. The findings clearly delineated evolutionary lineages corresponding to three major orders: Calanoida, Cyclopoida, and Harpacticoida. In the 18S rRNA, the overall mean genetic diversity (d) was slightly higher. The gamma distribution rate (Φ) showed site-specific variation in both of the markers. Furthermore, segregating sites and the total number of recombination frequency were higher in the COI gene compared to 18S rRNA. The analysis of nucleotide composition showed that the strongest (triple) G+C hydrogen-bond interactions were more abundant in the 18S rRNA sequences than in COI. Our findings demonstrate that both 18S rRNA and COI serve as reliable and informative markers for resolving cladogenetic patterns and evolutionary relationships among copepod taxa. Among various genetic diversity tools, their combined application enhances the accuracy of phylogenetic reconstruction and supports their use in integrative taxonomic studies of marine copepods.

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A white, Gram-negative, facultatively anaerobic, floc-forming bacterial strain with the ability of nitrate reduction, designated M4Q-1^T, was isolated from influent samples of the air flotation tank at a distillery effluent treatment plant. Strain M4Q-1^T was found to be a non-motile short rod or coccobacillus, oxidase-positive and catalase-negative. Growth was observed at 16–43 °C (optimum 37–40 °C), pH 4.5–8.0 (optimum 7.0), but not in 1.5% (w/v) NaCl (optimum 0%). The sole respiratory quinone of strain M4Q-1^T was ubiquinone-8 (Q-8), and the major polar lipids were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), aminophospholipid (APL), phosphatidylglycerol (PG), two unknown phospholipid (PL) and one unidentified polar lipid (L). The predominant fatty acids (> 10% of total fatty acids) were summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), summed feature 8 (C_18:1 ω6c and/or C_18:1 ω7c) and C_16:0. Strain M4Q-1^T exhibited the highest 16S rRNA gene sequence similarity to the type strain of Brachymonas denitrificans AS-P1^T (96.90%). Phylogenetic analysis based on 16S rRNA gene sequence and the whole-genome sequences revealed that strain M4Q-1^T formed a distinct clade closely neighboring the members of the genus Brachymonas. The G + C content of genomic DNA was 64.5 mol%. Combined with the analyses of the orthologous average nucleotide identities (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH), strain M4Q-1^T represented a novel species of the genus Brachymonas, for which the name Brachymonas moutaii sp. nov. is proposed, with the type strain M4Q-1^T (= MCCC 1K10055 = KCTC 18263).

A novel polysaccharide-degrading bacterial strain, designated ASW11-125^T, was isolated from intertidal sediments in Aoshan Bay, Qingdao, China. The strain was strictly aerobic, Gram-stain-negative, catalase-positive but oxidase-negative, short rod-shaped, and exhibited gliding motility without flagella. Growth occurred at 4–35°C (optimum 28°C), pH 6.0–8.0 (optimum pH 7.0), and in 0.5–16.0% NaCl (optimum 2.5–3.0%). The predominant polar lipid was phosphatidylethanolamine. Major fatty acids were iso-C_15:0 and iso-C_17:0 3-OH, and the primary respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic analyses of 16S rRNA gene sequences and 1542 single copy orthologous clusters, strain ASW11-125^T affiliated with the genus Christiangramia and was closely related to Christiangramia portivictoriae MCCC 1A00585^T (98.8%), Christiangramia aquimixticola KCTC 42706^T (98.8%) and Christiangramia marina KCTC 12366^T (98.6%). Comparative genomic analysis revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain ASW11-125^T and its closely related species were 74.6–91.5% and 18.6–44.3%, respectively, which were below the cutoff values for proposing a novel species. Based on a polyphasic characterization integrating phenotypic, phylogenetic, and chemotaxonomic evidence, strain ASW11-125^T represents a novel species of the genus Christiangramia, for which the name Christiangramia qingdaonensis sp. nov. is proposed. The draft genome of strain ASW11-125^T is 3.2 Mb in size with a G + C content of 38.3%. Notably, genomic analysis revealed an abundance of genes encoding putative carbohydrate-active enzymes (CAZymes), particularly those associated with starch, laminarin, and fructan utilization, suggesting its potential role in the marine carbon cycle. The type strain is ASW11-125^T (= KCTC 102340^T = MCCC 1K09555^T).

The rise of antibiotic-resistant Bacillus cereus strains, particularly those carrying the blaOXA gene encoding oxacillinase-type β-lactamase, has significantly limited treatment options for foodborne illnesses. This study aimed to identify blaOXA-positive Bacillus cereus from environmental samples and evaluate AI-optimized phytochemicals as novel inhibitors of the blaOXA enzyme. Soil-derived bacterial isolates were identified via 16S rRNA gene amplification and Sanger sequencing. Antibiotic susceptibility was assessed using the disc diffusion method. The blaOXA gene was amplified and sequenced, followed by phylogenetic analysis. The blaOXA protein was modeled using AlphaFold3 and validated by the Ramachandran plot and ERRAT. Thirty phytochemicals were screened using molecular docking against blaOXA protein. Piperine emerged as the top candidate and was optimized using the WADDAICA AI tool. AI-modified derivatives were evaluated through docking, ADMET, toxicity, density functional theory (DFT), molecular dynamics (MD) simulations, and pharmacophore analysis. The isolated strain MBBL37 was confirmed as B. cereus (NCBI Accession: PVO14952.1), resistant to ampicillin and cefoxitin. The blaOXA gene (632 bp; Accession: PV535213.1) showed phylogenetic similarity with Enterobacter and E. coli, suggesting potential horizontal transfer. The predicted blaOXA protein demonstrated high stereochemical reliability (87.8% residues in favored regions; ERRAT score: 100%). Piperine showed the best natural docking score (− 6.9 kcal/mol), while the AI-optimized compound 2 exhibited superior binding (− 7.3 kcal/mol) compared to standard antibiotics (e.g., cefotaxime, − 6.5 kcal/mol). MD simulations confirmed complex stability, and DFT analysis showed a favorable energy gap (0.20 a.u). AI-modified Piperine showed improved pharmacokinetics, reduced CYP interactions, and lower toxicity. However, these findings are based on in silico analyses and require further validation through in vitro and in vivo studies to confirm biological activity, safety, and therapeutic potential.

Amidst the escalating demand for biocompatible, biodegradable, and ecologically responsible materials in clinical biomaterial science, filamentous fungal hyphae have emerged as a compelling and underexplored resource for the development of medical sutures. This review consolidates and critically evaluates the utilization of fungal mycelial networks, primarily from filamentous fungi within the Zygomycota phylum, as structural frameworks for biofunctional surgical sutures. The hyphal architecture, characterized by its hierarchical organization, tensile robustness, and inherent biodegradability, presents a biologically congruent alternative to traditional synthetic polymers and animal-derived fibers. Emphasis is placed on fabrication methodologies such as wet-spinning and bioextrusion, which enable the morphological refinement and mechanical tuning of fungal filaments into monofilament and multifilament suture constructs. Furthermore, this review delineates the biocompatibility profiles, degradation kinetics, and sterilization challenges associated with fungal-based materials, while addressing regulatory considerations and translational hurdles. Collectively, the synthesis of interdisciplinary insights highlights the potential of filamentous fungal hyphae as a paradigm-shifting innovation in surgical sutures and sustainable medical textiles.

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A novel Gram stain–positive, endospore-forming, motile, rod-shaped, aerobic bacterial strain, designated PS06^T, was isolated from the rhizosphere soil of Stipa breviflora at the Siziwang Banner Research Station in Inner Mongolia, PR China. The strain could grow at 4–40 ℃ (optimum, 37 ℃), at pH 6.0–9.5 (optimum, pH 8.5), and in the presence of 0–5% NaCl (optimum, 1%). The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PS06^T was most closely related to Litchfieldia salsus IBRC-M 10078^T (16S rRNA similarity, 97.73%) and L. alkalitelluris DSM 16976^T (97.65%) and formed an independent clade with these two type species in the genus Litchfieldia. The genome analysis showed that the average nucleotide identity (ANI) values and digital DNA–DNA hybridization (dDDH) of strain PS06^T with L. salsus IBRC-M 10078^T and L. alkalitelluris DSM 16976^T were 78.0 and 76.1%, and 21.5 and 22.1%, respectively, which were significantly lower than the thresholds of 95% for ANI and 70% for dDDH for species delineation. The predominant cellular fatty acids (> 10%) were anteiso-C_15:0 and iso-C_15:0. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and five unknown lipids. The genomic G + C content of strain PS06^T was 37 mol%. Based on the phenotypic, genotypic, chemotaxonomic, and phylogenetic analyses, strain PS06^T was classified as a novel species of the genus Litchfieldia, and the species name proposed was L. stipae sp. nov. The type strain of the proposed novel species was PS06^T (= KCTC 43244^T = CGMCC 1.17355^T).

Coevolution is a widespread phenomenon, especially prominent in the dynamic interactions between bacteria and bacteriophages. The continuous antagonistic coevolution, characterized by cycles of bacterial resistance and phage infectivity, drives the diversification of phage adsorption structures and bacterial surface receptors, with significant ecological and evolutionary implications. This study investigated the short-term coevolution (40 days) between Pseudomonas sivasensis W-6 and its cold-adapted phage VW6S, isolated from the Napahai plateau wetland. Genomic resequencing revealed reciprocal adaptations, with mutations occurring in bacterial resistance genes and phage infection-related genes. We identified a putative receptor-binding mechanism wherein the phage-encoded tail fiber protein (gp28) specifically interacts with bacterial surface receptors, mediating host recognition and adsorption. Furthermore, variations in a prophage region during coevolution were found to influence phage adsorption efficiency, indicating that prophage-driven evolutionary changes can affect bacterial survival strategies beyond direct virus–host interactions.