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

Low-risk human papillomaviruses HPV-6 and HPV-11 impose a substantial global burden of benign disease. While genomically similar to high-risk HPV types, their codon usage patterns remain uncharacterized. This study systematically deciphers these patterns in HPV-6 and HPV-11. Analysis included 214 HPV-6 and 100 HPV-11 genomes from the NCBI GenBank database. Genomic analysis identified a strong preference for A/U-ending synonymous codons (over 85% of preferred codons) and low GC content at third codon positions (<35%). Relative dinucleotide abundance analysis further revealed underrepresentation of ApA, CpG, and UpC, and overrepresentation of CpA and UpG, which critically shaped synonymous codon selection in both genotypes. While Effective Number of Codons (ENC) values >49 indicated limited overall codon bias, multi-method analyses (Parity Rule 2, ENC-plot, neutrality plot) established natural selection as the dominant evolutionary force over mutational pressure. Despite moderate host adaptation, a strategic mismatch exists between viral codon preferences and human tRNA abundance, potentially moderating translational efficiency to favor immune evasion and persistence. The Relative Codon Deoptimization Index (RCDI) values approaching 2 further support a moderate adaptation to human codon usage patterns. These findings provide crucial insights into the molecular evolution of low-risk HPVs and inform the development of codon-optimized therapeutic strategies, including vaccines targeting pathologies like genital warts and recurrent respiratory papillomatosis.

Uropathogenic Escherichia coli (UPEC) is a primary etiological agent of urinary tract infections (UTIs) worldwide. The emergence of multidrug-resistant (MDR) UPEC strains, especially the globally disseminated ST131 clone, poses a critical health threat in regions like Pakistan, where comprehensive genomic data is limited. This study performed an in-depth genomic characterization of a newly isolated MDR UPEC strain (U1) and conducted a comparative pangenome analysis of 73 UPEC genomes from Pakistan. The overall cohort exhibited an average genome size of 5.2 Mb, an average GC content of 50.6%, and an average of 5180 coding sequences. In silico genomic analysis identified U1 as a high-risk ST131 lineage member (O25:H4, phylogroup B2). The strain exhibited an MDR profile, supported by the prediction of key antibiotic resistance genes (ARGs), including bla^CTX-M-15 and dfrA17, as well as several putative virulence factors (VFs) and four plasmid replicon types. The comparative analysis revealed a highly diverse and open pangenome (3280 core and 10,977 unique genes). The U1 genome’s total coding sequences (5273 genes) contribute ~ 30% share of the total pangenome gene families, indicating its status as a well-equipped strain with essential genes (core) and a substantial number of fitness and adaptability genes (accessory/unique). Core-genome phylogeny confirmed the prevalence of the ST131 lineage, with U1 clustering closely with other local isolates. Widespread VFs and ARGs highlight their critical role in UPEC adaptability. These findings demand urgent antimicrobial stewardship and enhanced genomic surveillance to control the spread of MDR UPEC, particularly the ST131 clone, in Pakistan.

Aeromonas spp. are associated with significant mortalities of economically important Channa striata. Antibiotic resistance and biofilm-forming capacity make them difficult to eradicate from the environment, and studies on antibiotics alternatives, such as Cinnamomum verum essential oil (CVO), in aquaculture are scarce. This study aims to characterise the phytochemicals of CVO and to investigate its in-vitro antibacterial, antibiofilm, and antioxidant potency against A. hydrophila and A. jandaei, isolated from diseased C. striata. The CVO was extracted from the bark of C. verum via hydrodistillation and its characterisation was performed using Gas Chromatography and Mass Spectrometry (GC/MS). The antibacterial potency was evaluated by determination of Zone of Inhibition (ZoI), Minimum Inhibitory Concentration (MIC), Minimum Bactericidal Concentration (MBC), growth kinetics assay, and antibiofilm assay. Additionally, antioxidant activity was analysed via DPPH and ABTS assay as a function of concentration of CVO and respective reference standard. The GC/MS analysis identified twelve compounds (89.85%), with E-cinnamaldehyde (42.735%) and Eugenol (18.583%) as the predominant compounds. Antibacterial assay demonstrated higher sensitivity of A. jandaei (maximum ZoI: 29.5 ± 0.50 mm; MIC: 156 µg/ml; MBC: 312.5 µg/ml) than A. hydrophila (maximum ZoI: 25.4± 0.40  mm; MIC: 312.5 µg/ml; MBC: 625 µg/ml). Strong biofilm inhibition potential (> 50%) of CVO was observed against A. hydrophila (range:7.07 ± 4.51% to 74.46 ± 2.12%) and A. jandaei (range:10.80 ± 5.5% to 80.17 ± 4.56%). The IC₅₀ indices obtained were 15.02 ± 0.64 µg/ml (DPPH) and 17.09 ± 0.92 µg/ml (ABTS), indicating a strong scavenging capacity of CVO. Our results highlight the potential use of CVO to control Aeromonas infection in aquaculture, presenting a safe and cost-effective alternative to conventional antibiotics.

Graphical abstract

A Gram-stain-negative, facultatively anaerobic, rod-shaped bacterial strain, namely F4206^T, was isolated from the sediments of Beihai Red Beach, China. The optimal temperature, pH, and NaCl concentration of F4206^T were 20–40 °C, pH 6.5, and 10%. The digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) values between strain F4206^T and its closest relatives ranged from 20.5 to 44.3%, 78.2 to 80.5% and 65.0 to 94.8% respectively, which are well below the established species delineation thresholds of 70%, 95% and 95%. This conclusive genomic evidence for novelty is further supported by phylogenetic analysis, which placed strain F4206^T within a distinct lineage closely related to Marinobacter qingdaonensis ASW11-75 ^T and Marinobacter arenosus CAU 1620 ^T, with a 16S rRNA gene sequence similarity of 98.22%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain F4206^T formed a distinct lineage within the genus Marinobacter. The digital DNA-DNA hybridization and average nucleotide identity values between strain F4206^T and closely related strains were 20.5–44.3% and 78.2–80.5%, much lower than the cutoff values of 70% and 95%, respectively. The dominant respiratory quinone of the strain was ubiquinone-9. The main fatty acids (> 5%) were C_16:0, C_18:1 ω9c, C_16:1 ω9c, summed feature 3, C_12:0 3-OH and C_12:0. The major polar lipids of strain F4206^T were phosphatidylethanolamine, phosphatidylglycerol, aminolipid, and aminophospholipid. The DNA G + C content of F4206^T was 58.5%. According to phenotypic, phylogenetic, and chemotaxonomic analysis, strain F4206^T was considered as a new species of Marinobacter, with the name of Marinobacter liaoningensis sp. nov. F4206^T. The type strain is F4206^T (= CGMCC 1.19487 ^T = KCTC 92054 ^T).

The genus Ganoderma is considered as the most prolific producer of novel myco-chemicals among medicinally significant mushrooms. More than 430 physiologically and medicinally active chemicals have been identified from several species of Ganoderma. This present study focuses on G. casuarinicola, an unexplored species of Ganoderma. This investigation aimed to extract its bioactive components using three distinct extraction techniques, viz., infusion, decoction, and hydroalcoholic extract, and to assess their mycochemical estimation, antioxidant capacity, antimicrobial efficacy, anti-inflammatory, and anticancer effects. After collection, the sample was preserved and by macroscopic, microscopic, and phylogenetic analysis the genus and species were established as G. casuarinicola. The extracts successfully scavenged 2,2'-azino-bis (3 ethylbenzthiazoline6-sulphonate) (ABTS) radicals, and 1,1-diphenyl-2-picrylhydrazyl (DPPH) as well as hydroxyl radicals. Hydroalcoholic extract demonstrated the highest ABTS and DPPH radical scavenging activity, antibacterial activity, and anticancer activity. In terms of anticancer properties, the hydroalcoholic extract showed potent cytotoxic and anti-proliferative effects against lung adenocarcinoma (A549 cells). It induced apoptotic cell death, as evidenced by changes in nuclear morphology. Hence, these inquiries yield substantiation for the wild variety of G. casuarinicola that was discovered to be an enormous reservoir of naturally occurring bioactive compounds with potential applications for human benefit.

The freshwater snail Cipangopaludina lecythis holds both ecological and medicinal importance, yet its microbiome remains unexplored. This study presents the first shotgun metagenomic profiling of edible tissues of C. lecythis. Illumina HiSeq sequencing generated over 42 million high-quality reads, revealing 38 bacterial phyla dominated by Pseudomonadota (32%), followed by Bacillota and Actinomycetota. At the genus level, Pseudomonas, Klebsiella, Acinetobacter, Bacillus, Clostridium, Staphylococcus, and Streptomyces were prevalent. Functionally important genera such as Aeromonas, Vibrio, and Pseudoalteromonas which are known for their probiotic and immunomodulatory properties were also detected. The dominant species included Pseudomonas sp. REST10, Escherichia coli, Klebsiella pneumoniae, and Streptomyces sp. T12, many of which were associated with fermentation and host microbe interactions. Interestingly, the microbial profiles differed from those in marine snails, indicating environment-specific microbiome signatures. Functional annotation revealed key enzymes including 17 beta-hydroxysteroid dehydrogenase type 3 (HSD17B3) and malonyl-CoA:ACP transacylase, involved in fatty acid metabolism and energy regulation. Enzymes such as glutathione S-transferase and arylacetamide deacetylase were also detected, along with chitinase and chitin synthases, suggesting host microbe interactions in chitin metabolism. High alpha diversity showed a rich and functional microbiome. Overall, this study highlights the metabolic potential and ecological relevance of the C. lecythis microbiome, supporting its application in biotechnology and nutraceutical industry.

Haematococcus pluvialis is mainly known by its high astaxanthin content. This carotenoid, with strong antioxidant properties, is naturally accumulated in microalgal cells under stressful conditions (light intensity variation, nutrient deprivation, osmotic stress, etc.). Nevertheless, the cost-effectiveness of such methods at a large scale is controversial, in addition to their negative impact on cell growth. We examined the effectiveness of major nutrients (nitrogen, phosphorus, copper, and iron) modification in the culture medium as well as light intensity. This study is the first to report continuous monitoring of the red stage over a 60-day culture period on final astaxanthin yield, through both biomass change and pigment accumulation. Reduced light intensity prolonged the green growth stage, while elevated light intensity (150 µmol m⁻² s⁻¹) induced astaxanthin accumulation by over 140 mg/g. Nevertheless, growth was stopped early. Under nutrient starvation or depletion (N, P, Fe, Cu), growth decreased proportionally to their concentration, and even astaxanthin accumulation in zoospores. The fourfold reduction of P and N concentration (P_/4, N_/4) in the medium resulted in the highest productivity at 30 days, reaching 9.91 and 9.09 g/L of astaxanthin, respectively. Although yields declined after 40 days in most treatments, N_/4 and N-limitation (N₀) maintained the best results, indicating their efficiency in sustaining both astaxanthin accumulation and overall biomass. These changes in nutrient availability influenced the cells’ transition to different forms, and the zoosporic form became a key stage for astaxanthin accumulation as the cells adapted to stress conditions.

Three endophytic Sphingobium strains, WW5^T, 11R-BB, and HT1-2^T, were isolated from Salix sitchensis stems, Populus trichocarpa roots, and Pluchea carolinensis shoots, respectively, growing on nutrient-limited rock substrates undergoing primary succession. Cells are Gram-negative, strictly aerobic, rod-shaped, catalase-positive, and motile by a single flagellum. Colonies formed within 2–3 days on nitrogen-limited combined carbon medium (NLCCM) and mannitol-glutamate/Luria (MGL) media. Growth occurred at 25–35 °C (optimum 30–32.5 °C), pH 5–8, and up to 2% NaCl for strains WW5^T and 11R-BB and 3% for strain HT1-2^T. Cellular fatty acid profiles were dominated by C_18:1 ω7c and C_16:1 ω7c. The predominant respiratory quinone was ubiquinone-10, and the principal polar lipids were phosphatidylethanolamine, sphingoglycolipids, and phosphatidylglycerol. Hybrid genome assemblies ranged from 5.49–5.72 Mb with 64.0–64.2 mol% GC, and 5404–5635 coding sequences. The 16S rRNA gene sequences of strains WW5^T, 11R-BB, and HT-12^T showed 99.5–99.9% identity to S. yanoikuyae JCM 7371^T, but formed a separate lineage in neighbor-joining, maximum-likelihood, and maximum-parsimony trees. Pairwise digital DNA–DNA hybridization (dDDH; 99.8%), average nucleotide identity based on BLAST (ANIb; 99.98%), and alignment fraction (AF; 99.5%) indicate that strains WW5^T and 11R-BB are conspecific and represent the same subspecies. Strain HT1-2^T showed lower relatedness (70% dDDH; 95.05–95.31% ANIb; 76–79% AF) but was more closely related to strains WW5^T and 11R-BB than to S. yanoikuyae JCM 7371^T, supporting its placement as a subspecies within the same species as strains WW5^T and 11R-BB. Based on phylogenomic, genomic, and phenotypic evidence, these strains constitute a novel species, Sphingobium salicis sp. nov., with the strain WW5^T (DSM 120182^T, NCCB 101075^T) designated as the type strain.

This study aimed to investigate the diversity of Acinetobacter spp. isolated from aquatic environments along the Brazilian coast, with a focus on environmental reservoirs of clinically relevant resistance genes. Twenty-three Acinetobacter isolates were recovered from marine animals, floating plastic, and surface water samples collected in two contrasting Brazilian regions: the heavily polluted Guanabara Bay (Rio de Janeiro) and the pristine Fernando de Noronha Archipelago (Pernambuco). Seven species were identified, with A. venetianus (n = 13) and A. johnsonii (n = 4) being the most frequent. Two A. johnsonii isolates carried the metallo-β-lactamase gene blaNDM-1, along with resistance to fluoroquinolones and carbapenems. Resistance to polymyxins and aminoglycosides was also observed in A. haemolyticus, A. baumannii, and A. modestus. ApaI-PFGE dendrogram and phylogenetic analyses based on single nucleotide position (SNPs) revealed high genetic diversity, and global comparisons placed the environmental isolates in lineages distinct from those commonly associated with healthcare-associated infections. This study highlights the diversity of Acinetobacter spp. in aquatic environments and their potential role as reservoirs of clinically important resistance genes, including blaNDM-1. By uncovering resistance mechanisms in environmental Acinetobacter strains, this work reinforces the relevance of environmental surveillance for One Health initiatives, particularly in regions with significant anthropogenic impact.

Lactic acid bacteria (LAB) are known to possess potent antifungal activity; however, the factors that affect this activity remain poorly investigated. In this study, we explored the influence of physicochemical and nutritional factors on the antifungal activity of five LAB strains namely Lactiplantibacillus pentosus 22B, Leuconostoc mesenteroides 8C2, Lactiplantibacillus plantarum 21B, Enterococcus faecium LC2V5 and Enterococcus faecium LC2P8. These factors included incubation period, medium initial pH, incubation temperature, long-term storage and carbon source. Results showed that these factors significantly influenced the antifungal activity of the studied LAB strains (p < 0.0001). The optimal conditions yielding the most potent inhibition (21 ± 0.4 mm to 19 ± 0.4 mm) were identified. Specifically, maximum activity was achieved after a 48-h incubation (late stationary phase), at 25–30 °C, an initial pH of 3–4, and with sucrose, galactose, or mannose as the carbon source, depending on the strain. Moreover, long-term storage at − 80 °C led to complete loss of activity in two strains (8C2 and LC2P8), while the other three remained stable. Furthermore, HPLC and GC–MS analyses were used to identify the antifungal compounds produced by these three stable strains. The results revealed the presence of various organic acids (lactic, acetic, formic, malic, and fumaric acids) and fatty acids, such as 9-octadecenoic acid, 11-dodecenoic acid, 10-hydroxy. Scanning electron microscopy confirmed that these compounds caused significant structural damage to fungal mycelia, supporting their demonstrated fungicidal effects. This study improves our understanding of the key factors and mechanisms underlying LAB antifungal activity, contributing to the optimization of their use as natural antifungal agents.