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

A novel Gram-staining-negative, rod-shaped, aerobic bacterial strain, designated as TSM-5 ^T, was isolated from surface seawater of a marine inlet. This strain grew well at 10–30 °C, pH 5.0–10.0 and in the presence of 0–4% (w/v) NaCl. Strain TSM-5 ^T was non-flagellated and positive for catalase and oxidase activities, and the major respiratory quinone was menaquinone-6 (MK-6). The major fatty acids present in the strain were iso-C_15:1 G, iso-C_15:0, iso-C_15:0 3-OH, iso-C_17:0 3-OH, and summed feature 3 (comprising C_16:1ω7c and/or C_16:1ω6c). The major polar lipid of the strain was phosphatidylethanolamine. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TSM-5 ^T shared 92.6 to 94.0% sequence similarity with valid species of the genus Cellulophaga, and the phylogenetic branch of this strain divided the genus into two groups. Based on the average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) with genomes from the closely related family Flavobacteriacea, strain TSM-5 ^T represents a lineage distinct from genus Cellulophaga, suggesting that this genus should be divided into two genera. Physiological and biochemical comparisons between strain TSM-5 ^T and closely related species revealed additional differences, including optimal NaCl concentrations and pH for growth, as well as metabolic traits such as flexirubin pigment reaction. Based on these results, we propose a novel species in a new genus, Allocellulophaga tsushimaensis gen. nov. sp. nov., with TSM-5 ^T (= KCTC 52508 ^T = NBRC 112430 ^T) as the type strain. Furthermore, we propose that Cellulophaga baltica, Cellulophaga pacifica, Cellulophaga tyrosinoxydans, and Cellulophaga algicola, currently valid species of the genus Cellulophaga, be reclassified into a novel genus, Paracellulophaga gen. nov., with Paracellulophaga baltica NN015840^T (= DSM 24729 ^T = ATCC 700862 ^T) as the type species.

In this study, we investigated the taxonomic identity and biotechnological potential of the actinobacterium Streptomyces sp. LaBMicrA B280, isolated from the rhizosphere of Inga edulis (Mart.). Our approach combined a phylogenomic approach, annotation of metabolic subsystems and biosynthetic gene clusters (BGCs), biological assays to assess antifungal, antimalarial, cytotoxic, and larvicidal activities, classical molecular networking analysis, and characterization of the major compound in the most active fraction (FR3). The digital DNA–DNA hybridization values, using the d2 (GGDC) and d4 (TYGS) formulas, average nucleotide identity, and average amino acid identity (< 70% and ≤ 95–96%, respectively) revealed LaBMicrA B280 as a novel species within the Streptomyces genus. Our genomic analysis revealed 39 BGCs, including the cluster responsible for pentamycin biosynthesis, 314 metabolic subsystems, and 24 gene categories. In the molecular networking analysis, pentamycin was the only compound identified. Biological assays with fraction FR3 at a concentration of 50 µg/mL showed 96.59% ± 0.03 and 72.39% ± 0.18 inhibition against Plasmodium falciparum strains W2 and 3D7, respectively, as well as 91.45% ± 0.55 cytotoxicity against the HEp-2 cancer cell line. Larvicidal activity assays demonstrated 100% efficacy against Aedes aegypti (FO) at 250 µg/mL after 48 h. Pentamycin, a known antifungal compound, was successfully isolated from the highly active FR3 fraction. These findings highlight that LaBMicrA B280 exhibits a broad biotechnological potential and represents a promising source of important secondary metabolites for future application.

Kineococcus wuchangensis DHX-1 was isolated from rice leaves at the wax-ripening stage and represents a novel species within the genus Kineococcus. In this study, the complete genome of strain DHX-1 was sequenced and assembled, revealing a genome size of 4,808,488 b with a GC content of 73.7%. Antimicrobial assays using the fermentation supernatant demonstrated that strain DHX-1 possesses potential antifungal activity against Fusarium culmorum and Fusarium sporotrichioides. Gas chromatography-mass spectrometry (GC–MS) analyses of volatile components in the strain DHX-1 fermentation broth supernatant, revealed that phenylethyl alcohol and 1,3-benzodioxole, 4-methoxy-6-(2-propenyl) contribute to the antifungal function. Strain DHX-1 exhibits potential as a biocontrol agent, and its discovery expands the known antifungal capabilities and biocontrol applications within the genus Kineococcus.

As an important food crop in China, hybrid rice is of significant importance for national food security and supply. Cytoplasmic male-sterile (CMS) rice is a key component of hybrid rice technology, while plant endophytes, especially seed endophytes, play a crucial role in promoting plant growth and reproduction. Therefore, understanding the diversity and community structure of seed endophytes in CMS rice is essential for hybrid rice technology. However, relevant research in this area remains scarce. This study systematically analyzed the diversity and community structure characteristics of seed endophytic bacteria in 14 Yunnan CMS rice varieties (totaling 42 samples) based on Illumina NovaSeq 6000 high-throughput sequencing technology, aiming to elucidate the core microbial community structure and diversity. A total of 503 operational taxonomic units (OTUs) were identified. At the phylum level, the dominant microbial groups in all samples were Proteobacteria (relative abundance 91.53–99.95%). At the genus level, the core microbial community consisted of Pantoea (64.29–93.11%), Xanthomonas (1.08–16.97%), and Kosakonia (0.46–12.66%). Both α- and β-diversity analyses revealed no significant inter-line differentiation, indicating a highly stable and conserved endophytic bacterial community across the Yunnan CMS rice germplasm. This study provides the first comprehensive characterization of the seed-associated core microbiome of Yunnan CMS rice lines.

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A gram-positive, endospore-forming bacterial strain CQH2019^T was isolated from pit mud samples used in the production of Chinese strong flavor Baijiu. Cells of strain CQH2019^T are anaerobic, Gram-positive, rod-shaped, with 0.5–0.8 µm in width and 3–5 µm in length. The optimal growth was observed at 37 °C, pH 5.5 and 0.5% (w/v) NaCl. This obligate chemoorganoheterotrophic strain utilizes complex organic compounds, carbohydrates (L-arabinose, D-xylose, D-galactose, D-fructose, D-mannose, L-rhamnose, and D-tagatose), organic salts (potassium gluconate), glycosides (amygdalin, arbutin, salicin). Strain CQH2019^T produced acetate, butyric acid and lactic acid as end products when cultured in the Reinforced Clostridial Medium (RCM). The predominant cellular fatty acids (> 10%) of strain CQH2019^T were anteiso-C_17:0 (29.95%), C_16:0 (17.47%) and anteiso-C_15:0 (14.42%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that closest relatives were Sporolactobacillus putidus JCM 15325^T (95.74%), Sporolactobacillus vineae SL153^T (95.74%), Sporolactobacillus pectinivorans GD201205^T (95.38%) and Sporolactobacillus shoreae BK92^T (95.19%). The genome size is 4.5 Mb with DNA G + C content of 47.58%. The digital DNA-DNA hybridization (dDDH) values between strain CQH2019^T and its closest relatives ranged from 19.3 to 26.8%, whereas the whole-genome average nucleotide identity (ANI) values ranged from 71.48—82.58%. Based on this polyphasic taxonomic analysis, the dDDH and ANI values fall below the established thresholds for species delineation. Therefore, strain CQH2019^T represents a novel species within the genus Sporolactobacillus, for which the name Sporolactobacillus fermentans sp. nov. is proposed. The type strain is CQH2019^T (= MCCC 1A19398^T = KACC 23552^T).

In agriculture, the presence of soil-borne phytopathogenic fungi represents a limiting factor that causes significant crop losses. In this context, Trichoderma brevicompactum represents a viable alternative to chemical fungicides, acting as an effective biological control agent for managing fungal diseases. The objective of this work was to characterize the antifungal activity of a native isolate of T. brevicompactum FCQ18, obtained from soil associated with tomato cultivation, against Macrophomina phaseolina, Rhizoctonia solani, and Sclerotinia sclerotiorum. Direct confrontation assays showed inhibition of the growth of all evaluated phytopathogens. Additionally, antibiosis assays using cellophane membranes and dialysis indicated that the inhibitory effect is mainly due to low molecular weight molecules, as similar inhibition percentages were observed in both assays. Furthermore, a bio-guided isolation of the metabolite involved in antibiosis was performed. The organic extract of T. brevicompactum FCQ18 was fractionated using chromatographic techniques and its antifungal activity was evaluated, leading to the identification of a fraction with 100% inhibitory activity against the tested phytopathogens. Subsequent purification of the fraction with the highest antifungal activity allowed the identification of the principal compound responsible for the observed antibiosis, whose spectroscopic data corresponds to the mycotoxin trichodermin. The antifungal activity of trichodermin against the agriculturally important pathogens M. phaseolina and S. sclerotiorum is described for the first time.

Xylanases are one of the most important hydrolytic enzymes involved in plant hemicellulose degradation with potential industrial as well as ecological significance. This study presents a comprehensive characterization of an endo-1,4-β-xylanase enzyme from Agrobacterium sp. Strain DKPNP3 isolated from the beetle gut of Gonocephalum sp. (Coleoptera: Tenebrionidae). Bioinformatics analyses were performed, including physicochemical characterization, phylogenetic assessment, conserved domain identification, secondary and tertiary structure prediction, subcellular localization prediction, homology modeling, structural validation, molecular docking and molecular dynamics simulation to assess the stability of this protein. The enzyme belongs to the glycoside hydrolase family 10 (GH10) with 339 amino acids, molecular weight of 37.8 kDa, and acidic in nature (pi 5.8). The homology model demonstrated high structural reliability, with an ERRAT score of 96.364% and a QMEAN Z-score of 0.59. Molecular dynamics simulations demonstrated that the enzyme is structurally stable in both its apo and ligand-bound forms. The apo form showed stability comparable to a well-characterized synthetic construct xylanase from Bacillus halodurans (GenBank accession number: MW311490), which was used as a positive control. Furthermore, simulations performed at multiple temperatures indicated retention of conformational integrity under different thermal conditions, suggesting potential thermostability. The intracellular nature of the enzyme, as predicted by in silico analysis, was confirmed by experimental validation using Congo Red-xylan agar assay and quantification with di nitro salicylic acid (DNSA).

The genus Burkholderia, particularly the Burkholderia cepacia complex (Bcc), encompasses Gram-negative bacteria of recognized ecological, biotechnological, and clinical relevance. Accurate identification of species within this complex is challenging due to high phenotypic and genetic similarity, impacting clinical diagnostics and epidemiological surveillance. This review addresses phenotypic, proteomic, and molecular methods for species- and clone-level identification, highlighting their advantages and limitations. Classical methods, including selective media, Burkholderia cepacia selective agar (BCSA), Oxidation-Fermentation Polymyxin Bacitracin Lactose agar (OFPBLA), and Pseudomonas cepacia agar (PCA), and biochemical tests are useful for initial screening but have limited resolution for differentiating closely related Bcc species. Automated systems, such as VITEK® 2, provide rapid genus-level identification, whereas Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and Fourier Transform Infrared Spectroscopy (FTIR) improve accuracy for species differentiation and clone typing, depending on the quality and currency of reference databases. Molecular methods, including Multilocus Sequence Typing (MLST), which sequences housekeeping genes such as gyrB and recA, and Whole-Genome Sequencing (WGS), offer high-resolution species- and clone-level identification, enabling detailed epidemiological monitoring. WGS represents the current gold standard, providing comprehensive information on identification, antimicrobial resistance, virulence factors, and clone typing. A tiered strategy is recommended, combining accessible methods for initial screening with advanced techniques for research centers and genomic surveillance. This study emphasizes the critical need for methodological standardization to enhance clinical diagnosis, epidemiological surveillance, and management of infections caused by species of the genus Burkholderia.

Leptospirosis, a bacterial zoonosis caused by select pathogenic spirochetes belonging to the genus Leptospira, can trigger a systemic inflammatory response syndrome due to a cytokine storm that can occur during infection. However, the molecular mechanisms underlying the extensive inflammatory responses during leptospiral infection remain poorly understood. In this study, we characterized a high temperature requirement protein A (HtrA) homologue encoded by the L. interrogans gene locus LIC12812, referred herein as LepHtrA. We used AlphaFold 3 to predict the structure of this protein. And we show that LepHtrA is located on the surface of L. interrogans, and its expression is upregulated by increased temperature. An in vitro enzyme assay using purified LepHtrA provides direct evidence of its serine protease activity. We demonstrate that LepHtrA induces a robust pro-inflammatory response in RAW264.7 cells, a mouse macrophage cell line, by promoting their differentiation into pro-inflammatory M1 macrophages. This differentiation leads to an increased production of pro-inflammatory cytokines and the generation of reactive oxygen species, ultimately inducing cellular apoptosis via modulation of Bcl-2/Bax expression. Collectively, our study suggests that LepHtrA is a temperature-induced and surface-exposed antigen that can contribute to cellular inflammation, stress, and apoptosis, potentially influencing the pathogenesis of leptospirosis.

Antimicrobial-resistant Aeromonas species are ubiquitous in aquatic environments and pose a growing risk to environmental, animal, and human health. This study assessed the occurrence, species diversity, antimicrobial resistance patterns, and associated resistomes of Aeromonas spp. isolated from the Asa River, Kwara State, Nigeria. A total of 108 water samples were collected monthly from upstream, midstream, and downstream locations between January and December 2021. Isolates were recovered using selective culture, identified by biochemical methods and 16S rRNA gene sequencing, and tested for antimicrobial susceptibility against ten commonly used antibiotics. Resistance genes were detected using the polymerase chain reaction. Seventy-eight Aeromonas isolates were identified, comprising A. hydrophila (40.8%), A. caviae (23.5%), A. allosaccharophila (15.3%), A. veronii (15.3%), and A. dhakensis (5.1%). High resistance rates were observed to oxytetracycline (83.3–100%), penicillin (50.0–100%), and cephalexin (33.3–100%), with most isolates exhibiting multidrug resistance. Principal component analysis showed similar resistance profiles among A. hydrophila, A. caviae, and A. veronii, while A. allosaccharophila and A. dhakensis displayed distinct clustering patterns. All isolates harboured the β-lactamase genes ampC and blaCTX-M (100%). The tetracycline resistance gene tetA was highly prevalent (80–100%), whereas tetB, blaTEM, class 1 integrons, and sulfonamide resistance genes occurred at lower, species-dependent frequencies. These findings demonstrate that the Asa River serves as an important environmental reservoir for multidrug-resistant Aeromonas spp. and clinically relevant resistance genes, with implications for aquatic health and the human–animal–environment interface. This underscores the need for continuous surveillance and One Health–based antimicrobial resistance control strategies.