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

Curd, a probiotic-enriched fermented dairy product is widely consumed for its functional and nutritional health benefits. However, microbial activity and product quality can be greatly influences by the various concentrations of sucrose and sodium This study aimed to investigate the effect of varying sucrose (3%, 6%, 9%, and 12%) and sodium chloride (3%, 6%, 9%, and 12%) concentrations on the physicochemical properties, sensory attributes, microstructural characteristics, and microbial growth of curd during room temperature and refrigerated storage conditions. The formulated samples were evaluated for pH, titratable acidity, sensory acceptability, microstructure and total plate count by the application of scanning electron microscopy (SEM). Results indicated that moderate amount of sucrose and sodium chloride promoted the increase in viable count of lactic acid bacteria and maintained desirable sensory quality, in contrast higher concentrations shows inhibitory effects on microbial activity and resulted in significant microstructural modifications. SEM examination demonstrated a well-organized protein matrix at moderate concentrations, whereas the significant microstructural changes are observed at higher concentration. In summary, the result indicated that controlled concentrations of sucrose and sodium chloride play a key role in affecting curd quality under laboratory conditions. The findings offer valuable insights for developing formulation strategies that optimize microbial activity and product acceptability.

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Enterococcus faecalis, a Gram-positive bacterium that causes nosocomial infections, has been reported to be resistant to several antibiotics, posing a significant threat to public healthcare. In the present study, we explored a combinatorial therapeutic approach involving conventional antibiotics alongside phytochemicals against E. faecalis. Vancomycin and ciprofloxacin were chosen for the current study due to their different modes of action. The minimum inhibitory concentration (MIC) of cuminaldehyde and thymoquinone was found to be 500 µg/mL and 30 µg/mL, respectively. Co-administering vancomycin with thymoquinone or cuminaldehyde reduced the MIC of vancomycin from 5 to 2 µg/mL, resulting in a 60% drop in MIC dose. Ciprofloxacin’s MIC reduced from 1.5 to 1 µg/mL in the presence of the same phytochemicals, resulting in 33% reduction in its MIC dose. Furthermore, fractional inhibitory concentration indices (FICI) suggested additive interactions (FICI range: 0.66–1) between the antibiotics and phytochemicals against E. faecalis. Since precision dosing is important for any combinatorial application, we explored response surface methodology (RSM) to optimize dosing regimens of the selected compounds. It was observed that the predicted optimal concentrations of the test compounds (in different combinations) could closely match the actual observations when tested under the in-vitro laboratory conditions (R² range: 0.97–0.99). These findings suggested that combining conventional antibiotics with phytochemicals may offer a promising strategy to enhance the antimicrobial efficacy for effective control of infections caused by E. faecalis.

The citrus industry is of significant global economic importance but faces substantial postharvest losses from soft rot disease. While chemical fungicides are commonly used for control, their application has raised concerns about pathogen resistance and environmental hazards. This concern underscores the urgent need for safe and sustainable alternatives. The current research focused on isolation and identification of primary pathogen responsible for soft rot in mandarin (Citrus unshiu Marc) and evaluated the efficacy of the antagonistic yeast Debaryomyces nepalensis as a biological control agent. A fungal pathogen was isolated from diseased citrus fruits, identified as Aspergillus niger through morphological and molecular analyses, and its soft rot pathogenicity was confirmed by inoculation experiments, leading to 100% disease incidence within nine days. The biocontrol efficacy of a D. nepalensis and a commercial agent ('LvKangWei') containing Bacillus amyloliquefaciens was tested against A. niger-induced soft rot. Both treatment with 'LvKangWei' and D. nepalensis significantly reduced disease severity, with a control efficacy of 31.54% and 22.98% respectively at 15 days post-inoculation. The research extends the study of effect of the yeast biocontrol agents that was associated with the induction of host defense responses, as evidenced by a significant increase in CAT, POD, and SOD activity and the maintenance of total sugar content compared to infected control fruit. Our findings demonstrate that D. nepalensis is an effective biocontrol agent against A. niger-induced soft rot in mandarin.

Mushrooms represent a taxonomically and ecologically diverse group of fungi with profound significance for ecosystems, biotechnology, and human welfare. However, their accurate identification and classification have long been hindered by morphological convergence, cryptic speciation, and limited diagnostic traits. This review synthesizes recent progress in DNA barcoding, phylogenomics, and multi-omics approaches that are reshaping the molecular systematics of mushrooms. The internal transcribed spacer (ITS) region remains the universal fungal barcode, yet its limitations have driven the adoption of multilocus and genome-scale datasets for deeper evolutionary resolution. Advances in high-throughput sequencing (HTS), whole-genome phylogenies, and core-gene frameworks have refined species boundaries and clarified evolutionary trajectories across major fungal lineages. The integration of multi-omics platforms including genomics, transcriptomics, proteomics, and metabolomics has enabled holistic insights into fungal metabolism, adaptation, and ecological functions. Despite these advances, challenges persist, including database inconsistencies, incomplete sampling, and analytical complexities. Addressing these issues through standardized molecular protocols, AI-driven data analytics, and global open-data collaboration will be essential for achieving reproducible and evolutionarily coherent fungal systematics. Ultimately, the convergence of barcoding, phylogenomics, and omics technologies represents a transformative step toward an integrative, data-driven framework for understanding and utilizing fungal diversity in science, sustainability, and innovation.

As a new kind of green and environmentally friendly fertilizer, plant growth promotion and disease resistance function microbial fertilizer has become a new trend of agricultural production. In this study, Bacillus velezensis YU18 with high protease yield was isolated from mangrove rhizosphere soil and its genome was analyzed. The fermentation process was optimized and applied to the development of functional microbial fertilizer. The optimal growth temperature of strain YU18 was 30℃, the optimal growth pH was 7, and the strain could adapt to 100 g/L high concentration salt environment. The optimum process of protease production was sucrose as fermentation carbon source, soybean meal or peanut bran as fermentation nitrogen source, Na⁺ or K⁺ as inorganic salt ion, fermentation temperature was 37℃, fermentation pH was 7. Inorganic nitrogen as fermentation nitrogen source hardly produces protease. There were abundant NRPS and PKS gene clusters in the genome of strain YU18, most of which were not similar to the known gene clusters, and there were resistance genes to Cu, As, Cr, Hg and Cd. In particular, it can tolerate Cu concentrations below 500 mg/L. The functional microbial fertilizer prepared by the fermentation of strain YU18 contains IAA and siderophores that promote plant growth, and has broad-spectrum antagonistic function against plant pathogens. These findings provide a basis for further promotion and development of the application of Bacillus velezensis.

Mediterranean wild legumes, including Ononis repens, represent an underexplored reservoir of rhizobial diversity with ecological and agronomic significance. In this study, three novel bacterial symbionts, namely, Mesorhizobium sp. strains ORM16^T, ORM5.1, and ORM12.1, were previously isolated from root nodules of O. repens in the Maâmora forest near Rabat, Morocco. Phylogenetic analysis based on 16S rRNA gene sequencing placed all three strains within the genus, Mesorhizobium, closely related to Mesorhizobium opportunistum WSM2075^T. Multilocus sequence analysis (MLSA) using housekeeping genes (recA, atpD, and glnII) and whole-genome sequencing (WGS) further confirmed the distinct taxonomic position of ORM16^T, with average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values of 87.63% and 31.2%, respectively, both of which were below the species delimitation thresholds. Genomic analysis revealed the presence of canonical nod genes on chromosomal DNA. The type strain, ORM16^T, is a gram-negative, aerobic, rod-shaped bacterium with moderate tolerance to salinity, osmotic, and thermal stress. Chemotaxonomic data highlighted the characteristic fatty acid profiles of this strain, which distinguished it from its closest relatives. Given this strain's genetic, phenotypic, and symbiotic uniqueness, we propose Mesorhizobium maamorense sp. nov., with strain ORM16^T as the type strain (= DSM120599^T = CCMM B1359^T). Its genomic distinctiveness makes ORM16^T an ideal candidate for expanding our knowledge of Mesorhizobium diversity, conducting taxonomic research, and exploring novel biotechnological applications in nitrogen fixation.

A short rod-shaped, Gram-negative, strictly aerobic, non-motile bacterium, designated as NW5^T, was isolated from a eutrophic pond in Jimo District, Qingdao, Shandong Province, China. The strain exhibited growth between 20–42 °C (optimal at 30 °C), pH 6.0–10.0 (optimal at pH 8.0), and 0–2.0% (w/v) NaCl (optimal at 0% NaCl). Based on 16S rRNA gene sequence analysis, strain NW5^T showed the highest similarity with ‘Pseudomonas oryzae’ CGMCC 1.12417^T (98.2%), followed by Pseudomonas oryzagri CGMCC 1.12618^T (97.8%), and Pseudomonas guguanensis JCM 18416^T (97.7%). Phylogenetic analysis based on 16S rRNA gene sequence and whole-genome sequence indicated that strain NW5^T belongs to the genus Pseudomonas. The genome size of strain NW5^T is approximately 2.6 Mb with a DNA G+C content of 65.3%, which is one of the smallest genomes reported to date among all Pseudomonas type strains. The average nucleotide identity and digital DNA-DNA hybridization values between strain NW5^T and the closely related type strains were in the range of 75.8–87.2% and 21.4–26.6%, respectively, which were below the species delineation thresholds. The major fatty acids (≥5.0%) were C_10:0 3-OH, C_12:0, C_16:0, summed feature 3 and summed feature 8. The predominant isoprenoid quinone was ubiquinone-8 (Q-8) and small amounts of Q-7 and Q-9 were also detected, which is quite different from the ubiquinone profile of Pseudomonas. Strain NW5^T harbored a relatively large number of genes in the metabolic pathway for multi-xenobiotics degradation. In addition, strain NW5^T was highly resistant to zinc (100 mM), consistent with the genotype. Based on the phenotypic, phylogenetic, chemotaxonomic, and physiological analyses, strain NW5^T is considered to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas eutrophicaquae sp. nov. is proposed. The type strain is NW5^T (=GDMCC 1.3065^T =MCCC 1K07223^T =JCM 35388^T).

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).