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

Streptococcus thermophilus plays a pivotal role in yogurt fermentation, yet strains from traditional fermented products remain largely unexplored compared to their industrial counterparts. This study aimed to characterize the genomic diversity and functional potential of 15 S. thermophilus strains isolated from Turkish traditional yogurts, and to compare them with industrial strains. Through whole-genome sequencing and advanced bioinformatics analyses, we revealed distinct phylogenetic patterns and genetic features that differentiate these traditional strains from industrial isolates. The genomes (1.68–1.86 Mb) exhibited high genetic homogeneity (ANI > 98.69%) while maintaining significant functional diversity. Pan-genome analysis identified 1160 core genes and 5694 accessory genes, highlighting substantial genomic plasticity that enables niche adaptation. Our analysis uncovered several distinctive features: (1) unique phylogenetic clustering patterns based on both housekeeping genes and whole-genome SNPs, suggesting geographical isolation effects; (2) an extensive repertoire of carbohydrate-active enzymes (CAZymes), comprising 111 Glycoside Hydrolases, 227 Glycosyl Transferases, and 44 Carbohydrate Esterases and 13 Carbohydrate-Binding Modules, demonstrating sophisticated carbohydrate metabolism adaptation significantly enriched compared to industrial strains; (3) widespread GABA biosynthesis pathways in 8 strains, including complete gadB gene, indicating potential health-promoting properties; (4) multiple genomic islands containing genes for galactose utilization and stress response, suggesting specific adaptation to traditional fermentation environments; (5) diverse exopolysaccharide biosynthesis and bacteriocin gene clusters; and (6) widespread CRISPR-Cas systems with variable spacer content. Notably, we identified vanY glycopeptide resistance genes across all strains, with two strains additionally harboring vanT. These results reveal the genetic mechanisms behind S. thermophilus adaptation to traditional yogurt environments, offering valuable insights for developing starter cultures and preserving the unique qualities and potential health benefits of traditional dairy products.

Twenty-one lactic acid bacteria (LAB) strains were isolated from Algerian fruits such as white mulberry (Morus alba L.), prickly pear (Opuntia ficus-indica), date (Phoenix dactylifera L.), grape (Vitis vinifera) and fig (Ficus carica). The initial screening showed that ten out of twenty-one strains were tolerant to acid pH and bile salts and were further identified as Lactiplantibacillus (L.) plantarum strains by MALDI-TOF mass spectrometry and 16S rDNA sequencing. The identified strains were then characterized for their surface properties such as self-aggregation, hydrophobicity and biofilm formation. The resulting data were then statistically processed using Principal Component Analysis (PCA), after which only 5 strains were selected for further analysis. These five strains, designated L. plantarum F8, F13, FB23, D21 and M1, were found to be safe and able to adhere to human epithelial colorectal adenocarcinoma Caco-2 cells. In particular, all these strains were active against Escherichia coli ATCC 8739 and Staphylococcus aureus ATCC 6538 through the production of lactic acid (up to 12 g.l⁻¹) or bacteriocins, namely plantaricins, or their combination. In addition, these strains showed high antioxidant activity against the synthetic free radicals 2,2-diphenyl-2-picrylhydrazyl (DPPH) and 2,2-azino-bis: 3-ethyl-benzothiazoline-6-sulphonic acid (ABTS +) radical. These results demonstrate the importance of these L. plantarum strains for the development of new functional foods and probiotics and as biopreservatives. This study deepens and enriches the knowledge of lactobacilli from plant raw materials by focusing on the functional properties of new strains of L. plantarum isolated from Algerian fruits. In fact, with the growing interest in natural preservatives and probiotics, the results of this study could contribute to the development of new biotechnological products aimed at improving gut health, reducing food-borne illnesses and extending the shelf life of food by preventing spoilage.

The evolutionary adaptation of pathogens to biological materials has led to an upsurge in drug-resistant superbugs that significantly threaten public health. Treating most infections is an uphill task, especially those associated with multi-drug-resistant pathogens, biofilm formation, persister cells, and pathogens that have acquired robust colonization and immune evasion mechanisms. Innovative diagnostic solutions are crucial for identifying and understanding these pathogens, initiating efficient treatment regimens, and curtailing their spread. While next-generation sequencing has proven invaluable in diagnosis over the years, the most glaring drawbacks must be addressed quickly. Many promising pathogen-associated and host biomarkers hold promise, but their sensitivity and specificity remain questionable. The integration of CRISPR-Cas9 enrichment with nanopore sequencing shows promise in rapid bacterial diagnosis from blood samples. Moreover, machine learning and artificial intelligence are proving indispensable in diagnosing pathogens. However, despite renewed efforts from all quarters to improve diagnosis, accelerated bacterial diagnosis, especially in Africa, remains a mystery to this day. In this review, we discuss current and emerging diagnostic approaches, pinpointing the limitations and challenges associated with each technique and their potential to help address drug-resistant bacterial threats. We further critically delve into the need for accelerated diagnosis in low- and middle-income countries, which harbor more infectious disease threats. Overall, this review provides an up-to-date overview of the diagnostic approaches needed for a prompt response to imminent or possible bacterial infectious disease outbreaks.

A novel endophytic actinomycete with antagonistic activity against Fusarium moniliforme, designated strain NEAU-BLH26^T, was isolated from the root of Adonis amurensis Regel collected at the horticultural experiment station of Northeast Agricultural University, Heilongjiang Province, northeast China. Strain NEAU-BLH26^T exhibited morphological and chemotaxonomic features of the genus Streptomyces. The diamino acid present in its cell wall was identified as LL-diaminopimelic acid, while galactose detected in whole-cell hydrolysates. The menaquinones were identified as MK-9(H₆), MK-9(H₈), and MK-9(H₄). The phospholipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified phospholipids and two unidentified aminolipids. The major fatty acids were determined to be iso-C_16:0 and C_16:0. The DNA G + C content, based on the genome sequence, was 70.5 mol%. Phylogenetic analyses of 16S rRNA gene and whole genome sequences analyses indicated that strain NEAU-BLH26^T was most closely related to Streptomyces geranii A301^T, with a 16S rRNA gene sequence similarity of 98.69%. However, the average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values confirmed that strain NEAU-BLH26^T represents a distinct species. This conclusion was further supported by phenotypic and chemotaxonomic differences between strain NEAU-BLH26^T and its closest relative. Additionally, the secondary metabolite biosynthetic gene clusters in strain NEAU-BLH26^T were predicted and analyzed. Based on phenotypic, chemotaxonomic and genotypic evidence, strain NEAU-BLH26^T is proposed as a novel species of the genus Streptomyces, for which the name Streptomyces adonidis sp. nov. is suggested. The type strain is NEAU-BLH26^T (= JCM 36414^T = MCCC 1K08678^T).

The conversion of filamentous fungus-based feedstock into Biodiesel holds potential as a sustainable and eco-conscious method for producing alternative liquid fuels. This study examined the comparison of individual Fatty Acid Methyl Esters (FAME) of Aspergillus niger and Curvularia lunata with the consortium of both filamentous fungal cocktail Fatty acid methyl esters (cFAME), following a transesterification process that turned the fungal lipids into myco-based biodiesel productions. cFAME weighs 23.89 g and accumulates to 20.43 g of lipid yield, with 86% of cellular lipids; in contrast, A. niger weighs 12.65 g and pile up 9.5 g of lipid yield, with 75% of cellular lipid, also C. lunata exhibits 8.35 g of dry weight with 4.89 g of lipid concentration, with 59% of cellular lipids. A. niger was known to contain C16–C18 saturated and unsaturated fatty acids possess LAME (C18:2), OAFA (C18:1), and PAME (C16:0) were shown in high percentages accounted for 86.6% in A. niger. The results showed that PUFA was predominant over MUFA and SFA. C. lunata chiefly produces C16 and C18 fatty acids, which are considered favorable for combustion properties with oleic acid (C18:1), linoleic acid (C18:2), palmitic acid (C16:0), and stearic acid (C18:0), on the comparison. However, the FAME profile of C. lunata occupies only 39.07% of the biodiesel quality. Pentadecanoic acid, palmitic acid, palmitoleic acid, Oleic acid, Linolenic acid, Linoleic acis, and Hexanoic acid with the carbon range of C6:0 – C18:3 were observed in cFAME. Based on the biodiesel yield, cFAME scored 20.55%, whereas A. niger with 11.05 and C.lunata 2.45%, respectively. The presence of methyl esters containing various long-chain fatty acids indicates very effective biodiesel assets, as confirmed by GC–MS analysis, which evidenced ignition efficiency, among others. cFAMEs were impacted by high ignition efficiency with > 4 min. Consortium strategies seize attention in different dimensions and have been confirmed by their upregulation in their fatty acid profiles; in the future, the combination of high lipid holders among the fungal kingdom can be an alternative in myco-based biodiesel production.

Graphical Abstract

Two Gram-negative, catalase- and oxidase-positive, cream-coloured, short rod-shaped, and motile bacterial strains, designated CS7^T and SSM6^T, were isolated from mud and marine water collected in Incheon, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Halomonas. Strain CS7^T exhibited the highest 16S rRNA similarity with Halomonas urmiana TBZ3^T (99.0%), while strain SSM6^T exhibited the highest 16S rRNA similarity with Halomonas saccharevitans AJ275^T (98.4%). Strain CS7^T was observed at temperatures ranging from 4 to 44 °C (optimum, 30 °C), at pH levels from 2.0 to 12.0 (optimum, pH 8–9), and in NaCl concentrations of 0–23% (w/v) (optimum, 9%). Strain SSM6^T was observed at temperatures ranging from 4 to 37 °C (optimum, 30 °C), at pH levels from 2.0 to 10.0 (optimum, pH 8–9), and in NaCl concentrations of 0% to 23% (w/v) (optimum, 9%). The DNA G + C content of CS7^T was 67.7 mol%, while that of SSM6^T was 65.1 mol%. Strains CS7^T and SSM6^T were identified to possess phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and diphosphatidylglycerol (DPG) as the major polar lipids. Predominant fatty acids (> 10%) in strain CS7^T were C_16:0, C_12:0 3-OH, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). Predominant fatty acids (> 10%) in strain SSM6^T were C_16:0, C_12:0 3-OH, cyclo-C_19:0 ω8c, and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). Based on phylogenetic, physicochemical, and biochemical data, CS7^T and SSM6^T represent novel species within the genus Halomonas. They have been designated as Halomonas pelophila sp. nov. (= KACC 23728^T = TBRC 19017^T) and Halomonas aquatica sp. nov. (= KACC 23729^T = TBRC 19018^T).

Pseudomonas aeruginosa, an opportunistic pathogen, is a major contributor to hospital-acquired infections. This Gram-negative bacterium relies on aerobic respiration and cannot ferment. Various mechanisms of antibiotic resistance closely link to its pathogenicity. This study aimed to determine how common the bla-TEM, blaOXA-10, blaSHV, and per-1 genes were in Pseudomonas aeruginosa samples taken from hospitalized patients. We conducted a retrospective cross-sectional analysis on 100 isolates of the bacterium. The double-disc test detected extended-spectrum beta-lactamase (ESBL) activity and assessed antibiotic susceptibility. Using polymerase chain reaction (PCR), we found that the bla-TEM, bla-SHV, blaOXA-10, and per-1 genes were present. Pseudomonas aeruginosa isolates were highly resistant to meropenem (80%), imipenem (77%), piperacillin (77%), and ceftazidime (76%). However, they were not resistant to colistin. 91% of the isolates exhibited multidrug resistance (MDR), and 76% phenotypically showed ESBL production.Gene analysis revealed that bla-TEM was the most prevalent (38%), then per-1 (31%), bla-SHV (15%), and OXA-10 (9%). We identified the bla-TEM gene in 50.8% of ESBL-positive Pseudomonas aeruginosa, the per-1 gene in 40.8%, and the bla-SHV and OXA-10 genes in 19.7% and 2.6% respectively. The phenotypic method failed to detect ESBL activity in 24 isolates with the per-1 gene and 7 isolates with the OXA-10 gene. In conclusion, clinical isolates of Pseudomonas aeruginosa show a high prevalence of ESBL activity, but reliance on phenotypic methods alone may overlook some cases. The most frequently detected ESBL-associated genes are bla-TEM, followed by per-1, bla-SHV, and OXA-10. Additionally, Pseudomonas aeruginosa isolates demonstrate a high incidence of multiple drug resistance.

It is believed that the larval stage infestation by Neurozerra conferta Walker of Aquilaria malaccensis trees followed by fungal infections assists in higher-quality agarwood formation. However, it remains unclear what these intricate interactions offer for higher-grade agarwood formation. In the earlier studies, fungal diversity associated with agarwood has been identified and their role in agarwood formation has been fairly well established. However, these studies cover a broad aspect of agarwood fungal diversity and interactions but lack specificity regarding insect infestation, particularly since agarwood can be obtained either naturally through insect-inflicted injuries or artificially induced by different methods. The present study therefore specifically examines the culturable fungal associates in resinous agarwood formed due to the infestation by N. conferta. A total of 12 fungi were isolated belonging to four fungal families, namely Endomelanconiopsidaceae, Hypocreaceae, Nectriaceae, and Trichocomaceae. Internal Transcribed Spacer (ITS) sequencing identified the isolates as Endomelanconiopsis microspore, Fonsecaea monophora, Fusarium incarnatum, Fusarium sp., Neocosmospora solani, Penicillium sp., and Trichoderma cf. harzianum. Screening for enzyme activity revealed the isolates with the highest rate of xylanase activity compared to cellulase and tannase activity. However, most of the fungal isolates could produce the tannase enzyme, implying its potential in overcoming the plant's defense process. N. solani exhibited abundance and, displayed variations in colony morphology as well as enzyme activities. Therefore, our findings provide a basis for understanding N. solani, as the significant fungal microbe contributing to the agarwood formation via resin development in the N. conferta infested A. malaccensis trees.

Mesoporous silica nanoparticles (MSNs), particularly SBA15 and SBA16, provide a versatile platform due to their ordered structures, high surface area, and biocompatibility. This study investigates their role as prebiotic agents by evaluating their effect on the growth of Bacillus coagulans, an industrially significant probiotic. SEM and TEM analyses revealed that SBA15 had mesh-like hexagonal structure, while SBA16 featured hexagonal pores with tubular channels, enhancing surface area and porosity for bacterial attachment and proliferation. BET analysis showed SBA15 had a surface area of 718 m²/g with 8.5 nm pores, whereas SBA16 exhibited 740 m²/g with 5.4 nm pores, influencing nutrient diffusion and bacterial interactions. UV–Vis spectroscopy confirmed structural stability with lambda maxima at 225 nm (SBA15) and 231 nm (SBA16). DLS analysis showed that SBA15 (267.7 nm) and SBA16 (367 nm) had high dispersibility in aqueous media, fostering a stable microenvironment. Optical density measurements and colony-forming unit assays demonstrated significant growth enhancement of Bacillus coagulans in the presence of MSNs, at lower concentrations (0.1–1 ppm). SBA15 promoted bacterial proliferation more effectively than SBA16, due to its larger pore size. The porosity facilitated bacterial adhesion and nutrient absorption, leading to enhanced metabolic activity. Enzyme assays confirmed a rise in ATP levels, suggesting increased energy metabolism, while a paradoxical increase in the Minimum Inhibitory Concentration (MIC) of Ampicillin was observed, attributed to nanoparticle-mediated antibiotic adsorption, reducing the bioavailability of the antibiotic and allowing bacterial survival. These findings highlight MSNs as growth modulators and antibiotic stress mitigators with applications in biotechnology and healthcare.

Graphical Abstract

The Ambystoma mexicanum axolotl is a highly threatened amphibian and a valuable research model, with very little information about bacterial diseases affecting it. The aim of this study was to perform an identification of bacteria responsible for septicemia in three individuals. For all of them, necropsies were made, bacteria classification was performed by traditional and DNA-based molecular methods and tissues were histologically examined. All animals showed edema and ascites, and other tissues such as the lungs, spleen, liver, and kidney were also affected, dermatitis also occurred, in one case, the dermatitis was severe. Two bacterial isolates showed genetic identities of 99% with Aeromonas veronii, one with Citrobacter freundii, and another with 100% identity with Citrobacter portucalensis. These and other Enterobacteriaceae species of Aeromonas genus have been reported to produce septicemia in Anura amphibians and fish, pointing out that they are a health hazard for aquatic animals. Future endeavors to determine these bacteria prevalence, the search for antibiotic resistance/susceptibility, factors that can trigger the pathology, and the development of early diagnostic tools should be done to improve our understanding.