Search Results (4,659)

Microorganisms live in a wide range of environments, performing diverse roles either independently or in association with other organisms forming consortia. This study is focused on those with the ability to bioremediate environments contaminated with petroleum hydrocarbons (PHCs), that is, the case of bacteria, fungi, algae, and consortia. PHC contamination constitutes a major global environmental issue, and presents a serious ecological risk. This research was conducted in the coastal waters of Haina Port (Dominican Republic) and the main objective was to characterise the bacterial communities with bioremediation capacity by sequencing the 16S rRNA. The samples were collected in sterile conditions, and physicochemical and molecular analyses were conducted. The results revealed the composition and distribution of bacterial communities in the area. At the phylum level, Proteobacteria is the dominant group, accounting for 70–90% of the community. At the class level, Gammaproteobacteria is the predominant group, followed by Alphaproteobacteria which ranks second in relative abundance. Bacillaceae appears as the most abundant family at most points. This 16S rRNA survey provides a taxonomic baseline of the microbial community, identifying taxa with documented degradative potential. Future functional analyses and culture studies are required to quantify and confirm the active metabolic pathways of the detected microorganisms. Full article

This study aimed to evaluate the microbiological quality of Brazilian dry-cured loin (Socol), as well as the presence of ochratoxin A (OTA) and its synthesis by the isolated Aspergillus ochraceus complex under different conditions (culture media, temperature, and time of incubation). Nine bacterial genera were isolated and identified by Matrix Assisted Laser Desorption Ionization—Time Of Flight/Mass Spectrometry (MALDI-TOF/MS), including Serratia spp. (32.4%), Citrobacter spp. (20.9%), Enterobacter spp. (13.6%), and Staphylococcus spp. (6.3%), among others. Salmonella spp. was not observed, and counts of thermotolerant coliforms and coagulase-positive Staphylococcus were below the confidence level. Fifteen fungal strains were isolated and identified as Aspergillus spp. (n = 5), Cladosporium sp. (n = 1), and Penicillium spp. (n = 9). OTA was quantified in Socol samples, and the enumeration of fungi showed a correlation (r = 0.77) with the mycotoxin detection. A. ochraceus complex produced OTA in Czapek Yeast Autolyzed (CYA) and Yeast Extract Sucrose (YES) agars at different times and temperatures. It was concluded that the microbiota of Socol is complex, encompassing spoilage bacteria. Undesirable fungi are also present, including those belonging to the A. ochraceus complex that produce OTA. Full article

Background and Clinical Significance: Chronic non-bacterial osteomyelitis (CNO) is a rare autoinflammatory bone disorder that primarily affects children and adolescents, with females more frequently impacted. The condition remains poorly understood, though cytokine dysregulation and inflammasome activation are believed to contribute to its pathogenesis. Clinically, CNO is often difficult to distinguish from infectious osteomyelitis, as presenting symptoms such as bone pain, swelling, and functional limitation are nonspecific, while cultures are frequently negative. As a diagnosis of exclusion, delays in recognition can lead to prolonged or unnecessary antibiotic exposure and uncertainty in management. Case Presentation: A 14-year-old male with a history of left second toe osteomyelitis initially diagnosed in 2021. Despite negative cultures and limited histopathologic findings, he received multiple antibiotic courses with little improvement, and the digit remained chronically swollen. Three years later, a repeat evaluation revealed osseous resorption of the middle and distal phalanges, and a biopsy confirmed acute and mild chronic fibrosing osteomyelitis, consistent with CNO. Given the risk of progression and possible amputation, surgical reconstruction was pursued. The patient underwent autologous calcaneal bone grafting with digital fusion using a K-wire. At three months and one year postoperatively, radiographs demonstrated solid fusion of the digit with maintained activity and resolution of pain. Conclusions: This case emphasizes the diagnostic complexity of CNO and the importance of considering it in children with culture-negative or recurrent osteomyelitis. It further illustrates how timely surgical intervention can preserve function and quality of life while avoiding unnecessary amputation. Full article

Lignin is a complex aromatic polymer that constitutes a major fraction of plant biomass and represents a valuable renewable carbon resource. Naturally decaying wood serves as an environmental reservoir of microorganisms capable of degrading lignin. In this study, we isolated and characterized sixteen bacterial strains from decaying Tilia cordata wood using an enrichment culture technique with lignin as the sole carbon source. Taxonomic identification via 16S rRNA gene sequencing revealed microbial diversity spanning the genera Bacillus, Pseudomonas, Stenotrophomonas, and several members of the Enterobacteriaceae family, including Raoultella terrigena isolates. Metagenomic sequencing of the wood substrate revealed an exceptionally rich and balanced bacterial community (Shannon index H′ = 5.07), dominated by Streptomyces, Bradyrhizobium, Bacillus, and Pseudomonas, likely reflecting a specialized consortium adapted to lignin rich late-stage decay. Functional phenotyping demonstrated that all isolates possess ligninolytic potential, evidenced by peroxidase/laccase-type activity through methylene blue decolorization. Dynamic Light Scattering (DLS) and HPLC analyses showed that some isolates, such as Raoultella terrigena MGMM806, effectively depolymerized lignosulfonate into low molecular weight fragments (1.23 nm), while others accumulated intermediate metabolites or completely mineralized the substrate. Growth profiling on monolignol substrates revealed a broad spectrum of catabolic specialization in lignin monomer degradation. The results demonstrate a complex system of metabolic partitioning within a natural bacterial consortium. This collection represents a foundational genetic resource for developing engineered biocatalysts and synthetic microbial communities aimed at the efficient conversion of lignin into valuable aromatic compounds. Full article

Bacillus licheniformis Mb1, a thermophilic strain isolated from the Yungas rainforest in northwestern Argentina, was analyzed through genomic and experimental approaches to explore its biotechnological potential. Phylogenomic analysis confirmed its close relationship with B. licheniformis reference strains. The genome revealed multiple genes associated with hydrolytic, oxidative, carbohydrate-active, and polyester-degrading activities, indicating a wide enzymatic capacity. Experimental assays demonstrated strong extracellular hydrolytic activities and efficient degradation of bis(2-hydroxyethyl) terephthalate (BHET), a key polyethylene terephthalate (PET) intermediate. In liquid cultures with 3 mg/mL BHET, B. licheniformis Mb1 achieved 99.9% depletion within four days, with transient BHET dimer accumulation and progressive terephthalic acid (TPA) production, reaching 1.17 mg/mL after 15 days. Mono (2-hydroxyethyl) terephthalate (MHET) and vanillic acid were not detected. Complete BHET and dimer degradation suggests the presence of versatile hydrolases acting on short-chain polyester intermediates. Sequence and molecular docking analyses identified a BHETase-like carboxylesterase as the main enzyme candidate, featuring a truncated lidC region that generates a more open catalytic cleft. This structural trait, not previously reported in bacterial BHETases, enables the accommodation of bulkier substrates such as BHET dimer. These findings highlight B. licheniformis Mb1 as a promising biocatalyst for polyester depolymerization and a valuable microbial resource for future enzyme discovery and plastic bioremediation strategies. Full article

Background/Objectives: It is of the utmost importance to study environmental bacteria, as these microorganisms remain poorly characterized regarding their diversity, antimicrobial resistance, and impact on the global ecosystem. This knowledge gap is particularly pronounced for marine bacteria. In this study, we aimed to isolate bacteria from different marine samples and to gain insights into the environmental bacterial resistome, an aspect that remains largely neglected. Methods: Bacteria were isolated from several marine sources using two different culture media, and their identification was based on 16S rRNA gene analysis. Whole-genome sequencing was performed for selected isolates belonging to novel taxa. Antimicrobial susceptibility to seven antibiotics was evaluated using the disk diffusion method. Results: A total of 171 bacterial isolates belonging to the phyla Pseudomonadota, Bacteroidota, Planctomycetota, Actinomycetota, and Bacillota were obtained from diverse marine samples. The most abundant group belonged to the class Alphaproteobacteria. Thirty isolates represented novel taxa, comprising 16 new species and one new genus. Despite the challenges associated with determining antibiotic resistance profiles in environmental bacteria, only one isolate (1.8%) was pan-susceptible, whereas 54 (98.2%) showed resistance to at least one of the tested antibiotics. Moreover, 33 isolates exhibited a multidrug-resistant phenotype. Genome analysis of four novel taxa revealed the presence of an incomplete AdeFGH efflux pump. Conclusions: This study highlights the high bacterial diversity in marine environments, the striking prevalence of antibiotic resistance, and the major methodological challenges in studying environmental bacteria. Importantly, it emphasizes the relevance of culturomics-based approaches for uncovering hidden microbial diversity and characterizing environmental resistomes. Full article

The widespread use of antibiotics has led to the persistence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in drinking water systems, posing potential public health risks at the point of use. In this study, a residential secondary water supply system (SWSS) in eastern China was investigated over one year to characterize microbial communities, ARB and ARG occurrence, and their associations with water quality in bulk water and biofilms. Culture-based methods, flow cytometry, quantitative PCR, and high-throughput 16S rRNA and ITS sequencing were applied. Although conventional treatment removed 94.8% of total bacteria, significant microbial regrowth occurred during secondary distribution, with the highest heterotrophic plate counts observed in rooftop storage tanks (up to 4718 CFU/mL). ARG concentrations increased along the distribution line, and the class 1 integron intI1 was enriched in downstream locations, indicating enhanced horizontal gene transfer potential. Sulfonamide resistance genes dominated the resistome, accounting for more than 60% of total ARG abundance in water samples. Seasonally, ARG levels were higher in autumn and winter, coinciding with elevated disinfectant residuals and lower temperatures. Chlorine was negatively associated with total bacterial abundance, while positive correlations were observed with the relative abundance of several ARGs when normalized to bacterial biomass, suggesting selective pressure under oxidative stress. Turbidity and bacterial abundance were positively correlated with ARB, particularly sulfonamide-resistant bacteria. Biofilms exhibited more stable microbial communities and provided microhabitats that facilitated microbial persistence. Notably, fungal abundance showed strong positive correlations with multiple ARGs, implying that microbial interactions may indirectly contribute to ARG persistence in SWSSs. These findings highlight the role of secondary distribution conditions, disinfectant pressure, and microbial interactions in shaping resistance risks in residential water supply systems, and provide insights for improving microbial risk management at the point of consumption. Full article

High culture medium costs economically constrain bacterial cellulose (BC) production. In parallel, agro-industrial wastes are plentiful but often underutilised sources of carbon and nitrogen substrates that could support microbial growth and metabolite production. This study aimed to bioconvert agro-industrial waste sustainably into BC using response surface methodology. A novel lactic acid bacterium, Levilactobacillus brevis DSS.01, isolated from nata de coco wastewater, was evaluated alongside Acetobacter tropicalis KBC and Komagataeibacter xylinus TISTR 086 for BC production using Australian agro-industrial wastes. Preliminary screening identified pear pomace and rice bran as optimal low-cost carbon and nitrogen sources, respectively. The response surface methodology employing Box–Behnken Design determined the optimal agro-industrial waste medium composition for L. brevis DSS.01 to produce BC at 1.56 ± 0.15 g/L. The optimised agro-industrial waste medium substituted 85% of standard Hestrin-Schramm medium components, suggesting a significant reduction in culture medium and production costs. Scanning electron microscopy revealed BC fibres from L. brevis DSS.01 maintained a uniform diameter. Fourier transform infrared spectroscopy and X-ray diffraction analyses indicated minimal structural deviation in BC produced from optimised agro-industrial waste medium versus standard medium. These findings demonstrate economic and sustainable BC production through valorisation of agro-industrial residues, establishing lactic acid bacteria as alternative BC producers with potential food-grade applications in circular economy frameworks. Full article

Clinical data on antimicrobial profiles are useful for dairy udder health treatment programmes and represents a component of antimicrobial stewardship. The study aimed to determine the bacterial aetiology of clinical mastitis in dairy herds in Western Australia and to evaluate their antibiotic resistance profiles. This retrospective study utilised clinical antimicrobial profile data from two referral diagnostic centres within the region of Western Australia. A total of 545 mastitic samples were submitted for antimicrobial culture and testing over a period of 10 years (2008–2018). Of these, 406 showed bacterial growth and 139 no bacterial growth was observed. The most common isolates were Streptococcus uberis (25.3%), Staphylococcus aureus (17.2%), and Escherichia coli (9.4%). No growth was identified in 25.5% of the mastitis milk samples. The antimicrobial profiles revealed high susceptibilities towards cefuroxime (95.7%), clavulox (89.4%), and oxytetracycline (89%), whilst showing high resistance towards novobiovin (70%). From this study, it is concluded that there was a decline in the resistance trends towards the isolates of both S. uberis and S. aureus over the 10-year period and contagious mastitis had a higher occurrence. There is a need to consider surveillance programmes that determine the patterns of on-farm antimicrobial usage and further characterise the pathogens based on the presence of resistance antimicrobial genes. Data on antimicrobial surveillance represent an important component of antimicrobial stewardship. Full article

Background/Objectives: Ulcerative colitis (UC) is an inflammatory bowel disease and a major cause of ulcers and chronic inflammation in the colon and rectum. Recurring symptoms include abdominal pain, rectal bleeding, and diarrhoea, and patients with UC are at a higher risk of developing comorbidities such as colorectal cancer and poor mental health. In UC, the decreased diversity and changed metabolic profile of gut microbiota, along with a diminished mucus layer, leads to disruption of the underlying epithelial barrier, with an ensuing excessive and detrimental inflammatory response. Treatment options currently rely on drugs that reduce the inflammation, but less emphasis has been placed on improving the resilience of the epithelial barrier. Macrolide antibiotics exhibit epithelial barrier-enhancing capacities unrelated to their antibacterial properties. Methods: We investigated two novel barriolides, macrolides with reduced antibacterial effects in common bacterial strains. Gut epithelial cell barrier resistance in the Caco-2 cell line, with and without co-culture with mucus-producing HT-29 cells, was increased when treated with barriolides. Using ^AXGut-on-Chip technology with inflammatory cytokine-stimulated Caco-2/HT-29 co-cultures, the effectiveness of the barriolides was confirmed. Lastly, we reveal the barrier-enhancing and inflammation-reducing effects of the barriolides in a dextran-sulphate sodium (DSS)-induced colitis mouse model. Results: We show the predictive power of the novel ^AXGut-on-Chip system and the effectiveness of the novel barriolides. Indications include reduced inflammatory response, increased epithelial barrier and decreased overall clinical score. Conclusions: The results of this study indicate the notion that barriolides could be used as a treatment option for UC. Full article

This study examined the association between biofilm growth and surface properties of 3D printed, milled, and conventional materials used for manufacturing fixed dental prostheses. Disc-shaped specimens were produced and finished from five 3D-printing resins (VarseoSmile Crown plus [VSC], NextDent C&B MFH [ND], VarseoSmile Temp [VST], Temp PRINT [TP], P Pro Crown & Bridge [P]), two polymer milling blocks (composite: TetricCAD [TC], PMMA: TelioCAD [TEL]), two conventional polymer materials (Tetric EvoCeram [TEC], Protemp 4 [PT]), and zirconia (ZR). Surface roughness (R_a), wettability, interfacial tension (IFT) and surface topography were examined. Three-day biofilms were grown on the specimens using A. naeslundii, S. gordonii, S. mutans, S. oralis, and S. sanguinis in a multi-species suspension. Biofilms were quantified by crystal violet staining and with a plating and culture method (CFU/mL). Linear regression analysis was computed to demonstrate associations between the surface properties and biofilm growth. The strength of this relationship was quantified by calculating Spearman’s ρ. TC exhibited the highest, and TP the lowest IFT. TEC showed the highest R_a, while TEL had the lowest, with significant differences detected particularly between milled and 3D-printed specimens. TP specimens exhibited the highest biofilm mass, while ZR surfaces retained the least. Bacterial viability within the biofilms remained similar across all tested materials. There was a strong negative correlation between total IFT and biofilm mass, and a moderate positive correlation between R_a and CFU/mL. Surface properties are shaped by material composition, microstructure, and manufacturing methods and play a crucial role in biofilm formation on dental restorations. Full article

Background/Objectives: Syndromic multiplex PCR assays such as BIOFIRE FilmArray^® Pneumonia (PN) panel enable rapid and simultaneous detection of bacterial and viral pathogens in respiratory specimens, improving diagnostic accuracy and patient management in lower respiratory tract infections (LRTIs). Methods: In this retrospective observational study, PN panel results in 410 bronchoalveolar lavage (BAL) samples from hospitalized patients with suspected pneumonia were analyzed and compared with those obtained using the conventional culture (CC) method. Results: The PN panel showed an overall positivity rate of 54%, detecting bacteria in 39.0% of samples, viruses in 7.1%, and atypical bacteria in 2.2%. Using the conventional culture (CC) method, 33.9% of samples tested positive. Overall, 83 (20.2%) samples that were positive by the PN panel were negative by CC, whereas only 14 specimens (3.4%) were positive by CC and negative by PN panel. The most frequently detected pathogen by both the PN panel and CC was Staphylococcus aureus (n = 67, 16.34% for PN; n = 40, 9.76% for CC). Regarding diagnostic performance, the PN panel demonstrated a sensitivity of 89.02%, a specificity of 97.86%, and an overall accuracy of 97.63%. Lower sensitivity values were observed only for the Enterobacter cloacae complex (57.14%) and the Klebsiella pneumoniae group (75%). Specificity exceeded 92% for all bacterial targets. Conclusions: The PN panel confirms enhanced pathogen detection and a shortened time-to-result. It serves as a valuable adjunct for the timely diagnosis of LRTIs, supporting antimicrobial stewardship through more precise and appropriate antibiotic selection. Full article

Probiotics are live microorganisms that provide health benefits when administered in adequate amounts. Due to the increasing popularity of probiotic supplements, concerns have arisen regarding their quality, microbial composition, and safety. This study aimed to evaluate the quantitative and qualitative characteristics of the selected probiotics available on the Polish market, including both dietary supplements and foods for special medical purposes, and to compare the obtained results with the information provided on the product labels. Fifteen commercial probiotic products were analysed. Viable microorganism counts were determined using the traditional culture-based plate count method and by flow cytometry for selected products. Species identification was performed using MALDI-TOF MS and qPCR, whereas microbiological purity testing was conducted to confirm the absence of pathogenic bacteria. Significant differences were observed between the declared and experimentally determined numbers of viable microorganisms. Only a few products maintained bacterial counts consistent with label claims, while most contained considerably low viable cells. Flow cytometry revealed higher viable cell counts than plate counting, indicating the presence of viable but non-culturable bacteria. The declared species composition of the strains was mostly confirmed, although in several cases, undeclared probiotic microorganisms were identified. All tested products were free from pathogens. The study indicates significant discrepancies in the quality of probiotic supplements available on the Polish market. From a consumer perspective, these findings highlight the importance of verifying probiotic quality and suggest that not all commercial products may guarantee the full range of claimed health benefits. The implementation of standardised analytical procedures and enhanced quality control measures is therefore essential to ensure the product safety, strain authenticity, and reliability of health-related claims. Full article

Between 2015 and 2022, we evaluated a novel broad-range (BR) 16S PCR rDNA PCR/Sanger sequencing assay to improve diagnosis of invasive infections in culture-negative specimens. Using dual-priming oligonucleotides (DPO), this assay analyzed ribosomal DNA from sterile fluids or tissues. A total of 762 specimens were analyzed from 661 patients: 61% had negative cultures and BR 16S PCR tests; 35% had negative cultures but positive BR 16S PCR tests; and only 4% had negative cultures with indeterminate BR 16S PCR results. After resolution of indeterminate BR 16S PCR results (i.e., 29 negative, 1 false-positive, and 1 positive) the assay showed a sensitivity of 98.26% (95% CI = 96.00–99.43%), specificity of 99.79% (95% CI: 99.82–99.99%), positive predictive value of 99.65% (95% CI: 97.56–99.95%), negative predictive value of 98.94% (95% CI: 97.51–99.55%), and accuracy of 99.21% (95% CI: 98.28–99.71%) for a disease prevalence of 38.10% (95% CI: 34.62–41.66%). Gram stain purulence predicted the BR 16S PCR result better (69.4%) than organisms (24.6%), but the latter had a higher PPV (78.5%). Increased peripheral WBC (86.1%) or CRP (71.8%) predicted positive BR 16S PCR results. Our DPO BR 16S PCR assay improved pathogen detection over culture and minimized contamination. Broad range 16S rDNA PCR/sequencing (BR 16S PCR) is an important diagnostic technique in cases with invasive infection due to fastidious or uncultivatable pathogens. However, appropriate case selection, the quality of clinical specimen, and the specific assay primers affect its performance. Our novel BR 16S PCR assay uses unique dual-priming oligonucleotides (DPO) primers and fast protocols for rapid, optimal detection of bacterial pathogens, while minimizing contamination. Fast BR 16S PCR assay reports occurred within 24–48 h. BR 16S PCR and culture analyzed a diverse range of clinical specimens from patients with invasive infections. BR 16S PCR demonstrated a high performance for accurately detecting pathogens, ruling out infections, and minimizing contamination. BR 16S PCR detection of a pathogen allowed the appropriate clinical management of one-third of patients in this cohort. BR 16S PCR is an essential tool for the clinical management of patients with invasive infection when primary cultures are negative or contaminated. Full article

Background: Intrachromosomal rearrangements in birds play a subtle but important role in shaping genomic evolution, phenotypic diversity and speciation. However, the avian sex chromosome system (homogametic ZZ males; heterogametic ZW females) remains relatively understudied, and evolutionary rearrangements of the Z chromosome have not been mapped in most species. To address this, we employed universally hybridizing avian Z chromosome probes to metaphases of 11 avian species from South America. Methods: Chromosome preparations were obtained from fibroblast cell cultures of 11 birds representing nine different orders; four bacterial artificial chromosome (BAC) probes were used in our interspecies fluorescence in situ hybridization (FISH) experiments. We identified chromosomal rearrangements in the species investigated, tracing the evolution of the Z chromosome in these species through comparison with reptiles from Southeast Asia (three snake species used as an outgroup), along with two reference species: chicken (Galliformes) and zebra finch (Passeriformes). Results: We observed high rates of intrachromosomal rearrangements in the avian Z chromosome, with most species showing different patterns from chicken and zebra finch. Nannopterum brasilianum (Suliformes) and Jacana jacana (Charadriiformes) showed the same BAC order as chicken, but centromere repositioning was evident. Apart from Piciformes, all other species exhibited a conserved Z chromosome size. The corresponding Z chromosome sequences were homologous to regions of the long arms of Chromosome 2 and W in snakes but not on the Z chromosomes. Conclusions: Comparative analysis of the Z chromosome across avian orders provides important insights into the dynamics of avian sex chromosomes and the evolution of sex chromosome systems in general. Full article