Search Results (354)

Wildfires can significantly alter soil physicochemical conditions and microbial communities in forest ecosystems. This study aimed to characterize the culturable soil fungal community and evaluate biological activity in Banco Totumo Bijibana, a protected dry tropical forest in Atlántico, Colombia, affected by a wildfire in 2014. Twenty soil samples were collected for microbiological (10 cm depth) and physicochemical (30 cm) analysis. Basal respiration was measured using Stotzky’s method, nitrogen mineralization via Rawls’ method, and fungal diversity through culture-based identification and colony-forming unit (CFU) counts. Diversity was assessed using Simpson, Shannon–Weaver, and ACE indices. The soils presented low organic matter (0.70%) and nitrogen content (0.035%), with reduced biological activity as indicated by basal respiration (0.12 kg C ha⁻¹ d⁻¹) and mineralized nitrogen (5.61 kg ha⁻¹). Four fungal morphotypes, likely from the genus Aspergillus, were identified. Simpson index indicated moderate dominance, while Shannon–Weaver values reflected low diversity. Correlation analysis showed Aspergillus-3 was positively associated with moisture, whereas Aspergillus-4 correlated negatively with pH and sand content. The species accumulation curve reached an asymptote, suggesting an adequate sampling effort. Although no control site was included, the findings provide a baseline characterization of post-fire soil microbial structure and function in a dry tropical ecosystem. Full article

Background: Urine microbial analysis is a frequently requested test that is often associated with contamination during specimen collection or storage, which leads to false-positive diagnoses and delayed reporting. In the era of digitalization, machine learning (ML) can serve as a valuable tool to support clinical decision-making. Methods: This study investigates the application of a simple artificial neural network (ANN) to pre-identify negative and contaminated (false-positive) specimens. An ML model was developed using 8181 urine samples, including cytology, dipstick tests, and culture results. The dataset was randomly split 2:1 for training and testing a multilayer perceptron (MLP). Input variables with a normalized importance below 0.2 were excluded. Results: The final model used only microbial and either urine color or urobilinogen pigment analysis as inputs; other physical, chemical, and cellular parameters were omitted. The frequency of positive and negative specimens for bacteria was 6.9% and 89.6%, respectively. Contaminated specimens represented 3.5% of cases and were predominantly misclassified as negative by the MLP. Thus, the negative predictive value (NPV) was 96.5% and the positive predictive value (PPV) was 87.2%, leading to 0.82% of the cultures being unnecessary microbial cultures (UMC). Conclusions: These results suggest that the MLP is reliable for screening out negative specimens but less effective at identifying positive ones. In conclusion, ANN models can effectively support the screening of negative urine samples, detect clinically significant bacteriuria, and potentially reduce unnecessary cultures. Incorporating morphological information data could further improve the accuracy of our model and minimize false negatives. Full article

Integrated rice–crayfish (Oryza sativa–Procambarus clarkii) co-culture (RC) systems have gained prominence due to their economic benefits and ecological sustainability; however, the interactions between soil properties and microbial communities in such systems remain poorly understood. This study evaluated the effects of the RC systems on soil physicochemical characteristics and microbial dynamics in paddy fields of southern Henan Province, China, over the 2023 growing season and subsequent fallow period. Using a randomized complete design, rice monoculture (RM, as the control) and RC treatments were compared across replicated plots. Soil and water samples were collected post-harvest and pre-transplanting to assess soil properties, extracellular enzyme activity, and microbial community structure. Results showed that RC significantly enhanced soil moisture by up to 30.2%, increased soil porosity by 9.6%, and nearly tripled soil organic carbon compared to RM. The RC system consistently elevated nitrogen (N), phosphorus (P), and potassium (K) throughout both the rice growth and fallow stages, indicating improved nutrient availability and retention. Elevated extracellular enzyme activities linked to carbon, N, and P cycling were observed under RC, with enzymatic stoichiometry revealing increased microbial nutrient limitation intensity and a shift toward P limitation. Microbial community composition was significantly altered under RC, showing increased biomass, a higher fungi-to-bacteria ratio, and greater relative abundance of Gram-positive bacteria, reflecting enhanced soil biodiversity and ecosystem resilience. Further analyses using the Mantel test and Random Forest identified extracellular enzyme activities, PLFAs, soil moisture, and bulk density as major factors shaping microbial communities. Redundancy analysis (RDA) confirmed that total potassium (TK), vector length (VL), soil pH, and total nitrogen (TN) were the strongest environmental predictors of microbial variation, jointly explaining 74.57% of the total variation. Our findings indicated that RC improves soil physicochemical conditions and microbial function, thereby supporting sustainable nutrient cycling and offering a promising, environmentally sound strategy for enhancing productivity and soil health in rice-based agro-ecosystems. Full article

Background/Objectives: Ulcerative colitis (UC) is characterized by the interplay between immune responses and dysbiosis in disease development. Aiming to provide additional insights into disease development and potential treatment strategies, the present study investigates the local effect of oral treatment with polysaccharides obtained from Auricularia auricula’s submerged culture in an experimental model of DSS-induced colitis and its impact on lesion resolution. Methods: The structure and monosaccharide composition of Auricularia polysaccharides were characterized through Nuclear Magnetic Resonance (NMR). To evaluate the effect of this polysaccharide on the murine model, wild-type and Dectin-1 knockout mice were treated or not with the exopolysaccharide (EPS) while under DSS consumption. During the experimental period, feces samples were collected to evaluate microbial shifts during disease development, and, finally, the colonic tissue was analyzed to assess the inflammatory process and cytokine production. Results: The EPS composition showed a polymeric mixture of glucans and fucogalactomannans. The treatment of the wild-type DSS-induced colitis group improved the inflammatory response by increasing gut–homeostatic cytokines, such as interleukin-10 (IL-10) and tumor necrosis factor-alpha (TNF-α). The Dectin-1 KO mice group did not show the same enhancement after EPS treatment. The microbiome analysis revealed a difference in the genotype, and the treatment modified the DSS microbiome modulation, with nine and four ASVs in WT and Dectin-1 KO mice, respectively. Conclusions: The EPS treatment demonstrated therapeutic potential in treating inflammatory intestinal diseases by modulating cytokine secretion and microbiota composition, which is dependent on the Dectin-1 receptor’s carbohydrate recognition. Full article

Objectives: Odontogenic sinusitis (ODS) is common but frequently overlooked condition that differs from rhinogenic sinusitis (CRS) and should be suspected in each case of unilateral sinusitis. Clinical symptoms such as foul smell, congestion, rhinorrhea, and unilateral maxillary sinus opacification with overt dental pathology on radiological scans are more suggestive of ODS than CRS, but the distinctive microbiological flora are another clinical factor in diagnosis. The aim of this study was to compare the microbiological load of ODS and CRS and their clinical presentation for better disease recognition and its predisposing factors. Methods: Adult patients scheduled for endoscopic sinus surgery were included in the study. Clinical data and radiological images were analyzed. The otolaryngologist assessed nasal endoscopy for mucopurulence or edema in middle meatus or sinuses, whereas dental specialist confirmed or ruled out the dental cause. Microbiological samples were collected after endoscopic maxillary antrostomy. After irrigation with 0,9% saline, the aspirated rinse was collected into sterile sets and sent for culturing. Results: The study group consisted of 84 patients, 55 with CRS and 29 with ODS. Streptococcus spp prevailed in the CRS group, whereas Staphylococcus spp prevailed in the ODS group. Statistically significant differences between the groups were found in type of discharge, degree of edema, and presence of polyps. However, no statistical correlations were noted for presence of bacteria in the culture and endoscopic or radiological findings. Conclusions: ODS and CRS share some common features: ODS more often presents with purulent discharge, localized maxillary involvement, and the presence of oral pathogens, and Staphylococcus spp in microbial profile. Full article

This study assessed the viable and culturable microbial diversity that remained on equipment surfaces after hygiene procedures in Brazilian poultry and fish slaughterhouses. Food-contact surface samples were collected using sterile swabs in poultry (n = 50) and fish (Oreochromis niloticus, n = 50) slaughterhouses. The swab samples were used to prepare culture plates to recover viable and culturable cells. The grown plates were washed, and the total DNA of the cell suspension was extracted with a commercial kit. Sequencing of the total DNA extracted from cultures was targeted at the V3 and V4 regions of the 16S rRNA. DNA reads were analyzed by QIIME2 software, with results expressed in relative frequency (%RF). Alpha and beta diversity indexes were analyzed considering the spots of sample collection, type of industry, surfaces (smooth or modular), and materials (polypropylene, stainless steel, or polyurethane). The results showed that in the poultry slaughterhouse, the most abundant genera were Acinetobacter (27.4%), Staphylococcus (7.7%), and Pseudomonas (5.3%), while for the fish slaughterhouse, there was a higher abundance of Staphylococcus (27.7%), Acinetobacter (17.2%), and Bacillus (12.5%). Surface characteristics influenced the microbial diversity, with Acinetobacter spp. dominating modular surfaces and Staphylococcus spp. prevailing on smooth surfaces. The results obtained indicate there is an important resident microbiota that persists even after hygiene processes, and surface-specific cleaning strategies should be developed. Full article

Background/Objectives: The main objective of the study is to assess the clinical utility of microbial cell-free DNA (mcfDNA) in neutropenic patients diagnosed with acute myeloid leukemia (AML) undergoing chemotherapy in the outpatient setting. Neutropenia is a common complication in this patient cohort and enhances the risk of fatal opportunistic bacterial and fungal infections. Accurate and timely diagnosis of these infections in outpatient asymptomatic individuals is critical. Methods: Fourteen patients were studied in this prospective observational case series. Traditional blood cultures (BCs) were obtained when clinically indicated and blood samples were collected for plasma mcfDNA metagenomic sequencing up to two times a week at outpatient oncology appointments. Results were compared in identifying potential infectious agents. Results: BCs identified pathogens in only two patients, despite several cases where infection was suspected. In contrast, mcfDNA testing detected pathogens in 11 of the 14 patients, including bacteria, such as Staphylococcus aureus, and invasive fungi, such as Candida and Aspergillus species, and Pneumocystis jirovecii. Conclusions: In the outpatient setting, mcfDNA surveillance offers a more reliable method for detecting pathogens. This approach identified actionable microbiologic results in immunocompromised individuals who did not meet standard clinical criteria for suspicion of infection. Further research is required to confirm the potential of mcfDNA surveillance in an outpatient setting to guide more accurate treatment decisions, reduce extensive clinical investigations, and improve neutropenic patient outcomes. Full article

In the African Sahel, fonio (Digitaria sp.) is a cereal crop that alleviates mid-season hunger before other main crops are harvested. As fonio is valued for its ability to grow under low nutrient and drought conditions, it was hypothesized that it may contain endophytic bacteria that can tolerate such extreme stress. White fonio seeds were obtained from a dry environment (Mali) and a moderate rainfall environment (Guinea). Plants were grown indoors on field soil mixed with sand to mimic Sahelian soils, grown at 30 °C, and exposed to drought, optimal water, and low nitrogen stress conditions. In total, 73 cultured bacteria were classified using full-length 16S rRNA sequencing followed by searching three 16S reference databases. Selected strains were tested in vitro for tolerance to relevant abiotic stresses. Including nine isolates from seeds, the candidate root/shoot endophytes spanned 27 genera and 18–39 top-match species. Several well-known nitrogen-fixing bacteria were cultured, including Ensifer. Leaves were dominated by Bacilli (spore-formers known to withstand dry conditions). There were five root isolates of Variovorax. Leifsonia was isolated from the leaves and showed 100% sequence identity with seed isolates, suggestive of transmission from seed to shoot. In vitro experiments showed that seed isolates, including Leifsonia, survived diverse abiotic stresses relevant to the Sahel. Combined, these results suggest that white fonio hosts stress-tolerant microbiota, and points to Leifsonia as a candidate seed-to-plant transmitted endophyte, pending confirmation by future whole genome sequencing. This microbial collection serves as a starting point for long-term experiments to understand stress tolerance in this under-studied crop. Full article

This study aims to identify the optimal conditions—host, plant material, seasonality, and agricultural practices—for isolating and developing a collection of culturable endophytic microorganisms to support sustainable Olea europaea L. cultivation. Samples were collected from three Sicilian olive cultivars (‘Nocellara del Belice’, ‘Nocellara Etnea’, and ‘Nocellara Messinese’) and six wild olive accessions across different phenological phases and under organic and conventional agronomic management. Endophytes were isolated from leaves and twigs using a culture-dependent approach, and their taxonomic diversity and plant-growth-promoting (PGP) traits were analyzed. A total of 133 endophytic isolates were identified, spanning bacterial (Proteobacteria, Firmicutes, and Actinobacteria) and fungal (Ascomycota and Basidiomycota) phyla. Wild olive trees contributed more than cultivated varieties to enriching the diversity and composition of culturable endophyte collection as well as twigs instead of leaves. Winter sampling allowed to implement the taxonomic genera of olive endophyte collection. Both farming systems favored an increase in the composition of microbial collection, though organic farming systems supported greater microbial richness. Functional analysis highlighted key PGP traits in a selection of bacterial isolates, including indole-3-acetic acid and siderophore production, nitrogen fixation, and antifungal activity. Bacillus spp. dominated enzymatic activities, such as amylase, protease, and lipase production, as well as antifungal activity against the olive fungal pathogen Neofusicoccum vitifusiforme. This research highlights the significant diversity and functional potential of Mediterranean olive endophytes. Our findings emphasize the role of native microbial communities as bio-inoculants, promoting plant growth, nutrient uptake, and disease resistance. These insights lay the groundwork for developing targeted olive-microbial consortia for biocontrol and stress tolerance applications. Full article

Traditional methods of microbial quantification of irrigation water using colony counts from agar culture require dedicated laboratory space and trained personnel, limiting their on-site applicability. Dehydrated Petrifilm™ plates are a simpler alternative but still require 2–3 days to culture. Adenosine triphosphate (ATP) tests may offer a fast and reliable method for quantifying microbes in water. In this study, we compared (a) microbial quantification based on ATP assays with Petrifilm™-based assays, and (b) we evaluated the effectiveness of cold plasma or ozone treatments in controlling microbial growth at various oxidation–reduction potential (ORP) levels. Lake water was recirculated through an ozone or cold plasma treatment system until a target ORP of 700 mV was reached. Samples were collected at various ORP levels and plated for aerobic bacteria and yeast and mold counts using Petrifilm™ plates. The free and total ATP concentrations were measured using the Hygiena EnSURE luminometer and its accompanying free and total ATP swabs. Microbial ATP was calculated by subtracting the free from the total ATP. Cold plasma and ozone showed similar effects on microbial inactivation at 700 mV (p < 0.05). Both treatments achieved complete fungal inactivation at 600–700 mV ORP, bacterial inactivation at 600 mV ORP, and near-complete inactivation of microbial ATP at 600–700 mV. A moderate positive correlation (Pearson’s correlation = 0.39 and Spearman’s rank correlation = 0.39) was observed between the Petrifilm™ bacterial counts and microbial ATP levels, suggesting ATP quantification could complement Petrifilm™ for rapid and non-selective onsite microbial assessment of irrigation water. Full article

This study aimed to evaluate the microbiological quality of colostrum on three dairy farms with different colostrum management hygiene practices and to compare it with the current colostrum quality guidelines. On farm A, colostrum was fed raw, while on farms B and C it was heat treated. On farms A and B, the feeding equipment was cleaned manually, while on farm C, an automated cleaning system was used. Samples were collected from the calf-feeding equipment and submitted for microbial culture: total plate count (TPC); total coliform count (TCC); and E. coli, enterobacteria (ENTB), staphylococci (STAP), and lactic acid bacteria counts. In addition, pH, water activity (a_W), and Brix were analyzed. Colostrum quality was defined as follows: good quality (GQ)—TPC < 100,000, TCC < 10,000, STAP < 50,000 cfu/mL, and Brix ≥ 22%; excellent quality (EQ)—TPC < 20,000, TCC < 100, STAP < 5000 cfu/mL, and Brix ≥ 25%. Mean concentrations were as follows: TPC was 3.99 × 10⁵ cfu/mL (min: 40.00, max: 1.32 × 10⁷ cfu/mL); TCC was 1.17 × 10⁴ cfu/mL (min: <detection limit, max: 6.37 × 10⁵ cfu/mL); and STAP was 1.77 × 10⁴ cfu/mL (min: <detection limit, max: 3.50 × 10⁵ cfu/mL). Approximately 54% (GQ) and 32% (EQ) of samples met the defined criteria. Farm C consistently showed lower microbial counts across all culture types. Colostrum from farm B had lower TCC, LAB, and E. coli counts than farm A but not TPC, STAP, and ENTB. These results showed that a considerable proportion of calves were fed colostrum with suboptimal quality, especially when less rigorous hygiene practices were implemented. Full article

Objectives: To introduce a novel method for apical lesion sampling using a protected paper point device and to evaluate its effectiveness and robustness during the sampling process in vitro. Methods: A prototype for apical sample collection was developed as an adaptation of the Micro-Apical Placement System—the device features a highly tapered screw head with a thin, hollow, stainless-steel tube and an internal wire piston. Standardized 5 mm paper points (ISO 10; PD Dental, Switzerland) served as carrier material. The prototype was tested using 30 × 3D-printed, single-rooted tooth models inoculated using two bacterial strains (Staphylococcus epidermidis and Escherichia coli) to simulate apical and intraradicular bacterial infections, respectively. The sampling process involved collecting and analyzing samples at specific timepoints, focusing on the presence or absence of E. coli contamination. Following sample collection, cultural detection of bacterial presence was performed by incubating the samples on agar plates to confirm the presence of E. coli. Samples were collected as follows: S0 (sterility control of the prototype), P0 (sterility control of the tooth model), P1 (apical sample collected with the CAPS (controlled apical sampling) device, and P2 (contamination control sample to check for the presence of E. coli inside the root canal). Results: Handling of the CAPS prototype was straightforward and reproducible. No loss of paper points or complications were observed during sample collection. All sterility samples (P0, S0) were negative for tested microorganisms, confirming the sterility of the setup. P2 samples confirmed the presence of E. coli in the root canal in all trials. The P1 samples were free from contamination in 86.67% of trials. Conclusions: The CAPS method for apical sampling demonstrated advances in the successful and precise sample collection of apically located S. epidermidis and will be a useful tool for endodontic microbiological analysis. Its user-friendly design and consistent performance highlight its potential for clinical application, contributing to more accurate microbial diagnostics and later patient-specific therapeutic approaches in endodontic treatments. Full article

Background/Objectives: Unexplained infertility is a worldwide problem affecting a significant proportion of couples of reproductive age. Recent studies suggest that alterations in the vaginal microbiota are related to female infertility, while supplementation with some probiotic strains has been shown to improve pregnancy rates in couples experiencing this problem. This study aimed to evaluate the impact of oral administration of Ligilactobacillus salivarius CECT5713 on pregnancy success rates in couples with unexplained infertility prior to in vitro fertilization (IVF). Methods: Seventy couples were randomized to receive either a placebo or a probiotic intervention (one capsule per day containing an excipient only or 3 × 10⁹ viable cells of L. salivarius CECT5713 plus an excipient, respectively); 57 couples completed the study. Baseline data on demographics, health status (including gynecological and reproductive history), and lifestyle habits were collected. Vaginal swabs and semen samples were obtained from each couple before the intervention and immediately prior to IVF or upon confirmed pregnancy and were analyzed for microbiological (using both culture-dependent and -independent methods) and immunological profiles. Results: Oral administration of L. salivarius CECT5713 in couples with unexplained infertility scheduled for IVF resulted in a significantly higher pregnancy success rate (48.1%) compared to the placebo group (20.0%) (one-tailed Chi-square test; p < 0.024). The probiotic intervention improved both vaginal and semen immunological profiles, with no substantial changes observed in their microbial composition. Conclusions: These preliminary findings support the potential of L. salivarius CECT5713 supplementation to enhance fertility outcomes in couples with unexplained infertility. Full article

Background/Objective: Urinary tract infections (UTIs) are a significant public health concern worldwide, yet longitudinal data from Portuguese hospital settings remain limited. This study aimed to characterize epidemiological trends, microbial etiology, antimicrobial resistance patterns, and associated risk factors of UTIs over a five-year period (2018–2022) in a central Portuguese hospital. Methods: In this retrospective observational study, 23,682 positive urine cultures were analyzed from specimens collected between January 2018 and December 2022. Data were extracted from the laboratory information system and included patient demographics, clinical service of origin, isolated microorganisms, resistance profiles, and annual antibiotic consumption (Defined Daily Dose (DDD) per 1000 patient-days). UTI prevalence was calculated as the proportion of positive cultures among all urine samples processed annually. Results: The positivity rate increased from 18.7% in 2018 to 22.7% in 2022, with a peak in 2019. Women represented around 70% of cases throughout the study period. Most infections originated from inpatient wards, followed by emergency services. Escherichia coli remained the leading pathogen (≈62%), followed by Klebsiella pneumoniae (≈14%) and Enterococcus faecalis (≈8%). Risk factors included catheterization (37.2%), prior UTI history (22.1%), and diabetes mellitus (18.5%). Longer hospital stays (>7 days) were associated with increased positivity. For E. coli, resistance ranged from 2% (amikacin) to 41% (ampicillin), with increasing resistance to ertapenem and fosfomycin and decreasing resistance to several key antibiotics. K. pneumoniae showed 4–36% resistance across antimicrobials, with notable increases for fosfomycin, meropenem, and cefuroxime axetil. Antibiotic usage trends reflected these patterns, with declining use of amikacin and rising use of cefuroxime axetil and meropenem. Conclusions: Over the five-year period, both UTI prevalence and resistance to critical antimicrobials increased, reinforcing the need to update empirical treatment guidelines. Identified risk factors may inform targeted prevention strategies. Ongoing surveillance and antimicrobial stewardship are crucial to mitigate the rising burden of UTIs and resistance Full article

Infections often occur in complex niches consisting of multiple bacteria. Despite the increasing awareness, there is a fundamental gap in understanding which interactions govern microbial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobial and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competition within co-cultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen’s multiple quorum-sensing (QS) systems in these interactions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI, and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR, control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with the ESKAPEE pathogens tested while disarming the pathogens’ ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously attenuating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections. Full article