Search Results (1,027)

The study of various microorganisms isolated from an Indian Ocean sponge, Scopalina hapalia ML-263, led to the selection of a promising Actinobacteria strain, Micromonospora sp. SH-82. Genomic analysis identified this strain as a new species, revealing the presence of 23 biosynthetic gene clusters (BGCs), some of which are associated with the synthesis of specialized metabolites such as polyketides deriving from polyketide synthases (PKSs). The strain was cultivated under favorable conditions for the production of bioactive molecules, resulting in the isolation and identification of seven microbial metabolites. Three of them are potentially novel, two erythronolides and one erythromycin, all characterized by a rare C10–C11 double bond. Some of these compounds also display atypical conformations, forming hemiacetals or spiroacetals. Their identification was achieved through detailed chemical analyses (NMR and ESI⁺-HRMS). A molecular networking approach was employed to assess the presence of potentially novel molecules in the microbial crude extract, supported by the identification of isolated molecules. Four molecules (1, 2, 3 and 5) were evaluated for their cytotoxic activities against cancer cell lines (HCT-116 and MDA-MB-231) and the immortalized retinal pigment epithelial RPE1 cells. No activity was observed in the latter, suggesting a lack of toxicity toward healthy cells. Moreover, megalomicin C1 (3), one of the isolated compounds, showed interesting antiplasmodial activity against Plasmodium falciparum 3D7, with an IC₅₀ of 6.37 ± 2.99 µM. Full article

Clinical manifestations of salmonellosis in humans typically include acute gastroenteritis, abdominal pain, diarrhea, nausea, and fever. Diarrhea and anorexia may persist for several days. In some cases, the organisms may invade the intestinal mucosa and cause septicemia, even in the absence of significant gastrointestinal symptoms. Most clinical signs are attributed to hematogenous dissemination of the pathogen. As with other microbial infections, disease severity is influenced by the serotype of the organism, bacterial load, and host susceptibility. Serotyping analysis of Salmonella spp. using the White–Kauffmann–Le Minor scheme remains the gold standard for strain typing. However, this method is expensive, time-consuming, and requires significant expertise and visual interpretation by trained personnel, which is why it is typically restricted to regional or national reference laboratories. In this study, we evaluated a spectroscopic technique coupled with chemometrics and multivariate machine learning algorithms for its ability to discriminate the main Salmonella spp. serogroups in a clinical routine setting. We analyzed 95 isolates of Salmonella that were randomly selected, including four strains of S. Typhi. The I-dOne Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) system (Alifax S.r.l., Polverara, Italy) also shows promising potential for distinguishing Salmonella Typhi within the D serogroup. The I-dOne system enables simultaneous identification of both species and subspecies using the same workflow and instrumentation, thus streamlining the diagnostic process. Full article

Light-flavor Baijiu (LFB) is renowned for its distinct flavor and long history, with the microbial community structure of low-temperature Daqu (LTD) serving as a crucial saccharification fermenter that significantly influences the quality and flavor of Baijiu. With the rapid advancement of biotechnology, research on LTD has become more in-depth, focusing on the identification of core microorganisms and the construction of Synthetic Microbial Communities (SynComs), which have emerged as research hotspots. Core microorganisms play a vital role in fermentation and flavor development, while SynComs are artificially constructed microbial combinations designed to optimize fermentation and improve liquor quality. This paper provides a systematic overview of the core microorganisms associated with LTD and their identification methods, as well as the concepts, advantages, applications, and construction methodologies of SynComs. It compiles relevant research findings to offer a theoretical foundation for a deeper understanding of the brewing mechanism and further optimization of the LFB brewing process, along with insights into future research directions. Full article

Background: Timely and accurate identification of wound infections is essential for effective management, yet remains clinically challenging. This study evaluated the utility of a near-infrared autofluorescence imaging system (Fluobeam^®, Fluoptics, Grenoble, France) and a thermal imaging system (FLIR^®, Teledyne LLC, Thousand Oaks, CA, USA) for detecting bacterial and fungal infections in chronic wounds. Fluobeam^® enables real-time visualization of microbial autofluorescence without exogenous contrast agents, whereas FLIR^® detects localized thermal changes associated with infection-related inflammation. Methods: This retrospective clinical study included 33 patients with suspected wound infections. All patients underwent autofluorescence imaging using Fluobeam^® and concurrent thermal imaging with FLIR^®. Imaging findings were compared with microbiological culture results, clinical signs of infection, and semi-quantitative microbial burdens. Results: Fluobeam^® achieved a sensitivity of 78.3% and specificity of 80.0% in detecting culture-positive infections. Fluorescence signal intensity correlated strongly with microbial burden (r = 0.76, p < 0.01) and clinical indicators, such as exudate, swelling, and malodor. Pathogens with high metabolic fluorescence, including Pseudomonas aeruginosa and Candida spp., were consistently identified. Representative cases demonstrate the utility of fluorescence imaging in guiding targeted debridement and enhancing intraoperative decision-making. Conclusions: Near-infrared autofluorescence imaging with Fluobeam^® and thermal imaging with FLIR^® offer complementary, noninvasive diagnostic insights into microbial burden and host inflammatory response. The combined use of these modalities may improve infection detection, support clinical decision-making, and enhance wound care outcomes. Full article

Background/Objectives: 16S ribosomal RNA sequencing has, for several years, been the main means of identifying bacterial and archaeal species. Low-throughput Sanger sequencing is often used for the detection and identification of microbial species, but this technique has several limitations. The use of high-throughput sequencers may be a good alternative to improve patient identification, especially for polyclonal infections and management. Kraken 2 and KrakenUniq are free, high-throughput tools providing a very rapid and accurate classification for metagenomic analyses. However, Kraken 2 can present false-positive results relative to KrakenUniq, which can be limiting in hospital settings requiring high levels of accuracy. The aim of this study was to establish an alternative next-generation sequencing technique to replace Sanger sequencing and to confirm that KrakenUniq is an excellent analysis tool that does not present false results relative to Kraken 2. Methods: DNA was extracted from reference bacterial samples for Laboratory Quality Controls (QCMDs) and the V2-V3 and V3-V4 regions of the 16S ribosomal gene were amplified. Amplified products were sequenced with the Illumina 16S Metagenomic Sequencing protocol with minor modifications to adapt and sequence an Illumina 16S library with a small 500-cycle nano-flow cell. The raw files (Fastq) were analyzed on a commercial Smartgene platform for comparison with Kraken 2 and KrakenUniq results. KrakenUniq was used with a standard bacterial database and with the 16S-specific Silva138, RDP11.5, and Greengenes 13.5 databases. Results: Seven of the eight (87.5%) QCMDs were correctly sequenced and identified by Sanger sequencing. The remaining QCMD, QCMD6, could not be identified through Sanger sequencing. All QCMDs were correctly sequenced and identified by MiSeq with the commercial Smartgene analysis platform. QCMD6 contained two bacteria, Acinetobacter and Klebsiella. KrakenUniq identification results were identical to those of Smartgene, whereas Kraken 2 yielded 25% false-positive results. Conclusions: If Sanger identification fails, MiSeq with a small nano-flow cell is a very good alternative for the identification of bacterial species. KrakenUniq is a free, fast, and easy-to-use tool for identifying and classifying bacterial infections. Full article

With the rise of environmental protection and health topics in recent years, microbial production of red pigments has gradually become a research hotspot. Red pigment possesses biological properties such as anticancer and antioxidant activities and has a wide range of potential applications in the fields of food and medicine. In this paper, a red pigment-producing strain was screened from rice soil to provide a reserve for obtaining natural and safe red pigments. Methods: The strain LSY1-2 was identified using morphological and 16S rDNA molecular biological identification. The fermentation conditions for red pigment production were optimised to improve pigment yield, and the best conditions were analysed using response surface methodology. Finally, the stabilisation conditions of red pigment were analysed to determine the difficulty of retention. Results: The molecular ecology was identified as the bacterium Arthrobacter sp. of the genus Arthrobacter. The optimal red pigment production medium for the strain was determined by a one-way test with the carbon source beef extract, the nitrogen source peptone, the inoculum size 2%, the temperature 27 °C, the pH value 7, and the rotational speed 160 rpm. Response surface optimisation determined the optimal red pigment production conditions as the incubation temperature of 26.43 °C, the pH value of 6.89, and the rotational speed of 162.77 rpm, which resulted in the yield of red pigment under these optimal conditions as 0.883 U/mL. The stability of red pigment was best under the condition without light, and poorer under conditions of above 50 °C, strong acid, strong alkali, and more than 3% oxidant, and Fe³⁺ had a greater effect on the stability. Conclusions: Strain LSY-1 can produce stable red pigment under the optimised red pigment-producing conditions, which provides a reference for the large-scale production of natural red pigment and subsequent related research. Full article

The Forensic Anthropology Research Facility (FARF) at Texas State University (TXST), San Marcos, TX, USA, is a leading human taphonomy facility (HTF), dedicated to advancing forensic science through the study of human decomposition. This systematic review synthesizes 15 scholarly outputs comprising 7 peer-reviewed journal articles and 8 dissertations centered on arthropod-associated research undertaken at FARF, with particular emphasis on its contribution to forensic entomology. The analyzed body of literature is organized into six overarching thematic domains: (1): refining postmortem interval (PMI) estimation; (2): developmental biology of forensic arthropods; (3): arthropod behavior and forensic implications; (4): Taxonomy and systematics; (5): microbial–arthropod interactions; and (6): forensic decomposition scenarios with arthropod involvement. Key contributions from these studies include refined methodologies for PMI estimation, the systematic revision of forensically relevant arthropods and identification of accidental arthropod activity. Additionally, studies at FARF have incorporated interdisciplinary approaches bridging entomology, microbiology and ecology. The semi-arid, subtropical environment and large open natural range of FARF provides some unique regional and specific insights concerning decomposition. This entomological review on FARF is the first to be completed concerning any HTF and adds to the knowledge of forensic evidence involving arthropods. Full article

Cryptosporidium is a major waterborne parasite that causes gastrointestinal illness. Conventional assays, including microscopy and immunological identification, often suffer from false positives or negatives due to non-specific binding or morphological differences between Cryptosporidium species. We developed a novel qPCR assay based on a Cryptosporidium-specific Conserved Signature Protein (CSP) to address the limitations of testing complex samples, including those from recreational waters. The CSP (hypothetical protein (cgd2_3830)) was identified as taxonomically unique to Cryptosporidium species. The CSP sequence and designed qPCR assay primers/probe demonstrated high specificity for the targeted Cryptosporidium species when tested against NCBI RefSeq databases. qPCR assay efficiency was determined as 95% and an R² value of 0.99, with a slope and intercept of −3.4 and 40.1, respectively. Additionally, the Lower Limit of Detection (ALLOD) was determined as three gene copies, suggesting the potential to detect even a single oocyst. No non-specific amplification products or primer dimers were observed when the qPCR assay was evaluated using recreational water, fecal solution, and wastewater, while spike-in-control tests indicated minimal interference with the sensitivity of the assay, highlighting application for testing complex environmental DNA extracts. These findings highlight the application of the novel CSP-based qPCR assay for the rapid and sensitive detection of Cryptosporidium sp., thereby circumventing the sequence variability and multi-copy limitations associated with existing molecular markers. This proof-of-concept study presents a diagnostic framework utilizing CSP-based markers for developing water quality monitoring strategies, with scope for expansion to other microbial pathogens and potential applications in clinical and food safety settings. Full article

16S rRNA next-generation sequencing (NGS) has significantly advanced cervicovaginal microbiome profiling, offering insights into the relationship between vaginal dysbiosis and HPV-associated carcinogenesis. However, reliance on a limited set of 16S hypervariable regions introduces inherent biases that impact results. This study developed standardized workflows for 16S/ITS NGS, with a focus on identifying methodological biases that influence microbial abundance and taxonomic specificity. Commercial NGS tools were employed, including the 16S/ITS QIAseq V1–V9 screening panel, ATCC vaginal microbial standard, and CLC Genomics Workbench integrated with a customized database (VAGIBIOTA) for analysis. The microbial communities of 66 cervical cytology samples were characterized. Among the regions tested, V3V4 exhibited the least quantitative bias, while V1V2 offered the highest specificity. Microbial profiles and Community State Types (CST) (I–V) were broadly consistent with prior studies, with Lactobacillus abundance clustering into three states: L.-dominant (CST I–III, V), L.-diminished (CST IV-A), and L.-depleted (CST IV-B). Differential abundance analysis revealed that anaerobic opportunistic pathogens dominant in CST IV-B (dysbiosis) were also enriched in HSIL and HPV-16 positive samples. Our findings revealed distinct differences in species identification across 16S rRNA hypervariable regions, emphasizing the importance of region selection in clarifying microbial contributions to HPV-associated carcinogenesis. Full article

Obesity is a global health challenge marked by substantial inter-individual differences in responses to dietary and lifestyle interventions. Traditional weight loss strategies often overlook critical biological variations in genetics, metabolic profiles, and gut microbiota composition, contributing to poor adherence and variable outcomes. Our primary aim is to identify key biological and behavioral effectors relevant to precision medicine for weight control, with a particular focus on nutrition, while also discussing their current and potential integration into digital health platforms. Thus, this review aligns more closely with the identification of influential factors within precision medicine (e.g., genetic, metabolic, and microbiome factors) but also explores how these factors are currently integrated into digital health tools. We synthesize recent advances in nutrigenomics, nutritional metabolomics, and microbiome-informed nutrition, highlighting how tailored dietary strategies—such as high-protein, low-glycemic, polyphenol-enriched, and fiber-based diets—can be aligned with specific genetic variants (e.g., FTO and MC4R), metabolic phenotypes (e.g., insulin resistance), and gut microbiota profiles (e.g., Akkermansia muciniphila abundance, SCFA production). In parallel, digital health tools—including mobile health applications, wearable devices, and AI-supported platforms—enhance self-monitoring, adherence, and dynamic feedback in real-world settings. Mechanistic pathways such as gut–brain axis regulation, microbial fermentation, gene–diet interactions, and anti-inflammatory responses are explored to explain inter-individual differences in dietary outcomes. However, challenges such as cost, accessibility, and patient motivation remain and should be addressed to ensure the effective implementation of these integrated strategies in real-world settings. Collectively, these insights underscore the pivotal role of precision nutrition as a cornerstone for personalized, scalable, and sustainable obesity interventions. Full article

Plant growth-promoting rhizobacteria (PGPRs) colonise the rhizosphere and root surfaces, enhancing crop development through a variety of mechanisms. This study evaluated microbial strains isolated from Triticum aestivum L. for key plant growth-promoting traits, including indole-3-acetic acid (IAA) production, phosphate and zinc (Zn) solubilisation, nitrogen (N₂) fixation, and antifungal activity. Among 36 isolates, 3 (AS8, AS23, AS31) exhibited strong growth-promoting potential. IAA production, citrate assimilation, carbohydrate fermentation, and catalase activity were observed to a comparable extent among the selected strains. AS8 showed the highest protease, lipase, and amylolytic activity, while AS23 demonstrated superior phosphate and Zn solubilisation. Notably, AS31 emerged as the most promising multi-trait isolate, exhibiting the highest levels of IAA production, N₂ fixation, antifungal activity against five phytopathogens (Fusarium graminearum, F. solani, F. oxysporum, Pythium aphanidermatum, and Alternaria alternata), potentially linked to its hydrogen sulphide (H₂S) production, and cellulolytic activity. Molecular identification based on 16S rRNA gene sequencing revealed the isolates as Stenotrophomonas indicatrix AS8, Pantoea agglomerans AS23, and Bacillus thuringiensis AS31. Seed germination assays confirmed the plant growth-promoting efficacy of these PGPR strains, with vigour index increases of up to 43.4-fold. Given their positive impact on seed germination and significant Zn-solubilising abilities, the selected strains represent promising candidates for use as bio-inoculants, offering a sustainable and eco-friendly strategy to enhance agricultural productivity in nutrient-deficient soils. Future research should validate the efficacy of these PGPR strains under pot conditions to confirm their potential for practical agricultural applications. Full article

Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based techniques and modern omics approaches. The review also focuses on interactions between these microorganisms and their host plants, emphasizing their roles in biocontrol, phytoremediation, and nanoparticle biosynthesis. While significant progress has been made in characterizing cultivable bacterial endophytes, challenges persist in accessing unculturable species and understanding strain-specific functional mechanisms. The integration of metagenomics, metatranscriptomics, and metabolomics has begun unraveling this hidden diversity, revealing novel metabolic pathways and plant–microbe communication systems. There have been limitations in endophyte isolation protocols and field applications, and therefore a need exists for standardized frameworks to bridge lab-based discoveries with agricultural practices. Cutting-edge multi-omics techniques, such as genomics, transcriptomics, metabolomics, proteomics, and phenomics, should be used more in future research to clarify the mechanistic underpinnings of plant–endophyte interactions to thoroughly profile the microbial communities and unlock their functional potential under diverse environmental conditions. Overall, bacterial endophytes present viable paths toward sustainable farming methods, supporting food security and crop resilience in the face of environmental difficulties by providing a transformative opportunity for next-generation agriculture, mitigating climate-related agricultural stressors, reducing dependence on synthetic agrochemicals, and enhancing crop productivity. Full article

Considering the clinical relevance of commensal yeasts (Malassezia and Candida) and zoophilic dermatophytes (Microsporum canis and Trichophyton mentagrophytes) in dogs and cats, this study determines the prevalence of fungal species involved in ear and superficial skin infections in dogs and cats in Grenada and examines their antifungal susceptibility. The etiological agents were isolated from ear, skin, and hair samples of suspected clinical fungal cases using Sabouraud Dextrose Agar (SAB). The isolates’ identification comprised morphological, biochemical, and molecular methods encompassing micro-/macroscopy analysis. Biochemically, yeast isolates were identified by the BD Phoenix M50 microbial identification system, and additional validation of all fungal isolates was performed by polymerase chain reaction (PCR) and sequencing of the ITS region. Furthermore, the E-Test (Epsilometer Test) was used to determine the susceptibility patterns for four azole drugs: ketoconazole, itraconazole, fluconazole, and voriconazole. A total of 405 samples (266 ear, 61 skin, and 78 hair) were collected from 136 dogs and 43 cats. The identified species were Malassezia pachydermatis, Candida tropicalis, and Trichophyton spp. All isolates demonstrated (100%) resistant activity to fluconazole. Importantly, this knowledge will significantly contribute to our understanding of the epidemiology of fungal infections as well as provide guidelines for preventive measures against fungal infections in Grenada. Full article

Background/Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) infections remain a significant challenge in healthcare. Conventional and molecular techniques used for MRSA identification are either time-consuming or costly. Alternatively, Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) offers a rapid method for microbial identification and has the potential to detect biomarkers that distinguish methicillin resistance in S. aureus isolates. The aim of this study was to identify methicillin-resistant discriminative biomarkers for S. aureus obtained using MALDI-TOF MS. Methods: A systematic review was conducted by searching databases such as PubMed and Web of Science for studies that focused on MRSA detection with biomarkers by MALDI-TOF MS, including all relevant studies published up to July 2024. The review protocol was registered in PROSPERO registry. Results: A total of 15 studies were selected for analysis. Data were extracted on study location, sample size, MALDI-TOF MS analyzer, sample preparation, methicillin resistance and sensitivity biomarkers, and the use of Artificial Intelligence (AI) models. Notably, PSM-mec and delta toxin were frequently reported as informative biomarkers, detectable at 2414 ± 2 Da and 3006 ± 2 Da, respectively. Additionally, eight studies used AI models to identify specific biomarkers differentiating methicillin-resistant and methicillin-sensitive strains, based on differences in peak intensities or the exclusive presence of certain peaks. Moreover, two studies employed detection of MRSA in low concentrations from biological samples and others employed an optimized matrix solution for improved analysis. Conclusions: Overall, MALDI-TOF MS is not only a powerful tool for the identification of bacterial isolates but also shows strong potential for rapid, cost-effective detection of methicillin resistance in S. aureus through biomarker analysis. Given that it is already implemented in several clinical laboratories, this approach could be adopted without significant additional cost. Full article

The precipitation of minerals, in particular carbonates, is a widespread phenomenon in all ecosystems, where it assumes a high relevance both from a geological and biogeochemical standpoint. Most carbonate rocks are of biological origin and made in an aquatic environment. In particular, bioprecipitation of carbonates is believed to have started in the Mesoproterozoic Era, thanks to a process often driven by photosynthetic microorganisms. Nevertheless, an important contribution to carbonate precipitation is also due to the metabolic activity of heterotrophic bacteria, which is not restricted to specific taxonomic groups or to specific environments, making this process a ubiquitous phenomenon. In this framework, the relationship between carbonatogenic microorganisms and other living organisms assumes a particular interest. This study aims to isolate and identify the culturable heterotrophic bacterial component associated with the coenosarc of Corallium rubrum in order to evaluate the occurrence of strains able to precipitate carbonates. In particular, the study was focused on the identification and characterisation of bacterial strains isolated from a coral coenosarc showing a high carbonatogenic capacity under laboratory conditions. Samples of C. rubrum were taken in the coastal waters of three Italian regions. The concentration of the aerobic heterotrophic microflora colonising C. rubrum coenosarc samples spanned from 3 to 6∙10⁶ CFU/cm². This variation in microbial populations colonising the C. rubrum coenosarc, spanning over 6 orders of magnitude, is not mirrored by a corresponding variability in the colony morphotypes recorded, with the mean being 5.1 (±2.1 sd). Among these bacteria, the carbonatogenic predominant species was Staphylococcus equorum (93% of the isolates), whereas Staphylococcus xylosus and Shewanella sp. accounted only for 3% of isolates each. All these strains showed a remarkable capacity of precipitating calcium carbonate, in the form of calcite crystals organised radially as well crystalised spherulites (S. equorum) or coalescing spherulites (Shewanella sp.). S. xylosus only produced amorphous precipitates of calcium carbonate. All bacterial strains identified were positive both for the production of urease and carbon anhydrase in vitro at 30 °C. It seems that they potentially possess the major biochemical abilities conducive to Ca²⁺ precipitation, as they showed in vitro. In addition, all our carbonatogenic isolates were able to hydrolyse the phytic acid calcium salt and then were potentially able to induce precipitation of calcium phosphates also through such a mechanism. Full article