Search Results (195)

Gut microbiota dysbiosis is implicated in metabolic disorders, yet taxonomic and functional alterations in canine diabetes remain incompletely defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 38 diabetic dogs and 37 healthy controls under controlled conditions (no recent antibiotic/probiotic exposure and stable commercial diets). Alpha-diversity indices did not differ between groups, whereas beta-diversity revealed significant separation of community structure at both genus and species levels (p < 0.05). Linear discriminant analysis effect size (LEfSe) identified enrichment of opportunistic-associated taxa in diabetic dogs, including Enterobacterales/Enterobacteriaceae (e.g., Escherichia coli, Klebsiella pneumoniae, Salmonella enterica) and Enterococcus faecalis. In contrast, healthy dogs were enriched for putatively beneficial taxa linked to bile acid and short-chain fatty acid (SCFA) metabolism, including Turicibacter spp. and Romboutsia spp. Functional profiling showed higher abundances of pathways related to carbohydrate/energy metabolism, membrane transport, and virulence/colonization in diabetic dogs; 17 KEGG level-3 pathways and 320 KOs differed at FDR < 0.05, with enriched modules including bacterial secretion systems, lipopolysaccharide biosynthesis, chemotaxis/flagellar assembly, and biofilm formation. Collectively, canine diabetes is associated with a remodeled gut microbiome characterized by expansion of opportunistic pathogens and elevated virulence and metabolic potential, supporting exploration of microbiota-targeted strategies as a complement to conventional management. Full article

Background/Objectives: The gut microbiome plays an important role in the colonization of an individual by Clostridioides difficile and in the development of Clostridioides difficile infection (CDI). The main purpose of this study was to compare the gut microbiomes of patients with CDI and healthy individuals. Methods: We prospectively included 48 individuals: 32 patients with CDI and 16 healthy individuals. Microbiomes were analyzed by sequencing the hypervariable regions of the 16S rRNA gene using an Ion GeneStudio™ S5 System. Further statistical analysis of microbiome data was performed with the open-source programming language R version 3.5.2. Results: Among the CDI patients, Firmicutes and Proteobacteria were the most abundant phyla, while Enterobacteriaceae and Enterococcaceae were the most abundant families. Genus-level analysis showed that Enterococcus was the dominant genus in CDI patients; in contrast, in healthy individuals, Faecalibacterium was the most abundant. The MaAsLin2 tool revealed that members of the family Enterococcaceae and the genus Enterococcus were more abundant in patients with CDI than in healthy individuals. Alpha and beta diversity did not reveal differences between the two study groups. Conclusions: We observed differences in microbiome patterns between healthy individuals and CDI patients that were consistent with the literature. Further studies are needed. Full article

Drawing on two indigenous chicken breeds that have adapted for centuries to the hyper-arid Tarim Basin, namely the Baicheng You Chicken and Hotan Black Chicken, this study provides a high-resolution map of their gut microbiota across the duodenum, jejunum, ileum and cecum and subsequently isolates putative probiotic strains from cecal contents using conventional culture techniques. In the duodenum, Lactobacillus dominated Hotan Black Chicken (43.16%), whereas Ligilactobacillus prevailed in Baicheng You Chicken (37.03%). This segregation persisted in the jejunum, with Lactobacillus accounting for 62.55% of Hotan Black Chicken reads and Ligilactobacillus accounting for 60.76% reads in Baicheng You Chicken. The ileal core of Hotan Black Chicken remained Lactobacillus (50.63%), while Baicheng You Chicken shifted to Enterococcus (32.37%). In the cecum, both breeds converged on the Rikenellaceae RC9 gut group as the single dominant lineage (Hotan Black Chicken, 46.87%; Baicheng You Chicken, 46.23%). At the genus level, Hotan Black Chicken was enriched in Lactobacillus and Ligilactobacillus, whereas Baicheng You Chicken harbored a greater proportion of Enterococcus. Concurrently, eight strains with in vitro probiotic attributes were isolated, four from each breed, identified as Ligilactobacillus salivarius, Limosilactobacillus reuteri, Lactobacillus gallinarum, Enterococcus lactis, Enterococcus faecium, Enterococcus faecalis, and Bacillus velezensis. This study deciphers the intestinal microbiome of two native Tarim Basin chicken breeds, Hotan Black Chicken and Baicheng You Chicken, and mines them for autochthonous probiotic strains. The obtained dataset has established a foundational resource for poultry-related probiotics adapted to extremely arid environments, providing theoretical insights and practical value for poultry nutritionists in water-scarce regions in the future. Full article

Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage–bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction–modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria–phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms. Full article

Lactic acid bacteria (LAB) are increasingly recognized for their role in food biopreservation due to their ability to synthesize antimicrobial compounds. Milk naturally harbors a wide variety of LAB, offering a promising source for identifying strains with biopreservative potential. This study investigated the antagonistic effects, safety characteristics, and technological properties of LAB strains isolated from traditionally fermented milk. Thirty-two dairy samples were analyzed, and the resulting LAB isolates were screened for inhibitory activity against Listeria monocytogenes CECT 4032 and Staphylococcus aureus CECT 976 using agar spot and well diffusion assays. All tested strains exhibited strong antimicrobial effects, with particularly notable inhibition of L. monocytogenes. After phenotypic screening, five representative isolates were selected for molecular identification and further assessment of safety-related attributes, functional capabilities, auto- and co-aggregation properties. 16S rRNA gene sequencing revealed that four strains belonged to the genus Enterococcus, specifically, one E. faecium and three E. durans, while one was classified as a Lactococcus species. Moreover, none of the strains showed proteolytic or lipolytic activities which highlights their potential use in dairy fermentation processes. Full article

The characterization of environmental Pseudomonas spp. from pharmaceutical industries is a relatively underexplored area of research. This study used 40 isolates of Pseudomonas from a pharmaceutical company that had been presumptively identified as Pseudomonas aeruginosa by VITEK^®2. The isolates were characterized using 16S rRNA sequencing, Multilocus Sequence Typing (MLST), Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass (MALDI–TOF MS), Fourier Transform Infrared (FT-IR) spectroscopy, ERIC-PCR, antimicrobial susceptibility profiling, and biofilm formation assessment on stainless steel surfaces. Twenty isolates were confirmed as P. aeruginosa. Sixteen isolates were only identified to the genus level of Pseudomonas, and the remaining four isolates were identified as Enterococcus faecalis (n = 2), Proteus spp. (n = 1), and Staphylococcus saprophyticus subsp. bovis/S. edaphicus/S. saprophyticus subsp. saprophyticus/S. pseudoxylosus/S. xylosus/S. caeli/S. ureilyticus. Typing of the 20 P. aeruginosa strains yielded 18 distinct FT-IR profiles and 19 ERIC-PCR profiles. The MLST analysis identified eight new sequence types (ST4292–ST4299). All strains were classified as multidrug-resistant (MDR), exhibiting resistance to multiple antimicrobial classes. Biofilm formation was observed in 28 (77.8%) Pseudomonas spp. strains on polystyrene surfaces, classified as moderately or strongly adherent, while all P. aeruginosa strains formed biofilms on stainless steel. Of the three disinfectants tested, sodium hypochlorite at 0.01% showed the best performance, reducing or eliminating biofilm formation in 24 (85.7%) strains. The regular evaluation of disinfection effectiveness in pharmaceutical industries is essential, as the presence of biofilm-forming strains can compromise production and contaminate final products. Full article

Gram-positive cocci of the Enterococcus genus, despite their prevalence in the environment and the microbiota of healthy people, have become a serious threat in hospitals as opportunistic pathogens. These bacteria have many virulence factors and intrinsic resistance to existing drugs, which significantly narrows the group of effective antimicrobials. Due to the spread of Multi-Drug-Resistant (MDR) strains, there is a need to search for new substances as potential antibiotics. Our work aimed to evaluate the antimicrobial effect of commercially available products (five oils containing cannabidiol (CBD) and its derivatives and one 99% CBD product in the form of crystals) on 20 clinical strains of E. faecalis and E. faecium. We determined the Minimal Inhibitory Concentration (MIC) of CBD oils using the microdilution method in Mueller–Hinton broth (MHB). The CBD displayed antibacterial properties against all tested Enterococcus spp. strains (MIC ≤ 1 μg/mL). The higher concentration of CBD resulted in a larger antibacterial effect. The obtained MICs of pure CBD and CBD crystals were statistically lower (W = 97, p < 0.001) for E. feacium than E. faecalis. This work confirms the antibacterial activity of CBD on Enterococcus spp., providing a solid basis for further research that can help identify new therapeutic options and gain a deeper understanding of the CBD mechanism of action. Full article

Mespilus germanica L. is one of the two species of the genus Mespilus L., and is distributed in several regions, including Southeastern Europe, Anatolia, the Caucasus, and parts of the Middle East. The fruits of the plant are consumed as food, and the fruits, leaves, and stem bark are traditionally used for various systemic disorders, including gastrointestinal, respiratory, urinary tract, and skin conditions, as well as menstrual irregularities. In our study, the anti-inflammatory potential and antimicrobial activities of aqueous-methanolic extracts prepared from ripe (MGRF) and unripe fruits (MGUF), leaves (MGL), and stem bark (MGB) of M. germanica were evaluated in vitro. Quercetin, catechin, epicatechin, ellagic acid, chlorogenic acid, and caffeic acid were analyzed using high-performance liquid chromatography. MGL exhibited the strongest activity against Staphylococcus aureus (MIC = 8 µg/mL), while MGB was most active against Enterococcus faecalis (MIC = 4 µg/mL), and fruit extracts were effective against resistant Acinetobacter baumannii (MIC = 16–32 µg/mL). Membrane-protective effects were more pronounced in MGUF and MGB, whereas MGL demonstrated the highest protein stabilization activity. Leaves also contained the highest levels of chlorogenic acid and epicatechin. These findings support the traditional use of M. germanica, though further studies are required to explore its therapeutic potential. Full article

Background and Objectives: Emerging evidence suggests that the genitourinary microbiota may influence the development and progression of urological malignancies, including bladder cancer. This study aimed to characterize the urinary microbiota at diagnosis in patients with bladder cancer and compare findings with healthy controls. Materials and Methods: Urine samples were collected from 30 patients with treatment-naïve bladder cancer and 20 age- and sex-matched healthy individuals. Microbiota composition was analyzed using 16S rRNA sequencing, and subgroup comparisons were made between muscle-invasive bladder cancer (MIBC) and non-muscle-invasive bladder cancer (NMIBC). Differentially abundant taxa were identified using linear discriminant analysis effect size (LEfSe) with an LDA threshold > 2 and p < 0.05. Results: No significant differences were observed in alpha or beta diversity between patients and controls or between MIBC and NMIBC. At the phylum level, Firmicutes was dominant in both groups but relatively more abundant in bladder cancer cases. Enterococcus was the most abundant genus in the cancer group (35.0%) and especially in MIBC (58.0%), while Lactobacillus was more prevalent in healthy controls (19.8% vs. 9.5%). At the species level, Veillonella dispar was notably enriched in MIBC cases (70.9%) compared to NMIBC (3.9%). LEfSe analysis revealed significant enrichment of Ralstonia, Microbacterium, and Facklamia in patients with bladder cancer, while Parvimonas, Sneathia, Gemella, and Acinetobacter guillouiae were more abundant in controls. Conclusions: These findings highlight preliminary microbiota differences associated with bladder cancer and tumor invasiveness; however, the results are exploratory and larger studies are required to evaluate their diagnostic or clinical relevance. Full article

Migratory birds travel long distances and interact with diverse environments, making them potential reservoirs and disseminators of antimicrobial-resistant bacteria. This study investigated the species distribution of migratory birds, bacterial isolates from bird internal organs, and the corresponding antimicrobial resistance (AMR) profiles in South Korea. A total of 35 bird carcasses representing 20 species were collected from five major stopover sites on the Sinan-gun islands along the East Asian–Australasian Flyway. More than half of the sampled birds belonged to the genus Emberiza, reflecting the prevalence of small migratory passerines in coastal habitats. From these carcasses, 54 bacterial isolates belonging to 24 species were identified, including Enterococcus spp., coliforms such as Enterobacter spp. and Escherichia coli, and opportunistic pathogens including Bacillus spp., Staphylococcus spp., and Serratia spp. Antimicrobial susceptibility testing revealed that 18 isolates (33.3%) were multidrug-resistant (MDR). Enterococcus isolates displayed high resistance to tigecycline and daptomycin, and two vancomycin-resistant strains were identified. Coliform isolates were resistant to third- and fourth-generation cephalosporins, carbapenems, and colistin. The two E. coli strains exhibited concurrent carbapenem–colistin resistance, posing a significant public health concern. These findings provide the first organ-level AMR dataset for migratory birds in South Korea and highlight the potential role of small passerines as ecological sentinels of environmental contamination. The detection of MDR strains underscores the need to integrate wildlife surveillance into One Health strategies for AMR monitoring. Full article

Natural whey starter (NWS) cultures are microbial consortia characterized by high microbial diversity in terms of genus and species, as well as strains, accounting for the variety of different characteristics and quality of the artisanal fermented food. By means of a combined approach, using plate counts, bacterial isolation, molecular identification, and genotyping, we analyzed 41 colonies isolated from NWS of cow milk used in the production of caciocavallo, a typical pasta filata Italian cheese. Results revealed that 27 of them were lactic acid bacteria (LAB), including Lactococcus lactis as the dominant species, followed by Streptococcus thermophilus, Enterococcus faecium, Limosilactobacillus fermentum, Lactobacillus helveticus, and Lacticaseibacillus rhamnosus. The remaining isolates were taxonomically identified as non-LAB, probably due to environmental contamination. These results were mostly confirmed by metagenomic analysis, with the exception of only three species. Finally, small-scale fermentation experiments were performed in both standard media and skimmed milk to further characterize the newly isolated LAB strains. Overall, our results show that, except for four of the Lactococcus isolates and one Streptococcus, which show multi-drug resistance, the isolated strains under study exhibit levels of acidifying, metabolic properties, and safety parameters, suggesting their potential as starter cultures in cheese production. Full article

Ventilator-associated pneumonia (VAP) is one of the most common hospital-acquired infections. Several studies have explored the potential role of the lung microbiome as a biomarker for identifying and predicting the prognosis of VAP. However, research on the respiratory microbiome in individuals with VAP caused by carbapenem-resistant Acinetobacter baumannii (CRAB) remains limited. Therefore, we aimed to analyze the respiratory microbiome of patients with CRAB VAP. Respiratory specimens were collected from patients who developed CRAB VAP. Microbiome diversity and composition were analyzed using 16S rRNA gene pyrosequencing. Patients were categorized into two groups based on mortality outcomes: intensive care unit (ICU) mortality or 28-day mortality after ICU discharge. Twenty patients with CRAB VAP were enrolled, including nine in the mortality group. No significant differences were observed in α-diversity indices between the study groups. However, multivariable Firth’s logistic regression revealed a significant association between a relative abundance of the Enterococcus genus ≥ 1% and mortality outcomes (odds ratio: 0.06; 95% confidence interval: 0.00–0.771; p = 0.029). This study characterized the respiratory microbiome of patients with CRAB VAP and highlighted the potential role of microbiome analysis in predicting disease prognosis. Further studies with larger sample sizes are warranted to validate these findings. Full article

Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6–24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (p < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log₂FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as Bifidobacterium longum, Faecalibacterium, Lactobacillus, and Eubacterium, alongside an enrichment of opportunistic taxa including Klebsiella, Enterococcus lactis, and Streptococcus spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions. Full article

Pampus argenteus (Zobaidy) is an important fish in Kuwait and the Gulf region due to its economic value in the fish industry. Analyzing the gut microbiome of Zobaidy can help determine the health status of the fish and its responses to environmental changes. In this study, we investigated the microbiome composition of the intestinal tract among seven wild-caught silver pomfret specimens sampled in the Arabian gulf. The 16S rRNA was sequenced using the Illumina platform; then, sequences were analyzed using several bioinformatics tools to identify the microbial diversity, taxonomical status, and functional aspects. The results were 5933 operational taxonomic units (OTUs) categorized into 35 phyla. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacterota were most abundant in the Zobaidy and water samples. At the genus level, we found high relative abundances of Acinetobacter. The results indicated that Lactococcus piscium, Enterococcus cecorum, Psychrobacter arenosus, Vagococcus salmoninarum, and Carnobacterium maltaromaticum are the most commonly present species in the analyzed Zobaidy samples. A heatmap analysis indicated notable differences in the functional categories of intestinal microflora within the Zobaidy2 sample compared to other Zobaidy samples. It should be noted that microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention, and increase sustainability in aquaculture production. Full article

Essential oils from the genus Piper are recognized for their chemical diversity and biological potential, yet Piper platylobum has been scarcely investigated. This study aimed to characterize the chemical composition of the leaf essential oil of P. platylobum and evaluate its antimicrobial, antioxidant, and anticholinesterase activities. The oil was obtained by steam distillation and analyzed through gas chromatography–mass spectrometry (GC-MS) and gas chromatography equipped with a flame ionization detector (GC-FID), leading to the identification of 35 compounds that accounted for 91.11% of the volatile fraction. Dillapiole (42.0%) was the principal constituent, followed by α-(E)-bergamotene (5.69%), (E)-caryophyllene (5.01%), and (E)-isocroweacin (3.75%). Biological assays revealed selective antimicrobial activity, with inhibition observed only against Enterococcus faecium (MIC = 1000 µg/mL), while no effect was detected against other bacterial or fungal strains tested. Antioxidant evaluation showed moderate activity in the ABTS assay (SC₅₀ = 335.71 ± 1.43 µg/mL; TEAC = 45.85 ± 1.68 µM Trolox/g EO), but no activity in the DPPH assay. The essential oil also displayed moderate inhibition of acetylcholinesterase (IC₅₀ = 76.86 ± 1.00 µg/mL), suggesting a potential role in neuroprotective applications. This study constitutes the first report on the chemical composition and biological activities of P. platylabum essential oil, highlighting its potential as a novel source of bioactive compounds. Full article