Search Results (288)

Background/Objectives: Helicobacter pylori (H. pylori) is a common gastric pathogen linked to gastritis, gastroduodenal ulcers, and gastric cancer. Rising antimicrobial resistance (AMR) poses challenges for effective treatment and has prompted the WHO to classify H. pylori as a high-priority pathogen. This study aimed to detect the prevalence of AMR genes in H. pylori-positive gastric samples from patients in Algarve, Portugal, where regional data is scarce. Methods: Eighteen H. pylori-positive gastric biopsy samples from patients undergoing upper gastrointestinal endoscopy were analyzed. PCR and sequencing were used to identify genes associated with resistance to amoxicillin (Pbp1A), metronidazole (rdxA, frxA), tetracycline (16S rRNA mutation) and clarithromycin (23S rRNA). Sequence identity and homologies were verified using tBLASTx and the Comprehensive Antibiotic Resistance Database (CARD). Results: Out of the 18 H. pylori-positive samples, 16 (88.9%) contained at least one AMR gene. The most frequent genes were rdxA (83.3%) and frxA (66.7%) for metronidazole resistance, and the 16S rRNA mutation (66.7%) for tetracycline. Resistance to amoxicillin and clarithromycin was detected in 27.8% and 16.7% of cases, respectively. Most samples (72.2%) had multiple resistance genes. A significantly strong association was found between female sex and the presence of the rdxA gene (p = 0.043). Conclusions: The study reveals a high prevalence of H. pylori resistance genes in Algarve, particularly against metronidazole and tetracycline. These findings highlight the need for local surveillance and tailored treatment strategies. Further research with larger populations is warranted to assess regional resistance patterns and improve eradication efforts. Full article

In Brazil, Plasmodium infections in non-human primates (NHPs) have been associated with P. simium and P. brasilianum, which are morphologically and genetically similar to the human-infecting species P. vivax and P. malariae, respectively. Surveillance and monitoring of wild NHPs are crucial for understanding the distribution of these parasites and assessing the risk of zoonotic transmission. This study aimed to detect the presence of Plasmodium spp. genetic material in Platyrrhini primates from 47 municipalities in the states of Bahia and Minas Gerais. The animals were captured using Tomahawk-type live traps baited with fruit or immobilized with tranquilizer darts. Free-ranging individuals were chemically restrained via inhalation anesthesia using VetBag^® or intramuscular anesthesia injection. Blood samples were collected from the femoral vein. A total of 298 blood and tissue samples were collected from 10 primate species across five genera: Alouatta caraya (25), Alouatta guariba clamitans (1), Callicebus melanochir (1), Callithrix geoffroyi (28), Callithrix jacchus (4), Callithrix kuhlii (31), Callithrix penicillata (175), Callithrix spp. hybrids (15), Leontopithecus chrysomelas (16), Sapajus robustus (1), and Sapajus xanthosthernos (1). Molecular diagnosis was performed using a nested PCR targeting the 18S small subunit ribosomal RNA (18S SSU rRNA) gene, followed by sequencing. Of the 298 samples analyzed, only one (0.3%) from Bahia tested positive for Plasmodium brasilianum/P. malariae. This represents the first detection of this parasite in a free-living C. geoffroyi in Brazil. These findings highlight the importance of continued surveillance of Plasmodium infections in NHPs to identify regions at risk for zoonotic transmission. Full article

Background/Objectives: An increasing number of apparently healthy individuals are adhering to a gluten-free lifestyle without any underlying medical indications, although the evidence for the health benefits in these individuals remains unclear. Although it has already been shown that a low- or gluten-free diet alters the gut microbiota, few studies have examined the effects of this diet on healthy subjects. Therefore, our aim was to evaluate whether and how a prolonged low-gluten diet impacts gut microbiota composition and function in healthy adults, bearing in mind its intimate link to the host’s health. Methods: Forty healthy volunteers habitually consuming a gluten-containing diet (HGD, high-gluten diet) were included in a randomised control trial consisting of two successive 8-week dietary intervention periods on a low-gluten diet (LGD). After each 8-week period, gut microbiota composition was assessed by 16S rRNA gene sequencing, molecular quantification by qPCR, and a cultural approach, while its metabolic capacity was evaluated through measuring faecal fermentative metabolites by ¹H NMR. Results: A prolonged period of LGD for 16 weeks reduced gut microbiota richness and decreased the relative abundance of bacterial species with previously reported potential health benefits such as Akkermansia muciniphila and Bifidobacterium sp. A decrease in certain plant cell wall polysaccharide-degrading species was also observed. While there was no major modification affecting the main short-chain fatty acid profiles, the concentration of the intermediate metabolite, ethanol, was increased in faecal samples. Conclusions: A 16-week LGD significantly altered both composition and metabolic production of the gut microbiota in healthy individuals, towards a more dysbiotic profile previously linked to adverse effects on the host’s health. Therefore, the evaluation of longer-term LDG would consolidate these results and enable a more in-depth examination of its impact on the host’s physiology, immunity, and metabolism. Full article

Background/Objectives: Obesity is increasingly recognized as a global health concern due to its association with metabolic disorders and gut microbiota dysbiosis. While probiotics offer promise in regulating gut microbiota and improving host metabolism, strain-specific effects remain underexplored, particularly for canine-derived probiotics. This study aimed to isolate and characterize a novel probiotic strain, Ligilactobacillus animalis LA-1, and evaluate its anti-obesity effects and underlying mechanisms using a high-fat diet (HFD)-induced obese mouse model. Methods: LA-1 was isolated from the feces of a healthy dog and assessed for probiotic potential in vitro, including gastrointestinal tolerance, bile salt hydrolase activity, cholesterol-lowering capacity, and fatty acid absorption. Male C57BL/6J mice were fed either a standard chow diet or an HFD for 16 weeks, with HFD mice receiving oral LA-1 supplementation (2 × 10⁹ CFU/day). Multi-omics analyses, including 16S rRNA gene sequencing, short-chain fatty acid (SCFA) quantification, and untargeted liver metabolomics, were employed to investigate the effects of LA-1 on gut microbiota composition, metabolic pathways, and obesity-related phenotypes. Results: LA-1 supplementation significantly alleviated HFD-induced weight gain, hepatic lipid accumulation, and adipose tissue hypertrophy, without affecting food intake. It improved serum lipid profiles, reduced liver injury markers, and partially restored gut microbiota composition, decreasing the Firmicutes/Bacteroidetes ratio and enriching SCFA-producing genera. Total SCFA levels, particularly acetate, propionate, and butyrate, increased following LA-1 treatment. Liver metabolomics revealed that LA-1 modulated pathways involved in lipid and amino acid metabolism, resulting in decreased levels of acetyl-CoA, triglycerides, and bile acids. Conclusions: L. animalis LA-1 exerts anti-obesity effects via gut microbiota modulation, enhanced SCFA production, and hepatic metabolic reprogramming. These findings highlight its potential as a targeted probiotic intervention for obesity and metabolic disorders. Full article

Urban river ecosystems are increasingly threatened by anthropogenic activities, with wastewater discharge being a significant contributor. The complex nature and diverse sources of wastewater pose challenges in assessing its impact on water quality and ecological health. This study investigated the distribution, toxicity, and ecological effects of organic pollutants in an urban river system during the dry season. A comprehensive analysis was conducted of 16 phthalate esters (PAEs), 16 polycyclic aromatic hydrocarbons (PAHs), and 8 antibiotics, with a focus on several key pollutants. The results revealed distinct pollutant profiles: Dibutyl phthalate (DBP), Dimethyl phthalate (DEHP), and Diisobutyl phthalate (DIBP) were the predominant PAEs, while Chrysene was the most abundant PAH. Among antibiotics, Oxytetracycline and Norfloxacin were the dominant compounds. Wastewater treatment plant (WWTP) effluents significantly altered the composition of organic pollutants in receiving waters. Although dilution reduced the concentrations of some pollutants, certain organic compounds were detected for the first time downstream of the WWTP, and some specific compounds exhibited increased concentrations. Toxicity prediction using the Concentration Addition (CA) model identified DBP as the primary contributor to overall toxicity, accounting for the highest toxic load among all detected pollutants. Furthermore, WWTP effluents induced significant shifts in microbial community structure downstream, with incomplete recovery to upstream conditions. Integrated analysis of 16S rRNA gene sequencing, water quality assessment, and toxicity prediction elucidated the multifaceted impacts of pollution sources on aquatic ecosystems. This study provides critical insights into the composition, spatial distribution, and toxicity characteristics of organic pollutants in urban rivers, as well as their effects on bacterial community structure. The findings offer a scientific foundation for urban river water quality management and ecological protection strategies. Full article

Background: Obesity is characterized by a chronic state of low-grade inflammation. Investigating immune-critical genes and their biological functions in the adipose tissue of postmenopausal obese women is crucial for elucidating the underlying mechanisms of immune dysregulation associated with obesity. Methods: In this study, microarray (GSE151839) and single-cell RNA-seq (GSE176171) datasets were obtained from the Gene Expression Omnibus (GEO). For microarray data analysis, weighted gene co-expression network analysis (WGCNA), protein–protein interaction network (PPI) analysis, and immune infiltration analysis (ssGSEA) were employed to identify obesity-related immune-critical genes. Subsequently, the candidate genes were validated using scRNA-seq data to explore their expression patterns at the single-cell level. Finally, the expression levels of these immune-critical genes were experimentally verified in adipose tissue from obese and control zebrafish models using RT-qPCR. Results: Analysis of microarray data through WGCNA, PPI and ssGSEA identified 16 obesity-related immune-critical genes, including IL7R, CD3E, CD2, CCR5, CD3D, MS4A1, TRAT1, SLAMF8, CCL3L1, SPP1, CCL5, IL2RG, CD3G, TLR8, ITK, and CCL3. Differential expression of SPP1, ITK and CCL5 was confirmed in scRNA-seq data, with ITK and CCL5 showing distinct expression patterns in natural killer (NK) cells. Furthermore, RT-qPCR analysis revealed upregulation of SPP1 and ITK in adipose tissue of obese zebrafish compared to lean controls. Conclusions: This study identifies SPP1, ITK and CCL5 as key immune hub genes in the adipose tissue of postmenopausal obese women, with NK cells playing a significant role in adipose tissue inflammation through the expression of these genes. These findings provide novel insights into potential therapeutic targets for the prevention and treatment of obesity in postmenopausal women. Full article

Zygotic genome activation (ZGA) marks the critical transition from reliance on maternal transcripts to the initiation of embryonic transcription early in development. Despite extensive characterization in model species, the regulatory framework of ZGA in sheep remains poorly defined. Here, we applied single-cell RNA sequencing (Smart-seq2) to in vivo- and in vitro-derived sheep embryos at the 8-, 16-, and 32-cell stages. Differential expression analysis revealed 114, 1628, and 1465 genes altered in the 8- vs. 16-, 16- vs. 32-, and 8- vs. 32-cell transitions, respectively, with the core pluripotency factors SOX2, NANOG, POU5F1, and KLF4 upregulated during major ZGA. To uncover coordinated regulatory modules, we constructed a weighted gene co-expression network using WGCNA, identifying the MEred module as most tightly correlated with developmental progression (r = 0.48, p = 8.6 × 10⁻¹⁴). The integration of MERed genes into the STRING v11 protein–protein interaction network furnished a high-confidence scaffold for community detection. Louvain partitioning delineated two discrete communities: Community 0 was enriched in ER–Golgi vesicle-mediated transport, transmembrane transport, and cytoskeletal dynamics, suggesting roles in membrane protein processing, secretion, and early signaling; Community 1 was enriched in G2/M cell-cycle transition and RNA splicing/processing, indicating a coordinated network for accurate post-ZGA cell division and transcript maturation. Together, these integrated analyses reveal a modular regulatory architecture underlying sheep ZGA and provide a framework for dissecting early embryonic development in this species. Full article

Background: Cow-milk-induced allergic proctocolitis (CMIAP) is a non-IgE-mediated food hypersensitivity that often resolves spontaneously but may predispose infants to IgE-mediated allergies and eosinophilic gastrointestinal disorders. Understanding its pathophysiology is crucial for microbiota-based interventions. Methods: We enrolled 32 exclusively breastfed infants—16 with confirmed cases of CMIAP and 16 age-matched healthy controls. The cohorts were sex-balanced (8 F/8 M), term-born (gestational age ± SD: 40 ± 1.2 vs. 39 ± 1.3 weeks), vaginally delivered, and sampled at a mean age of 2.0 ± 0.44 months (range 1.5–3.0) vs. 2.4 ± 0.66 months (range 1.5–3.5). Faecal samples underwent 16S rRNA gene sequencing on the Illumina NovaSeq platform, with diversity and differential abundance analyses. Results: The maternal dairy intake was similar (total dairy: 250 ± 80 vs. 240 ± 75 mL/day; yoghurt: 2.3 ± 1.0 vs. 2.5 ± 1.2 days/week; p = 0.72). Bray–Curtis dissimilarity assessments revealed distinct microbiota in infants with CMIAP. Infants with CMIAP had a lower abundance of Bifidobacterium (log₂FC−2.27; q = 0.022; ANCOM-BC), Collinsella (−29.35; padj < 0.0001; DESeq2), and Limosilactobacillus (−8.01; padj = 0.0285; DESeq2; q < 0.0001; ANCOM-BC) compared with controls. In contrast, Hungatella (+24.99; padj < 0.0001; DESeq2), Veillonella (+4.73; padj = 0.0221; DESeq2), Citrobacter (+10.44; padj = 0.0124; DESeq2), and Ruminococcus gnavus (+2.69; q < 0.0001; ANCOM–BC) were more abundant in the CMIAP group. Conclusions: Infants with CMIAP exhibit gut dysbiosis, which is characterised by the depletion of beneficial commensals and the enrichment of potential pathogens, independent of maternal dairy intake. Further studies should establish whether these microbiota alterations are causal or consequential in CMIAP. Full article

The Rio Bravo/Grande River is a binational water resource between Mexico and the United States and supports diverse anthropogenic activities. However, limited studies on its microbiological composition focus on molecular techniques. Therefore, the aim of this study was to characterize the bacteriome and identify potentially pathogenic bacteria in surface waters of the Rio Bravo/Grande in northeastern Tamaulipas, Mexico, using the 16S rRNA gene metabarcoding technique. Surface water samples were collected from the localities of Diaz Ordaz, Reynosa, and Matamoros between 2016 and 2017. DNA extraction and sequencing were performed, focusing on the V3–V4 region of the 16S rRNA gene. A taxonomic analysis revealed the presence of 13 bacterial phyla, with Proteobacteria (40%), Firmicutes (28%), and Actinobacteria (10.2%) being the most abundant. At the genus level, Bacillus, Pseudomonas, and Acinetobacter were predominant, while 16 potentially pathogenic species, including Acinetobacter baumannii and Vibrio vulnificus, were identified. Alpha and beta diversity analyses highlighted significant differences in the bacterial diversity among the sampling sites, indicating that the river has some capacity to recover from anthropogenic and environmental disturbances. This study underscores the need for the continuous monitoring of the Rio Bravo/Grande to protect public health and maintain the water quality in the face of increasing anthropogenic pressures. Full article

The objectives of this study comprise the identification of key miRNAs and their target genes associated with severe tolerance in individuals exposed to aluminum and welding fumes, and the elucidation of the underlying regulatory mechanisms. In this study, the levels of seven miRNAs (hsa-miR-19a-3p, hsa-miR-130b-3p, hsa-miR-25-3p, hsa-miR-363-3p, hsa-miR-92a-3p, hsa-miR-24-3p, and hsa-miR-19b-3p) were analyzed using both hsa-miR-16-5p and RNU6 (U6 snRNA) as reference miRNAs to validate normalization reliability. The qRT-PCR method was used on blood serum samples from 16 workers who were exposed to aluminum, 16 workers who were exposed to welding fumes, and 16 healthy controls who were not exposed to aluminum or welding fumes. We determined heavy metal levels from serum samples of workers exposed to aluminum and welding fumes and control groups using the ICP-OES method. The expression levels of hsa-miR-19a-3p and hsa-miR-19b-3p in aluminum-exposed and control groups were found to be statistically significant (p < 0.05). When workers exposed to welding fumes were compared with the those in the control groups, the expression levels of hsa-miR-19a-3p, hsa-miR-130b-3p, hsa-miR-92a-3p, and hsa-miR-24-3p were observed to be statistically significant (p < 0.05). This study shows that the identification of miRNAs and target genes in different biological functions and pathways plays an important role in understanding the molecular mechanisms of responses to heavy metal toxicity. We share the view that the study will make a significant contribution to the literature in that seven candidate miRNAs can be used as possible biomarkers for exposure to aluminum and welding fumes in humans. Full article

Maternal nutrition’s impact on liver transcriptome in beef cattle offspring is still underexplored. We investigated the long-term effects of maternal nutrition strategies on the liver transcriptome of pre-slaughter Nelore bulls. Pregnant cows were divided into three groups, each receiving different nutritional regimens: NP (control, only mineral supplementation), PP (late gestation protein–energy supplementation), and FP (protein–energy supplementation throughout pregnancy). Liver samples were collected from male offspring aged 22.5 ± 1 months and analyzed using RNA-Seq (n = 5 per treatment). Principal component analysis (PCA) and differential gene expression analysis were carried out in an R statistical environment. Genes were considered significant when FDR < 0.05. The over-representation analysis (ORA) was performed using the clusterProfiler package from R. Metabolic pathways were considered significant when the Q-value < 0.1. The PCA showed overlapping clusters among the groups. We identified 16 differentially expressed genes (DEGs) associated with PP × NP contrast, four with FP × NP, and two with FP × PP. The ORA revealed two significant pathways (thiamine and butanoate metabolism). The identified genes and pathways were associated with vitamins, energy, oxidative metabolism, and immune function. This study emphasizes the more significant long-term effects of the PP treatment on the offspring’s liver transcriptome compared to the FP treatment. Full article

The Ghd7 gene in rice plays a crucial role in determining heading date, plant height, and grain yield. However, the variations in Ghd7 and their functional implications across different rice accessions are not fully understood. Based on the release of a large amount of rice genome data in recent years, we investigated Ghd7 through pan-genome analysis of 372 diverse rice varieties and figured out the structural variations (SVs) in the Ghd7 locus. However, due to the high cost of pan-genomes, most genomes are based on next-generation sequencing (NGS) data now. Therefore, we developed a method for identifying SVs using NGS data and Polymerase Chain Reaction (PCR) based on the results of pan-genome analysis and identified 977 accessions carrying such SVs of Ghd7. Furthermore, we identified 46 single-nucleotide polymorphisms (SNPs) and one insertion-deletion (InDel) in the coding region of Ghd7. They are classified into 49 haplotypes. Notably, a splice-site mutation in haplotype H6 causes aberrant mRNA splicing. Using prime editing (PE) technology, we successfully restored the functional of Ghd7 in Yixiang 1B (YX1B), delaying the heading date by approximately 16 days. This modification synchronized the heading date between YX1B and the restorer line Yahui 2115 (YH2115R), enhancing the hybrid rice seed production efficiency. In conclusion, our findings highlight the potential of integrating pan-genomics and precision gene editing to accelerate crop improvement and enhance agronomic traits. Full article

Background: Smilax glabra (S. glabra) and Smilax zeylanica (S. zeylanica), two medicinally important species within the genus Smilax, have been widely used in Traditional Chinese Medicine (TCM) for the treatment of rheumatism, traumatic injuries, and related ailments. Despite their medicinal significance, research on the mitochondrial DNA (mtDNA) of Smilax species remains limited. Methods: We utilized NovaSeq 6000 and PromethION sequencing platforms to assemble the complete mitochondrial genomes of Smilax glabra and Smilax zeylanica, and conducted in-depth comparative genomic and evolutionary analyses. Results: The complete mitochondrial genomes of S. glabra and S. zeylanica were assembled and annotated, with total lengths of 535,215 bp and 471,049 bp, respectively. Both genomes encode 40 unique protein-coding genes (PCGs), composed of 24 core and 16 non-core genes, alongside multiple tRNA and rRNA genes. Repetitive element analysis identified 158 and 403 dispersed repeats in S. glabra and S. zeylanica, respectively, as well as 123 and 139 simple sequence repeats (SSRs). RNA editing site predictions revealed C-to-U conversions in both species. Additionally, chloroplast-to-mitochondrial DNA migration analysis detected 34 homologous fragments in S. glabra and 28 homologous fragments in S. zeylanica. Phylogenetically, S. glabra and S. zeylanica cluster within the Liliales order and Smilacaceae family, closely related to Lilium species. Collinearity analysis indicated numerous syntenic blocks between Smilax and three other Liliopsida species, though gene order was not conserved. Conclusions: This study presents high-quality mitochondrial genome assemblies for S. glabra and S. zeylanica, providing valuable insights into molecular identification and conservation efforts of these traditional medicinal plants. Full article

Coenzyme Q10 (CoQ10), a high-value-added nutraceutical antioxidant, exhibits an excellent ability to prevent cardiovascular disease. Here, a novel Cereibacter azotoformans strain, designated YS02, was isolated for its ability to produce CoQ10 and genetically characterized by whole genome sequencing (WGS). The CoQ10 biosynthesis and metabolism differences of YS02 under various culture conditions were also systematically investigated. Phylogenetic analysis based on 16 S rRNA genes, along with taxonomic verification using average nucleotide identity (ANI) analysis, confirmed its classification as C. azotoformans. Enzymatic genes dxs, dxr, idi, ubiA, and ubiG were annotated in YS02, which are critical genetic hallmarks for CoQ10 biosynthesis. Under aerobic–dark cultivation, YS02 grows well, and CoQ10 production can reach 201 mg/kg. A total of 542 small-molecule metabolites were identified from YS02 in aerobic–dark and anaerobic–light cultivation via ultra-high performance liquid chromatography–coupled quadrupole orbitrap high-resolution mass spectrometry (UPLC-Q-Exactive Orbitrap MS). Additionally, 40 differential metabolites were screened through multivariate statistical analysis. Metabolic pathway analysis revealed that the biosynthesis of phenylalanine, tyrosine, and tryptophan might be latent factors influencing CoQ10 production discrepancies within YS02 under both cultural modes. These findings represent new insights into the metabolic mechanism of YS02 and underscore its potential as an alternative strain source for industrial CoQ10 production, enriching the existing resources. Full article

The increasing use of computed tomography (CT) has led to a rise in cumulative radiation dose due to medical imaging, raising concerns about potential long-term adverse effects. Large-scale epidemiological studies indicate a higher tumor incidence associated with CT examinations, but the underlying biological mechanisms remain largely unexplained. To gain further insights into the cellular response triggered by routine CT diagnostics, we investigated CT-induced changes of gene expression in peripheral blood cells using whole transcriptome sequencing. RNA was isolated from peripheral blood cells of 40 male patients with asymptomatic microhematuria, sampled before and after multi-phase abdominal CT (CTDIvol: 3.75–26.95 mGy, median: 6.55 mGy). On average, 22.11 million sequence reads (SD 5.71) per sample were generated to identify differentially expressed genes 6 h post-exposure by means of DESeq2. To assess the dose dependency of CT-induced effects, we additionally divided samples into three categories: low exposure (≤6.55 mGy, n = 20), medium exposure (>6.55 mGy and <12 mGy, n = 16), and high exposure (≥12 mGy, n = 4), and repeated gene expression analysis for each subset and their corresponding prae-exposure sample. CT exposure caused consistent and dose-dependent upregulation of six genes (EDA2R, AEN, FDXR, DDB2, PHLDA3, and MIR34AHG; padj < 0.1). These genes share several functional commonalities, including regulation by TP53 and involvement in the DNA damage response. The biological pathways highlighted by Gene Set Enrichment Analysis (GSEA) suggest a dose-dependent increase of cellular damage and metabolic particularities in the low-exposure subset, which may be related to a potential adaptive cellular response to low-dose irradiation. Irrespective of applied dose, AEN emerged as the most robust biomarker for CT exposure among all genes. Routine abdominal CT scans cause dose-dependent gene deregulation in association with DNA damage in peripheral blood cells after in vivo exposure. Regarding risk assessment of CT, our results support the commonly applied “As Low–As –Reasonably Achievable (ALARA)” principle. Evidence of additional gene expression changes associated with metabolic processes indicates a rather complex molecular response beyond DNA damage after CT exposure, and emphasizes the need for further targeted investigations. Full article