Search Results (620)

During China’s 41st Antarctic research expedition, samples were collected from wildlife on the Fildes Peninsula, South Shetland Islands, Antarctica. Real-time RT-PCR screening confirmed H5N1 positivity, representing the first identification of the virus in brown skuas on the Fildes Peninsula. Whole-genome sequences obtained from positive samples via next-generation sequencing were subjected to phylogenetic and phylogeographic analyses. The results revealed that these Antarctic strains are most closely related to H5N1 viruses circulating in South America, particularly from Peru and Chile, suggesting a likely introduction via avian migration routes. Furthermore, a unique 17-amino-acid deletion was identified in the stalk region of the neuraminidase (NA) gene, which is uncommon among globally sampled clade 2.3.4.4b variants. This study confirms the arrival of HPAI H5N1 in the Antarctic continent and underscores the necessity for enhanced surveillance to understand the viral ecology and potential risks within this unique ecosystem. Full article

Multiple sclerosis (MS) is a chronic autoimmune neurodegenerative disorder characterized by progressive demyelination and axonal degeneration within the central nervous system, driven by complex genomic and epigenomic dysregulation. Its pathogenesis involves aberrant DNA methylation patterns at CpG islands of numbers of genes like OLIG1 and OLIG2 disrupting protein expression at myelin with compromised oligodendrocyte differentiation. Furthermore, histone modifications, particularly H3K4me3 and H3K27ac, alter the promoter regions of genes responsible for myelination, affecting myelin synthesis. MS exhibits chromosomal instability and copy number variations in immune-regulatory gene loci, contributing to the elevated expression of genes for pro-inflammatory cytokines (TNF-α, IL-6) and reductions in anti-inflammatory molecules (IL-10, TGF-β1). Vitamin D deficiency correlates with compromised immune regulation through hypermethylation and reduced chromatin accessibility of vitamin D receptor (VDR) dysfunction and is reported to be associated with dopaminergic neuronal loss. Vitamin D supplementation demonstrates therapeutic potential through binding with VDR, which facilitates nuclear translocation and subsequent transcriptional activation of target genes via vitamin D response elements (VDREs), resulting in suppression of NF-κB signalling, enhancement of regulatory T-cell (T_reg) responses due to upregulation of specific genes like FOXP3, downregulation of pro-inflammatory pathways, and potential restoration of the chromatin accessibility of oligodendrocyte-specific gene promoters, which normalizes oligodendrocyte activity. Identification of differentially methylated regions (DMRs) and differentially expressed genes (DEGs) that are in proximity to VDR-mediated gene regulation supports vitamin D supplementation as a promising, economically viable, and sustainable therapeutic strategy for MS. This systematic review integrates clinical evidence and eventual bioinformatical meta-analyses that reference transcriptome and methylome profiling and identify prospective molecular targets that represent potential genetic and epigenetic biomarkers for personalized therapeutic intervention. Full article

Background/Objectives: Biofilms are key in spreading antibiotic resistance in various ecosystems. This study employed comparative genomics to examine the resistance and adaptability mechanisms of the Vibrio parahaemolyticus strain Vaw-5, isolated from a seafood market biofilm. Methods: A comparative examination of Vaw-5 and 32 publicly available V. parahaemolyticus genomes identified a distinct set of genetic resistance characteristics. Results: Unlike clinical strains, Vaw-5 lacks acquired antimicrobial resistance genes like the blaCARB and qnr variations. Instead, its resistance potential is based on chromosomal alterations, efflux pump systems (vmeAB, vcmD), and a unique repertoire of 16 strain-specific transposons, including Tn5501 and Tn5393, which are well-known vectors for antibiotic resistance gene (ARG) mobilization. Although not multidrug-resistant, Vaw-5 possesses unique genomic islands that share negligible homology with those of clinical strains, enriched with gene clusters for environmental adaptation, such as exopolysaccharide production and a fully functional Type VI Secretion System. Vaw-5 carries a distinctive plasmid with the resistance gene aac(2${}^{\prime }$)-Ia. Conclusions: Biofilm adaptation promotes structural integrity, inherent processes, and resistance above standard ARG acquisition. This study focuses on how biofilm communities in the food chain can operate as covert incubators for mobilizable resistance determinants, emphasizing the significance of ecological monitoring within a One Health paradigm to reduce possible public health hazards. Full article

Marine Bacteroidota are recognized bacterial producers of bioactive metabolites, yet their biosynthetic potential remains cryptic under standard laboratory conditions. Here, we developed chemically defined media for Fulvivirga kasyanovii 48LL (Cytophagia) and Tenacibaculum mesophilum fLL (Flavobacteriia) to evaluate the effect of environmentally relevant carbon sources on growth and secondary metabolism. F. kasyanovii utilized 31 of 34 tested carbon sources whereas T. mesophilum grew on only five substrates, underscoring a distinct nutritional preferences. Substrate significantly influenced the antibacterial activity of F. kasyanovii extracts. Growth on β-1,3-glucan, glycerol, poly(β-hydroxybutyrate) (PHB), fish gelatin, or pectin resulted in extracts generating the largest inhibition zones (10–13 mm) against Bacillus subtilis or Rossellomorea marisflavi. Genome analysis revealed F. kasyanovii to be enriched in biosynthetic gene clusters (BGCs), notably harboring a ~570 kb genomic island comprising five large NRPS/PKS-type clusters. Quantitative PCR confirmed carbon-source-dependent regulation of these operons: glucose induced BGC1, BGC3, and BGC4, while κ-carrageenan and PHB upregulated BGC2. Conversely, yeast–peptone medium (analogous to standard marine broth) repressed transcription across all active clusters. These findings demonstrate that naturally occurring carbon sources can selectively activate cryptic BGCs and modulate antibacterial activity in F. kasyanovii, suggesting that similar strategy can be used for natural-product discovery in marine Bacteroidota. Full article

This study evaluated the diffusion of Listeria monocytogenes (LM) in a beef steak tartare production chain, aiming to (1) evaluate Listeria spp. diffusion in finishing farms supplying beef cattle, (2) evaluate LM prevalence in carcasses, and (3) map LM diffusion in the production plant. A detection rate of 6/76 was observed in the farm, while carcasses after skinning and before refrigeration tested positive in 19/30 and 11/30, respectively. During tartare production, 57/154 meat and 35/191 environmental samples tested positive. A total of 114 LM isolates were characterized via a whole-genome sequencing approach. Five clonal complexes (CCs) and seven sequence types (STs) were identified, with CC9-ST580 being the most prevalent. Four clusters were identified from both the slaughtering and production phases. Genes related to resistance to fosfomycin, quinolones, sulfonamides, lincosamide, and tetracycline were detected. Two hypervirulent strains (CC6-ST6 and CC2-ST145), harboring a full-length inlA, several virulence genes, and stress islands, were detected. Stress Survival Islet 1 was found in almost all the isolates. The wide diffusion of LM in steak tartare requires the management of some critical phases of the production chain (mainly slaughtering); genomic methodologies could be useful in describing the circulation and virulence of LM strains. Full article

K-mer analysis is a powerful tool for understanding genome structure and evolution. A “k-mer” refers to a short DNA sequence made up of k nucleotides (where k is a specific integer), while an “m-mer” is a similar concept but with a shorter sequence length. The functional mechanisms of CG-containing k-mers, as well as their potential role in evolutionary processes, remain unclear. To explore this issue, we analyzed 8-mers in several species with varying genomic complexities and evolutionary divergences: Homo sapiens, Saccharomyces cerevisiae, Bombyx mori, Ciona intestinalis, Danio rerio, and Caenorhabditis elegans, which were grouped by CG dinucleotide content (0CG, 1CG, and 2CG). We examined the relative frequencies of shorter m-mers (with m = 3 and 4) within each CG-defined group, using information-theoretic, distance-based, and angular metrics. Our results show that 0CG motifs follow random patterns, while 1CG and 2CG motifs display significant deviations, likely due to functional constraints such as nucleosome-binding and CpG island association. The observed unimodal distribution of 8-mers arises from the convergence of the three CG-defined groups. Among them, the 2CG group shows the highest divergence in m-mer composition, followed by 1CG, reflecting varying degrees of selective pressure. Furthermore, species-specific differences in CG-classified 8-mer patterns could provide valuable insights into phylogenetic relationships. Through extensive comparison, we explore how CG content and sequence composition influence genomic organization and contribute to evolutionary divergence across different taxa. These findings deepen our understanding of short motif functions, genome organization, and sequence evolution. Full article

Mixed infections of Mannheimia haemolytica and Mycoplasma bovis are relatively common in bovine respiratory diseases, presenting severe respiratory symptoms and high mortality that severely endanger the cattle industry. In this study, a serotype A1 strain of Mannheimia haemolytica, designated as XJCJMh1, was isolated and identified from the lung tissue of a hybrid Simmental calf infected with Mycoplasma bovis. The pathogenicity of this strain was evaluated using Kunming mice as a model. The results indicated that infection with XJCJMh1 caused pathological manifestations such as pulmonary hemorrhage and edema in mice. Subsequently, the genome of this strain was sequenced and assembled using Illumina sequencing to obtain general genomic features. The genome was annotated and analyzed for gene functions using the Swiss-Prot, NR, GO, COG, KEGG, CAZy, TCDB, and Pfam databases. Additionally, the virulence factors and resistance genes of this strain were annotated using the PHI, VFDB, and CARD databases. The genome of Mannheimia haemolytica XJCJMh1 is 2,595,489 base pairs (bp) in length, with a GC content of 40.93%. Notably, this strain exhibits three distinct genomic islands and contains 98 effectors associated with the type III secretion system (T3SS). The XJCJMh1 strain harbors 74 virulence genes and 45 resistance genes. We annotated the proteins, genes, and associated GO and KEGG pathways of the XJCJMh1 strain; exploring the relationship between these annotations and the strain’s pathogenicity is of considerable value. This study is of great significance for clarifying the pathogenic mechanism and genetic characteristics of the Mannheimia haemolytica strain XJCJMh1 in cattle, and its results provide a scientific reference for analyzing the genomic basis of pathogenicity and drug resistance of Mannheimia haemolytica under co-infection conditions. Full article

Areca palm velarivirus 1 (APV1), the causal agent of yellow leaf disease (YLD), poses a serious threat to the economically important areca palm industry in the Hainan Province, China, yet its evolutionary dynamics remain poorly understood. Here, we performed a large-scale molecular survey by sequencing the coat protein (CP) gene from 364 APV1-infected samples collected across major cultivation regions of Hainan. Population genetic analyses revealed extremely high haplotype diversity (H_d = 0.997) but very low nucleotide diversity (π = 0.017). Neutrality tests (Tajima’s D = −2.266; Fu’s F_S = −23.697) and a unimodal mismatch distribution supported a scenario of recent demographic expansion from a restricted ancestral pool. Evolutionary analyses indicated that the CP gene is subject to strong purifying selection, although eight codons exhibited episodic positive selection, suggesting ongoing viral adaptation. Furthermore, we identified three distinct genetic clusters with significant geographic structuring, indicating that viral dissemination is shaped by local factors. Together, these results reveal a recent explosive invasion of APV1 characterized by rapid island-wide expansion and emerging local differentiation. This work provides novel insights into the evolutionary trajectory of APV1 and establishes a genomic basis for improved surveillance and management of YLD. Full article

Listeria monocytogenes (L. monocytogenes) is an important foodborne pathogen that poses great risks to food safety and public health, and knowledge about its presence and diversity in potential sources is crucial for effectively tracking and controlling it in the food chain. In this study, we investigated the prevalence, antimicrobial susceptibility, and genomic characteristics of Listeria monocytogenes (L. monocytogenes) collected from retail chicken meat samples in Qingdao, China, in 2022. A total of 38 (10.6%, 38/360) L. monocytogenes isolates were recovered from 360 retail chickens. All 38 isolates were classified into two lineages (I and II), three serogroups (IIa, IIb, IIc), eight sequence types (STs), eight clonal complexes (CCs), eight Sublineages (SLs) and nine cgMLSTs (CTs). ST121 and ST9 were the most prevalent STs in this study. The ST121 strains from China had heterogeneity with those from other countries, while the Chinese ST9 strains had homogeneity with those from other countries. One resistance cassette tet(M)-entS-msr(D) was identified in eight L2-SL121-ST121-CT13265 isolates, the genetic structure of which was identical to that of three reference genomes. All isolates carried the L. monocytogenes pathogenic island (LIPI)-1, with only one carrying LIPI-3 and three carrying LIPI-4. In addition, 11 isolates subtyped as L2-SL121-ST121-CT13265 were found to have a premature stop codon (PMSC) in the inlA gene in this study. Our data revealed the antimicrobial susceptibility, genomic characteristics and evolutionary relationships of L. monocytogenes in retail chicken in Qingdao, China. The characterization of genotypes, virulence, stress and antimicrobial markers of strains circulating in retail chicken in Qingdao, as described in this study, provides the opportunity to improve risk assessments of L. monocytogenes exposure. Full article

Background/Objectives: Developmental biologist Conrad Waddington proposed that evolution is shaped not only by genetic mutations and natural selection but also by environmentally responsive developmental mechanisms. Building on this premise, the epigenetic regulation of three master genes central to mammalian embryogenesis—OCT4, SOX2, and hTERT—focusing on their intragenic CpG islands (iCpGIs), which are crucial for transcriptional control and chromatin state modulation, were investigated. Methods: By performing a phylo-epigenetic comparison across 12 primate species, strong conservation of CpG-rich regions, punctuated by lineage-specific CpG transitions, particularly CpG→TpG and CpG→CpA was identified. Results: These mutational patterns align with methylation-dependent deamination mechanisms and highlight iCpGIs as evolutionarily constrained, epigenetically plastic elements. Notably, CpG variation alone recapitulated known primate phylogenies, suggesting that methylation-sensitive sites within iCpGIs encode both developmental and evolutionary information. Conclusions: It is proposed that such sites are prone to Environmentally Determined Epimutations (EDEMs)—methylation-driven, nutrition-sensitive changes that persist across generations and modulate gene regulatory capacity. This integrative framework advances Waddington’s concept of canalization by providing a molecular mechanism through which environmental factors can reshape developmental trajectories and contribute to evolutionary innovation. Full article

Strains of Aeromonas salmonicida subsp. salmonicida, a major pathogen of salmonids, typically do not grow at temperatures above 30 °C. The effects of thermal stress on this bacterium have been extensively studied. Recently, we demonstrated that repeated exposure to cyclical thermal stress, reaching up to 37 °C, can induce permanent thermoadaptation in certain strains of this bacterium. Many aspects of this adaptation process remain poorly understood. We generated 88 thermoadapted strains of A. salmonicida subsp. salmonicida capable of sustained growth at 33 °C or higher demonstrating that prolonged heat exposure can shift a substantial proportion of psychrophilic strains toward a more mesophilic-like behavior. Although growth at 35 °C was still weaker than in naturally mesophilic A. salmonicida strains, some thermoadapted strains were able to grow up to 37 °C. North American strains harboring the genomic island AsaGEI1a, a known biomarker, exhibited a significantly reduced capacity for thermoadaptation, suggesting a possible genetic constraint, although genomic analyses indicate that AsaGEI1a itself is not directly responsible for this limitation. Genotyping and phenotypic analyses revealed that thermoadaptation is frequently associated with the loss of Type III secretion system and the A-layer, two key virulence factors. Only 7% of the thermoadapted strains retained both features. Overall, our findings suggest that thermoadaptation may represent a potential mechanism influencing the persistence of some psychrophilic A. salmonicida subsp. salmonicida strains in warming aquatic environments under climate change. Full article

Marine-derived Actinomycetota have emerged as promising sources of bioactive natural products, particularly filamentous actinomycetes (e.g., Streptomyces). However, members from non-filamentous genera have showed potential biotechnological importance. In this study, we performed a comprehensive genomic characterization of two bioactive Brevibacterium strains, Brevibacterium luteolum (B. luteolum) 26C and Brevibacterium casei (B. casei) 13A, isolated from two Red Sea sponges. Whole-genome sequencing and taxonomic analysis confirmed species-level identification, marking the first documented report of these species within the Red Sea ecosystem. The two strains displayed antimicrobial activity against Staphylococcus aureus, Escherichia coli, and Candida albicans. Additionally, functional annotation revealed multiple genomic islands (GIs) enriched with genes conferring heavy metal resistance, DNA repair enzymes, nutrient acquisition, and mobile genetic elements, highlighting potential evolutionary adaptations to the harsh physicochemical conditions of the Red Sea. Genome mining identified biosynthetic gene clusters, including those encoding ε-poly-L-lysine, tropodithietic acid, ectoine, and carotenoids. The comparative analysis of orthologous gene clusters from both strains and their counterparts from terrestrial ecosystems highlighted potential marine adaptive genetic mechanisms. This study highlights the biosynthetic potential of B. luteolum 26C and B. casei 13A and their ecological role as active competitors and potential defensive associates within the sponge microbiome. Full article

This study examines the genetic variation and structure of the spectacled caiman (Caiman crocodilus) on Gorgona Island, Colombia, compared to continental populations. We analyzed 178 partial Cytochrome b gene sequences, most of which were obtained from GenBank, and identified 23 haplogroups, with five of these specifically found on the Island. Phylogenetic analysis using maximum likelihood placed C. crocodilus, including the Gorgona Island population, in a distinct monophyletic group. Genetic structure analysis identified two main clusters, with Gorgona Island caimans primarily assigned to the Trans-Andean cluster. The haplogroup network illustrates the two major groups, with a maximum of 12 mutational steps between them. Additionally, Tajima’s D statistic suggests an excess of rare alleles in the spectacled caiman. Genetic differentiation across regions suggests historical isolation, likely shaped by geographical barriers and limited gene flow. The distinct genetic patterns of island populations highlight their disparity in terms of evolutionary dynamics and conservation importance. Further genomic analysis is recommended to explore demographic history. Conservation strategies should prioritize the maintenance of genetic diversity to mitigate the effects of isolation, while also incorporating insights from the species’ biogeographic history. Our findings highlight the unique contribution of the small population in Gorgona Island to the species’ spatial genetic structure. Full article

Owing to their remarkable biological activities and health benefits, probiotics have gained widespread application in enhancing pet health and welfare. Host-derived probiotics are considered optimal due to their unique digestive tract environments. This study isolated Lactobacillus acidophilus L1 from the feces of a 2-month-old Shiba Inu puppy and conducted a comprehensive evaluation of its potential as a probiotic candidate for pet health. Strain L1 demonstrated high tolerance to acidic conditions (survival rates of 90.41%, 92.90% and 98.81% at pH 2, 2.5, and 3.0, respectively) and bile salts (survival rates of 98.05%, 95.68%, and 82.21% at 0.1%, 0.2%, and 0.3% concentrations, respectively). Adhesion to Caco-2 intestinal epithelial cells reached 38.33%, with hydrophobicity of 97.81% and auto-aggregation of 32.28%. L1 also displayed pronounced antioxidant activity, with DPPH and ABTS radical scavenging rates of 71.15% and 83.20%. Both the bacterial suspension and the cell-free supernatant had potent inhibition of pathogenic bacteria, while the strain showed a non-hemolytic phenotype and remained sensitive to clinically relevant antibiotics (e.g., penicillin). On the other hand, animal experiments conducted in ICR mice (randomly divided into four groups) demonstrated that oral administration of L1 had no toxic effects on the mice and increased serum SOD and CAT levels, while reducing MDA levels. Furthermore, whole-genome sequencing revealed that L1 is 2,106,895 bp in size and contains 2098 coding sequences, two CRISPR arrays, ten genomic islands, and two prophage regions. Collectively, the in vitro and in vivo data presented here indicate that L. acidophilus L1, originally isolated from canine feces, supports further evaluation as a candidate strain for incorporation into functional pet foods. Full article

Background/Objectives: Dülmen wild horses are kept in a fenced wooden and marsh area around Dülmen in Westphalia, Germany, since 1856. Previous analyses supported early genetic divergence from other domesticated horse populations and the Przewalski horse. Therefore, the objective of this study was to evaluate genetic diversity using high-density genomic data. Methods: We collected 337 one-year-old male Dülmen wild horses, captured at 12 annual auctions, for genotyping on the Illumina GGP Equine Plus Beadchip. All analyses were performed for 63,123 autosomal SNPs. Results: On average, each horse had 27.96 ROH with an average length of 8.237 Mb, resulting in an average genomic inbreeding coefficient F_ROH of 0.107. ROH with a length of 2–4 Mb were most frequent, and the next frequent ROH fall into the length categories of 4–8 and 8–16 Mb. The effective population size (N_e) steadily decreased in the last 100 generations by 4.57 individuals per generation from 498 to 41. We identified 10 ROH islands on equine chromosomes 1, 4, 5, 7, 9, and 10. Only one ROH island on ECA 1 was shared by 45% of the horses. Overrepresented genes of ROH islands were associated with glycerophospholipid catabolism through phospholipase A2 genes, skeletal muscle contraction (TNNI3, TNNT1), synapse activity and structure (CTTNBP2), regulation of inflammatory response (NLRP genes), and zinc finger protein genes, which are involved in many cellular processes and may also act as tumor suppressors and oncogenes. Conclusions: This study highlights the development of genomic inbreeding and shows the importance of the stallions selected for breeding on the genetic diversity of the Dülmen wild horses. The results of this study should be used to develop strategies to slow down increase in inbreeding and prevent transmitting unfavorable alleles from the stallions to the next generation. Full article