Search Results (306)

Background: Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥90%, contamination ≤5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim–sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia. Full article

Evolutionary history of the host may influence the skeletal morphology of scleractinian corals. However, its effects on the assembly and function of endolithic microbiomes remain unknown. We analyzed bacterial and archaeal microbiomes from the coral skeleton by using 16S rRNA gene sequencing. We collected the samples of seven coral genera distributed among the diverse “Complex” and “Robust” clades. In this study, bacterial α-diversity was significantly higher in the Complex clade relative to the Robust clade. Archaea, on the other hand, remained stable and showed no significant differences between the two host clades, and were most abundantly Nanoarchaeota and Thermoproteota. Analysis of the network topologies showed that network structures were different between the Complex group and the Robust clade. The Robust clade formed a dense and closely knit network among bacteria and archaea. The Com-plex group formed a more modular network structure. Functional predictions further highlighted lineage-specific metabolic strategies. Enrichment was apparent in both nitrification genes (amoB, amoC) and denitrification genes (nirK, nirS) in the Complex clade. This suggests that the coupling of these nitrogen cycles is possible. The opposite was observed for the Robust clade, which had low potential for both types of nitrogen cycling. This reflects the degree of diffusion limitation in the more massive skeleton of this host lineage. Overall, species evolutionary lineage is a pre-eminent driver for the selective filtering of endolithic assembly. It generates discrete skeletal micro-niches on which microbial strategies diverge. In particular, Complex corals favor fast metabolic flux, and Robust corals favor strong network connectivity. Full article

Influenza D virus (IDV), an emerging orthomyxovirus with zoonotic potential, infects diverse hosts, causes respiratory disease, and remains poorly characterized in China despite its global expansion. From October 2023 to January 2025, we collected 563 nasal swabs from cattle across 28 farms in Jilin Province, Northeast China, and identified seven IDV-positive samples (1.2%), recovering two viable isolates (JL/YB2024 and JL/CC2024). Full-genome sequencing revealed complete, stable seven-segment genomes with high nucleotide identity (up to 99.9%) to contemporary Chinese D/Yamagata/2019 strains and no evidence of reassortment. Maximum-likelihood and time-resolved Bayesian phylogenies of 231 global hemagglutinin-esterase-fusion (HEF) sequences placed the Jilin isolates within the East Asian D/Yamagata/2019 clade and traced their most recent common ancestor to approximately 2017 (95% highest posterior density: 2016–2018), suggesting a cross-border introduction likely associated with regional cattle movement. No IDV was detected in parallel surveillance of swine, underscoring cattle as the principal reservoir and amplifying host. Bayesian skyline analysis demonstrated a marked decline in global IDV genetic diversity during 2020–2022, coinciding with livestock-movement restrictions imposed during the COVID-19 pandemic. Collectively, these findings indicate that IDV circulation in China is sporadic and geographically localized, dominated by the D/Yamagata/2019 lineage, and shaped by multiple independent incursions rather than a single emergence. Both the incorporation of IDV diagnostics into routine bovine respiratory disease surveillance and cattle-import quarantine programs, and the adoption of a One Health framework to monitor potential human spillover and future viral evolution, were recommend. Full article

Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background “blood microbiome”, the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking (“stress test”) of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted “blood microbiome” enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0–12.0%) in CAD and 21.8% (5.4–31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually “enriched” taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays. Full article

Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and crop improvement. Using multi-region 16S rRNA sequencing, we compared the rhizosphere and endosphere bacterial communities of cultivated tomato (Solanum lycopersicum cv. Moneymaker) with six wild relatives (S. pimpinellifolium, S. huaylasense, S. peruvianum, S. chilense, S. habrochaites, and S. pennellii) spanning the main wild lineages within Solanum sect. Lycopersicon. Bacterial community structure in the rhizosphere was broadly conserved across all seven hosts, and diversity remained comparable among genotypes. Despite this overall stability, the rhizosphere microbiomes were ordered along a gradient consistent with host phylogeny, with Moneymaker clustering near S. pimpinellifolium, the four green-fruited Eriopersicon species forming a cohesive block, and S. pennellii occupying the most distinct position. Within this hierarchy, individual hosts showed specific recruitment preferences, including enrichment of Streptomycetaceae in S. pimpinellifolium, Bacillaceae in S. chilense, and contrasting patterns of nitrifiers among Eriopersicon species and S. pennellii. Differential abundance testing in the endosphere revealed consistent reductions in several bacterial families in wild accessions, alongside the enrichment of Streptomycetaceae and Rhodobiaceae in multiple wild species. Overall, our study suggests that domestication exerted a modest effect on tomato root microbiomes, while wild relatives retained microbial association traits that could be harnessed in microbiome-informed breeding to improve resilience in cultivated tomato. Full article

Root rot disease severely threatens tropical fruit production, leading to plant mortality and reduced yields; however, the mechanisms of host defense responses and pathogen infection remain poorly understood. In this study, Fusarium acutatum was isolated from diseased Annona squamosa roots and identified through morphological features and ITS phylogeny (99.8% identity). Infection triggered a marked activation of antioxidant defenses, with elevated POD, SOD, PAL, PPO, and CAT activities. Transcriptomic and TMT-based quantitative proteomic analyses identified 23,791 and 74,403 differentially expressed genes (DEGs) and 367 and 609 differentially expressed proteins (DEPs) in root at 5 and 10 days post inoculation, respectively, relative to the control. These DEGs and DEPs were consistently enriched in pathways involving redox regulation, protein synthesis and processing, ubiquitin-mediated proteolysis, phenylpropanoid and flavonoid metabolism, cell wall remodeling, plant–pathogen interaction and MAPK signaling. Integrated transcriptomic–proteomic correlation analysis showed clear positive associations between key defense-related genes and proteins, suggesting that phenylpropanoid metabolism and reactive oxygen species (ROS) scavenging play central roles in resistance. Key genes such as CHI2, CHS, and CYP were strongly induced and validated by qPCR, supporting coordinated activation of the defense systems. Furthermore, F. acutatum exhibited upregulation of 50 pathogenic-related proteins, including 4 cell wall-degrading enzymes (e.g., CBH1, pectate lyase), 5 metabolic regulation or signal transduction enzymes (e.g., gabD, TPI, and ENO) and 3 potential effectors, suggesting coordinated pathogen strategies for host colonization. Collectively, this study provides comprehensive multi-omics insight into the molecular mechanisms underlying A. squamosa defense against F. acutatum and offers candidate targets supported by omics evidence, serving as a theoretical reference for the management of root rot. Full article

As a major export crop in China, Saccharina japonica cultivation suffers from significant economic losses due to disease outbreaks, with pathogen identification remaining a critical bottleneck for mariculture. In this study, a dominant bacterial strain, LJ53, was isolated from the diseased farmed S. japonica. Artificial challenge assay confirmed that this strain is the direct causative agent of bleaching symptoms on sporophytes. Based on morphological characteristics and 16S rRNA gene-based phylogeny, it was identified as Pseudoalteromonas agarivorans LJ53. Ultrastructural observation revealed that this strain destroyed host cells and caused typical pathological changes such as chloroplast disintegration. Interestingly, metagenomic analysis showed no significant difference in the relative abundance of this pathogen between healthy and diseased S. japonica tissues. However, the co-occurrence network of the disease community exhibited increased connectivity, altered modularity, and features characteristic of microbial dysbiosis. This dysbiosis disrupts the water ecological balance by destabilizing microbial symbiosis and nutrient cycling, which are essential for overall ecosystem resilience. As a result, these imbalances can exacerbate disease transmission and weaken the self-regulating capacity of marine environment, highlighting the need for integrated management strategies to restore equilibrium. These findings provide a theoretical basis for elucidating the mechanisms of bacterial diseases in S. japonica and developing future control strategies. Full article

Rotavirus alphagastroenteritidis (rotavirus) infects a broad range of hosts, including humans and various animal species. Its genome comprises 11 segments of double-stranded RNA, making it highly prone to genetic diversity through gene reassortment. Although rotavirus strains are typically host-specific, novel human strains with global impact often originate from interspecies transmission of animal rotaviruses. This review explores the critical role of interspecies transmission coupled with genetic reassortment in rotavirus adaptation to humans, contextualizing key studies and methodological advances. Central to this progress was the development of tools to analyse entire genomes and distinguish homologous from heterologous strains. We trace the evolution from RNA-RNA hybridisation to whole-genome sequencing, which underpins genotype constellation and sub-genotype phylogeny. A decade-long surveillance of the bovine-like G8 rotavirus in Vietnam offers a compelling model: for an animal rotavirus to become a successful human pathogen, it must replace its animal-derived genes with human-derived counterparts through reassortment. Retaining the animal-origin G8 VP7 gene is enabled by acquiring a compatible human VP4 gene (specifically P[8]) and DS-1-like backbone genes. Building on this model of reassortment-driven adaptation, our investigation into the unusual G1P[6] strain AU19, of wholly porcine origin, supports the hypothesis that the predominant human G1 rotavirus also evolved from a successful interspecies transmission event. Phylogenetic analysis suggests the ancestral human G1 gene emerged from a porcine rotavirus between 1915 and 1948, later reassorting with human strains to acquire Wa-like backbone genes, ultimately becoming a stable and dominant part of the human rotavirus population. In conclusion, genetic reassortment is a key mechanism transforming sporadic zoonotic events into sustained human-pathogens, although other factors remain to be fully defined. We conclude by highlighting key areas for further research. Full article

During a survey of plant litter-associated microfungi in Guangdong and Jiangxi Provinces, China, several specimens that have carbonaceous ascomata were collected. Morphological characteristics combined with multi-gene (LSU, SSU, and tef1-α) phylogeny revealed that they belong to the Aigialaceae, Astrosphaeriellaceae, and Pseudoastrosphaeriellaceae families. Phylogenetic analyses were conducted using Maximum Likelihood (ML) and Bayesian Inference (BI) approaches. Caryospora pruni and Pseudoastrosphaeriella zingiberacearum are introduced as new species, and Astrosphaeriella bambusae, C. quercus, Fissuroma caryotae, and Neoastrosphaeriella aquatica are introduced as new host records. In addition, Caryospora minima is synonymized under C. aquatica based on close morphological and phylogenetic relationships. All the newly introduced species fit well with their respective generic concepts and can be distinguished from closely related species in their morphology and DNA molecular data. The new host records also provide similar morphological characteristics to their respective type species, and multi-gene phylogeny analyses also offer evidence for their placements. In addition, we compiled the geographical distribution and host associations of species in Aigialaceae, Astrosphaeriellaceae, and Pseudoastrosphaeriellaceae. This provides a database for future studies to understand the ecological interactions and geographical variations. Full article

The global spread of carbapenem-resistant Acinetobacter baumannii (CRAB) poses a severe public health threat, driving growing interest in phage-based precision antibacterial strategies. This systematic review synthesizes recent advances in the field of A. baumannii phage. Modern taxonomy, based on whole-genome phylogeny, has reclassified the majority of A. baumannii phages into the class Caudoviricetes, revealing distinct evolutionary clades that correlate with host tropism and biological properties, superseding the traditional morphological families (Myoviridae, Siphoviridae, Podoviridae). To overcome limitations of natural phage therapy, such as narrow host range, cocktail therapies (ex vivo resistance mutation rates < 5%) and phage-antibiotic synergism (enabling antibiotic efficacy at 1/4 minimum inhibitory concentration) have significantly enhanced antibacterial efficacy. Preclinical models demonstrate that phage therapy efficiently clears pathogens in pneumonia models and promotes the healing of burn wounds and diabetic ulcers via immunomodulatory mechanisms. Technical optimizations include nebulized inhalation delivery achieving 42% alveolar deposition, and thermosensitive hydrogels enabling sustained release over 72 h. Genetic engineering approaches, such as host range expansion through tail fiber recombination and CRISPR/Cas-mediated elimination of lysogeny, show promise. However, the genetic stability of engineered phages requires further validation. Current challenges remain, including limited host spectrum, the absence of clinical translation standards, and lagging regulatory frameworks. Future efforts must integrate metagenomic mining and synthetic biology strategies to establish a precision medicine framework encompassing resistance monitoring and personalized phage formulation, offering innovative solutions against CRAB infections. Full article

Longhorn beetles mainly harm trees, flowers, and certain crops. They are closely associated with their host plants and often climb on vertical trunks, branches, and the underside of leaves. Their tarsi have numerous micro-scale adhesive setae on the ventral side. These setae provide sufficient force to enable the beetles to adhere firmly to smooth or slightly micro-structured surfaces. This study observed and analyzed the ultrastructures of the adhesive setae of three species from different subfamilies of Cerambycidae and one species from Vesperidae using a scanning electron microscope. The comparative analysis focused on characterizing the types, morphology, distribution patterns and adhesion mechanisms of the adhesive ultrastructures in four longhorn beetle species. The results showed that the longhorn beetles generally had pseudotetramerous tarsi (except An. chinensis, which had tetramerous tarsi), and that tarsomeres I–III were expanded and widened to increase the contact area between the tarsi and the substrate. Furthermore, a large number of micro-scale adhesive setae were present on the ventral surface of these tarsomeres. In total, five types of adhesive setae were found in the four species studied. The three species belonging to the Cerambycidae family exhibited adhesive setae with numerous short setules, while in the species Mantitheus pekinensis belonging to Vesperidae, there are two types of adhesive setae without any short setules. The differentiation of the adhesive structures in longhorn beetles is shaped by the combined effects of phylogeny, sexual dimorphism, and host-plant adaptations. Full article

The structure and assembly mechanism of wild animal gut microbiota represent persistent research hotspots. Among, the impact of geographic factors on the bacterial co-occurrence network characteristics and assembly mechanism of the gut microbiome remains unclear. Therefore, this study analyzed the gut microbiome of Niviventer confucianus and Apodemus agrarius from Anhui and Hubei provinces. The same alpha diversity pattern was found in the gut microbiome of species from the same region. The gut microbiome of the two rodent species in Anhui region exhibited “small world” characteristics, such as nodes with more local connections to allow interaction information (such as metabolites) to rapidly spread throughout the entire microbial community. In addition, dispersal limitations and heterogeneous selection accounted for higher proportions of the gut microbiome in the rodents from the Anhui and Hubei regions, respectively. The higher proportion of heterogeneous selection may exacerbate selection pressure in the Hubei region. Multiple regression on distance matrices analysis revealed that geographic region exerted a limited but significant influence (0 < R² < 0.2, * p < 0.05) on the gut microbiome, surpassing the effects of host phylogeny, gender, and weight. Nevertheless, the roles of regional factors—such as environmental microbes, pollutants, and diet—remain unexamined, and their potential as key drivers of microbiota variation in these rodents warrants further investigation. Full article

The amphibian microbiome plays a vital role in host health, yet the bacterial communities of caecilians (Order: Gymnophiona) remain largely uncharacterised. We investigated this by providing the first characterisation of the gut and skin microbiome of larval Ichthyophis bannanicus, a carnivorous caecilian, using 16S rRNA gene metabarcoding. Our analyses show distinct communities between the faecal samples and skin, with significant enrichment of Laribacter in faeces and Flavobacterium on skin. Despite significant variation in their community structures, the core genera Escherichia-Shigella were shared between both regions, suggesting similar microbial exchange in the aquatic environments. Skin bacterial diversity exhibited relatively higher richness, but lower evenness than that of faeces. Further, the skin bacterial community exhibited more complex interactions, suggesting stronger resilience to changes. The relationships and interactions of skin and faecal bacterial communities suggest their interactive effects on the host’s overall health. Compared with anuran tadpoles, the I. bannanicus larval microbiome showed taxonomic overlap, but possessed certain unique core bacteria. This work on an understudied amphibian lineage is foundational, highlighting how diet, phylogeny, and aquatic environment shape microbial communities and informing future research into amphibian health and disease. Full article

The Ponto-Caspian invader, the gravel snail Lithoglyphus naticoides (C. Pfeiffer, 1828), is infected with a diverse community of digenetic trematodes in its colonized range and most often serves as first intermediate host. We have performed the parasitological examination of L. naticoides snails sampled in Kaunas water reservoir (Lithuania) and found yet unknown strigeid metacercariae of the tetracotyle type using these snails as second intermediate host. In this study, we report data on morphology and molecular analysis based on two markers, the partial 28S rDNA gene and the ITS2 region of these metacercariae. Based on the comparative molecular and phylogenetic analysis, the metacercaria detected in L. naticoides was identified as Cotylurus cornutus (Rudolphi 1809) Szidat, 1928. Differences in metacercariae infection between snail sexes were assessed. The prevalence of infection in L. naticoides was significantly higher in males than in females. Additional molecular markers of tetracotyle of C. cornutus from Stagnicola palustris (O. F. Müller, 1774) and furcocercaria of Cotylurus strigeoides Dubois, 1958 from Physa fontinalis (Linnaeus, 1758), sampled in Curonian Lagoon, Lithuania, were obtained for the first time and used for comparative phylogenetic analysis. Full article

The highly fatal rabbit hemorrhagic disease (RHD) that first emerged in 1984 in China has spread worldwide and affects both domestic and wild rabbits. The disease was originally caused by RHD virus (Lagovirus europaeus, L.europaeus) of GI.1 genotype, but over the years, two further pathogenic forms, known as the antigenic and genetic variant RHDVa (GI.1a) and RHDV2 (genotype GI.2), have been identified. RHD was first reported in Poland in 1988, when two RHDV strains were isolated, currently classified as GI.1c, while RHDVa and RHDV2 emerged in 2003 and 2016, respectively. In this study, using virological and molecular methods, we characterized five new RHDV strains belonging to GI.1 (RHDV)/GI.1a (RHDVa) and GI.2 (RHDV2) genotypes isolated in Poland in 2020–2022, in domestic rabbits from backyard farm and companion animals. We showed that two strains of L. europaeus (NRU 2020 and LIB 2020) from 2020 in the phylogenies of nonstructural proteins (NSP) and structural capsid protein (SP-VP60) clustered in a homogeneous GI.1a variant group. We stated that three strains of L. europaeus from 2020 to 2022 (KOB 2020, ZWO 2021, WAE 2022) in the VP60 phylogeny were positioned in the GI.2 (RHDV2) genotype, while in the NSP phylogeny, they are genetically related to recombinants with the GI.3/GI.2 genotype. Unexpectedly, in two RHD cases identified in the same small geographical area of south-eastern Poland (Libusza and Kobylanka), the close coexistence of RHDVa (LIB2020) and RHDV2 (KOB2020) strains capable of causing independent infections at the same time was found. This leads to the conclusion that the close natural coexistence of RHDV strains belonging to different genotypes does not necessarily have to directly lead to the emergence of new genetic or antigenic variants, which confirms the distinctness of both genetic forms and indicates different evolutionary paths leading to the best possible adaptation to the host. Full article