搜索结果：diversity

Clavibacter nebraskensis (Cn) is a Gram-positive bacterial plant pathogen that infects the vascular tissue of maize, causing Goss's Wilt and Leaf Blight. Detection of highly virulent strains since the mid-2000s suggests that genetic divergence has contributed to the re-emergence of the disease following its effective management and subsequent disappearance in the 1980s. However, few genomic resources exist for this pathogen, and little is known about genomic variation in the species. Our study aimed to characterize genomic diversity across a set of differentially virulent strains isolated from both historic epidemics and recent outbreaks. We sequenced 17 Cn strains of varying virulence isolated from epidemics spanning their earliest detection to subsequent outbreaks in the mid-2010s across various US states and Manitoba, Canada. Contrary to previous studies, we found no strong population structure associated with geographic origin or year of isolation based on haplotype analysis. We detected five heterogeneous plasmids in strains CDK032, CDK039, CDK044, CDK045, and CDK046, whereas to date, only one plasmid has been sequenced in a single Cn strain. Genomic islands were detected in all strains, and the putative virulence gene celA was found to be encoded in one such island. Secreted CAZymes, hypothesized to be involved in pathogenicity, are well conserved across all Cn genomes, indicating that allelic or expression diversity, and not gene copy number, might be implicated in virulence diversity. Importantly, we identified deletions in a secreted cellulase within the linker peptide region between the carbohydrate-binding domain and the cellulase domain that have not been reported in the literature previously. Our analyses provide insight into genomic diversity within the species, revealing five novel plasmids and genomic islands harboring CAzymes, including the celA gene. Genes encoding cell wall degrading enzymes are well-conserved across strains of all virulence phenotypes. Deletions within a secreted cellulase not previously reported have been described for future functional analysis.

Immunonutrition examines how diet influences immune development. Complementary feeding represents a critical window for long-term health. We aimed to map evidence linking complementary feeding to immune outcomes, allergy, infection, and growth in infants and toddlers (≤ 3 years). We conducted a scoping review and evidence-gap mapping, following PRISMA-ScR. MEDLINE and Epistemonikos were searched from inception to November 2024. Concepts included diet diversity/patterns, feeding practices/models, and timing of allergen introduction, timing of complementary feeding, macronutrients, micronutrients, foods, supplementation, and ultra-processed foods. We included systematic reviews and recent primary studies meeting criteria. From 13,512 records screened, 108 systematic reviews were included, comprising 99 randomized controlled trials, 41 cohorts, 22 case-control, and 14 cross-sectional studies. Most reviews addressed nutrient intake, supplementation, or timing of allergen introduction, while fewer reviews explored diet diversity, foods, or ultra-processed food intake. Responsive complementary feeding was consistently associated with healthier growth and lower obesity risk, whereas restrictive practices showed adverse effects. Greater diet diversity was linked to reduced asthma and food allergy risk, though eczema findings were inconsistent. Western-style diets high in processed foods, fat, sugar, and meat correlated with higher allergy risk, while home-prepared diets were protective. Micronutrient supplementation (iron, zinc, vitamin D) reduced infection and anemia risk but had mixed effects on allergy. Early allergen introduction reduced food allergy incidence. Complementary feeding research now extends beyond calorie counting, macronutrients, and early allergen introduction to dietary patterns and early life nutrition that supports the microbiome. Evidence supports dietary diversity, timely food allergen introduction, and responsive feeding, while discouraging restrictive practices and ultra-processed foods. Future work should harmonize definitions and investigate plant-based diets, advanced glycation end products, and processed food exposures.

Current understanding of how multiple stressors shape freshwater biodiversity at continental scales relies heavily on evidence from postindustrial temperate regions, potentially misrepresenting the dynamics of ecosystems facing rapid development and extreme environmental heterogeneity. Here, we present a standardized, continental-scale field survey of benthic macroinvertebrates across 502 sites in China to test the universality of established macroecological patterns. Contrary to the expectation that physical habitat and climatic gradients primarily drive community structure, we found that organic pollution, with a focus on oxygen-demand assays (COD and BOD), emerged as the single most influential variable, explaining the largest proportion of variation in taxonomic, functional, and phylogenetic diversity. Together with total nitrogen and total phosphorus loading, this chemical pressure largely overrode the explanatory contribution of land-use and climatic drivers, with stressor interactions characterized by asymmetric dominance rather than the synergistic amplification commonly predicted. Furthermore, despite steep environmental gradients that theoretically favor deterministic sorting, community assembly was overwhelmingly dominated by stochastic processes ( ∼ $$ \sim $$ 86%, based on overall pairwise comparisons across all sites). We suggest this pattern is consistent with a "stochastic trap" hypothesis, potentially arising from high-frequency anthropogenic disturbances that weaken trait-environment matching. These findings indicate that biodiversity frameworks derived from stabilized, temperate systems may not generalize to the compressed modernity of developing regions. We propose that global conservation strategies should consider prioritizing the reduction of chemical bottlenecks, which may act as critical physiological constraints on freshwater resilience in the Anthropocene.

To investigate the effects of storage time and temperature on the quality of fecal samples and to provide a reference for clinical laboratories and biobanks in formulating sample storage operation guidelines. Fresh fecal samples were collected from healthy volunteers and immediately aliquoted into aliquots. Different temperature and time gradients were established to simulate common pre-analytical storage processes in clinical practice, with samples snap-frozen in liquid nitrogen immediately after collection as the control group. 16S rRNA gene sequencing and untargeted lipid metabolomics were employed to determine changes in microbial diversity, species abundance, and metabolite concentrations under different storage conditions, and sample quality was evaluated based on these indicators. Storage at 4°C significantly minimized fluctuations in α-diversity indices, with the most pronounced protective effect observed within 2-4 hours; beyond 4 hours, changes in microbial community structure intensified. β-diversity analysis revealed that 4°C storage delayed the increase in microbial dissimilarity between samples and the liquid nitrogen-frozen control group, among which samples stored for 2-4 hours exhibited the highest similarity to the control. At the phylum level, the abundance of Firmicutes increased significantly after 6 hours of storage at room temperature, while 4°C storage effectively delayed this change. Metabolomic analysis identified more metabolomic differences (including bile acids and amino acids) in samples stored at room temperature, whereas only minor changes in fatty acid metabolites were observed at 4°C. 3β-hydroxy-5-cholenic acid exhibited a continuous upward trend with prolonged storage at both temperatures, suggesting its potential as a biomarker for evaluating sample storage quality. Short-term storage at 4°C (≤4 hours) can effectively delay the quality degradation of fecal microbial communities and metabolites, making it the optimal transitional storage strategy when immediate liquid nitrogen freezing is not feasible in clinical practice. These findings provide critical experimental data for the establishment of standardized fecal sample storage protocols.

Copy number variation (CNV) is a major source of genomic diversity that shapes gene family evolution and may contribute to ecological differentiation, yet its genome-wide ecological relevance remains poorly understood. Here, we analyzed CNV across four Brassicaceae species (Arabidopsis thaliana, A. lyrata, A. halleri, and Arabis alpina) to identify gene families undergoing rapid expansion or contraction. Using a birth-death model, we identified 231 rapidly evolving gene families spanning diverse functional categories. We then characterized CNV within populations of A. thaliana and A. lyrata using population-scale long-read assemblies. CNV exhibited strong heterogeneity across gene families and species, with contrasting evolutionary outcomes: A. thaliana showed greater retention of duplicated copies, whereas A. lyrata exhibited higher pseudogenization and turnover. CNV profiles were strongly structured geographically, reflecting known demographic and phylogeographic patterns in both species. Environmental association analyses revealed species-specific architectures: CNV in A. thaliana showed a diffuse, polygenic association with climate, whereas in A. lyrata associations were more strongly coupled to population structure. Despite the functional diversity of rapidly evolving families, environmentally associated CNVs were significantly enriched in defense- and stress-related functions. These results demonstrate that CNV-environment relationships emerge at the level of gene family networks and are shaped by genomic architecture and lineage history, highlighting CNV as a context-dependent driver of genome evolution and ecological differentiation.

Background Fluoroquinolone resistance in Escherichia coli is increasingly associated with the dissemination of high-risk lineages such as ST131. However, data integrating resistance phenotypes with molecular characteristics remain limited in local clinical settings. This study aimed to describe the distribution of ST131 and associated resistance determinants in a single-center cohort.Methods We analyzed 90 non-duplicate clinical E. coli isolates collected at a tertiary-care hospital in Turkey. Fluoroquinolone resistance was assessed using ciprofloxacin and pefloxacin. Molecular assays targeted phylogenetic groups, ST131 (including H30-Rx), ESBL genes (blaCTX-M with group assignment), plasmid-mediated quinolone resistance (PMQR) markers, and selected virulence genes. ERIC-PCR was used for genotyping and clustering. Comparative analyses were performed between ciprofloxacin-resistant and -susceptible isolates using appropriate categorical and non-parametric tests.Results Ciprofloxacin resistance was detected in 35/90 isolates (38.9%). Overall, presumptive ST131 (PCR-defined) was identified in 10/90 isolates (11.1%) and was strongly enriched among ciprofloxacin-resistant isolates (25.7% vs. 1.8%, p&#x2009;<&#x2009;0.001); H30-Rx was also more frequent in ciprofloxacin-resistant isolates (14.3% vs. 1.8%, p&#x2009;=&#x2009;0.031). CTX-M was detected in 31/90 isolates (34.4%) and was significantly associated with ciprofloxacin resistance (65.7% vs. 14.5%, p&#x2009;<&#x2009;0.001). Among CTX-M-positive isolates (n&#x2009;=&#x2009;31), group 1 predominated (87.1%), followed by group 2 (41.9%) and group 9 (6.5%); group 1&#x2009;+&#x2009;2 co-detection occurred in 38.7%, and 6.5% remained untypeable. PMQR markers included qnrS (11.1%), qnrB (4.4%), and aac(6')-Ib-cr (8.9%). Phylogroup B2 was dominant (76.7%). ERIC-PCR identified 59 profiles with high diversity (Simpson's index 0.9898); 60.0% of isolates belonged to clusters (largest cluster n&#x2009;=&#x2009;4), indicating high fingerprint diversity inconsistent with a single dominant outbreak clone.Conclusion Presumptive ST131 isolates were enriched among ciprofloxacin-resistant E. coli in this single-center cohort. These findings reflect local molecular surveillance patterns rather than population-level prevalence. The high ERIC-PCR diversity suggests multiple lineages rather than a single outbreak clone, underscoring the need for sustained molecular surveillance and antimicrobial stewardship.

Autoimmune diseases are chronic and heterogeneous disorders resulting from the breakdown of immune tolerance and subsequent tissue damage. Beyond genetic predisposition, viral infections are increasingly recognized as pivotal environmental contributors to disease onset. In this study, we performed comprehensive viral metagenomic profiling of blood samples from 205 patients with systemic lupus erythematosus (SLE), Sj&#xf6;gren's syndrome (SS), ankylosing spondylitis (AS), and undifferentiated connective tissue disease (UCTD). A total of approximately 103.98&#xa0;million sequencing reads were analyzed, revealing 44 viral families, including 30 DNA and 14 RNA families. RNA viruses dominated the virome composition, accounting for 71% of total reads, with Picobirnaviridae being consistently prevalent and abundant across all disease groups. Alpha and beta diversity analyses revealed significant heterogeneity in viral community structures among different disease groups, with a marked diversity skew observed in the SS group. Disease-specific viral composition patterns were prominent, and the number of core viral species shared across the four groups was limited. Of particular note, Anelloviridae was significantly enriched in the AS and UCTD groups, suggesting its potential as a biomarker for immunosuppressive states. Furthermore, bacteriophages such as Microviridae exhibited differential abundance across groups, reflecting the potential role of virus-microbe-host immune interactions in disease pathogenesis. In conclusion, this study provides a comprehensive profile of the blood virome in four autoimmune diseases, highlighting the potential role of viral communities in immune regulation and offering new perspectives for the development of related biomarkers.

Understanding how biological communities are structured across space and time is a fundamental goal in ecology and evolution. Traditional genetic approaches require sampling many individuals, an effort that is often logistically challenging, limited in geographic coverage, and taxonomically biased towards easily sampled species. Environmental DNA (eDNA) offers a transformative alternative, enabling simultaneous characterisation of both community composition and genetic variation across hundreds of species. However, a key challenge for this approach is determining the frequencies of genotypes and haplotypes from mixed environmental samples containing many taxa and individuals. This could be limiting for marine species that have high gene flow, as genetic differentiation is often characterised by changes in gene frequencies, not the presence of unique haplotypes. Here, we directly tested the accuracy of eDNA-derived mitochondrial DNA diversity and genetic differentiation estimates for 18 Hawaiian marine vertebrates against benchmarks from traditional, individual-based tissue sampling. eDNA reliably recovered dominant haplotypes at their relative frequencies, and measures of sequence diversity were significantly correlated between approaches. In contrast, population structure metrics were only weakly correlated at this spatial scale, because eDNA more frequently returned positive values of &#x3a6;ST than tissue-based methods. Overall, eDNA successfully converted complex mixed samples into accurate estimates of haplotype composition and relative frequencies, enabling comparative population genetic analyses across entire marine communities and revealing both the strengths and limitations of frequency-based inference from environmental samples.

Agricultural intensification is a major driver of land use change, thereby reducing biodiversity and leading to population declines across various animal groups. In response, animals can mediate some negative fitness impacts and navigate through agricultural landscapes with reduced resource availability by changing their habitat selection via movement decisions - particularly when constrained by central-place foraging, which requires balancing travel costs against energetic returns. Here, using miniature ATLAS tags (Advanced Tracking and Localisation of Animals in real-life Systems), we tracked 101 house martins and 87 barn swallows at high-resolution to investigate their state-specific habitat selection and mapped the insect abundance and diversity across an intensively used agricultural landscape. Both species mainly avoided arable fields and increasingly selected for forests and water bodies with distance from the colonies. House martins ranged farther from colonies than barn swallows and also showed strong distance-dependent selection for structurally complex habitats, such as extensive grasslands and green areas within villages. Furthermore, house martins selected for proximity to water bodies, while barn swallows' selection focused on proximity to woody vegetation structures. During our 2023 insect sampling window, habitat selection tracked mapped insect richness more closely than mapped insect abundance. Distance-dependent divergence in space use suggests horizontal niche differentiation between sympatric central-place foragers, with potential implications for coexistence. Combined, our findings point to the importance of maintaining extensively used grasslands and small-scale habitat structures within intensively managed farmland to improve the abundance and diversity of prey for farmland passerines.

Allogeneic haematopoietic stem cell transplantation (HSCT) is a cornerstone therapy for haematological and genetic disorders. Owing to the limited availability of HLA-identical related donors, umbilical cord blood (UCB) has become a valuable alternative source of haematopoietic progenitors. However, many UCB units are excluded from banking based on quality criteria, despite potentially harbouring rare and underrepresented HLA profiles, particularly within certain demographic groups. This study evaluated the strategic value of immunogenetically rare but low-quality UCB units in expanding donor options for patients with uncommon HLA profiles. HLA-A, -B, and -DRB1 typing was performed on 577 UCB units, and allelic, haplotypic, and genetic diversity analyses were conducted using the HLA-net GENE[RATE] tool. Units were categorised using the Search Prognosis Application as good (6/6), fair (5/6), or poor (<&#x2009;5/6 matches). Genotype frequency was used as a proxy for immunogenetic rarity and evaluated as an operational criterion for defining retention thresholds. ROC analyses were interpreted as concordance analyses between genotype frequency and Search Prognosis classification rather than as independent predictive validation. Statistical significance was assessed by chi-square and residual analyses. The cohort displayed remarkable allelic diversity, particularly at the HLA-B locus, strong linkage disequilibrium among loci, and a large proportion of unique genotypes. Matching-prognosis classification identified 66.72% of units as good, 31.54% as fair, and 1.73% as poor. Caucasian genotypes were overrepresented in the good category, whereas Asian-Pacific-Islander and African-American haplotypes were enriched in poorer matching-prognosis categories. ROC analysis showed strong concordance between genotype frequency and Search Prognosis classification (AUC 0.80-0.99) and population-specific genotype frequency thresholds. Our findings suggest that immunogenetic rarity provides complementary value to conventional quality metrics. While low-cell-dose units may have limited direct clinical utility, those with rare HLA genotypes may retain strategic importance, particularly for patients with uncommon immunogenetic profiles. Integrative approaches combining biological and immunogenetic parameters may improve cord blood banking strategies.

Tree seeds harbor diverse fungal communities, including both pathogens and mutualists, that can influence plant health. These communities comprise living, metabolically active organisms as well as dormant or dead cells. Because only active fungi interact with their hosts, distinguishing active from inactive taxa is crucial, especially for environmental and phytosanitary monitoring. Traditional culturing methods capture living fungi but account for only a small fraction of the total fungal diversity. Currently, these methods are increasingly replaced by high-throughput DNA metabarcoding, which detects a broader range of taxa. However, DNA persists after cell death and occurs in dormant cells, preventing distinction between active and inactive fungi. In contrast, RNA metabarcoding may better reflect living fungal communities than the other two methods, though its use in assessing plant-associated fungi remains underexplored. We used culturing, DNA-, and RNA-based metabarcoding to compare fungal communities associated with seeds of three key European tree species (Fagus sylvatica, Abies alba, Pinus sylvestris). Dominant fungal communities in seeds were strongly shaped by host species identity and were largely shared across DNA and RNA metabarcoding datasets, with roughly half of the most abundant genera detected by both methods. Differences between DNA- and RNA-derived communities were predominantly associated with rare taxa in the RNA dataset, although distinguishing true biological signals from noise introduced by different methodological workflows remains challenging. Several cultured genera, likely both abundant and metabolically active, were consistently detected by both approaches. These results highlight the complementary nature of the three methods for characterising seed-associated fungi. Combining culturing, DNA- and RNA-based metabarcoding may provide the most comprehensive assessment of fungal diversity, while RNA metabarcoding alone offers a promising opportunity to identify the active members of fungal communities for improved environmental and phytosanitary monitoring.

Enteroviruses (EV) represent a significant public health concern due to their widespread prevalent and ability to cause disease in humans. Due to the limitations of routine surveillance, which primarily only detect clinically symptomatic cases, environment surveillance of urban sewage has emerged as a valuable and complementary strategy for EV surveillance. A total of 48 sewage samples were collected monthly from two wastewater treatment plants (WWTPs) in Hangzhou, Zhejiang Province from January 2023 to December 2024. Virus isolation and direct next-generation sequencing (NGS) were performed to characterize the EV serotypes profiles in sewage. Reverse transcription polymerase chain reaction (RT-PCR) was used to amplify VP1 gene sequences for molecular epidemiological analysis of EV serotypes. Ten distinct serotypes were isolated and identified from WWTP-QT and sixteen from WWTP-XS via virus isolation. EV-B was the dominant group in both treatment plants, with E3 and E11 representing the most frequently isolated serotypes. Phylogenetic analysis showed that the predominant genotypes in E3 was C6, whereas all E11 included phylogenetic analysis were classified into genotype D5. On the other hand, direct NGS uncovered as many as 108 distinct EV serotypes covering four human-infective species across both WWTPs. CVA4 and CVA6 were the dominant serotypes identified via NGS. Additionally, multiple uncommon serotypes as EV-A76, A89, A90, A92, A114, B74, B79, B98, B101, B106, B107, C96, C99, C113, C116, D70, D94, D111, D120 were detected in sewage. Environment surveillance is an important tool for monitoring EV circulation in the population. Furthermore, direct NGS can serve as a supplementary tool to the routine virus isolation method, particularly in detecting EV serotype diversity and evolution, and identifying uncommon serotypes.

The genus Cladophora (Cladophorales, Ulvophyceae) has a long history of taxonomic challenges due to morphological plasticity and incongruence between traditional classifications and molecular phylogenies. Here, we propose Mysticladia gen. nov. to accommodate species previously assigned to Cladophora but phylogenetically placed within the Siphonocladus clade. Analyses of concatenated SSU&#x2009;+&#x2009;LSU rDNA gene sequences from specimens collected along the Brazilian coast revealed that populations morphologically identified as C. prolifera and C. aokii form a distinct and phylogenetically distant clade from Cladophora sensu stricto. Genetic divergence and morphological comparisons supported the recognition of two new cryptic species: Mysticladia nigra sp. nov. and M.&#x2009;edisonii sp. nov. Both seemingly restricted to the southwestern Atlantic. These species are morphologically indistinguishable from their closest relatives but distinguishable by DNA sequences. Additionally, we transfer C. prolifera, C. aokii, and C. coelothrix to Mysticladia. Our findings broaden the widespread cryptic diversity within the Cladophorales and emphasize the critical need for molecular analyses across populations in this group, including those already and correctly identified based on morphology alone. Such efforts are essential for elucidating cryptic lineages and species boundaries in simple filamentous green algae, where phenotypic plasticity often disguises true evolutionary relationships.

Sesame (Sesamum indicum L., 2n&#x2009;=&#x2009;26) is one of the oldest oilseed crops and is often called the 'queen of oilseeds' due to its high content of unsaturated fatty acids and natural antioxidants. Despite its long history, the origin and global spread of cultivated sesame remain unresolved. We assembled a telomere-to-telomere (T2T), high-quality reference genome of sesame (cv. Yuzhi11) to investigate sequence differences between genomes and its origin and the local adaptation evolution of flowering time (DF). We generated a 305&#x2009;Mb T2T sesame reference genome (cv. Yuzhi11) with >&#x2009;99.99% base-level accuracy, identifying 31&#x2009;063 protein-coding genes. Repetitive elements accounted for 52.03% of the genome. Population genomic analysis of 927 accessions from 14 regions identified four major groups. Integrative analyses of linkage disequilibrium decay (LD), nucleotide diversity (&#x3c0;), and fixation index (FST) support East Africa as the center of origin, with subsequent migration through the Middle East, to South Asia, South-East Asia, East Asia and ultimately to other parts of the world. Genome-wide association studies (GWAS) and selection scans identified 30 genes associated with flowering time. SiUBP16 is a candidate associated with 7.6% of DF variation. Early-flowering accessions carried up to 225 favourable alleles. A flowering time prediction model for high-latitude regions achieved 96% accuracy. We present a high-quality T2T reference genome for cultivated sesame, shedding light on its origin, evolutionary history, and regional flowering time adaptation. This genome insights valuable tools for breeding programs aimed at improving yield and environmental adaptation in sesame and related crops.