Antibacterial resistance represents a major global health challenge, particularly due to drug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA), which is known for causing persistent, biofilm-associated infections. In this study, we introduce self-assembling, tryptophan-rich peptide nanofibrils derived from DVFLGREEWWWWC (D4W) as potent antibacterial agents against Staphylococcus species, including MRSA. These self-assembling D4W units form amyloid fibril-like structures through controlled polarity reversal, enhancing their structural stability and antibacterial efficacy. The DVFLG motif enables selective recognition of Staphylococci, while the WWWW segment facilitates β-sheet formation and deep membrane penetration via hydrophobic interactions, effectively disrupting bacterial membranes. Moreover, D4W-derived nanofibrils engage in multivalent interactions with bacterial surfaces, significantly enhancing targeting precision and antibacterial efficacy. Beyond eradicating planktonic Staphylococci, D4W-derived nanofibrils significantly inhibit biofilm formation, a main factor in antibiotic resistance. Notably, D4W-derived nanofibrils exhibit low cytotoxicity and hemotoxicity, addressing their therapeutic potential. Their efficacy was validated in ex vivo pig skin and in vivo zebrafish embryo models, where they successfully inhibited MRSA growth. In addition, molecular dynamics simulations were employed to elucidate the interactions between D4W and model lipid membranes. This study introduces a strategy for designing effective antibacterial agents with enhanced stability, selectivity, and biofilm-prevention capabilities against drug-resistant Staphylococci. Our results indicate the promise of self-assembling peptide-based therapeutics in combating antibiotic-resistant Staphylococcal infections.
Loop-mediated isothermal amplification (LAMP) continuously generates strand-displaced single-stranded DNA intermediates, providing the possibility of assembling DNA fragments. Here, we developed a novel two-DNA-fragment fusion technique, termed fusion LAMP, which is an isothermal DNA-fusion strategy that enables the fusion of two independent DNA fragments within a single amplification reaction. By combining fusion LAMP with CRISPR/Cas13a, we further established an "AND-gate" nucleic acid detection platform, termed Fusion LAMP-Coupled CRISPR/Cas13a (FLCC), which enables concurrent detection of two targets by reading the fusion product-triggered fluorescence signals. This platform generates signals only when two targets are present simultaneously. To prove this concept, we then employed FLCC to identify the methicillin-resistant Staphylococcus aureus (MRSA). This method achieved a limit of detection of 10 copies/μL of MRSA genomic DNA and showed no cross-reactivity with closely related bacterial strains. Furthermore, we validated its feasibility by detecting 19 clinical isolates, demonstrating a simple and accurate approach for MRSA detection. Collectively, the FLCC platform ensures identifying pathogens accurately and provides a promising diagnostic approach for detecting complex genetic targets.
The full utilization of both photocatalytic reduction and oxidation reactions is highly attractive for atom-economic and sustainable chemical synthesis. However, coupling CO2 reduction with oxidation of liquid organics is challenging, as their disparate physicochemical properties lead to mismatched adsorption, diffusion, and activation at a common interface. Effective integration requires precise molecular recognition to selectively bind each substrate molecule and tailored spatial confinement to bring them into reactive proximity. Herein, we engineered dual functionality by assembling a cyclodextrin metal-organic framework (CD-MOF) onto ZnCdS nanoparticles. The γ-CD cavities exhibit molecular recognition of benzyl alcohol via host-guest interactions, while the porous framework has spatial confinement effects and accumulates CO2 molecules. This well-defined microenvironment with an interfacial dipole field enhances charge separation, accelerates interfacial electron transfer, and drives efficient tandem photoreactions. Under visible light illumination, CO has been produced at a rate of 1195.1 µmol·g- 1·h- 1 (14.5-folds higher than pristine ZnCdS). Meanwhile, benzyl alcohol is oxidized to benzaldehyde with nearly 100% selectivity, rivaling state-of-the-art performance among non-precious metal systems. This work establishes a supramolecular paradigm of programmable host-guest microenvironments to orchestrate photoredox transformations.
Graphene can support spin transport over long distances, yet achieving large electrical spin signals remains challenging because spin injection and detection are highly sensitive to disorder at tunnel-barrier interfaces. Here we demonstrate that suppressing such interfacial disorder enables high-fidelity spin injection and detection in graphene. We fabricate van der Waals graphene spin valves by exfoliating and assembling constituent two-dimensional crystals inside an inert glovebox, combined with contamination-suppressing lamination and thorough post-transfer cleaning to realize atomically flat hexagonal boron nitride tunnel barriers. Our four-terminal nonlocal devices exhibit exceptionally large spin polarizations approaching 90 percent and nonlocal spin signals up to 1.6 kΩ. The high tunnel-barrier quality enables robust spin detection down to nanoampere excitation currents and gate-tunable magnetoresistance exceeding 80 percent. Spin precession measurements reveal Elliott-Yafet-type relaxation with nearly isotropic spin dynamics. These results establish interface-controlled van der Waals fabrication as an effective route to high-signal spin transport in graphene.
While conventional nanocarriers like liposomes are effective for small-molecule delivery, their fabrication often involves complex, multi-step processes. This work provides a proof-of-concept demonstrating a bacterial lipoprotein as a viable, genetically encoded, and self-assembling nanocarrier. We show specifically that the detergent-solubilized lipoprotein LipoMetQ from Neisseria meningitidis spontaneously forms micelle-like nanoparticles (termed LipoLoad), which entrap the small molecule Rose Bengal (RB) using a simple procedure of mixing and centrifugal ultrafiltration. The resulting LipoLoad: RB formulation was analyzed by dynamic light scattering and negative-stain TEM. Entrapment was found to decrease RB aggregation and enable a sustained release profile in vitro relative to the free drug. Furthermore, MTT assays performed on a subset of cancer cell lines revealed that LipoLoad: RB increased the intrinsic cytotoxic activity of RB. These results establish LipoLoad as a novel, biologically encoded nanocarrier. The facile production method, which does not require specialized equipment, and the formulation's stability underscore the broad potential of bacterial lipoproteins as a modular platform for nanotechnology.
The clinical intractability of diabetic foot ulcers stems from a profound uncoupling of cutaneous neurovascular networks, rendering standard metabolic and topical interventions largely palliative. Paradoxically, remote orthopedic trauma robustly accelerates distal skin repair, yet the systemic molecular mediators driving this "bone-skin crosstalk" remain undefined, precluding its translation into non-invasive therapies. Here, we establish that macroscopic bone fracture expedites diabetic wound healing through the systemic release of exosomal miR-130b-3p, a potent orchestrator of coupled angiogenesis and neurogenesis. To recapitulate this physiological axis non-invasively, we engineered a self-assembling, cholesterol-modified agomir-130b-3p nanocomplex that could bypass endolysosomal degradation. For sustained spatial delivery, these carrier-free nanoassemblies were incorporated into an in situ photocrosslinkable methacrylated collagen/silk fibroin hydrogel, creating a bio-instructive extracellular matrix that prolongs microRNA bioavailability. In streptozotocin-induced diabetic mice, hydrogel-mediated agomir delivery achieved 97.2% full-thickness wound closure. Advanced volumetric light-sheet imaging of chemically cleared whole-mount skin confirmed the robust spatiotemporal reconstruction of deep vascular and neural networks. These findings decode a distinct exosome-mediated inter-organ repair mechanism and demonstrate that biomimetic microRNA nanoformulations can effectively translate systemic physiological cues into localized, high-efficacy therapeutics for ischemic neuropathic wounds.
A fundamental obstacle in photocatalytic overall water splitting lies in the simultaneous evolution of H2 and O2 gases, which complicates gas separation. Decoupling hydrogen and oxygen evolution via a redox electron mediator offers an attractive route to overcome this limitation; however, its success critically depends on the development of electron mediators that satisfy both suitable redox potentials and rapid interfacial charge-transfer kinetics. Here, we demonstrate tunable redox potential in cobalt bipyridine complexes, [Co(bpy)2Cl2]Cl, through ligand functionalization. Electron-donating groups (-OCH3, -CH3) induce negative shifts in the redox potential, whereas electron-withdrawing substituents (-Cl) leads to positive shifts, yielding a broad potential range from 0.15 to 0.62 V versus NHE. The optimized electron mediator, [Co(bpy-CH3)2Cl2]Cl, exhibits enhanced electron transfer and water oxidation activity on BiVO4 photocatalyst. Coupled with selective assembling of Pt on the electron-rich {010} facets, an Pt-Cl interfacial charge-transfer channel was established, which accelerates electron transfer and promotes the adsorption/desorption of electron mediator. This integrated system achieves efficient photocatalytic water oxidation with an apparent quantum efficiency of up to 90% at 420 nm. Using [Co(bpy-CH3)2Cl2]Cl electron mediator, the work demonstrated the spatial separation of hydrogen and oxygen evolution reactions in particulate photocatalytic water splitting.
Corneal neovascularization (CNV) is one of the leading causes of corneal blindness, affecting millions of people worldwide. Anti-vascular endothelial growth factor agents, such as Bevacizumab (Beva), offer high specificity and low side effects. However, their limited ability to penetrate the corneal barrier necessitates invasive administration, significantly restricting their clinical application. Herein, we engineered (Beva&C₂G₂R₉)@Zn nanoparticles formed by co-assembling Beva, C₂G₂R₉ peptide and Zn2+, which decrease in size over time, as an efficient strategy for noninvasive Beva delivery across the corneal barrier to treat CNV. By combining various technologies (DLS, TEM, XPS, FTIR, and computer simulation), we discovered that the coordination between Beva and Zn2+ drives the nanoparticle formation, while the C₂G₂R₉ peptide facilitates its size evolution. Compared to size-stable nanoparticles of Beva@Zn and (Beva&R₉)@Zn, (Beva&C₂G₂R₉)@Zn nanoparticles exhibit rapid cellular internalization, efficient lysosomal escape, and effective corneal barrier penetration, leading to efficiently inhibit HUVEC cell migration and tube formation. Importantly, in a rat alkali-burned CNV model, (Beva&C₂G₂R₉)@Zn nanoparticles exhibited superior efficacy in inhibiting corneal neovascularization compared to size-stable nanoparticles, with the lowest inflammation index. The results of this study highlight the importance of controlling the size of nanoparticles to enable non-invasive delivery of macromolecular drugs across the corneal biological barrier, offering new insights for the design of future nanoparticle-based drug delivery systems.
Rapidly decreasing costs of sequencing whole genomes has caused a boom in genomic resources for many species. However, many key nonmodel systems that were sequenced early in the genomic revolution lack assemblies that reflect the quality and contiguity that are routine with current technology. Some of these "early for assembly, late for contiguity" genomes belong to the butterfly genus Heliconius, a remarkably fruitful clade for exploring questions of phenotypic mimicry, speciation dynamics, and population genetics. We de novo assembled five new reference genomes of Heliconius butterflies based on PacBio HiFi sequencing: two subspecies of H. erato, two subspecies of H. melpomene, and a closely related species, H. numata. While independent assemblies of multiple subspecies are already a valuable resource, these specific genomes are important for exploration of the genomic basis of mimicry, because the four H. erato and H. melpomene genomes represent two pairs of H. erato/H. melpomene local comimics. These genomes prove to be high quality (merqury quality score 51-58) and approach completeness (>98% BUSCO complete genes) over a lower number of longer contigs than earlier Heliconius genomes, illustrating how PacBio long-read technology alone can unlock untapped genomic resources. This set of high-quality, uniformly processed genomes represents an important resource for exploring the genomics of adaptation, hybridization, and speciation. Although a Heliconius butterfly was among the first animal genomes to be sequenced, the genus lacks high-quality, publicly accessible, de novo reference genomes for most of its species. This is particularly important for Heliconius because independent and complete genomes are necessary to unambiguously determine the history of introgression and phenotypic innovation that makes this system so relevant for evolutionary research. We address this gap by generating deep-coverage PacBio long-read data from 5 Heliconius subspecies, assembling genomes de novo with a uniform and reproducible Snakemake processing pipeline. We recover excellent genome contiguity, quality, and completeness scores using only long-read data. We further annotate these genomes with subspecies-specific RNA-seq data to produce annotations with >97% BUSCO completeness. This group of Heliconius genomes represent an important contribution of identically processed, high-quality genomes for comparative genomic investigation into the evolution and innovation of ecologically relevant phenotypes.
Trait-based frameworks, notably Grime's competitor-stress-tolerant-ruderal theory, offer a powerful lens for predicting how environmental fluctuations govern community structure. Yet, classical ecological models assume environments combining extreme stress and intense disturbance are non-viable for sustained colonisation, leaving a critical bottleneck in our ability to predict how microbial systems withstand compounded operational pressures. This gap severely hinders the predictive management of engineered microbiomes critical for global waste-to-energy conversion. Here we extend the application of classic ecological frameworks by demonstrating that anaerobic digester microbiomes deploy distinct, predictable life-history strategies across a 182-day compounded gradient of biomass turnover and organic loading. High-intensity single-event disturbances drive severe volatile fatty acid accumulation (propionate reaching 2,955 mg L-1), selectively shifting the microbiome toward stress-tolerant and stress-tolerant-ruderal strategies. Traits associated with ribosome function, molecular chaperones, and enzymatic reactive oxygen species detoxification were particularly enriched under highly disturbed conditions. Conversely, intermediate regimes were associated with ruderal strategies that prioritise rapid growth over resource-uptake efficiency, dropping total chemical oxygen demand removal to 41%. Cross-system comparisons encompassing anaerobic digestion, activated sludge, and soil ecosystems, revealed both universal and context-dependent ecological traits. Survival-associated traits linked to cell maintenance and repair, protective mechanisms, and cell motility were universally associated with stress-tolerant or ruderal strategies across ecosystems, whereas nutrient transport and metabolic traits exhibited greater context dependency. These insights establish a gene-resolved framework that reconciles microbial trait selection with ecological theory, providing a roadmap to engineer microbiome resilience against process failures.
The primary symbiont Candidatus Portiera is essential for nutrient provisioning in whiteflies. Genomic instability is a hallmark of Bemisia tabaci-associated Portiera, but the specific molecular evolutions and their metabolic consequences compared to Portiera from other whiteflies remain unclear. To overcome the limited sampling of previous studies, we assembled novel Portiera genomes from seven additional B. tabaci cryptic species. Comparative genomic, phylogenetic, and species delimitation analyses were conducted with other publicly available Portiera genomes. Branch-model selection analysis identified differentially evolved genes in the B. tabaci-associated Portiera, which were significantly enriched in amino acid biosynthetic pathways. The composition of essential amino acids biosynthetic pathways was systematically analyzed across Portiera, host nuclear, and secondary symbiont genomes. B. tabaci-associated Portiera formed a monophyletic lineage with larger genomes, lower coding density, and accelerated evolutionary rates, classified as a single species distinct from Portiera in other whiteflies. Twenty-two genes showed significantly different evolutionary rates with enrichment in amino acid biosynthetic pathways. Key genes for lysine and arginine biosynthesis were lost or pseudogenized in B. tabaci-associated Portiera but remained intact in other whiteflies like Trialeurodes vaporariorum. The synthesis of most other essential amino acids was similarly incomplete across all Portiera, relying on host or secondary symbiont genes for pathway completion. The B. tabaci-associated Portiera represents a unique symbiotic metabolic architecture where host horizontally transferred genes may potentially compensate for Portiera's genomic erosion, contrasting with the more autonomous Portiera in other whiteflies. This study reveals divergent evolutionary trajectories and metabolic integration strategies in whitefly symbiotic systems.
A photosensitizer-free, visible-light-driven hydrosilylation is reported. Mixing a nonaromatic substrate, tris(trimethylsilyl)silane, and Cs2CO3 generates a visible-light-absorbing species, which upon 456 nm irradiation produces silicon-centered radicals without an exogenous photocatalyst. These radicals enable hydrosilylation of diverse alkenes and alkynes, and also serve as halogen-atom transfer reagents for dehalogenation. This strategy eliminates the need for external initiators, photocatalysts, or HAT mediators.
Mesoporous membranes with tunable architectures and robust mechanical properties remain challenging to fabricate, owing to the difficulty of simultaneously achieving structural order and mechanical stability. We report a general strategy to construct programmable polymeric mesoporous membranes by exploiting confined physical entanglement within polymer-grafted nanocrystal (NC) superlattices. Two-dimensional superlattices, self-assembled at the liquid-air interface from size-, shape-, and composition-controlled NCs, serve as structural templates, and thermal annealing activates polymer entanglement to stabilize the superlattice framework. Subsequent selective removal of NC cores yields free-standing, long-range-ordered polymeric mesoporous membranes that exhibit remarkable specific moduli and deformability. Importantly, this approach enables independent control over pore size, wall thickness, and pore symmetry, offering precise structural programmability beyond conventional templating methods. This strategy is compatible with a wide range of building blocks and binary superlattice configurations, enabling the rational design of mechanically robust mesoporous membranes with hierarchical structural order.
Neritidae is one of the most diverse families in Neritomorpha, with approximately 300 extant species inhabiting various aquatic environments worldwide. Despite their ecological importance and popularity among aquarium hobbyists, genomic resources for this family remain limited, and their taxonomy is incompletely resolved. Here, we present de novo assembled transcriptomes from seven neritid species representing three genera collected from China, including Clithon pulchellum, C. retropictum, Neripteron violaceum, N. pileolus, Nerita insculpta, N. albicilla, and N. ocellata. Assembly was performed using Trinity, resulting in average contig lengths ranging from 1,098 to 1,336 bp and transcript numbers ranging from 94,216 to 160,086. All species exhibited N50 values exceeding 2,200 bp. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis showed complete BUSCO percentages ranging from 48.7% to 71.8%. Functional annotation of transcripts for each species yielded over 18,000 BLAST hits against the UniProtKB/Swiss-Prot database, with more than 17,000 GO terms, 15,000 KEGG pathways, and 7,750 Pfam accessions. Additionally, the major mitochondrial genes (comprising all 13 protein-coding genes and 2 rRNAs) were successfully assembled, among which the COI and 16S genes were utilized for species identification verification. This study provides valuable transcriptomic resources for Neritidae research, which can be applied to investigations of biodiversity, phylogenetic relationships, comparative genomics, physiological ecology, and conservation strategies for this ecologically important gastropod family.
Hypericum wightianum is a medicinal plant (section Monanthema) . In this study, we assembled, annotated and characterized the complete plastid genome of H. wightianum. The plastome is 137,760 bp in length and exhibits a standard quadripartite layout. In total, 119 genes were identified, comprising 35 tRNAs, 8 rRNAs, 3 pseudogenes, and 73 protein-coding genes with biased synonymous codon usage. Phylogenetic inference indicated that H. wightianum and H. petiolulatum form a well-supported sister clade, suggesting a close evolutionary relationship between sections Monanthema and Elodeoida. This data provide critical resources for species delimitation and evolutionary studies within the genus Hypericum.
Mung bean (Vigna radiata) is a globally important legume crop valued for its short growing cycle, nitrogen-fixing capacity and high nutritional value, particularly in developing countries. Here we report a comprehensive graph-based pan-genome assembled from 11 genetically diverse global accessions. The framework captures 75,268 gene families (50.86% core, 35.19% dispensable and 13.95% private) and 66,862 nonredundant structural variants. Integrating these structural variants and single nucleotide polymorphisms, genome-wide association studies across five environments identified candidate genes for 20 agronomic traits, underscoring the pivotal roles of these variants in driving mung bean domestication and improvement. Mechanistically, we demonstrate that a 68-bp promoter insertion in VrTIFY6B and a 136-bp promoter deletion in VrPGIP1 regulate flavonoid content and confer bruchid resistance, respectively. These genomic resources and actionable functional variants provide a powerful toolkit to accelerate mung bean improvement through marker-assisted breeding, genomic selection and genome editing to address global food security.
Candida auris is an emerging multidrug resistant fungal pathogen associated with high mortality rates, rapid global dissemination and resistance to conventional antifungal therapies. It's remarkable ability to evade host immune responses and persist in health care setting demands the development of effective immunotherapeutic strategies. In this study, a reverse vaccinology and immunoinformatics based approach was employed to design a novel chimeric multi-epitope vaccine targeting surface expose N-terminal domain of the agglutinin like protein involved in host pathogen interactions. High affinity B-cell and T-cell (MHC class I and II) epitopes were identified and screened based on antigenicity, allergenicity, toxicity and population coverage. Selected epitopes were assembled using optimized linkers (EAAAK, AAY and GPGPG) along with an adjuvant to enhance immunogenicity and structural stability. Physicochemical characterization, structural validation, molecular docking with human Toll-like receptor 4 (TLR4), Normal Mode Analysis (NMA), immune simulation, codon optimization and in silico cloning into the pET28a+ vector were performed to evaluate the vaccine construct. The selected epitopes demonstrated a global population coverage of 97.31%. the final vaccine construct was predicted to highly antigenic, non-allergenic, structurally stable and soluble. Molecular docking analysis revealed strong and stable interactions between the vaccine construct and human TLR4, with a binding energy of - 906.1 kcal/mol. Normal Mode Analysis further supported the structural stability of the vaccine receptor complex. Immune simulations predicted robust primary and secondary responses characterized by elevated IgG and IgM antibodies along with a Th1-skewed cytokine profile dominated by IFN-γ and IL-2 expression. Codon optimization and in-silico cloning indicated favorable translational efficiency in the pET28a+ expression system. The designed chimeric multi epitope vaccine demonstrated promising immunogenic, structural and receptor binding properties against Candida auris. These findings suggest that the proposed vaccine construct may serve as a potential candidate for further experimental validation and future development of effective immunotherapeutic interventions against multidrug- resistant fungal infections.
This study proposes a novel combined intraosseous-subperiosteal hybrid implant to rehabilitate severely atrophic edentulous mandibles. We aimed to elucidate its biomechanical behavior through finite element analysis. Using CBCT data from an edentulous patient, we reconstructed a 3D mandibular model. We designed intraosseous fixtures tailored to the residual bone volume and fused them with superstructure abutments and a customized subperiosteal titanium mesh using 3-matic software. Four finite element models were assembled, varying in implant design and abutment count. These models were subjected to four loading conditions: anterior vertical, unilateral molar vertical, bilateral molar vertical, and unilateral molar lateral occlusions. Biomechanical performance was assessed by evaluating the maximum and minimum principal stresses in the peri-implant bone and the von Mises stresses in the prosthetic components. Under simulated masticatory loads, the novel combined intraosseous-subperiosteal hybrid implant exhibited stress levels well within the elastic range of the material, avoiding plastic deformation. Notably, the six-abutment configuration proved superior under posterior loading, reducing peak von Mises stress in screws by roughly 33% and in implants by 25.5% relative to ultra-short implants. The proposed combined intraosseous-subperiosteal hybrid implant exhibits superior biomechanical stability for severe mandibular atrophy scenarios. By significantly mitigating stress concentrations, particularly in the six-abutment setup, this design presents a viable clinical alternative to overcome common prosthetic rehabilitation challenges.
Insect-associated viruses (viromes) shape insect biology and agroecosystems, yet aphid viromes remain undercharacterized. The cotton aphid, Aphis gossypii, is a globally distributed pest with a broad plant host range and demonstrated virus-vector competence, making it well suited for investigating virome composition at the plant-insect-virus interface. In this study, we profiled the virome of field-collected aphid alates, which were dominated by A. gossypii but included additional aphid species in some samples, across 15 cotton fields in Alabama, USA, to assess taxonomic diversity, relative viral abundance, and focal aphid-associated viruses. Metatranscriptomic sequencing of aphid alates revealed differences in taxonomic composition among county-level libraries, including viruses and diverse prokaryotic and eukaryotic taxa. Fifty-eight viral contigs > 1 kb were assembled, of which 20 were assigned to seven families: Dicistroviridae, Iflaviridae, Mitoviridae, Nudiviridae, Partitiviridae, Phasmaviridae, and Solemoviridae. Representative contigs from six families (all except Phasmaviridae) and five additional family-unassigned viruses were validated by PCR and Sanger sequencing. Three iflaviruses (RrIV, AgIV1, and AgIV2), positive-sense single-stranded RNA viruses, were discovered, including one associated with Rhopalosiphum rufiabdominale and two with A. gossypii. Their complete genomes were determined using PCR-based resequencing and 5'/3' RACE, each comprising a single open reading frame that encodes a polyprotein. Sequence identity and phylogenetic analyses indicate that the newly identified viruses are putative new species and form a distinct clade together with previously reported aphid iflaviruses within Iflaviridae. AgIV1 and AgIV2, despite being associated with the same host species, were not monophyletic within this clade, consistent with cross-species transmission among aphid hosts. Strand-specific RT-PCR detected negative-strand RNA for AgIV1 and AgIV2, suggesting replication in aphids. Given their low field prevalence, we propose the names Iflavirus furtiva (RrIV), Iflavirus obscurata (AgIV1), and Iflavirus rarivira (AgIV2). The aphid virome is taxonomically diverse and shows county-level differences in relative viral contig abundance. We identified seven viral families and three complete iflavirus genomes, providing a foundation for further investigating their host range, transmission, and potential impacts on aphid biology and cotton production.
Functional characterization of microbiomes often relies on the sequencing of metagenomic DNA extracted from environmental samples, with current approaches using metagenome-assembled genomes (MAGs). Although glycoside hydrolases (GHs) are central to carbon cycling, accurate annotation of GHs in metagenomic datasets remains challenging due to the multidomain architecture of carbohydrate-active enzymes and the prevalence of unassembled short reads due to limitations in the MAG-generation process. Here, we present CAZyOGH (CAZymes Open-source GH annotation), a curated reference database for the domain-specific identification of 135 protein domains spanning 99 GH families with well-defined catalytic domain signatures. CAZyOGH focuses on individual GH domains, enabling robust annotation of both assembled and unassembled metagenomic data. We validated CAZyOGH by reanalyzing genomes listed in CAZy db, where predicted GH profiles closely matched reported values. Next, we used CAZyOGH to analyze 12 human gut metagenomes and 12 newly sequenced soil microbiomes to reveal environment-specific GH repertoires. By accurately detecting catalytic domains independent of the genomic context, CAZyOGH improves sensitivity and specificity in short-read metagenomic annotation. This framework provides a scalable and reproducible approach to investigate carbohydrate-active enzymes across ecosystems, advancing our capacity to characterize microbial functional potential in global carbon cycling. CAZyOGH data is available on figshare (https://figshare.com/projects/CAZyO_GH/267770).