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Today, 1:52 PM
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Protein filaments, ordered self-assembled protein aggregates, are versatile biopolymers with unique structural and physicochemical properties. Their potential as high-performance materials is driving significant interest for a wide range of applications within the food industry. In this context, this review covers the fundamentals of both native and synthesized protein filaments. It systematically surveys their multifaceted applications in the food industry, including their use for texture modification, interfacial stabilization, encapsulation and delivery, biosensing, contaminant removal, biobased packaging, and as scaffolds for cultured foods. Overall, protein filaments represent a class of highly versatile biomaterials with dual functionality─as both direct food ingredients and enabling materials for safety and processing─highlighting their multifaceted potential to address various needs in the food industry.
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Today, 1:28 PM
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The phyllosphere encompasses all above-ground plant parts, covering ~109 km2 and hosting as many as 1026 microbial cells, yet its chemical ecology remains understudied compared to the rhizosphere. This review synthesizes recent advances in metabolite-mediated communication orchestrating phyllosphere microbiome assembly, function and host feedback. Leaf structural traits, host immune genes, developmental stage, and fluctuating environmental drivers create spatiotemporal chemical niches that filter incoming microbes. We then examine four major classes of plant-derived signals, including primary metabolites, secondary metabolites and phytohormones, with an emphasis on their dual functionality. Microbial feedback occurs through phytohormone synthesis/catabolism, volatile and soluble effectors and antimicrobial metabolites that collectively modulate plant immunity, growth and stress tolerance while structuring inter-microbial competition. These bidirectional exchanges form a dynamic network where plants and microbes continuously negotiate cooperation and conflict under diurnal and seasonal oscillations. We outline translational prospects, including probiotic foliar applications, metabolite priming and breeding for beneficial consortia, while identifying key challenges in signal attribution, microbiota stabilization and deciphering community-level crosstalk dynamics for sustainable crop protection.
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Today, 1:10 PM
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Prokaryotic defense-associated reverse transcriptase (DRT) systems confer host resistance to viral infection through DNA synthesis; however, the molecular mechanisms underlying their function remain poorly understood. Here, we demonstrate that DRT4, a single-gene antiphage defense system, synthesizes single-stranded DNA (ssDNA) products of random sequences in a template-independent manner. High-resolution cryo-EM structures of DRT4 in multiple functional states elucidate its oligomeric architecture, catalytic metal ion coordination, and substrate/DNA product binding, offering mechanistic insights into its promiscuous polymerization activity. Structural and biochemical analyses further identify a conserved tyrosine residue that acts as the priming site for the initiation of DNA synthesis. Upon phage infection, a phage-encoded DNA-binding protein, ORF55, protects the 3’ end of the DRT4-synthesized ssDNA from host exonuclease degradation, likely resulting in toxic ssDNA accumulation that leads to cell death. Remarkably, ORF55 also activates DRT6, a structural homolog of DRT4, suggesting a conserved activation mechanism among related DRT systems. These findings provide structural and mechanistic insights into DRT4-mediated antiviral defense, establishing a distinct paradigm for antiviral reverse transcriptase in bacterial immunity. Prokaryotic defense-associated reverse transcriptase (DRT) systems confer resistance to viral infection through DNA synthesis. Here, the authors dissect DRT4 mechanism of function and show that ORF55, a phage-encoded DNA-binding protein, protects the 3’ end of the DRT4- synthesized ssDNA, activating the anti-phage defense program.
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Today, 1:00 PM
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Microbiome breeding through host-mediated selection is a technique to artificially select for microbiomes conferring beneficial properties to plants. Using a systematic selection protocol that maximises the heritability of microbiome effects, transmission fidelity, and microbiome stability through multiple selection cycles, we previously developed root-associated microbial communities conferring sodium and aluminium tolerance to Brachypodium distachyon, a model for cereal crops. Here, we explore the physiological mechanisms underlying our selected microbiomes’ effect on plant fitness and analyse how our selection protocol shaped the composition and structure of these microbiomes. We analysed the effects of our selected microbiomes on plant fitness and tissue-nutrient concentration, then used 16S rRNA amplicon sequencing to examine microbial community composition and co-occurrence network patterns. Our sodium-selected microbiomes reduced leaf sodium concentration by ~ 50%, whereas the aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying the microbiome-mediated stress tolerance. By testing the selected microbiomes in a cross-fostering experiment, we show that our artificially selected microbiomes attained (a) ecological robustness contributing to transplantability (i.e. inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting salt-stress tolerance. Combined, these findings elucidate critical mechanisms underlying host-mediated artificial selection as a framework to breed microbiomes with targeted benefits for plants under salt stresses, with significant implications for sustainable agriculture. Video Abstract
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Today, 12:53 PM
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Tissue expansion, originally developed for super-resolution imaging, has become a foundation for expansion omics (ExO), a growing field that uses physical tissue expansion to enable spatially resolved omics profiling. In this perspective, we explore how ExO integrates multi-omics through chemical anchoring strategies that ensure selective retention of diverse molecular species, together with improved spatial resolution from the subcellular resolution for profiling to the sub-nanometer scale for imaging, allowing precise detection of biomolecules and their link with biological function. These capabilities have empowered tissue expansion to be successfully applied across multiple spatial omics modalities, including epigenomics, transcriptomics, proteomics, and lipidomics, enabling high-resolution mapping of chromatin states, gene expression, protein localization, and lipid distributions. Moreover, ExO supports spatial multi-omics approaches that jointly capture and correlate multiple biomolecular dimensions within the same tissue context. However, challenges remain in expansion resolution, molecular retention, hydrogel adaptability, data scalability, and AI-driven analysis. As tissue expansion evolves, its integration of super-resolution imaging and spatial omics establishes it as a core technology for whole-slide, single-cell multi-omics and the development of the Artificial Intelligence Virtual Cell, advancing spatial biology and medicine.
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Today, 2:14 AM
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Filamentous fungi play key roles in ecosystems, agriculture, biotechnology, symbiosis, and disease, yet the large-scale characterization of gene function in these organisms remains limited by low transformation efficiencies and their multinucleate, syncytial cells, which complicate high-throughput screening strategies. To address the challenge of high-throughput screening in filamentous fungi, we developed methods to construct a genome-wide barcoded insertional mutant library in Trichoderma atroviride, a filamentous fungus widely used as a biocontrol agent against bacterial and fungal plant pathogens. Our strategy leveraged randomly barcoded transfer DNA insertions from plasmid libraries containing hundreds of millions of unique DNA barcodes and a broad host-range drug resistance marker delivered via Agrobacterium tumefaciens into T. atroviride. By optimizing transformation conditions, we achieved up to 600 independent transformants per infection event, resulting in a library of over 31,000 mapped insertions disrupting 7,115 of the 11,828 predicted genes in the T. atroviride genome. This resource establishes a scalable platform for high-throughput functional genomics in filamentous fungi, enabling both fundamental investigations of fungal biology and engineering approaches toward improved medical applications, biotechnology, and sustainable agriculture.
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Today, 2:04 AM
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Biological nitrogen fixation (BNF), which is catalyzed by a large nitrogenase enzyme complex, has evolved in both bacteria and archaea. Indeed, nitrogen-fixing species are found in diverse living environments, and BNF has evolved even in aerobic bacteria, although the function of nitrogenase is inhibited by oxygen. BNF is, however, highly energy-costing, requiring 16 ATPs in a single nitrogen fixation reaction. To explain this paradox, we hypothesized that nitrogen-fixing species gain not only nitrogen-fixing (nif) genes but also non-nif genes to facilitate nitrogen fixation. We examined over 3500 nitrogen-fixing genomes and found that they have gained genes directly or indirectly related to BNF in diverse types of living environments, so that nitrogen-fixing species tend to have larger genomes than their non-nitrogen-fixing relatives. Interestingly, the non-nif genes gained tend to be located near nif-gene clusters, probably to achieve proximity effects such as coordinated gene regulation. For example, the most frequent among the genes gained are ABC transporter genes, which facilitate the absorption and physiological metabolism of carbon (e.g., sugars), nitrogen (e.g., amino acids), and trace elements (e.g., molybdenum), and many ABC transporter genes lie close to nif-gene clusters. From our findings, we propose the following scenario: BNF evolved in many archaea and bacteria because BNF is advantageous to its hosts, although it incurs a high energy cost. Then, gaining genes to facilitate BNF compensates the cost of BNF, facilitating the spread of nitrogen fixers to all living habitats. This expansion benefits the biosphere, as nitrogen is essential for all organisms.
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Today, 1:30 AM
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Diseases caused by plant pathogens are a major factor decreasing crop yields that lead to food insecurity. To protect against pathogen threats, plants possess a multifaceted immune system that perceive threats derived from plant pathogens, resulting in the activation of immune responses. Evolutionary pressures allow plant pathogens to evolve rapidly and evade recognition by nucleotide-binding leucine-rich repeat (NLR) receptors. In recent years, advancements in our understanding of the molecular and structural basis of effector recognition by NLRs have enabled targeted strategies for engineered receptors that contain novel or expanded recognition profiles. In conjunction with advancements in structural modeling and synthetic biology tools, this has transformed our ability to manipulate plant receptors with precision. Here, we highlight structure-based approaches toward engineering plant NLRs, including integrated domain (ID) engineering and leucine-rich repeat resurfacing, discuss challenges associated with NLR engineering, and highlight future engineering approaches to enhance the plant immune system against pathogen threats.
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Today, 1:05 AM
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Archaeal transcription is a hybrid of eukaryotic and prokaryotic features: an RNA polymerase II (RNAPII)-like polymerase transcribes genes organized in circular chromosomes within cells devoid of a nucleus. Consequently, archaeal genomes are depleted of transcriptional regulators found in other domains of life. Here, we outline the discovery of a cryptic, archaea-specific family of ligand-binding regulatory transcription factors (TFs), called AmzR (archaeal metabolite-sensing zipper-like regulators). We identify AmzR using an evolution-based genetic screen and show that it is a repressor of methanogenic growth on methylamines in the archaeon Methanosarcina acetivorans. AmzR binds its target promoters as an oligomer using paired basic α-helices akin to eukaryotic leucine zippers. AmzR also binds methylamines, which reduces its DNA-binding affinity and allows it to function as a one-component system commonly found in prokaryotes, while containing a eukaryotic-like DNA-binding motif. The AmzR family of TFs are widespread in archaea and broaden the scope of innovations at the prokaryote-eukaryote interface.
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Today, 12:55 AM
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Classical microbiology has focused on directly suppressing pathogens using drugs, ignoring other harmless microbial species living alongside the pathogens. We now have a much better understanding of how species interact and affect one another's growth within microbial communities, for example through chemical production. Here we capitalize on this understanding to demonstrate how one can manipulate and control the strength of interactions between bacterial species, and combine this with antibiotics to fully suppress and eliminate pathogens. Using experiments and a mathematical model, we first show how Citrobacter freundii can reduce the environmental pH to enhance the effect of ampicillin on the pathogen Pseudomonas aeruginosa. This negative interaction from C. freundii to P. aeruginosa can be strengthened by increasing glucose concentrations. Our proof-of-concept approach also worked against other pathogens: Klebsiella pneumoniae and Agrobacterium tumefaciens, and a different commensal: Lactobacillus plantarum, a common probiotic species. Overall, we show that taking advantage of the community and chemical context in which microbes live can help to develop efficient strategies to control them. In the medical context, this approach can help to eliminate pathogens thereby reducing our reliance on antibiotics.
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Today, 12:46 AM
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The design of RNA molecules with bespoke three-dimensional structures and functions is a central goal in synthetic biology and biotechnology. However, progress has been limited by the challenges of designing complex tertiary interactions such as pseudoknots, as well as engineering novel catalytic functions—problems that have remained largely intractable for automated methods. Here we present and experimentally validate a high-throughput generative AI pipeline for inverse design of RNA structure and function. Central to the pipeline is gRNAde, an RNA language model conditioned on 3D backbone structures and sequence constraints. In a community-wide, blinded RNA design competition on the Eterna platform, the gRNAde pipeline designs complex pseudoknotted RNAs at high success rates matching that of human experts, significantly outperforming other physics- and AI-based automated algorithms. We further demonstrate gRNAde's capability to generatively design functional RNA polymerase ribozymes with up to 20% sequence divergence from the wild type, discovering highly active variants in a functional landscape previously inaccessible to rational design and directed evolution. gRNAde thus provides an experimentally validated, open-source platform for automated design of complex RNA structures, paving the way for fully programmable RNA catalysts and nanostructures.
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Today, 12:35 AM
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We report for the first time the isolation and functional characterization of a novel promoter inducible by Agrobacterium tumefaciens, the causative agent of crown gall disease, which leads to significant crop losses. Chemical control of this neoplastic disease is ineffective, since bacterial presence is not essential for T-DNA mediated tumor development. Moreover, A. tumefaciens-mediated transformation, a cornerstone of plant biotechnology, fails in many recalcitrant species due to poorly understood mechanisms. A unique 1086 bp promoter (HyPRO) sharing only ~ 7% similarity with known sequences in NCBI was isolated upstream of the hyp1 gene from Hypericum perforatum. In silico analysis revealed multiple cis regulatory elements (CREs), including WRKY710S, W box, PALBOX, GT1, and VRE, associated with biotic stress responses. Transgenic tobacco plants expressing β glucuronidase (GUS) under HyPRO showed strong induction by A. tumefaciens, significantly higher than induction by Pseudomonas syringae. Upstream truncation of the promoter significantly reduced GUS expression, indicating essential regulatory elements lie upstream of position − 728. This A. tumefaciens responsive promoter offers a valuable tool to dissect plant defense and could enable innovative transgenic strategies for crop improvement and resistance to neoplastic diseases. Characterization of A. tumefaciens-specific CREs using the truncation approach is currently underway in our laboratory.
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Today, 12:21 AM
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The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community. This Consensus Statement presents the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines.
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Today, 1:38 PM
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Bacteria-mediated cancer therapy offers great promise for tumor targeting and immune activation but faces challenges of limited potency and biosafety. Here, a reinforced platform, E@PB, is developed by coating E. coli Nissle 1917 with polydopamine (PDA) and a cationic BODIPY-based photosensitizer (BOD-QAS). This dual-photosensitized system integrates photothermal and photodynamic modalities while maintaining bacterial viability. The PDA coating enhances tumor colonization and immune stimulation through 808 nm laser-induced hyperthermia, whereas BOD-QAS enables 660 nm-triggered reactive oxygen species generation for tumor cell apoptosis and bacterial growth regulation. The photosensitizer shell also provides real-time fluorescence imaging, improving therapeutic precision. A two-stage “green-to-red light” strategy allows spatiotemporal control of bacterial activity, maximizing both efficacy and safety. E@PB accumulates rapidly at tumor sites within 8 h and remains for extended periods, enabling sustained therapeutic action. In vivo evaluation demonstrates an 89.8% reduction in tumor volume, highlighting the potential of this triple-modal system to synergize phototherapy and immune activation in bacteria-based cancer treatment.
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Today, 1:22 PM
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Bacteria exist in competitive and rapidly changing environments in which the nature of future threats cannot be easily predicted. Streptomyces coelicolor produces three antibacterial umbrella particles that harbor distinct polymorphic toxin domains and an overlapping set of six diversified lectins. Here, we show that the exquisite specificity of umbrella particles derives from lectin-mediated species-specific binding to previously undescribed hypervariable surface glycoconjugates. A cryo-electron microscopy (cryo-EM) structure of one such lectin in complex with its oligosaccharide substrate defines the molecular basis for targeting through the coordinated recognition of multiple glycan features. Biochemical and genetic studies of several target species, in conjunction with lectin-swapping experiments, support a model whereby S. coelicolor umbrella toxin diversification at the levels of lectin composition and toxin polymorphism represents a unique, two-tiered bet-hedging strategy. Bioinformatic analyses support this as a means by which the unusual architecture of umbrella toxins offers Streptomyces a generalizable strategy to antagonize an unpredictable array of competitors.
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Today, 1:03 PM
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This paper reviews the design and application of mammalian synthetic gene circuits for biopharmaceutical manufacturing. It discusses key design principles and outlines transcription factors, DNA-binding proteins, and RNA as input and regulatory modules, while also presenting computational modelling as a driver for circuit optimisation. The review highlights potential applications towards the production of next-generation biotherapeutics by providing examples on monoclonal antibody glycosylation control, CAR-T cell therapy safety, and gene therapy viral vector yields.
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Today, 12:57 PM
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Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts. Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families. We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes.
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Today, 12:46 PM
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Heme is an iron-containing porphyrin that plays an indispensable role in biological system, involved in oxygen transport, electron transfer, gas sensing, enzyme catalysis, etc. Beyond its physiological functions, heme also has wide-ranging applications in pharmaceuticals, food additives, and biotechnology. However, conventional production methods—such as chemical synthesis and extraction from animal blood are hindered by high costs, ethical concerns, environmental burdens, and safety risks. Recent progresses in metabolic engineering and synthetic biology have made it possible to produce free heme using microorganisms, offering a scalable, cost-effective, and sustainable alternative. This review provides a comprehensive overview of bio-based heme production, focusing on: 1) Structure, functions, and synonyms of different heme types; 2) Conserved and divergent heme biosynthetic pathways; 3) Heme biosynthesis regulation involving transcription factors, protein interactions, and small molecules; 4) Recent advances in microbial production of heme and porphyrin intermediates using metabolic engineering strategies; 5) Methods for heme detection, including spectroscopy, chromatography, enzyme-linked immunosorbent assays (ELISA) and whole-cell biosensors. Finally, current challenges and future opportunities, highlighting microbial heme production as a transformative and sustainable strategy to meet growing global demand are discussed.
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Today, 2:10 AM
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Microbial necromass carbon (MNC) constitutes a critical component of soil organic carbon. Yet, how MNC regulates microbial arsenic (As) methylation processes in soil remains unclear. Across major Chinese rice-growing regions, bacterial and fungal necromass carbon showed significant positive correlations (P < 0.05) with the transcribed arsM gene. Soil incubation experiments with seven soils explored how straw and three types of MNC—gram-positive bacterial necromass carbon (G+-NC), gram-negative bacterial necromass carbon (G−-NC), and fungal necromass carbon (F-NC)—affect As methylation. Our results demonstrated that all types of MNC enhanced As methylation, and G−-NC exhibiting the most pronounced effect on methylated As accumulation. The addition of 10 to 60 mg G−-NC maximally increased As(III) by 43.0 to 75.9% and enhanced methylated As by 4.4- to 18.0-fold in soil porewater vs. the control. Further, metagenomic and metatranscriptomic analyses demonstrated that G−-NC addition upregulated the relative abundance of transcribed arsM and arsC2 genes, which were mostly assigned to Acidobacteriota, Pseudomonadota, Planctomycetota, and Bacteroidota. Notably, the transcriptional activity of arsM-harboring Methanosarcinales and Moorellales was markedly enhanced at the order level. By promoting As reduction process, G−-NC provides more substrates for As methylation process in soil. Furthermore, G−-NC could be used as a carbon source for As-methylating microorganisms, stimulating the transcriptional activity of arsM, which has been confirmed by the incubation experiment with pure culture of Paraclostridium benzoelyticum TC8. This study highlights the critical role of MNC in regulating As biogeochemistry, establishing a basis for predicting the extent of As methylation and risk of rice straighthead disease in paddy ecosystems.
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Today, 1:59 AM
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Transmembrane and extracellular proteins play crucial roles in diverse cellular functions and communication, affecting the progression and treatment of various diseases by mediating vital cellular processes. Whereas targeted protein degradation (TPD) represents an advancing therapeutic modality that leverages cellular degradation machinery to eliminate proteins of interest, present strategies have been largely confined to intracellular targets. Now, emerging strategies toward transmembrane and extracellular proteins are rapidly expanding the horizon of this powerful technology. Here, we review TPD in the transmembrane and extracellular space (meTPD) and discuss platform technologies, features, applications, and limitations. We focus on the conceptual innovations used in developing the present meTPD technology as well as its potential value for biological research and therapeutic interventions.
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Today, 1:23 AM
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Bacillus strains are widely used in food fermentation and plant disease control. An efficient transformation method is crucial for genetic manipulation in these organisms. To enhance the transformation efficiency of three Bacillus strains—Bacillus amyloliquefaciens YN-J3 (B.a YN-J3), Bacillus velezensis JN-Y2 (B.v JN-Y2) and Bacillus subtilis S-16 (B.s S-16), we optimized transformation conditions using orthogonal experiments combined with response surface analysis. Additionally, we tested various cell wall agents to improve competence. Our results showed that the optimal transformation parameters for B.a YN-J3 and B.v JN-Y2 had an OD600 of 0.70, a competent cell volume of 91 μL, a plasmid concentration of 1040 ng·μL⁻1, and a field strength of 18.1 kV·cm⁻1. For B.s S-16, the optimal conditions were an OD600 of 0.71, a competent cell volume of 92 μL, a plasmid concentration of 1052 ng·μL⁻1, and a field strength of 18.2 kV·cm⁻1. Under these optimal conditions, the transformation efficiencies for B.a YN-J3, B.v JN-Y2, and B.s S-16 were 22,198.33 CFU·μg⁻1 DNA, 24,498.67 CFU·μg⁻1 DNA, and 23,305.00 CFU·μg⁻1 DNA, respectively. Screening of cell wall agents revealed that 50 mg/mL glycine significantly boosted transformation efficiency by 40, 36, and 24 times for B.a YN-J3, B.v JN-Y2, and B.s S-16, respectively. These findings demonstrate that combining glycine treatment with optimized transformation conditions provides an efficient approach for the genetic manipulation of Bacillus strains.
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Today, 12:57 AM
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The Aer chemoreceptor in E. coli is known to perform oxygen- or aero-taxis by sensing metabolic flux through ETC via an FAD cofactor bound to its PAS domain. We show in this study that Aer also senses oxidative stress and performs FAD-dependent negative chemotaxis in response to the known ROS H2O2. The ability of Aer to detect both oxidizing and reducing intracellular environments redefines its functional range and establishes Aer as a bidirectional redox sensor. We show in addition that the ability of bacterial swarms to move away from bactericidal antibiotics is Aer-dependent and is abolished by expression of the catalase–peroxidase enzyme KatG, which scavenges intracellular ROS. Our study thus provides independent behavioral evidence that certain antibiotics generate intracellular ROS, while also offering a sensitive assay for detecting these reactive species.
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Today, 12:51 AM
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Core members of the fungal root microbiota include pathogens capable of colonizing multiple hosts, yet the underlying genetic determinants remain unknown. We report that Plectosphaerella cucumerina is a core member of the Arabidopsis thaliana root microbiota displaying high pathogenic potential and multi-host colonization capabilities. Establishment of a Plectosphaerella reference culture collection, followed by whole-genome sequencing of 72 strains reveals subtle phenotypic and genotypic variation that associate with fungal phylogeny, but not host plant identity. Transcriptome profiling of a model P. cucumerina isolate in roots of multiple hosts identifies core and host-specific fungal processes linked to carbon catabolism and root cell wall deconstruction of the hosts. A fungal gene encoding a candidate Beta-1,3-glucanase (GH64) was identified as a key genetic factor driving infection and disease in plants that diverged 110 million years ago. The gene is enriched in plant-colonizing fungi and consistently functions as a disease determinant in the root pathogen Colletotrichum incanum. We conclude that diverse and tunable fungal repertoires of carbohydrate-active enzymes act as disease determinants and drive multi-host compatibility belowground.
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Today, 12:40 AM
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The increasing number of fully sequenced bacterial plasmids being annotated and cataloged has prompted the development of computational tools for comparing and classifying them. Existing approaches typically compare full-length DNA sequences (e.g., Mash, BLASTn) or translated open reading frames (ORFs) (e.g., BLASTp, DIAMOND), with plasmid-level scores obtained by aggregating ORF-to-ORF similarities; however, they are either restricted to closely related plasmids or become computationally demanding in large-scale analyses. We describe pLAST (plasmid Language Analysis and Search Tool), a plasmid-search tool built using word2vec representations capturing both ORF-to-ORF similarity and gene neighborhood conservation. Benchmarks indicate that pLAST outperforms both DNA- and ORF-based methods in identifying functionally similar plasmids and, compared to the widely used Mash, it achieves 37%, 30%, and 13% improvements in detecting shared mating-pair formation (MPF) system, relaxase, and oriT types, respectively. This performance scales to datasets comprising thousands of sequences, as exemplified by clustering analyses of ~56,000 plasmids, which reveal expected functional groups. Beyond global similarity, pLAST also returns per-ORF plasmid-plasmid alignments, enabling detection of shared functional modules. Availability and implementation. web server at https://plast.lbs.cent.uw.edu.pl/ Python module along with a precomputed database at https://github.com/labstructbioinf/pLAST
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Today, 12:28 AM
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Several human-associated microbial communities exist in multiple configurations and can change their composition in response to perturbations, remaining in an altered state even after the perturbation ends. Multistability has been previously proposed to explain this behavior for gut microbiota in particular, but has not been clearly demonstrated experimentally. Here, we first investigate the life history strategies of three common human gut bacteria to identify mechanisms driving alternative states. We then use this data to build and parameterize a kinetic model, which predicts that alternative states emerge due to phenotype switching between subpopulations of the same species. Perturbation experiments support these predictions, and confirm the existence of alternative states. Finally, simulations show that phenotype switching can also explain alternative states in larger communities. Thus, a transient perturbation combined with metabolic flexibility is sufficient for alternative communities to emerge. In this study, the authors use a combination of experimental and modeling approaches to show that a human gut bacterial community can exist in different states under the same conditions. The mechanism behind these alternative states is likely based on metabolic change in response to nutrient depletion.
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r-2st. Necromass