Plasmid typing challenges in the era of genomic antimicrobial resistance surveillance

Plasmids are central drivers of antimicrobial resistance (AMR) dissemination, yet their modular, recombinogenic genomes defy concepts of relatedness derived from bacterial chromosomes. Long-read sequencing now routinely yields complete plasmid sequences, exposing a key gap: we can reconstruct plasmids but lack agreed principles for comparing them. In response, diverse clustering tools have emerged that emphasise different signals, such as marker genes, whole-sequence similarity, gene content, backbone structure, or explicit rearrangement events. Each encodes a distinct notion of plasmid distance. This review organises these tools into conceptual families, highlights how their assumptions shape surveillance outputs, and proposes hierarchical, multitool strategies and clearer models of plasmid evolution as the basis for scalable and interpretable plasmid-based AMR surveillance.

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From resistance genes to resistance states and enzymatic context-dependence in antimicrobial resistance

Antimicrobial resistance is often inferred from resistance genes and susceptibility phenotypes measured under standardized conditions. We argue that for many resistance genes, resistance is better vie...

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The who, how, and when of mother–infant microbial sharing

The establishment of the infant gut microbiome is strongly linked to health outcomes throughout life. Recently, Mueller et al. reported that the majority of strains shared between a mother and an infant are gut-derived, as opposed to vaginally derived, and strain sharing could be observed into the second year of life.

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Wetland virus exposes blind spots in orthonairovirus pathogenesis

Newly recognized human-associated orthonairoviruses are emerging across East Asia, yet their pathogenic mechanisms remain poorly defined. Wang et al. reveal how Wetland virus converges on caspase-3–gasdermin E pyroptosis and fatty acid synthase-dependent hepatic lipid accumulation Wang and colleagues, linking cell death to metabolic injury and exposing major gaps in pathogenesis and host-directed therapy.

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Micronutrients, the gut microbiota, and infection susceptibility in infants

Micronutrient deficiencies are common during infancy, particularly in settings with a high burden of infectious diseases. At the same time, the developing infant gut microbiota is a key determinant of susceptibility to infection from both resident pathobionts and incoming enteric pathogens. Recent human and experimental studies suggest that micronutrients regulate this developing microbial ecosystem in a highly context-dependent manner, with effects varying according to developmental stage, nutritional status, intestinal location, and environmental exposure. In this review, we synthesise current evidence linking micronutrient-microbiota interactions to microbial competition and metabolism, epithelial barrier integrity, and mucosal immunity, and discuss how these interactions may shape susceptibility to enteric and invasive bacterial infections during infancy.

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The textile web as a probiotic interface

Microbiome of the Built Environment research exhibits a marked ‘hard-surface bias’, overlooking the dynamic soft materials that dominate human-microbial exchange. We propose a theoretical reorientation: the home as a textile web of dynamic, porous microbial reactors. Grounded in immunology’s Danger Theory and the principle of ‘tissue-based class control’, these soft interfaces function as an external tissue analog. By treating textiles as designable interfaces (ranging from airway exchange nodes to laundry bioreactors), architecture becomes a site for proactive probiotic rituals. This framework leverages competitive exclusion to support externalized mucosal ‘guard duty’, transitioning from prophylactic sterility to a choreography of domestic care. Notably, this reframing recognizes that hygiene encompasses more than infection prevention: domestic cleaning rituals also shape the microbial ecology that educates the immune system. Ultimately, we frame the living home as a tolerogenic exoskeleton, biologically calibrated to protect and prime the human holobiont.

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From resistance genes to resistance states and enzymatic context-dependence in antimicrobial resistance

Antimicrobial resistance is often inferred from resistance genes and susceptibility phenotypes measured under standardized conditions. We argue that for many resistance genes, resistance is better viewed as a context-dependent functional state; the same gene can produce different phenotypes depending on the local microenvironment, enzyme kinetics, antibiotic exposure, and bacterial physiology.

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Serratia plymuthica

Serratia plymuthica is a ubiquitous bacterium with broad ecological relevance that can be isolated from soil, water, insects, plants, and fruits. Although widely distributed, it is most frequently isolated from the plant rhizosphere, where it occurs both as a free-living rhizobacterium and as a non-rhizobial endophyte. While several Serratia species are recognized as opportunistic pathogens (e.g., Serratia marcescens), S. plymuthica is primarily recognized for its beneficial interactions with plants and is widely regarded as a plant growth-promoting and biocontrol bacterium.

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Antifungal drug resistance in Candida auris: molecular mechanisms and emerging therapeutic approaches

The human fungal pathogen Candida auris (Candidozyma auris) has emerged as a major global health threat due to its pronounced skin tropism, efficient healthcare-associated transmission, as well as frequent resistance to antifungal therapy. These features have enabled outbreaks in healthcare settings worldwide and have complicated the management of life-threatening invasive infections. Understanding the molecular basis of antifungal multidrug resistance in C. auris is therefore essential for improving clinical management and developing new therapeutic strategies. In this review, we discuss current knowledge of C. auris and related emerging fungal pathogens, summarize the mechanisms underlying clinical resistance, and highlight recent advances in antifungal drug discovery and therapeutic approaches.

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Atopic dermatitis and beyond: Staphylococcus aureus skin adaptation

Chronic skin conditions are natural experiments in within-host bacterial evolution. Taking atopic dermatitis as the main example, we discuss how studies starting from collections of clinical skin isolates identify Staphylococcus aureus variants that arise independently in different patients, and how this convergence can prioritize candidates for functional genetics.

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Molecular pathways linking the gut microbiome to antitumor immunity

Accumulating evidence supports the important role played by the gut microbiota in controlling antitumor immune responses that impact tumor development. Extensive studies of bacterial species known to impact tumor growth have identified metabolites, produced by either bacteria or the host, that may alter efficacy of chemo- and/or immune-based therapies. Here, we summarize our current knowledge of those metabolites and the related bacterial species that influence activities linked with antitumor immunity, including epigenetic changes, the aryl hydrocarbon receptor signaling, cytokine and chemokine production, Janus kinase/signal transducer and activator of transcription signaling, and toll-like receptor signaling. We focus on specific metabolites, produced in the gut microbiome, which can alter molecular pathways associated with antitumor immunity, findings that warrant further evaluation in preclinical or clinical settings.

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The bacterial immune system: identifying evolved defense adaptations

Recent years have witnessed a rapid expansion in bacterial defense mechanisms. Alongside established defenses against molecular parasites, hundreds of novel mechanisms are being described annually, contributing to an ever-expanding ‘bacterial immune system’. Terms like ‘defense’ and ‘immune’ are often used as shorthand for an observed anti-infection phenotype, but can also imply an evolutionary adaptation with a specific anti-infection function. Despite the field’s growth, no agreed-upon framework exists for identifying defense adaptations. When is a defense mechanism an evolved adaptation? Here, we review prior debates in evolutionary biology and propose a four-part framework to evaluate the case for a defense mechanism being an evolved adaptation. Beyond bacterial immunity, these criteria offer a research roadmap to address functional controversies across microbiology.

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Aphanomyces euteiches

Aphanomyces euteiches is a formidable soil-borne pathogen that induces severe root rot in pea, lentil, and other legume crops. Although it grows as filamentous, fungus-like hyphae, A. euteiches is an oomycete of the stramenopile lineage and is evolutionarily more closely related to brown algae and diatoms than to true fungi. First described in 1925 in the United States, it is the most destructive soil-borne pathogen of pea, lentil, and alfalfa and also affects other legumes such as snap bean, clover, and vetch, causing yield losses of up to 80% in heavily infested fields.

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Leveraging traveller genomics for LMIC diarrhoeal disease management

Diarrhoeal pathogens impose a substantial global health burden, disproportionately affecting low- and middle-income countries (LMICs). However, in these settings, health-seeking behaviours, suboptimal microbiological capacity, and challenges in establishing genomics capacity constrain effective surveillance, including surveillance of antimicrobial resistance (AMR). In contrast, high-income countries routinely generate and share large volumes of diarrhoeal pathogen genomes through established systems, with a significant proportion originating from travellers returning from LMICs. These data reveal strong geographical structuring of lineages and clinically relevant AMR patterns, demonstrating untapped potential to support improvements in geographically granulated surveillance to support antimicrobial treatment recommendations. In this opinion article, we outline the potential to integrate traveller-derived microbial genomic data into LMIC public health decision-making and highlight the scientific, ethical, practical, and governance considerations for implementation.

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Mechanisms of sulbactam–durlobactam resistance in Acinetobacter baumannii

Sulbactam–durlobactam is the first-line agent against carbapenem-resistant Acinetobacter baumannii. Resistance can be conferred by metallo-β-lactamases alone or penicillin-binding protein 3 alterations plus β-lactamase overproduction or enhanced efflux. Other reported mechanisms remain associative and resistance in guideline-recommended carbapenem addition is unclear, underscoring the need for mechanistic validation and further studies.

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Methanogens: vital but threatened members of the human microbiome?

Methanogens are an ancestral group of archaea that occupy a unique niche within the human gut microbiome by virtue of their methane production. In this process, they serve as hydrogen sinks, allowing continued bacterial fermentation and influencing short-chain fatty acid production. Available evidence suggests that methanogen abundance may be declining in parallel with the broader reduction in gut microbial diversity accompanying industrialization. We describe the evolution of methanogens, their ecological roles in the human microbiome, and evidence for their apparent decline. If confirmed, reductions in methanogen prevalence and abundance may have substantial metabolic consequences, reframing these archaea as keystone species in need of scientific attention and conservation efforts.

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The importance of interbacterial relationships in shaping cyanobacterial ecology

Cyanobacteria are a globally abundant bacterial phylum that make key contributions to primary production and nutrient cycling in aquatic ecosystems. However, some cyanobacteria also cause substantial adverse environmental impacts through harmful blooms and the production of potent toxins. Given their global significance, understanding the processes governing cyanobacterial ecology is critical for assessing aquatic ecosystem function. While abiotic environmental factors have traditionally been considered most important, a growing body of literature indicates that interactions with other microorganisms, in particular heterotrophic bacteria, shape cyanobacterial growth, population dynamics, and ecological success. In this review, we provide a synthesis of the importance of interbacterial interactions in controlling cyanobacterial populations and their ecological impacts on natural aquatic environments and argue that these relationships should be incorporated into conceptual and predictive frameworks of cyanobacterial ecology.

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The multifaceted role of atomic force microscopy in bacteriology

Atomic force microscopy (AFM) has become a powerful tool to provide nanoscale insights into the spatial organization, biomechanics, and intermolecular interactions of the cell envelopes of living bacteria in real time and under near-native conditions. Focusing on recent literature, we discuss how AFM has advanced our understanding of Gram-positive, Gram-negative, and mycobacterial cell envelope architectures, as well as the mechanisms of action of established and novel antimicrobials. We also summarize how AFM can be used to probe the adhesion, virulence, and immune evasion of pathogens through single-molecule and single-cell force spectroscopy.

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Engineering nitrogen-fixing symbiosis: bridging signaling and intracellular entry

Nitrogen availability is a major constraint on plant growth and agricultural productivity. Legumes and several other plant lineages circumvent this limitation by establishing symbiotic associations with nitrogen-fixing microorganisms, which convert atmospheric dinitrogen into ammonia that the host assimilates. Since root nodules were first recognized as sites of biological nitrogen fixation in the late 19th century, engineering this capacity in nonlegume crops has remained a long-standing goal. However, two key challenges remain: enabling intracellular rhizobial infection and establishing a molecular framework that supports nitrogen fixation. Recent advances in the molecular, cellular, and evolutionary mechanisms underlying root nodule symbiosis now provide a conceptual framework toward this goal. In this review, we synthesize these advances and outline staged strategies for engineering nitrogen-fixing symbiosis.

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Shiny metal catalysts at the origin of metabolism

Metabolism is the reaction network that converts inanimate matter into living cells. There is no life without it. The network of approximately 400 enzymatic reactions that synthesize amino acids, nucleosides, and cofactors from compounds in the environment is conserved across life. Before enzymes, how did metabolism arise? The subsurface chemical environment of Earth’s crust reveals clues. Serpentinizing (H2 producing) hydrothermal vents contain naturally deposited, shiny metals in their reduced (native) state and phosphite, a reduced form of phosphate. In the laboratory, native metal catalysts fix CO2, replacing hydrogenases, the acetyl-CoA pathway to pyruvate, the Krebs cycle, amino acid syntheses, NADH, and ferredoxin. Native metals also phosphorylate organic compounds in water using phosphite, uncovering a new source of energy at the origin of metabolism.

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Tripartite toxin–antitoxin systems: expanding the paradigm of molecular interplay and antiphage defense

Prokaryotic toxin–antitoxin (TA) systems are genetic modules involved in stress responses, including antiphage defense and the maintenance of mobile genetic elements. Although canonical TA systems consist of two neighboring genes encoding one toxin and one antitoxin, many have evolved into tripartite systems through the incorporation of a third component that serves as a chaperone, a regulator, or an additional antitoxin or toxin to increase functional diversity and regulatory potential. This review compares tripartite TA systems [TA-chaperone (TAC), TA-regulator (TAR), dual-antitoxin, and dual-toxin systems] with bipartite systems, summarizing their neutralizing mechanisms and phage-triggered activation pathways. The regulatory capacity and modularity of tripartite TAs illuminate the evolutionary trajectory of these ‘selfish’ genetic elements, reflecting complex coevolutionary dynamics among TA systems, host bacteria, and phages.

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The meta-holobiont: rethinking marine species interactions through microbial connectivity

Positive species interactions underpin ecological resilience, which is critical for counteracting anthropogenic pressures on ecosystems. Current research focuses on intra-holobiont interactions between hosts and their microbiomes, reflecting their recognized importance for host well-being, but overlooks interactions among holobionts. We introduce the meta-holobiont framework for the marine environment, which conceptualizes ecological communities as networks of interacting holobionts connected through microbial transmission and metabolite production. Marine connectivity can facilitate horizontal transmission of microorganisms, potentially enhancing host fitness and stress tolerance across all life stages. Conceptual and empirical findings from sessile benthic species support this view. We argue that investigating meta-holobiont interactions is crucial for advancing knowledge of ecological dynamics and may have important practical implications, particularly for marine restoration strategies.

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The narrowing prokaryote–eukaryote divide reveals a complexity spectrum

Cellular organisms can be divided into two basic types of cells: the prokaryotic cells of Bacteria and Archaea and the eukaryotic cells. The rapidly expanding knowledge of the diversity and ultrastructure of prokaryotic cells has revealed cellular intricacies that warrant a critical reappraisal of the profundity of the prokaryote–eukaryote divide.

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Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism

Microbial metabolism is a complex, emergent system driven by the coordinated interplay of intricate and dynamic molecular processes. To elucidate cellular behavior and enable biotechnological applications, quantitative models that address the inherent complexity of metabolism have been developed from a resource allocation perspective. Here, we synthesize recent advances in coarse-grained resource allocation frameworks and their applications in understanding microbial physiology and guiding gene circuit design. These frameworks reveal global regulatory constraints and predict cellular adaptation to nutrient and environmental changes. In addition, they enable the quantification of metabolic costs, the dissection of circuit–host interactions, and the development of strategies for burden mitigation. Collectively, these modeling frameworks provide a powerful platform for uncovering quantitative principles of microbial growth and engineering robust synthetic biological systems.

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Biological language models uncover hidden bacterial antiviral immunity repertoires

Biological language models, including protein and genomic language models, are accelerating the discovery of bacterial antiviral defenses by identifying defense-associated proteins that lack detectable homology to known systems. These approaches reveal a vast, previously unexplored repertoire of defense-associated genes and suggest that antiviral defense-associated functions are more diverse and distributed across genomic contexts than previously appreciated.

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Microbial methane oxidation in aerated subterranean ecosystems: an upscaling and intervention framework for climate change mitigation

Aerated subterranean ecosystems are emerging as globally widespread yet understudied sinks for atmospheric greenhouse gases (GHGs), especially methane. Subterranean GHG cycling is driven by atmospheric exchange between the surface and subsurface, and by uptake by aerotrophic bacteria inhabiting cave surfaces. Despite growing evidence for these novel biogeochemical processes, aerated subterranean ecosystems remain largely omitted from Earth system models, GHG budgets, ecosystem service valuations, and climate change mitigation efforts. Here, we synthesise the current understanding of the subterranean microbial methane sink and provide a framework for upscaling uptake based on ventilation and biological determinants. We propose that enhanced subterranean aerotrophy could provide a novel pathway for atmospheric methane removal by leveraging caves and cave proxies as passive methane biofilters. We speculate that decommissioned mines might provide a similar opportunity. Based on this mechanistic understanding, we discuss key uncertainties and outline a research agenda to direct future research on subterranean ecosystems as a new potential lever for climate change mitigation.

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Applications of machine learning in microbial source tracking

Microbial source tracking (MST) has become important in environmental ecology, food safety, and forensic investigation. With advances in microbiome technologies, MST has shifted from single-indicator methods to community-level inference, creating demand for stronger analytical frameworks. Machine learning (ML) now plays a central role in handling large-scale microbiome data and capturing complex relationships between microbial communities and their sources. This review summarizes major ML methods used in MST, representative tools, and applications in pollution tracing, geospatial attribution, food safety, and forensics. Current studies show that ML substantially improves the accuracy, resolution, and scalability of MST. We also discuss key challenges, including limited interpretability, ecological dynamics, and a lack of benchmark datasets with explicit ground truth and evaluation criteria, and highlight how next-generation AI, especially deep learning, may further advance robust and intelligent MST.

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