FEMS microbiology reviews最新文献

Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.

Previously understudied for their lack of protein-coding capacity and assumed functional irrelevance, non-coding RNAs (ncRNAs) have emerged as crucial regulators of biological pathways. Technological advancements including optimised RNA sequencing methods have begun unearthing the extent of ncRNA contributions to cellular processes, however, many ncRNAs remain partially characterised. Nevertheless, ncRNAs have cemented their role as crucial regulators of gene expression, reinforced by ncRNA dysregulation being implicated in the development and progression of a wide range of human diseases. Viruses have evolved intricate mechanisms to override host immune strategies and propagate viral replication. Many of these involve manipulating host ncRNA networks or encoding viral ncRNA species to fine-tune the cellular milieu into one most permissive for viral biology. Yet, due to their regulatory potential, ncRNAs are also integral to cellular immune strategies and defence mechanisms, such that ncRNAs remain one of the main tools hosts use to subdue viral infections. Herein we describe the complex and dynamic interplay between viruses and host non-coding regulatory RNA species. We characterise the various classes of ncRNAs in comprehensive detail and explore their respective contributions to viral biology. We then discuss the therapeutic potential of ncRNAs, and their putative roles as specific biomarkers.

Bacteriophages are considered to have great potential as naturally occurring, antimicrobial agents for use in food production. Phages are ubiquitous in nature and can be isolated from almost all habitats. This review outlines the possibilities, as well as limitations of their use in food production. Application of phages in the food sector are described and the limitations of their use as well as potential risks are discussed. Approaches for a possible classification as either processing aid or food additive are considered, and the current status of their use in and outside the EU is presented. Finally, the need for research to close identified knowledge gaps is highlighted.

With the growing severity of antimicrobial resistance (AMR), phage therapy has garnered attention as a novel therapeutic alternative. In particular, phage cocktails, which combine multiple phages, potentially offer broader antimicrobial spectra than single-phage applications and may suppress the emergence of resistant bacteria. This comprehensive review systematically examines cutting-edge technologies and effective strategies for designing phage cocktails. Special attention was given to the combination of phages recognizing different receptors, designs based on phage-bacteria infection network analysis, and synergistic effects with antibiotics. Additionally, the analysis of large-scale clinical studies has identified challenges in practical implementation, including ensuring cocktail stability and addressing immune responses. These insights are expected to contribute to the design of more effective phage cocktails and the establishment of novel therapeutic strategies to address AMR.

Cyclic di-GMP (c-di-GMP) is a highly conserved bacterial second messenger that regulates important processes such as motility, biofilm formation and virulence. In this review, we investigate the architecture and regulatory functions of c-di-GMP signaling in classical Bordetella species, including B. bronchiseptica, B. parapertussis and B. pertussis. We examine how the c-di-GMP signaling pathway interacts with the BvgAS two-component system and other signaling pathways to coordinate virulence gene expression and surface-associated behaviors in these respiratory pathogens. In particular, we highlight the functions of characterized diguanylate cyclases (DGCs), phosphodiesterases (PDEs) and dual-domain proteins, focusing on regulatory modules such as the BdcA-DdpA scaffold complex, the oxygen-sensing DGC BpeGReg and the LapD-LapG proteolytic switch that controls BrtA adhesin. We also propose a model for the function of BvgR, a PDE-like protein lacking catalytic residues, and discuss how c-di-GMP suppresses the type III secretion system. Importantly, we highlight the diversity of the c-di-GMP network in classical Bordetella species, likely reflecting their evolutionary specialization. To conclude, we outline important open questions and suggest future research directions, including the identification of sensory ligands and c-di-GMP effectors. Overall, our review illustrates the importance of c-di-GMP as a critical, but still incompletely understood, regulatory hub in Bordetella pathogenesis.

World agriculture depends in part on the crop-associated microbiome for improved plant growth, health, and productivity. In particular, endophytic fungi (EF) with plant growth-promoting activities fulfill some of these roles and are central as bioinoculant agents. In the case of arbuscular mycorrhizal fungi (AMF), they form a symbiosis with their host plants, enhancing the uptake of water, phosphorus, nitrogen, and other micronutrients, while the plants provide them with photosynthates. This work reviews the differences in the colonization of internal plant niches between these beneficial fungi, as well as other distinctive ecological traits. It also explores mechanisms of seedborne vertical transmission in AMF and their classification. Genomic and transcriptomic advances in fungal endophytes are highlighted, shedding light on genes and expression profiles that define their lifestyle and plant associations. In addition, recent studies on their abilities to promote plant growth are analyzed, especially focusing on Trichoderma spp., Epichloë spp., Serendipita indica (formerly Piriformospora indica), and entomopathogens like Beauveria spp. and Metarhizium spp. Finally, the multiple interactions among EF, AMF, and other members of the plant microbiome-notably plant growth-promoting bacteria (PGPB)-are discussed, emphasizing how these organisms synergistically benefit the host. A deeper understanding of these fungi and their plant-beneficial effects should facilitate commercialization and help farmers achieve sustainable production, especially under challenges posed by global climate change.

Antimicrobial resistance poses a pressing global health challenge in the 21st century. The rapid increase and prevalence of multidrug-resistant bacteria will require novel approaches to develop new antibiotics. Major advances in nucleic acid-based therapeutics, particularly antisense technologies, could be one solution for developing precision antibiotics. The selectivity and specificity in the drug design of antibacterial antisense oligomers (ASOs) allows precise gene-specific silencing and ultimately enables targeting of currently undruggable gene products. Our goal here is to comprehensively review the advances in asobiotics (antisense oligomer biotics) leading to therapeutic success, including modifications in the nucleic acid backbone of ASOs, which have improved their properties and progresses in delivery. We will discuss utilization of ASOs against several pathogens, strategies to overcome resistance, and finally future scenarios and prospects for asobiotics as pathogen-specific therapy in the clinic.

This review addresses the crucial and emerging field of bacterial adaptation to antimicrobial nanomaterials, challenging prior assumptions that their multi-level action prevents the development of reduced bacterial sensitivity. It provides a comprehensive overview of experimentally induced adaptation mechanisms across various nanomaterials (e.g. AgNPs, ZnO) and bacterial species. Bacterial adaptations encompass genetic adaptations (e.g. efflux systems, mutagenesis), biomolecule production (e.g. flagellin, exopolysaccharides forming biofilms, protein coronas), and structural changes (e.g. altered shape, cell wall thickening, enhanced motility, membrane permeability changes). The described adaptation mechanisms to nanomaterials are compared with antibiotic resistance mechanisms, emphasizing common strategies such as efflux and envelope changes, but also unique adaptations specific to nanoparticles, such as aggregation and different roles of biomolecules. The review offers insights and emerging strategies for designing safer, more effective nano-antimicrobials, including membrane potential disruption, biofilm inhibition, and size modulation. It emphasizes the need for standardized evaluation methods and future research on cross-resistance.

The honeybee gut microbiome has emerged as a model system in microbial ecology, valued for its structural stability and host specificity, and has garnered significant attention for elucidating universal principles of host-microbe interactions. This review advocates for the honeybee as a multidisciplinary model organism, highlighting the unique role of its gut microbiota in maintaining colony immune homeostasis, driving host co-evolution, unraveling the transmission mechanisms of antibiotic resistance genes (ARGs), and enhancing host adaptability to environmental stressors. By integrating multidimensional factors, including environmental gradients and apicultural practices, we construct an "Environment-Microbiota-Host Health" interaction framework to transcend the limitations of single-factor analyses. This framework provides a novel paradigm for the ecological containment of antimicrobial resistance, the conservation of pollinator resources, and microbiome-based engineering interventions. The review underscores the unique value of the honeybee model in unraveling social insect-microbe coevolution and resistance transmission dynamics, while also prospecting its application potential in developing novel antimicrobial peptides, designing probiotic formulations, and monitoring environmental resistance.

Gram-negative bacteria are equipped with a unique cell envelope structure that includes an outer membrane populated by diverse outer membrane proteins (OMPs). These OMPs are not only essential for bacterial survival, mediating critical functions such as nutrient transport, antibiotic resistance, and structural integrity, but they also play pivotal roles as virulence factors during host-pathogen interactions. Recent research highlights the ability of OMPs to manipulate host cellular processes, often targeting mitochondria to induce cell death or modulate immune responses. This review explores the multifunctional roles of bacterial OMPs, emphasizing their structural features, biogenesis, and pathogenic mechanisms. Furthermore, it delves into how bacterial OMPs exploit host cell machinery, particularly mitochondria, to promote infection, as well as their potential as targets for innovative antimicrobial strategies. Specifically, this review focuses on β-barrel OMPs that reach host mitochondria, detailing their delivery routes and mechanisms of organelle manipulation, while excluding non-β-barrel toxins and secretion-system effectors, to provide a defined perspective on mitochondria-targeting OMP virulence mechanisms.