FEMS microbiology reviews最新文献

The disease burden from Legionella spp. infections has been increasing in many industrialized countries and, despite decades of scientific advances, ranks amongst the highest for waterborne diseases. We review here several key research areas from a multidisciplinary perspective and list critical research needs to address some of the challenges of Legionella spp. management in engineered environments. These include: (i) a consideration of Legionella species diversity and cooccurrence, beyond Legionella pneumophila only; (ii) an assessment of their environmental prevalence and clinical relevance, and how that may affect legislation, management, and intervention prioritization; (iii) a consideration of Legionella spp. sources, their definition and prioritization; (iv) the factors affecting Legionnaires' disease seasonality, how they link to sources, Legionella spp. proliferation and ecology, and how these may be affected by climate change; (v) the challenge of saving energy in buildings while controlling Legionella spp. with high water temperatures and chemical disinfection; and (vi) the ecological interactions of Legionella spp. with other microbes, and their potential as a biological control strategy. Ultimately, we call for increased interdisciplinary collaboration between multiple research domains, as well as transdisciplinary engagement and collaboration across government, industry, and science as the way toward controlling and reducing Legionella-derived infections.

The microbiomes of skin and gill mucosal surfaces are critical components in fish health and homeostasis by competitively excluding pathogens, secreting beneficial compounds, and priming the immune system. Disruption of these microbiomes can compromise their capacity for disease resilience and maintaining host homeostasis. However, the extent and nature of microbiome disruption required to impact fish health negatively remains poorly understood. This review examines how various stressors influence the community composition and functionality of fish skin and gill microbiomes, and the subsequent effects on fish health. Our findings highlight that the impact of stressors on skin and gill microbiomes may differ for different body sites and are highly context-dependent, influenced by a complex interplay of host-specific factors, stressor characteristics, and environmental conditions. By evaluating current knowledge on the genesis and homeostasis of these microbiomes, we highlight a strong influence of environmental factors especially on skin and gill microbiomes compared with fish gut microbiomes, which appear to be more closely regulated by the host's homeostatic and immunological systems. This review emphasizes the importance of understanding the ecology and plasticity of fish skin and gill microbiomes to identify critical thresholds for microbiome shifts that impact fish health and disease resilience.

Pathogenic microorganisms can infect a variety of niches in the human body. During infection, these microbes can only persist if they adapt adequately to the dynamic host environment and the stresses imposed by the immune system. While viruses entirely rely on host cells to replicate, bacteria and fungi use their pathogenicity mechanisms for the acquisition of essential nutrients that lie under host restriction. An inappropriate deployment of pathogenicity mechanisms will alert host defence mechanisms that aim to eradicate the pathogen. Thus, these adaptations require tight regulation to guarantee nutritional access without eliciting strong immune activation. To work efficiently, the immune system relies on a complex signalling network, involving a myriad of immune mediators, some of which are quite directly associated with imminent danger for the pathogen. To manipulate the host immune system, viruses have evolved cytokine receptors and viral cytokines. However, among bacteria and fungi, selected pathogens have evolved the capacity to use these inflammatory response-specific signals to regulate their pathogenicity. In this review, we explore how bacterial and fungal pathogens can sense the immune system and use adaptive pathogenicity strategies to evade and escape host defence to ensure their persistence in the host.

Microbial volatile organic compounds (MVOCs) are diverse molecules produced by microorganisms, ranging from mere waste byproducts to important signalling molecules. While the interest in MVOCs has been increasing steadily, there is a significant gap in our knowledge of MVOCs in extreme environments with e.g. extreme temperatures or acidity. Microorganisms in these conditions are subjected to additional stress compared to their counterparts in moderate environments and in many cases have evolved unique adaptations, including the production of specialized MVOCs. This review highlights the diversity of MVOCs identified in extreme environments or produced by isolated extremophiles. Furthermore, we explore potential applications already investigated and discuss broader implications for biotechnology, environmental biology, and astrobiology.

Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities-shedding light on cell-to-cell variability in gene expression, regulatory dynamics, and metabolic potential. These approaches have shown that microbial populations are more heterogeneous and functionally complex than previously thought. However, direct probing of single-cell physiology-arguably more ecologically relevant by focusing on functional traits such as growth, metabolic activity, and enzymatic activity-remains underexplored. Droplet microfluidics provides a practical and high-throughput approach to address this gap, allowing functional characterization of individual microbial cells within complex communities and offering new opportunities to study ecological processes at high resolution. In this review, we look at the state of droplet microfluidics for single-cell microbial ecology. We revisit the fundamentals of microbial droplet workflows, we overview the current capabilities of droplet microfluidics that exist for microbial ecology and we look at the phenomena these workflows have uncovered and understanding they have generated. Finally, we integrate these capabilities to envision future droplet workflows that could enhance our understanding of single-cell physiology and discuss the fundamental limitations that go together with the droplet format.

Candidatus Cardinium hertigii (Cardinium) are maternally transmitted obligate intracellular bacteria found in a wide range of invertebrate hosts, including arthropods and nematodes. Infection with Cardinium has substantial consequences for host biology, with many strains manipulating host reproduction to favor symbiont transmission by (i) feminizing male hosts, (ii) altering host sex allocation, (iii) inducing parthenogenesis, or (iv) causing cytoplasmic incompatibility. Other Cardinium strains can confer benefits to their host or alter host behavior. Cardinium-modified host phenotypes can result in selective sweeps of cytological elements through host populations and potentially reinforce host speciation. Cardinium has potential for applications in controlling arthropod pest species and arthropod-vectored disease transmission, although much remains to be explored regarding Cardinium physiology and host interactions. In this review, we provide an overview of Cardinium evolution and host distribution. We describe the various host phenotypes associated with Cardinium and how biological and environmental factors influence these symbioses. We also provide an overview of Cardinium metabolism, physiology, and potential mechanisms for interactions with hosts based on recent studies using genomics and transcriptomics. Finally, we discuss new methodologies and directions for Cardinium research, including improving our understanding of Cardinium physiology, response to environmental stress, and potential for controlling arthropod pest populations.

Mtb subverts host immune surveillance by damaging phagolysosomal membranes, exploiting them as replication niches. In response, host cells initiate a coordinated LDR, integrating membrane repair, selective autophagy, and de novo biogenesis. This review delineates a systems-level model of lysosomal quality control governed by three critical regulatory axes: LGALS3/8/9, TRIM E3 ubiquitin ligases, and the AMPK-TFEB signaling pathway. LGALSs detect exposed glycans on ruptured membranes, triggering ESCRT-mediated repair and recruiting ARs. TRIM proteins mediate context-specific ubiquitination, enhancing cargo selection and facilitating transcriptional reprogramming via TFEB. Simultaneously, AMPK-TFEB signaling links metabolic stress to lysosomal regeneration, reinforcing immune defense and cellular adaptation. We highlight emerging mechanisms, including ATG8ylation, CASM, Ca2 + leakage, and SG formation, that refine this multilayered response. Mtb virulence factors selectively disrupt these pathways, revealing their relevance to pathogen persistence. Beyond infection, this triadic network maintains lysosomal integrity in neurodegeneration, inflammation, and lysosomal storage disorders. Understanding its modular design reveals novel therapeutic targets and HDTs for combatting drug-resistant TB. This review integrates recent advances into a coherent framework that redefines lysosomal function as a dynamic, immune-regulatory hub essential for cellular resilience under infectious and metabolic stress.

Coenzyme A (CoA) biosynthesis is a crucial process in living organisms, characterized by the production of conserved intermediates through enzyme-catalysed steps that vary across species. The synthesis of CoA entails several conversions, starting from pantothenate. Pantothenate is an essential vitamin in humans and is synthesized by certain bacterial species. Intermediates of the biosynthetic pathway have been shown to impact bacteria, especially in community settings such as the intestinal microbiota. Additionally, various diseases have been associated with specific CoA precursors and metabolic pathways downstream of CoA in the gut microbiota, underscoring the significance of evaluating the current knowledge on how the CoA pathway influences the metabolic state of bacteria. This also highlights the importance of having standardized methodologies that can be employed to better understand the metabolism of the microbiome. In this review, we explore the current literature on bacterial CoA metabolism, with a particular focus on gut bacteria and the impact of CoA-related metabolites on bacterial composition, function and metabolism. Furthermore, we discuss previous and current methodologies employed to investigate CoA biosynthesis. Our goal is to provide valuable insights into the intricate relationship between CoA metabolism, gut microbiota and their implications for health and disease, offering a foundation for future research and therapeutic approaches.

Bacteria and ectomycorrhizal fungi (EcMF) represent two of the most dominant plant root-associated microbial groups on Earth, and their interactions continue to gain recognition as significant factors that shape forest health and resilience. Yet, we currently lack a focused review that explains the state of bacteria-EcMF interaction research in the context of experimental approaches and technological advancements. To these ends, we illustrate the utility of studying bacteria-EcMF interactions, detail outstanding questions, outline research priorities in the field, and provide a suite of approaches that can be used to promote experimental reproducibility, field advancement, and collaboration. Though this review centers on the ecology of bacteria, EcMF, and trees, it by default offers experimental and conceptual insights that can be adapted to various subfields of microbiology and microbial ecology.

Metabolic engineering is a key enabling technology for rewiring cellular metabolism to enhance production of chemicals, biofuels, and materials from renewable resources. However, how to make cells into efficient factories is still challenging due to its robust metabolic networks. To open this door, metabolic engineering has realized great breakthroughs through three waves of technological research and innovations, especially the third wave. To understand the third wave of metabolic engineering better, we discuss its mainstream strategies and examples of its application at five hierarchies, including part, pathway, network, genome, and cell level, and provide insights as to how to rewire cellular metabolism in the context of maximizing product titer, yield, and productivity. Finally, we highlight future perspectives on metabolic engineering for the successful development of cell factories.