Abstract Tuberculosis (TB) granulomas are complex multicellular structures central to disease pathogenesis and treatment challenges, notably due to bacterial persistence and immune modulation. Existing animal and in vitro models do not fully capture granuloma heterogeneity and immune complexity. Here, we review the biology and applications of Granuloma-Like Structures (GLS) derived from human peripheral blood mononuclear cells infected with Mycobacterium tuberculosis, which recapitulate key features of early granuloma formation, including macrophage differentiation, lymphocyte involvement, and cytokine dynamics. Quantitative analysis identifies conserved bacterial growth trajectories and recurrent aggregate sizes, despite protocol diversity and donor variability. Furthermore, a minimal theoretical model illustrates how aggregate size may influence drug efficacy, through physical and biological mechanisms. Although underutilized in drug screening, GLS offer a promising intermediate platform by bridging simple cell monolayers to animal models, particularly for evaluating host-directed therapies. Standardized metrics and integration with computational models are needed to enhance reproducibility and translational relevance. GLS thus represent a valuable tool to investigate host–pathogen interactions and advance TB drug development under controlled immune conditions.
Abstract Fungal pathogens have historically been studied as autonomous agents, as self-contained units independent of their associated microbiota, with disease outcomes attributed to fungal virulence factors acting on susceptible hosts. However, many pathogenic fungi harbor bacterial associates that influence their ecology, persistence and virulence. The pathobiome concept addressed this limitation by framing disease as an outcome of multi-kingdom interactions. Yet most pathobiome studies rely on correlative analyses of microbial abundances with pathogens, lacking spatial resolution to identify which microorganisms physically interact with pathogenic structures. Conversely, the hyphosphere provides micrometer-scale spatial resolution but has been investigated predominantly in non-pathogenic fungi. Here, we propose the pathomycosphere as a spatially defined and experimentally tractable subset of the pathobiome: a hypha-associated microbial assemblage in which physical association with the pathogenic member, prolonged or transient has a consequence for the pathogen’s biology, with pathogenicity residing in the fungus, an associated microorganism or their interaction. This framework bridges the pathobiome and hyphosphere concepts by anchoring disease-associated microbial interactions to hyphal interface, where mechanistic investigation becomes feasible. Pathomycosphere provides operational tractability to explore microbial partnerships contributing to pathogenesis, and positions fungal-associated bacterial consortia as important components of pathogen biology with relevance to disease ecology beyond agricultural systems.
Human immunodeficiency virus (HIV) infection remains a major global health challenge despite the success of antiretroviral therapy, largely due to the persistence of viral reservoirs and chronic immune dysregulation. Extracellular vesicles (EVs) have emerged as important mediators of intercellular communication during viral infection, operating at the interface between viral and host cellular pathways. Depending on their cellular origin and molecular cargo, EVs can exert context-dependent effects, with studies suggesting roles in both viral dissemination and persistence, as well as in the modulation of antiviral immune responses. This review examines the molecular mechanisms through which EVs have been proposed to contribute to HIV infection, focusing on host-virus interactions, immune regulation, chronic inflammation, and viral latency. We further discuss emerging therapeutic strategies targeting EV biology, including approaches aimed at modulating EV biogenesis and cargo composition, as well as the development of engineered EVs as platforms for drug delivery, gene editing, and immune modulation. Overall, this study highlights the emerging roles of EVs in HIV infection, emphasizing both their potential relevance and the limitations that currently complicate the interpretation of EV-associated effects.
Glycoside metabolization is a crucial function in bacteria and a key feature in fermentation and synthetic biology. To feed on various glycosides with complex structures, bacteria have developed very diverse mechanisms to recognize, transport, and degrade them. Despite their crucial role, transporters are hard to identify and study due to challenges in expressing membrane proteins in recombinant form and the fact that most bacteria are uncultivable. In this review, we present the available methods and technologies for identifying and characterizing bacterial glycoside transporters. We consolidate existing knowledge on experimentally validated glycoside transporters from different families, including TonB-dependent transporters, ATP-binding cassette transporters, the phosphotransferase system, and the major facilitator superfamily, highlighting their taxonomic, functional, mechanistic, and structural diversity. The disparity between the number of functionally characterized glycoside transporters and the vast amount of sequence data available underlines the need for more efficient approaches to determine their specificity and to better understand the molecular mechanisms of glycoside utilization in bacteria.
Enterohemorrhagic Escherichia coli (EHEC) is a major foodborne pathogen that causes hemorrhagic colitis and hemolytic uremic syndrome. Increasing evidence indicates that the gut microbiota plays a central role in modulating EHEC pathogenesis through complex metabolic and signaling networks. Beneficial commensals, including Bifidobacterium, Lactobacillus, and segmented filamentous bacteria, contribute to colonization resistance by competing for nutrients and adhesion sites, producing antimicrobial metabolites, and enhancing epithelial barrier integrity. In contrast, certain species such as Bacteroides thetaiotaomicron and Enterococcus faecalis may promote EHEC virulence by altering intestinal nutrient availability or triggering the expression of virulence genes. Microbiota-derived metabolites, including short-chain fatty acids, succinate, indole, riboflavin, nicotinamide, ethanolamine, and L-malate, act as important regulatory signals that connect microbial metabolism with LEE-mediated virulence pathways. Understanding these host-microbe-pathogen interactions provides a mechanistic basis for developing microbiota-targeted interventions such as probiotics, prebiotics, and fecal microbiota transplantation that enhance colonization resistance and attenuate virulence. Integration of AI-based analytics with multi-omics approaches is expected to facilitate the design of personalized, mechanism-driven therapeutic strategies for the control of EHEC infection.
