Biological functions and biogenesis of secreted bacterial outer membrane vesicles

Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10-deficient mouse model

Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD is understudied, and the underlying molecular mechanisms remain unknown. In this study, colonization of Il10-deficient mice with Alistipes timonensis DSM 27924 delays colitis development. Colonization does not significantly alter the gut microbiome composition, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are detected in the plasma of colonized mice, carrying potentially immunomodulatory metabolites into the host circulatory system. Fractions of A. timonensis OMVs suppress LPS-induced Il6, Il1b, and Tnfa expression in vitro in murine macrophages. We detect putative bioactive lipids in the OMVs, including immunomodulatory sulfonolipids (SoLs) in the active fraction, which are also increased in the blood of colonized mice. Treating Il10-deficient mice with purified SoL B, a representative SoL, suppresses colitis development, suggesting its contribution to the anti-inflammatory phenotype observed with A. timonensis colonization. Thus, A. timonensis OMVs represent a potential mechanism for Alistipes-mediated delay of colitis in Il10-deficient mice via delivery of immunomodulatory lipids and modulation of the host plasma lipidome.

Bacterial extracellular vesicles in the initiation, progression and treatment of atherosclerosis

Atherosclerosis is the primary cause of cardiovascular and cerebrovascular diseases. However, current anti-atherosclerosis drugs have shown conflicting therapeutic outcomes, thereby spurring the search for novel and effective treatments. Recent research indicates the crucial involvement of oral and gastrointestinal microbiota in atherosclerosis. While gut microbiota metabolites, such as choline derivatives, have been extensively studied and reviewed, emerging evidence suggests that bacterial extracellular vesicles (BEVs), which are membrane-derived lipid bilayers secreted by bacteria, also play a significant role in this process. However, the role of BEVs in host-microbiota interactions remains insufficiently explored. This review aims to elucidate the complex communication mediated by BEVs along the gut-heart axis. In this review, we summarize current knowledge on BEVs, with a specific focus on how pathogen-derived BEVs contribute to the promotion of atherosclerosis, as well as how BEVs from gut symbionts and probiotics may mitigate its progression. We also explore the potential and challenges associated with engineered BEVs in the prevention and treatment of atherosclerosis. Finally, we discuss the benefits and challenges of using BEVs in atherosclerosis diagnosis and treatment, and propose future research directions to address these issues.

Dual-seq transcriptomics of Aeromonas salmonicida infection in Atlantic salmon (Salmo salar) primary macrophages reveals lysosome and apoptosis impairments

A. salmonicida subsp. salmonicida is one of the oldest-known marine pathogens causing furunculosis in freshwater to marine fish species. A. salmonicida causes septicemia and fish death due to a systemic shock. Early stages of A. salmonicida infection, including intracellular macrophage infection, are not fully comprehended. Here, we conducted a dual RNA-seq study and functional analyses in Atlantic salmon primary macrophages infected with A. salmonicida to identify relevant genes for fish cellular immunity and A. salmonicida pathogenesis. At 1-h post-infection (hpi), A. salmonicida modulated the expression of genes associated with inflammation, fatty acids synthesis, and apoptosis. While at 2 hpi A. salmonicida hijacked pathways related to myeloid cell differentiation, cytoskeleton and actin filament organization, lysosome maturation, and apoptosis. In contrast, A. salmonicida upregulated genes encoding for hemolysin, aerolysin, type IVa pili, and T3SS effectors. In conclusion, these results suggest that A. salmonicida induces endocytosis, impairs lysosome maturation, and reduces apoptosis.

Intestinal bacteria-derived extracellular vesicles in metabolic dysfunction-associated steatotic liver disease: From mechanisms to therapeutics

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a progressive disease that affects the health of approximately one-third of the world's population. It is the primary cause of end-stage liver disease, liver malignancy, and liver transplantation, resulting in a great medical burden. No medications have yet been approved by the US Food and Drug Administration for treating MASLD without liver inflammation or scarring. Therefore, the development of specific drugs to treat MASLD remains a key task in the ongoing research objective. Extracellular vesicles (EVs) play an important role in the communication between organs, tissues, and cells. Recent studies have found that intestinal microbiota are closely related to the pathogenesis and progression of MASLD. EVs produced by bacteria (BEVs) play an indispensable role in this process. Thus, this study provides a new direction for MASLD treatment. However, the mechanism by which BEVs affect MASLD remains unclear. Therefore, this study investigated the influence and function of intestinal microbiota in MASLD. Additionally, we focus on the research progress of BEVs in recent years and explain the relationship between BEVs and MASLD from the perspectives of glucose and lipid metabolism, immune responses, and intestinal homeostasis. Finally, we summarized the potential therapeutic value of BEVs and EVs from other sources, such as adipocytes, immunocytes, stem cells, and plants.

AbOmpA in Acinetobacter baumannii: exploring virulence mechanisms of outer membrane-integrated and outer membrane vesicle-associated AbOmpA and developing anti-infective agents targeting AbOmpA

Acinetobacter baumannii is notorious for its antimicrobial resistance and its potential to cause epidemics in hospital settings, which pose a global health threat. Although this microorganism is traditionally considered a low-virulence pathogen, extensive research has been conducted on its virulence and pathogenesis in recent years. Advances in understanding the virulence mechanisms of A. baumannii have prompted a shift in the development of anti-infective agents. The outer membrane protein A (AbOmpA) of A. baumannii is a key virulence factor both in vitro and in vivo. AbOmpA exists in three forms: outer membrane-integrated AbOmpA, outer membrane vesicle (OMV)-associated AbOmpA, and free proteins. Given that outer membrane-integrated AbOmpA has been implicated in the virulence and antimicrobial resistance of A. baumannii, many studies have focused on outer membrane-integrated AbOmpA as a therapeutic target for combating drug-resistant A. baumannii, and have led to the discovery of small molecules, polypeptides, and antimicrobial peptides targeting AbOmpA. However, the pathophysiological role of OMV-associated AbOmpA and its impact on AbOmpA-targeting agents remain unclear. This review summarizes the current knowledge of AbOmpA and critically discusses OMV-associated AbOmpA in relation to virulence and its potential impact on AbOmpA-targeted therapies to provide a better understanding of AbOmpA for the development of novel therapeutics against A. baumannii.

Characterization of outer membrane vesicles of Aggregatibacter actinomycetemcomitans serotypes a, b and c and their interactions with human neutrophils

Aggregatibacter actinomycetemcomitans (Aa) is a Gram-negative oral pathogen associated with periodontitis and systemic diseases. Seven serotypes of Aa are known, with serotypes a, b and c being most prevalent worldwide. Interestingly, serotype a, b and c isolates present differences in virulence. This focuses interest on their secreted virulence factors. Gram-negative bacteria evolved a specific protein secretion mechanism, based on the release of outer membrane vesicles (OMVs) with a protein cargo. The present study was therefore aimed at investigating whether differences in the protein cargo of OMVs could be associated with the differential virulence of Aa serotypes a, b or c. Accordingly, the different OMV proteomes were defined by mass spectrometry and infection assays were performed with human neutrophils that represent the main innate defense against oral pathogens like Aa. Subsequently, we correlated the OMV proteome data with the observed OMV-neutrophil interactions. A total of 276 OMV-associated proteins was identified, including 53 known virulence factors. Interestingly, OMVs from Aa isolates with different serotypes displayed similar protein cargo, but the relative quantities differed. OMVs of serotype a isolates were exceptional in carrying CRISPR proteins with a potential role in virulence. Intriguingly, Aa OMVs mostly coated the neutrophil surface, triggering formation of neutrophil extracellular traps (NETs). Conversely, the NETs captured Aa OMVs. Since the observed OMV-neutrophil interplay will occur at a distance from the OMV-producing bacteria, we postulate that it allows the bacteria to evade capture and elimination by neutrophils.

Emerging Roles of Periodontal Pathogen-Derived Outer Membrane Vesicles in NAFLD

The rising incidence of nonalcoholic fatty liver disease (NAFLD) poses a great socioeconomic burden worldwide. Also, periodontitis is the most common chronic inflammatory disease caused by a group of oral pathogens, affecting both oral health and systemic conditions, especially liver disease. Although accumulating evidence has elucidated an association between periodontal pathogens and NAFLD, the role of periodontal pathogen-derived outer membrane vesicles (OMVs) has not yet been clarified. In this comprehensive review, we aim to address this gap by summarising the progression and pathogenesis of NAFLD and revealing the relationship between periodontal disease and NAFLD multidimensionally. Additionally, this review sheds light on the multifunctional roles of periodontal pathogens OMVs and emphasises that periodontal pathogen-derived OMVs promote the development of NAFLD by stimulating Kupffer cells to produce inflammatory factors and inducing the activation of Hepatic stellate cells. However, it is still controversial whether periodontal pathogen-derived OMVs can be transferred to the liver through the bloodstream route or the oral-gut-liver axis. This highlights the pressing need for continued research efforts to develop new and optimised research schemes to observe the formation of the systemic distribution pathway of periodontal pathogen-derived OMVs. Finally, it is notable that there are currently no relevant clinical treatment guidelines to make specific provisions on controlling the level of periodontal pathogen-derived OMVs in patients with NAFLD. Guidelines developed based on our findings may contribute to the standardisation of practices. It can also provide effective strategies and potential therapeutic targets for NAFLD patients with periodontitis to alleviate the development of NAFLD diseases by inhibiting periodontal pathogens OMVs.

The Transformation Experiment of Frederick Griffith II: Inclusion of Cellular Heredity for the Creation of Novel Microorganisms

So far, synthetic biology approaches for the construction of artificial microorganisms have fostered the transformation of acceptor cells with genomes from donor cells. However, this strategy seems to be limited to closely related bacterial species only, due to the need for a "fit" between donor and acceptor proteomes and structures. "Fitting" of cellular regulation of metabolite fluxes and turnover between donor and acceptor cells, i.e. cybernetic heredity, may be even more difficult to achieve. The bacterial transformation experiment design 1.0, as introduced by Frederick Griffith almost one century ago, may support integration of DNA, macromolecular, topological, cybernetic and cellular heredity: (i) attenuation of donor Pneumococci of (S) serotype fosters release of DNA, and hypothetically of non-DNA structures compatible with subsequent transfer to and transformation of acceptor Pneumococci from (R) to (S) serotype; (ii) use of intact donor cells rather than of subcellular or purified fractions may guarantee maximal diversity of the structural and cybernetic matter and information transferred; (iii) "Blending" or mixing and fusion of donor and acceptor Pneumococci may occur under accompanying transfer of metabolites and regulatory circuits. A Griffith transformation experiment design 2.0 is suggested, which may enable efficient exchange of DNA as well as non-DNA structural and cybernetic matter and information, leading to unicellular hybrid microorganisms with large morphological/metabolic phenotypic differences and major features compared to predeceding cells. The prerequisites of horizontal gene and somatic cell nuclear transfer, the molecular mechanism of transformation, the machineries for the biogenesis of bacterial cytoskeleton, micelle-like complexes and membrane landscapes are briefly reviewed on the basis of underlying conceptions, ranging from Darwin's "gemmules" to "stirps", cytoplasmic and "plasmon" inheritance, "rhizene agency", "communicology", "transdisciplinary membranology" to up to Kirschner's "facilitated variation".

Bacterial Extracellular Vesicles: Bridging Pathogen Biology and Therapeutic Innovation

The main role of bacterial extracellular vesicles (BEVs) has been associated with various processes such as intercellular communication and host-pathogen interactions. This comprehensive review explores the multifaceted functions of BEVs across different biological domains, emphasizing their dual nature as contributors to disease and potential vehicles for therapeutic intervention. We examine the intricate interactions of BEVs within bacterial communities and between bacteria and hosts, their involvement in disease development through cargo delivery mechanisms, and their beneficial impact on microbial ecology. The review also highlights BEVs' applications in biomedical field, where they are revolutionizing vaccine development, targeted drug delivery, and cancer therapy. By utilizing the inherent properties of BEVs for controlled drug release, targeted antigen delivery, and immune modulation, they offer a promising frontier in precision medicine. In addition, the diagnostic potential of BEVs is explored through their utility as biomarkers, providing valuable insights into disease states and treatment efficacy. Looking forward, this review underscores the challenges and opportunities in translating BEV research to clinical practice, promoting the need of standardized methods in BEV characterization and scaling up production. The diverse abilities of BEVs, ranging from contributing to pathogen virulence to driving therapeutic innovation, highlight their potential as a cornerstone in the future of biomedical advancements. STATEMENT OF SIGNIFICANCE: Bacterial extracellular vesicles (BEVs) are emerging as pivotal players in both pathogenesis and therapeutic innovation. This review explores their dual nature as agents of disease and as promising biomaterials for biomedical applications, and provides a comprehensive survey on their involvement in disease mechanisms and microbial ecology, and their potential in biomedical applications such as vaccine development, targeted drug delivery, cancer therapy, and diagnosis. It highlights the complex interactions of BEVs within bacterial communities and between bacteria and hosts. This review also addresses current advancements, challenges, and opportunities in translating BEV research into clinical practice. The insights presented here position BEVs as a cornerstone in the future of biomedical advancements, advocating for standardized methods in BEV characterization and scalable production techniques.

Unanticipated Lipid Redistribution Mechanism of Action by Conjugated Oligoelectrolyte Antibiotics

Antimicrobial resistance (AMR) is one of the most pressing global health threats, urgently requiring new classes of antibiotics with differentiated mechanisms of action (MOA). Conjugated oligoelectrolytes (COEs) represent a molecular platform for designing antimicrobial agents structurally distinct from commercially available drugs. However, questions remain regarding their MOA. Herein, we show that COE treatment causes distinct phenotypes from well-established membrane-active antibiotics, with differences arising from structural variations, such as pendant group hydrophobicity. This was revealed through bacterial cytological profiling approaches, single-cell quantitative morphological analysis, and dye localization following treatment against Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. E. coli treatment with PNH2 and 1B resulted in micrometer-sized membrane vesicles, which are absent in 2-2H-treated cells. COE-treated B. subtilis featured overproduction of regions of increased fluidity (RIFs), relative to untreated cells. In contrast to the originally postulated membrane pinching mechanism, these findings support a MOA for COEs that relies predominantly on membrane restructuring, thereby providing new guidelines for further COE-based antibiotic design.

Nitrate supplementation affects taste by changing the oral metabolome and microbiome

Nitrate, an inorganic anion found in various foods is also present in saliva and has emerged as a potential prebiotic for the oral microbiome. Salivary glands concentrate nitrate from the bloodstream and release it into the oral cavity via the anion transporter sialin SLC17A5. In previous studies dietary nitrate supplementation altered oral bacteria composition, favouring genera like Rothia and Neisseria while reducing Streptococcus, Veillonella, Prevotella, and Actinomyces. The present study hypothesized that taste intensity might adapt to changes in the oral microbiome caused by nitrate supplementation. Participants underwent taste tests before, during, and after supplementation. All subjects showed greater levels of salivary nitrate during supplementation and had higher levels of Neisseria compared to before. Subjects were then grouped according to taste tests (before vs. during) as responders (ANOVA p < 0.05, n = 7), and non-responders (ANOVA p > 0.05, n = 6) and their salivary metabolome and oral microbiome further analysed. Responders had significantly less 5-amino pentanoate, formate, propionate and butyrate in saliva while non-responders showed no metabolite changes between before and during supplementation. In contrast, non-responders had increased Capnocytophaga gingivalis and altered lysosomal degradation pathways. Overall, nitrate supplementation shifted the oral microbiome composition in all subjects and when taste intensity was altered this correlated to bacteria-derived short-chain fatty acid production. This suggests taste perception is affected by the oral microbiome.

Comprehensive method for isolation and functional characterization of bacterial vesicles from human biological samples

Bacterial vesicles (BVs) are membrane-bound extracellular vesicles (EV) released from bacteria. They are known to play crucial role in bacterial communication, host-pathogen interactions, transfer of virulence factors, contribute to immune modulation and are the key players in microbial pathogenesis and survival in the host. Despite their significance, isolation and investigating BVs from human samples remains challenging, necessitating an easy, reliable and reproducible protocol. BVs have been limited due to methodological difficulties in isolating them from host-derived EVs, and the existing knowledge primarily relies on bacteria cultured under controlled laboratory conditions. This study presents a method, where we can identify the enriched BVs and characterizing them from plasma and stool samples of healthy individuals. Blood and fecal samples were collected, processed to density gradient ultracentrifugation to isolate and enrich BVs. Morphological characterization was performed using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA). Further, molecular markers OmpA (BV marker) was used to differentiate from host EVs (Alix as marker) using Western blot. Further the BV fraction was analyzed for LPS and LTA using ELISA. To understand functional relevance, BVs proteomics was performed from BV enriched plasma and stool using mass spectrometry from healthy individuals. The enriched BVs were also co-cultured with healthy peripheral blood mononuclear cells, labelled with Pkh26 dye and analysed at different time points for mRNA expression of candidate genes involved in immune regulation by qRT-PCR. Both TEM and NTA confirmed the presence of BVs, with sizes ranging from 25 nm to 250 nm. The western blot analysis revealed the fractions 6-9 are enriched with host EVs with the presence of Alix and fractions 10-13 contains BVs with the presence of OmpA. Interestingly, the proteomic analysis identified 439 proteins associated with plasma-derived BVs and 327 in stool-derived BVs, with 300 common to both. The Gene ontology and KEGG pathway analysis revealed the majority of proteins associated were immune regulation, cell activation, binding, and catalytic activity. Next, the functional assays indicated BVs were uptaken by PBMCs within 10 mins and it upregulated Toll-like receptor 2 (TLR-2) expression within 30 min. Hence, study establishes a reliable method to identify enriched BV population from human samples. Revealed the proteins associated with BVs in healthy individuals and their role in immune regulation. These findings may provide a platform to investigate BVs potential for diagnostic and therapeutic applications in various diseases.

Does the Hfq Protein Contribute to RNA Cargo Translocation into Bacterial Outer Membrane Vesicles?

Gram-negative bacteria release outer membrane vesicles (OMVs) that deliver various molecules, including virulence factors, to interact with their host. Recent studies have suggested that OMVs may also serve as carriers for RNAs, particularly small regulatory noncoding RNAs (sRNAs). For these RNAs to function effectively, they typically require a protein cofactor, Hfq, known as an RNA chaperone. In previous work, using molecular imaging, Circular Dichroism CD, and InfraRed FTIR spectroscopies, we demonstrated that Hfq interacts with the bacterial inner membrane and forms pores, suggesting a possible role in translocating RNA from the cytoplasm to periplasm and then to OMVs. In this study, we expand on our previous findings and provide evidence that RNA molecules bind to the Escherichia coli inner membrane in an Hfq-dependent manner. Moreover, we show that the lipid nature, in particular the presence of a cardiolipin-rich domain, is crucial for this interaction. These results reveal a new aspect of RNA translocation through the inner membrane, for further packaging in OMVs, and underscore the importance of Hfq in this mechanism.

Co-purification of the GroEL chaperone during outer membrane vesicle purification: insights from Aeromonas salmonicida subsp. salmonicida

Outer membrane vesicles (OMVs) are naturally produced by Gram-negative bacteria and originate from their outer membrane. They can be extracted using ultracentrifugation or ultrafiltration using concentration columns, followed by purification with a density gradient. However, these methods may co-purify contaminants with similar physical properties. Several studies have identified GroEL, a chaperonin, as a major protein in OMV preparations. Using Aeromonas salmonicida subsp. salmonicida as a model, we detected GroEL by mass spectrometry and observed it in transmission electron microscopy images as separate from OMVs. As a cytoplasmic protein complex, GroEL is more likely a contaminant resulting from bacterial lysis during growth rather than an intrinsic OMV component. The model A. salmonicida subsp. salmonicida proved valuable in reaching this conclusion because it produces high levels of extracellular GroEL and low amounts of OMVs. This study emphasizes the need for caution when interpreting the presence of GroEL in OMV preparations and highlights the importance of rigorous purification methods to ensure OMV purity.

Potential of bacterial outer membrane vesicles in tumor vaccine: characteristics, advancements, and future directions

Bacterial outer membrane vesicles (OMVs), naturally released by Gram-negative bacteria, are a type of lipid bilayer nanoparticles containing many components found within the parent bacterium. Despite OMVs were first considered mere by-products of bacterial growth, recent studies have shown them as a highly adaptable platform for tumor vaccine. Here, we first demonstrate the biogenesis of OMVs, then review the strong immunogenicity of OMVs as an immune adjuvant in tumor vaccine and its excellent vaccine delivery capability, and finally discuss OMVs' engineering potentials through summarizing recent scientific advancements in genetic engineering, chemical modification, and nanotechnology. We also point out the clinical trials and future challenges of OMV-based vaccine. Overall, this review offers valuable insights into cancer immunotherapy, providing a roadmap for leveraging OMVs as a versatile platform for next-generation cancer vaccines.

Spatially resolved charge-transfer kinetics at the quantum dot-microbe interface using fluorescence lifetime imaging microscopy

Integrating the optoelectronic properties of quantum dots (QDs) with biological enzymatic systems to form microbe-semiconductor biohybrids offers promising prospects for both solar-to-chemical conversion and light-modulated biochemical processes. Developing these nano-bio hybrid systems necessitates a deep understanding of charge-transfer dynamics at the nano-bio interface. Photoexcited carrier transfer from QDs to microbes is driven by complex interactions, with emerging insights into the relevant thermodynamic and kinetic factors. The heterogeneities of both microbes and QD ensembles pose significant challenges in mechanistic understanding, which is critical for designing advanced nano-bio hybrids. We used fluorescence lifetime imaging microscopy to analyze charge transfer between a CdSe QD film and Shewanella oneidensis microbes. We correlated the spatiotemporal fluorescence data with an analytical model. Our analysis revealed two distinct distributions of QD de-excitation pathways. The characteristics of these distributions: 1) a faster transfer rate ([Formula: see text]), with a lower acceptor number ([Formula: see text]) and 2) a slower transfer rate ([Formula: see text]) with a higher acceptor number ([Formula: see text]). We assign these distributions to the indirect and direct electron transfer mechanisms, respectively. Our findings demonstrate how spectroscopic imaging can uncover fundamental electron transfer mechanisms at complex interfaces, offering valuable design principles for future nano-bio hybrids.

Exosomes as Therapeutic and Diagnostic Tools: Advances, Challenges, and Future Directions

Exosomes are tiny extracellular vesicles that are essential for intercellular communication and have shown great promise in the detection and treatment of disease. They are especially useful in the treatment of cancer, cardiovascular conditions, and neurological diseases because of their capacity to transport bioactive substances including proteins, lipids, and nucleic acids. Because of their low immunogenicity, ability to traverse biological barriers, and biocompatibility, exosome-based medicines have benefits over conventional treatments. Large-scale production, standardization of separation methods, possible immunological reactions, and worries about unforeseen biological effects are some of the obstacles that still need to be overcome. Furthermore, there are major barriers to the clinical use of exosomes due to their complex cargo sorting mechanisms and heterogeneity. Future studies should concentrate on enhancing separation and purification procedures, optimizing exosome engineering techniques, and creating plans to reduce immune system modifications. This review examines the most recent developments in exosome-based diagnostics and treatments, identifies current issues, and suggests ways to improve their clinical translation in the future.

The Transformation Experiment of Frederick Griffith I: Its Narrowing and Potential for the Creation of Novel Microorganisms

The construction of artificial microorganisms often relies on the transfer of genomes from donor to acceptor cells. This synthetic biology approach has been considerably fostered by the J. Craig Venter Institute but apparently depends on the use of microorganisms, which are very closely related. One reason for this limitation of the "creative potential" of "classical" transformation is the requirement for adequate "fitting" of newly synthesized polypeptide components, directed by the donor genome, to interacting counterparts encoded by the pre-existing acceptor genome. Transformation was introduced in 1928 by Frederick Griffith in the course of the demonstration of the instability of pneumococci and their conversion from rough, non-pathogenic into smooth, virulent variants. Subsequently, this method turned out to be critical for the identification of DNA as the sole matter of inheritance. Importantly, the initial experimental design (1.0) also considered the inheritance of both structural (e.g., plasma membranes) and cybernetic information (e.g., metabolite fluxes), which, in cooperation, determine topological and cellular heredity, as well as fusion and blending of bacterial cells. In contrast, subsequent experimental designs (1.X) were focused on the use of whole-cell homogenates and, thereafter, of soluble and water-clear fractions deprived of all information and macromolecules other than those directing protein synthesis, including outer-membrane vesicles, bacterial prions, lipopolysaccharides, lipoproteins, cytoskeletal elements, and complexes thereof. Identification of the reasons for this narrowing may be helpful in understanding the potential of transformation for the creation of novel microorganisms.

Reducing severity of inflammatory bowel disease through colonization of Lactiplantibacillus plantarum and its extracellular vesicles release

Inflammatory bowel disease (IBD) is characterized by compromised intestinal barrier function and a lack of effective treatments. Probiotics have shown promise in managing IBD due to their ability to modulate the gut microbiota, enhance intestinal barrier function, and exert anti-inflammatory effects. However, the specific mechanisms through which probiotics exert these therapeutic effects in IBD treatment remain poorly understood. Our research revealed a significant reduction of Lactiplantibacillus plantarum (L. plantarum) in the gut microbiota of IBD patients. L. plantarum is a well-known probiotic strain in the list of edible probiotics, recognized for its beneficial effects on gut health, including its ability to strengthen the intestinal barrier and reduce inflammation. We demonstrated that supplementation with L. plantarum could alleviate IBD symptoms in mice, primarily by inhibiting apoptosis in intestinal epithelial cells through L. plantarum's bacterial extracellular vesicles (L. plant-EVs). This protective effect is dependent on the efficient uptake of L. plant-EVs by intestinal cells. Intriguingly, watermelon enhances L. plantarum colonization and L. plant-EVs release, further promoting intestinal barrier repair. Our findings contribute to the understanding of L. plant-EVs in the probiotic-based therapeutic approach for IBD, as they are promising candidates for nanoparticle-based therapeutic methods that are enhanced by natural diets such as watermelon. This study thereby offers a potential breakthrough in the management and treatment of IBD.

Bacterial outer membrane vesicles in tumor prevention and treatment: advancements in research and application

As one of the major challenges to global health, the innovation of prevention and treatment methods for tumors has consistently been a focal point in medical research. In recent years, bacterial membrane vesicles (MVs), particularly outer membrane vesicles (OMVs) secreted by Gram-negative bacteria, have garnered significant attention due to their unique biological characteristics and potential anti-tumor effects. OMVs are bilayer lipid nanocapsules that are actively released by bacteria during their growth, typically ranging in diameter from 20 to 300 nm. They are rich in various biomolecules, including lipids, proteins, nucleic acids, and other small molecules. These components not only reflect the outer membrane structure of bacteria but also contain numerous pathogen-associated molecular patterns (PAMPs) related to bacterial pathogenicity and immunogenicity. Consequently, OMVs play an important role in bacterial resistance, antimicrobial activity, gene transfer, signal transduction, and immune regulation. Research and application of OMVs in anti-tumor therapy have made significant progress. This paper reviews the classification, characteristics, preparation, safety evaluation, biological functions, and specific research advancements of OMVs as antitumor drugs, immunomodulators, and carriers. Additionally, common methods for the preparation and modification of OMVs, including preliminary extraction, purification, characterization, and drug loading, are discussed. This paper also summarizes the challenges faced by OMVs in anti-tumor research and outlines future development directions, aiming to provide a reference for the further application of OMVs in tumor treatment.

Advances in molecular mechanisms and therapeutic strategies for central nervous system diseases based on gut microbiota imbalance

BACKGROUD

Central nervous system (CNS) diseases pose a serious threat to human health, but the regulatory mechanisms and therapeutic strategies of CNS diseases need to be further explored. It has been demonstrated that the gut microbiota (GM) is closely related to CNS disease. GM structure disorders, abnormal microbial metabolites, intestinal barrier destruction and elevated inflammation exist in patients with CNS diseases and promote the development of CNS diseases. More importantly, GM remodeling alleviates CNS pathology to some extent.

AIM OF REVIEW

Here, we have summarized the regulatory mechanism of the GM in CNS diseases and the potential treatment strategies for CNS repair based on GM regulation, aiming to provide safer and more effective strategies for CNS repair from the perspective of GM regulation.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The abundance and composition of GM is closely associated with the CNS diseases. On the basis of in-depth analysis of GM changes in mice with CNS disease, as well as the changes in its metabolites, therapeutic strategies, such as probiotics, prebiotics, and FMT, may be used to regulate GM balance and affect its microbial metabolites, thereby promoting the recovery of CNS diseases.

Monocyte activation test (MAT) as an ethical alternative to animal testing

Ethical considerations surrounding the utilization of animals in scientific research have prompted a widespread search for alternative methodologies. This review explores the historical context and ethical dilemmas associated with traditional animal testing methods, before introducing the Monocyte Activation Test (MAT) as a promising alternative, and outlining its basic principles, historical development, and advantages over conventional animal testing. The role of monocytes in the immune system and the activation pathways utilized in MAT are elucidated, while regulatory acceptance and guidelines for MAT validation are introduced, alongside case studies proving its reliability and reproducibility. The applications of MAT in pharmaceutical and medical device testing are summarized, together with its potential future uses. Although the MAT faces limitations and challenges, the global perspective to reduce unnecessary animal tests has become a general concept in animal welfare and scientific research. [BMB Reports 2025; 58(3): 105-115].

Unveiling the wonders of bacteria-derived extracellular vesicles: From fundamental functions to beneficial applications

Extracellular vesicles (EVs), are critical mediators of intercellular communication and exhibit significant potential across various biomedical domains. These nano-sized, membrane-encapsulated entities have captured substantial interest due to their diverse roles in pathogenesis and promising therapeutic applications. EVs manage numerous physiological processes by transferring bioactive molecules, including proteins, lipids, and nucleic acids, between cells. This review delves into the factors influencing the properties of EVs, such as temperature and stress conditions, which collectively influence their size, composition, and functional attributes. We also describe the emerging roles of EVs, emphasizing their involvement in microbial interactions, immune modulation, antimicrobial resistance spread and their potential as innovative diagnostic and therapeutic instruments. Despite their promising applications, the advancement of EV-based therapies faces several challenges, which will also be discussed. By elucidating these critical elements, we aim to provide a comprehensive overview of the transformative potential of EVs in revolutionizing diagnostics and therapeutics in medicine.

Extracellular Vesicles as Biomarkers in Infectious Diseases

Extracellular vesicles (EVs) are nanosized vesicles that are secreted by all cells into the extracellular space. EVs are involved in cell-to-cell communication and can be found in different bodily fluids (bronchoalveolar lavage fluid, sputum, and urine), tissues, and in circulation; the composition of EVs reflects the physiological condition of the releasing cell. The ability to use EVs from bodily fluids for minimally invasive detection to monitor diseases makes them an attractive target. EVs carry a snapshot of the releasing cell's internal state, and they can serve as powerful biomarkers for diagnosing diseases. EVs also play a role in the body's immune and pathogen detection responses. Pathogens, such as bacteria and viruses, can exploit EVs to enhance their survival and spread and to evade detection by the immune system. Changes in the number or contents of EVs can signal the presence of an infection, offering a potential avenue for developing new diagnostic methods for infectious diseases. Ongoing research in this area aims to address current challenges and the potential of EVs as biomarkers in diagnosing a range of diseases, including infections and infectious diseases. There is limited literature on the development of EVs as diagnostic biomarkers for infectious diseases using existing molecular biology approaches. We aim to address this gap by reviewing recent EV-related investigations in infectious disease studies.

Highly Pleomorphic Strains of the Vibrio Predator Pseudoalteromonas piscicida and Their Outer Membrane Vesicles: A Scanning Electron Micrographic Study

Pseudoalteromonas species are recognized for their probiotic roles in reducing pathogens in aquaculture products by secreting a broad range of antimicrobial compounds. Some species, like P. piscicida, are also predators that attack susceptible prey bacteria, including V. parahaemolyticus, by transferring outer membrane vesicles (OMVs) containing digestive compounds to the surface of their prey. These vesicles digest holes in the prey's cell wall releasing nutrients upon which the Pseudoalteromonas feed. In the present study, scanning electron microscopy was performed on two P. piscicida strains grown in sterile seawater and nutrient-enriched seawater, without the presence of bacterial prey, to determine if the presence of prey or low-nutrient media was required to induce vesicle formation. Micrographs revealed OMV formation and high pleomorphism of P. piscicida in the absence of prey cells and regardless of the nutrient levels of the seawater. Phenotypic characteristics included the presence of (i) vesiculated and non-vesiculated bacteria, (ii) large bulbous OMV versus small OMV, (iii) pilus-like connectors of widely varying lengths to which vesicles were attached, (iv) highly elongated (10 µm long) Pseudoalteromonas cells, and (v) cells that appeared to extend to 50 µm long and to be septating and dividing into short chains and individual cells. The possible contribution of these novel phenotypes to Pseudoalteromonas predation is discussed.

Enhancement of aerobic sludge granulation by quorum sensing signaling molecules mediated by biomimetic bacterial extracellular vesicles

The addition of exogenous quorum sensing signaling molecules to the activated sludge system enables rapid sludge granulation. However, signaling molecules exposed to the environment are easily degraded, and their quorum sensing effects cannot be maintained in the long term. Therefore, they must be frequently added, which leads to an increase in operational costs. In this study, signaling molecules, acylated homoserine lactones (AHLs), were packaged into biomimetic bacterial extracellular vesicles-lipid vesicles (AHLs@ZZT), and the mediating role of lipid vesicles for AHLs was utilized to improve the utilization efficiency of signaling molecules. The results show that packaging of AHLs into vesicles slowed down the release of AHLs and protected them from degradation by porcine renal acylase. Moreover, the chemical properties of lipid vesicles are similar to the structure of bacterial cell walls, making it easier for the packaged AHLs to bind to target bacteria, thereby generating more EPS and accelerating the aggregation of microorganisms. After adding the lipid vesicles loaded with AHLs into the activated sludge system, the sludge granulation process was accelerated. Furthermore, the frequency of AHLs@ZZT addition was reduced by three times compared to that of unpackaged AHLs, resulting in a granular sludge with a smoother and denser surface. High-throughput sequencing of the sludge genome in the system indicated that adding AHLs@ZZT could promote microbial diversity and enrich functional microorganisms. Three-dimensional fluorescence spectra further revealed that the tryptophan and tyrosine proteins in extracellular polymeric substances secreted by these microorganisms facilitated sludge granulation. In summary, the lipid vesicle-mediated signaling molecular strategy can promote the rapid formation of granular sludge and maintain the long-term stability of the granular sludge structure, representing an economic and feasible regulation strategy.

Plant memory and communication of encounters

Plants can communicate with each other and other living organisms in a very sophisticated manner. They use biological molecules and even physical cues to establish a molecular dialogue with beneficial organisms as well as with their predators and pathogens. Several studies were recently published that explore how plants communicate with each other about their previous encounters or stressful experiences. However, there is an almost complete lack of knowledge about how these intra- and interspecies communications are directly regulated at the epigenetic level. In this perspective article we provide new hypotheses for the possible epigenetic modifications that regulate plant responses at the communication level.

A look beyond topography: Transient phenomena of Escherichia coli cell division captured with high-speed in-line force mapping

Life on the nanoscale has been made accessible in recent decades by the development of fast and noninvasive techniques. High-speed atomic force microscopy (HS-AFM) is one such technique that shed light on single protein dynamics. Extending HS-AFM to effortlessly incorporate mechanical property mapping while maintaining fast imaging speed allows a look deeper than topography and reveal details of nanoscale mechanisms that govern life. Here, we present high-speed in-line force mapping (HS-iFM) to record mechanical properties and topography maps with high spatiotemporal resolution. Using HS-iFM, a comprehensive study of the nanoscale mechanical properties of living Escherichia coli revealed localized stiffening and details during cell division, formation and diffusion of pores in the membrane, and the impact of depressurization of a cell. The frame time was as low as 15 seconds with a spatial resolution of 5.5 nanometers per pixel in topography and 22 nanometers per pixel in force maps, allowing the capture of transient phenomena on bacterial surfaces in striking detail.

In situ NMR reveals a pH sensor motif in an outer membrane protein that drives bacterial vesicle production

The outer membrane vesicles (OMVs) produced by diderm bacteria have important roles in cell envelope homeostasis, secretion, interbacterial communication, and pathogenesis. The facultative intracellular pathogen Salmonella enterica Typhimurium (STm) activates OMV biogenesis inside the acidic vacuoles of host cells by upregulating the expression of the outer membrane (OM) protein PagC, one of the most robustly activated genes in a host environment. Here, we used solid-state nuclear magnetic resonance (NMR) and electron microscopy (EM), with native bacterial OMVs, to demonstrate that three histidines, essential for the OMV biogenic function of PagC, constitute a key pH-sensing motif. The NMR spectra of PagC in OMVs show that they become protonated around pH 6, and His protonation is associated with specific perturbations of select regions of PagC. The use of bacterial OMVs is an essential aspect of this work enabling NMR structural studies in the context of the physiological environment. PagC expression upregulates OMV production in E. coli, replicating its function in STm. Moreover, the presence of PagC drives a striking aggregation of OMVs and increases bacterial cell pellicle formation at acidic pH, pointing to a potential role as an adhesin active in biofilm formation. The data provide experimental evidence for a pH-dependent mechanism of OMV biogenesis and aggregation driven by an outer membrane protein.

Engineered Therapeutic Bacteria with High-Yield Membrane Vesicle Production Inspired by Eukaryotic Membrane Curvature for Treating Inflammatory Bowel Disease

Bacterial membrane vesicles (BMVs) are emerging as powerful natural nanoparticles with transformative potential in medicine and industry. Despite their promise, scaling up BMV production and ensuring stable isolation and storage remain formidable challenges that limit their broader application. Inspired by eukaryotic mechanisms of membrane curvature, we engineered Escherichia coli DH5α to serve as a high-efficiency BMV factory. By fusing the ethanolamine utilization microcompartment shell protein EutS with the outer membrane via the ompA signal peptide, we induced dramatic membrane curvatures that drove enhanced vesiculation. Simultaneously, overexpression of fatty acyl reductase led to the production of amphiphilic fatty alcohols, further amplifying the BMV yield. Dynamic modulation of peptidoglycan hydrolase (PGase) expression facilitated efficient BMV release, resulting in a striking 149.11-fold increase in vesicle production. Notably, the high-yield BMVs from our engineered strain, without the need for purification, significantly bolstered innate immune responses and demonstrated therapeutic efficacy in treating inflammatory bowel disease (IBD). This study presents a strategy to overcome BMV production barriers, showcasing the therapeutic potential of engineered bacteria and BMVs for IBD treatment, while highlighting their potential applications in diverse biomedical fields.

Opportunities and challenges of bacterial extracellular vesicles in regenerative medicine

Extracellular vesicles (EVs) are membrane-bound vesicles that are shed or secreted from the cell membrane and enveloped by a lipid bilayer. They possess stability, low immunogenicity, and non-cytotoxicity, exhibiting extensive prospects in regenerative medicine (RM). However, natural EVs pose challenges, such as insufficient targeting capabilities, potential biosafety concerns, and limited acquisition pathways. Although engineered EVs demonstrate excellent therapeutic efficacy, challenges such as low production yield and the complexity of engineering modifications constrain their further clinical applications. Bacteria have advantages such as rapid proliferation, diverse gene editing methods, mature cultivation techniques, and relatively easy preparation of bacterial EVs (BEVs), which can be used to effectively address the challenges currently encountered in the field of EVs. This review provides a description of the biogenesis and pathophysiological functions of BEVs, and strategies for optimizing BEVs preparation to attain efficiency and safety are discussed. An analysis of natural characteristics of BEVs is also conducted to explore how to leverage their advantages or mitigate their limitations, thereby overcoming constraints on the application of BEVs in RM. In summary, engineered BEVs possess characteristics such as high production yield, excellent stability, and high drug-delivering capabilities, laying the foundation for their application in RM.

Uncovering a new family of conserved virulence factors that promote the production of host-damaging outer membrane vesicles in gram-negative bacteria

CprA is a short-chain dehydrogenase/reductase (SDR) that contributes to resistance against colistin and antimicrobial peptides. The cprA gene is conserved across Pseudomonas aeruginosa clades and its expression is directly regulated by the two-component system PmrAB. We have shown that cprA expression leads to the production of outer membrane vesicles (OMVs) that block autophagic flux and have a greater capacity to activate the non-canonical inflammasome pathway. In a murine model of sepsis, a P. aeruginosa strain deleted for cprA was less virulent than the wild-type (WT) strain. These results demonstrate the important role of CprA in the pathogenicity of P. aeruginosa. It is worth noting that CprA is also a functional ortholog of hemolysin F (HlyF), which is encoded by virulence plasmids of Escherichia coli. We have shown that other cryptic SDRs encoded by mammalian and plant pathogens, such as Yersinia pestis and Ralstonia solanacearum are functional orthologs of CprA and HlyF. These SDRs also induce the production of OMVs which block autophagic flux. This study uncovers a new family of virulence determinants in Gram-negative bacteria, offering potential for innovative therapeutic interventions and deeper insights into bacterial pathogenesis.

Gut Microbiota as Emerging Players in the Development of Alcohol-Related Liver Disease

The global incidence and mortality rates of alcohol-related liver disease are on the rise, reflecting a growing health concern worldwide. Alcohol-related liver disease develops due to a complex interplay of multiple reasons, including oxidative stress generated during the metabolism of ethanol, immune response activated by immunogenic substances, and subsequent inflammatory processes. Recent research highlights the gut microbiota's significant role in the progression of alcohol-related liver disease. In patients with alcohol-related liver disease, the relative abundance of pathogenic bacteria, including Enterococcus faecalis, increases and is positively correlated with the level of severity exhibited by alcohol-related liver disease. Supplement probiotics like Lactobacillus, as well as Bifidobacterium, have been found to alleviate alcohol-related liver disease. The gut microbiota is speculated to trigger specific signaling pathways, influence metabolite profiles, and modulate immune responses in the gut and liver. This research aimed to investigate the role of gut microorganisms in the onset and advancement of alcohol-related liver disease, as well as to uncover the underlying mechanisms by which the gut microbiota may contribute to its development. This review outlines current treatments for reversing gut dysbiosis, including probiotics, fecal microbiota transplantation, and targeted phage therapy. Particularly, targeted therapy will be a vital aspect of future alcohol-related liver disease treatment. It is to be hoped that this article will prove beneficial for the treatment of alcohol-related liver disease.

Akkermansia muciniphila- and Pathogenic Bacteria-Derived Endotoxins Differently Regulate Human Dendritic Cell Generation and γδ T Lymphocyte Activation

Lipopolysaccharide (LPS) is a potent endotoxin released at high concentrations in acute infections, causing massive host inflammatory response. Accumulating evidence indicates that dysbiosis-associated chronic low levels of circulating LPS can sustain a prolonged sterile low-grade inflammation that increases the risk of several non-communicable diseases. Interventions aimed at increasing the abundance of beneficial/probiotic bacteria, including Akkermansia muciniphila, result in reduced inflammation, favoring metabolic and immune health. Immunosuppression is a common feature in conditions of chronic inflammation, and dendritic cells (DCs) represent key targets given their ability to shift the balance toward immunity or tolerance. In this study, the effects of low concentrations of LPS from pathogenic (Escherichia coli and Salmonella enterica) and probiotic (Akkermansia muciniphila) bacterial species on human DC generation and functions were compared. We report that monocyte precursor priming with Escherichia coli and Salmonella enterica LPS forces the differentiation of PD-L1-expressing DCs, releasing high levels of IL-6 and IL-10, and impairs their capacity to drive full TCR-Vδ2 T cell activation. Conversely, comparable concentrations of Akkermansia muciniphila promoted the generation of DCs with preserved activating potential and immunostimulatory properties. These results shed light on potential mechanisms underlying the impact of low endotoxemia on disease risk and pathogenesis, and increase our understanding of the immunomodulatory effects of Akkermansia muciniphila.

Comparative Genome Analysis of Piscine Vibrio vulnificus: Virulence-Associated Metabolic Pathways

Vibriosis caused by Vibrio vulnificus is a major problem in aquatic animals, particularly brown marble groupers (Epinephelus fuscoguttatus). V. vulnificus biotype I has recently been isolated and classified into subgroups SUKU_G1, SUKU_G2, and SUKU_G3 according to the different types of virulence genes. In a previous study, we have shown that biotype I V. vulnificus strains were classified into three subgroups according to the different types of virulence genes, which exhibited different phenotypes in terms of growth rate and virulence. To gain insight into the different genetic features revealed by the potential virulence mechanisms of V. vulnificus in relation to a spectrum of pathogenesis, comparative genomic analyses of three biotype I V. vulnificus strains belonging to different subgroups (SUKU_G1, SUKU_G2, and SUKU_G3) were performed. The V. vulnificus genome is composed of two circular chromosomes with average sizes of 3 Mbp and 1.7 Mbp that are evolutionarily related based on the analysis of orthologous genes. A comparative genome analysis of V. vulnificus revealed 5200 coding sequences, of which 3887 represented the core genome and the remaining 1313 constituted the dispensable genome. The most virulent isolate (SUKU_G1) carries unique enzymes that are important for lipopolysaccharide (LPS) and capsular polysaccharide (CPS) synthesis, as well as flagellar glycosylation, and harbors another type of repeat in toxin (RTX) and bacterial defense mechanisms. The less virulent isolate (SUKU_G2) shares enzymes related to CPS biosynthesis or flagellar glycosylation, while the avirulent isolate (SUKU_G3) and a less virulent isolate (SUKU_G2) share enzymes related to the production of rare sugars. Interestingly, the isolates from the three subgroups containing specific CMP-N-acetylneuraminate-producing enzymes that are correlated with their growth abilities. Collectively, these observations provide an understanding of the molecular mechanisms underlying disease pathogenesis and support the development of strategies for bacterial disease prevention and control.

High-resolution cryo-EM analysis of a Streptococcus pyogenes M-protein/human plasminogen complex

The importance of human plasminogen (hPg)/plasmin (hPm)/cell receptor complexes in invasiveness of cells has been amply established. The objective of this investigation was to determine a high-resolution structure of a major Group A Streptococcus (GAS) bacterial receptor (PAM) for hPg/hPm when bound on a cell surface to its major ligand, hPg. As a model cell surface with endogenous PAM, we employed engineered PAM-expressing lentivirus (LV) particles. We show that the ectodomain of a PAM-type M-Protein (M-Prt), in complex with hPg, is folded through distinct intra- and inter-domain interactions to a more compact form on the cell surface, thus establishing a new paradigm for membrane-bound M-Prt/ligand structures. These studies provide a framework for addressing the need for treatments of GAS disease by providing a molecular platform to solve structures of virulence-determining membrane proteins.

Immune Responses Elicited by Outer Membrane Vesicles of Gram-Negative Bacteria: Important Players in Vaccine Development

The attractiveness of OMVs derived from Gram-negative bacteria lies in the fact that they have two biomembranes sandwiching a peptidoglycan layer. It is well known that the envelope of OMVs consists of the outer bacterial membrane [OM] and not of the inner one [IM] of the source bacterium. This implies that all outer membranous molecules found in the OM act as antigens. However, under specific conditions, some of the inner membrane proteins can be exported into the outer membrane layer and perform as antigens. A key information was that the used purification procedures for OMVs, the induction methods to increase the production of OMVs as well as the specific mutant strains obtained via genetic engineering affect the composition of potential antigens on the surface and in the lumen of the OMVs. The available literature allowed us to list the major antigens that could be defined on OMVs. The functions of the antigens within the source bacterium are discussed for a better understanding of the various available hypotheses on the biogenesis of vesicle formation. Also, the impacts of OMV antigens on the immune system using animal models are assessed. Furthermore, information on the pathways of OMVs entering the host cell is presented. An example of a bacterial infection that causes epidemic diseases, namely via Neisseria meningitidis, is used to demonstrate that OMVs derived from this pathogen elicit protective immune responses when administered as a vaccine. Furthermore, information on OMV vaccines under development is presented. The assembled knowledge allowed us to formulate a number of reasons why OMVs are attractive as vaccine platforms, as their undesirable side effects remain small, and to provide an outlook on the potential use of OMVs as a vaccine platform.

Differences in clinical manifestations and the fecal microbiome between irritable bowel syndrome and small intestinal bacterial overgrowth

BACKGROUND

Irritable bowel syndrome (IBS) and small intestinal bacterial overgrowth (SIBO) share similar abdominal symptoms; however, their differentiation remains controversial.

AIMS

To illustrate the differences between the two conditions.

METHODS

Patients and healthy controls completed questionnaires and provided stool samples for analysis.

RESULTS

IBS presented with the most severe symptoms and was specifically characterized by intense abdominal pain and frequent episodes of diarrhea. Patients with IBS displayed more dysregulated taxonomy within the fecal microbiota than SIBO. Opportunistic pathogens, including Lachnoclostridium, Escherichia-Shigella, and Enterobacter were enriched in the IBS group which contributed to increased bacterial pathogenicity and positively correlated with abdominal pain and bloating, meanwhile, Lachnoclostridium and Escherichia-Shigella were found to be associated with metabolites affiliated to bile acids, alcohols and derivatives. Bacteria enriched in SIBO group correlated with constipation. The bacterial co-occurrence network within the SIBO group was the most intricate. Ruminococcaceae Group were defined as core bacteria in SIBO. Differential metabolites affiliated to androstane steroids and phenylacetic acids were associated with core bacteria.

CONCLUSIONS

Our study elucidates the differences between IBS and SIBO in terms of symptoms, microbiota and functions, which provides insights into a better understanding of both diseases and evidence for different treatment strategies.

Recent advances in bacterial outer membrane vesicles: Effects on the immune system, mechanisms and their usage for tumor treatment

Tumor treatment remains a significant medical challenge, with many traditional therapies causing notable side effects. Recent research has led to the development of immunotherapy, which offers numerous advantages. Bacteria inherently possess motility, allowing them to preferentially colonize tumors and modulate the tumor immune microenvironment, thus influencing the efficacy of immunotherapy. Bacterial outer membrane vesicles (OMVs) secreted by gram-negative bacteria are nanoscale lipid bilayer structures rich in bacterial antigens, pathogen-associated molecular patterns (PAMPs), various proteins, and vesicle structures. These features allow OMVs to stimulate immune system activation, generate immune responses, and serve as efficient drug delivery vehicles. This dual capability enhances the effectiveness of immunotherapy combined with chemotherapy or phototherapy, thereby improving anticancer drug efficacy. Current research has concentrated on engineering OMVs to enhance production yield, minimize cytotoxicity, and improve the safety and efficacy of treatments. Consequently, OMVs hold great promise for applications in tumor immunotherapy, tumor vaccine development, and drug delivery. This article provides an overview of the structural composition and immune mechanisms of OMVs, details various OMVs modification strategies, and reviews the progress in using OMVs for tumor treatment and their anti-tumor mechanisms. Additionally, it discusses the challenges faced in translating OMV-based anti-tumor therapies into clinical practice, aiming to provide a comprehensive understanding of OMVs' potential for in-depth research and clinical application.

Novel Nano Drug-Loaded Hydrogel Coatings for the Prevention and Treatment of CAUTI

Catheter-associated urinary tract infection (CAUTI) is a prevalent type of hospital-acquired infection, affecting approximately 15% to 25% of patients with urinary catheters. Long-term use of the catheter can lead to colonization of microorganisms and biofilm formation, and may develop into bacterial CAUTI. However, the frequent replacement of catheters in clinical settings can result in tissue damage, inflammation, ulceration, and additional complications, causing discomfort and pain for patients. In light of these challenges, a novel nanodrug-supported hydrogel coating called NP-AM/FK@OMV-P/H has been developed in this study. Through in vitro experiments, it is confirmed that OMV nano-loaded liquid gel coating has an effective reaction against E.coli HAase and releases antibacterial drugs. This coating has also demonstrated strong inhibition of E.coli and has shown the ability to inhibit the formation of bacterial biofilm. These findings highlight the potential of the OMV nanoparticle gel coating in preventing and treating bacterial infections. Notably, NP-AM/FK@OMV-P/H has exhibited greater efficacy against multidrug-resistant E.coli associated with UTIs compared to coatings containing single antimicrobial peptides or antibiotics. Additionally, it has demonstrated good biosecurity. In conclusion, the NP-AM/FK@OMV-P/H coating holds great potential in providing benefits to patients with CAUTI.

Single-use polyethylene terephthalate bottle-derived nanoplastics propagate antibiotic resistance in bacteria via transformation and outer membrane vesicle secretion

Plastic pollution arising from single-use plastic bottles (SUPBs) and containers leads to the formation of micro/nanoplastics (NPs). These NPs raise concerns due to their potential toxicity and interactions with microorganisms. In various environments, including our digestive system, both microorganisms and plastics coexist. The interactions between these NPs and microorganisms can have far-reaching consequences, potentially affecting the ecosystems and human health. Therefore, understanding these interactions is crucial for addressing the challenges posed by plastic pollution. This study investigated the role of NPs in propagating antibiotic resistance (AR), specifically through outer membrane vesicles (OMVs), which is a mechanism that has not been fully explored to date in terms of NPs' effects. To explore this, NPs were synthesized using polyethylene terephthalate (PET) SUPBs, mimicking the natural chemical composition of environmental nanoplastics, unlike previous studies, which used pure PET, polystyrene (PS) or other pure plastic materials. The resulting PET bottle-derived nanoplastics (PBNPs), which exhibited diverse shapes and sizes (50-850 nm), were found to facilitate horizontal gene transfer (HGT) through transformation and outer membrane vesicles (OMVs), enabling the transport of plasmids among bacteria. In transformation, PBNPs physically carried plasmids across the bacterial membrane. In another scenario, PBNPs induced oxidative stress and bacterial surface damage, which led to the upregulation of stress response-associated genes and the escalation of OMV secretion in E. coli. This novel pathway highlights how PBNPs contribute to AR gene dissemination, potentially exacerbating the global antibiotic resistance crisis. Furthermore, PBNPs mediate cross-species gene transfer from E. coli to Lactobacillus acidophilus, underscoring their impact on diverse microorganisms, including those in the human gut. Our findings suggest that nanoplastics may be an unrecognized contributor to the rising tide of antibiotic resistance, with significant consequences for human health and the environment. Molecular analyses revealed the upregulated expression of genes associated with stress response and OMV secretion, offering deeper insights into the biological mechanisms affected by PBNPs. This study offers crucial insights into the interactions of NPs and microorganisms for developing strategies to address the ecological and health implications of nanoplastic contamination.

Pseudomonas aeruginosa- mediated cardiac dysfunction is driven by extracellular vesicles released during infection

Pseudomonas aeruginosa (P.a.) is a gram-negative, opportunistic bacterium abundantly present in the environment. Often P.a. infections cause severe pneumonia, if left untreated. Surprisingly, up to 30% of patients admitted to the hospital for community- acquired pneumonia develop adverse cardiovascular complications such as myocardial infarction, arrhythmia, left ventricular dysfunction, and heart failure. However, the underlying mechanism of infection-mediated cardiac dysfunction is not yet known. Recently, we demonstrated that P.a. infection of the lungs led to severe cardiac electrical abnormalities and left ventricular dysfunction with limited P.a. dissemination to the heart tissue. To understand the mechanism of cardiac dysfunction during P.a. infection, we utilized both in vitro and in vivo models. Our results revealed that inflammatory cytokines contribute but are not solely responsible for severe contractile dysfunction in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Instead, exposure of hiPSC-CMs with conditioned media from P.a. infected human monocyte-derived macrophages (hMDMs) was sufficient to cause severe contractile dysfunction and arrhythmia in hiPSC-CMs. Specifically, exosomes released from infected hMDMs and bacterial outer membrane vesicles (OMVs) are the major drivers of cardiomyocyte contractile dysfunction. By using LC-MS/MS, we identified bacterial proteins, including toxins that are packaged in the exosomes and OMVs, which are responsible for contractile dysfunction. Furthermore, we demonstrated that systemic delivery of bacterial OMVs to mice caused severe cardiac dysfunction, mimicking the natural bacterial infection. In summary, we conclude that OMVs released during infection enter circulation and drive cardiac dysfunction.

Production and purification of outer membrane vesicles encapsulating green fluorescent protein from Escherichia coli: a step towards scalable OMV technologies

Outer membrane vesicles (OMVs) are spherical structures that contain a small fraction of the periplasm of Gram-negative bacteria, surrounded by its outer membrane. They are naturally produced and detached from the bacterial surface, participate in diverse biological processes, and their diameter size is in the range of 10-300 nm. OMVs have gained interest in different applications, such as the development of biosensors, vaccines, protein chips, and the encapsulation of heterologous proteins and peptides expressed by these microorganisms. However, the use of OMVs in these applications is limited due to the low yields and high purification costs. In this study, we produced green fluorescent protein (GFP) encapsulated into OMVs using Escherichia coli JC8031 transformed with pTRC99A-ssTorA-GFP to establish the production and purification route. Results showed that the motility of the strain prevents its immobilization in alginate, which hampers the purification of OMVs. To address this issue, a zeolite-based column was used to chromatographically separate the OMVs from smaller particles. Further experiments will be focused on standardizing the production and purification of OMVs at a scalable level.

A molecular toolkit for heterologous protein secretion across Bacteroides species

Bacteroides species are abundant, prevalent, and stable members of the human gut microbiota, making them a promising chassis for developing long-term interventions for chronic diseases. Engineering Bacteroides as in situ bio-factories, however, requires efficient protein secretion tools, which are currently lacking. Here, we systematically investigate methods to enable heterologous protein secretion in Bacteroides. We identify a collection of secretion carriers that can export functional proteins across multiple Bacteroides species at high titers. To understand the mechanistic drivers of Bacteroides secretion, we characterize signal peptide sequence features, post-secretion extracellular fate, and the size limit of protein cargo. To increase titers and enable flexible control of protein secretion, we develop a strong, self-contained, inducible expression circuit. Finally, we validate the functionality of our secretion carriers in vivo in a mouse model. This toolkit promises to enable expanded development of long-term living therapeutic interventions for chronic gastrointestinal disease.

First report on the physicochemical and proteomic characterization of Proteus mirabilis outer membrane vesicles under urine-mimicking growth conditions: comparative analysis with Escherichia coli

Introduction

Uropathogenic bacteria employ multiple strategies to colonize the urinary tract, including biofilm formation, invasion of urothelial cells, and the production of adhesins, toxins, and siderophores. Among the most prevalent pathogens causing urinary tract infections (UTIs) are Uropathogenic Escherichia coli and Proteus mirabilis. A notable feature of Gram-negative bacteria is their ability to produce outer membrane vesicles (OMVs), which play critical roles in bacterial survival, virulence, and host-pathogen interactions, including UTIs.

Methods

In this study, OMVs were isolated and characterized from two clinical strains, E. coli U144 and P. mirabilis 2,921, cultured in both Luria-Bertani broth and artificial urine.

Result and discussion

The OMVs ranged in size from 85 to 260 nm, with the largest vesicles observed in artificial urine. Proteomic analysis allowed the identification of 282 proteins in OMVs from E. coli and 353 proteins from P. mirabilis when cultured LB medium, while 215 were identified from E. coli and 103 from P. mirabilis when cultured in artificial urine. The majority of these proteins originated from the bacterial envelope, while others were linked to motility and adhesion. Notably, the protein composition of OMVs varied depending on the growth medium, and proteins associated with zinc and iron uptake being more prominent in artificial urine, suggesting their importance in the urinary environment. Crucially, this is the first report to characterize P. mirabilis OMVs under different culture conditions, offering novel insights into the role of OMVs in UTI pathogenesis. These findings provide a deeper understanding of the molecular mechanisms by which OMVs contribute to bacterial virulence, establishing the foundation for potential therapeutic interventions targeting OMV-mediated processes in UTIs.

Bacterial membrane vesicles combined with nanoparticles for bacterial vaccines and cancer immunotherapy

Similar to mammalian cells, most bacteria can release nano-sized membrane vesicles (MVs) into the extracellular environment. MVs contain lipids, bioactive proteins, nucleic acids, and metabolites, and play important roles in microbial physiology. MVs have great potential for immunotherapeutic applications, such as bacterial vaccines and cancer immunotherapy. However, because of the diversity in content and heterogeneity in size of MVs, the clinical application of MVs has been limited. Recently, the use of MVs combined with nanoparticles (NPs) has been shown to be effective in improving the homogeneity, stability and function of MVs. In this review, we focus on studies of MVs combined with NPs (MV-NPs) and describe the use of these MV-NPs in biotechnology, especially in bacterial vaccine and cancer immunotherapy.

Prokaryotic morphological features and maintenance activities governed by seasonal productivity conditions

Prokaryotic maintenance respiration and associated metabolic activities constitute a considerable proportion of the total respiration of carbon to CO2 in the ocean's mixed layer. However, seasonal influences on prokaryotic maintenance activities in terms of morphological and metabolic adaptations at low (winter) and high productivity (summer) are still unclear. To address this, we examined the natural prokaryotic communities at the mesocosm scale to analyse the differences in their morphological features and gene expression at low and high maintenance respiration, experimentally manipulated with the specific growth rate. Here, we showed that morphological features including membrane blebbing, membrane vesicles, and cell‒cell connections occurred under high productivity. Metabolic adaptations associated with maintenance activities were observed under low productivity. Several Kyoto Encyclopedia of Genes and Genomes categories related to signal transduction, energy metabolism, and translational machinery supported maintenance activities under simulated winter conditions. Differential abundances of genes related to transporters, osmoregulation, nitrogen metabolism, ribosome biogenesis, and cold stress were observed. Our results demonstrate how specific growth rate in different seasons can influence resource allocation at the levels of morphological features and metabolic adaptations. This motivates further study of morphological features and their ecological role during high productivity, while investigations of metabolic adaptations during low productivity can advance our knowledge about maintenance activities.

Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10 -deficient mouse model

Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD has not been studied and the underlying molecular mechanisms also remain unknown. In this study, colonization of Il10 -deficient mice with Alistipes timonensis DSM 27924 delays the development of colitis. Colonization with Alistipes does not significantly alter the gut microbiome composition during colitis development, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are also detected in the plasma of colonized mice, which carry metabolites with immunomodulatory potential into the host circulatory system. We further demonstrate that fractions of A. timonensis OMVs suppress LPS-induced Il6 , Il1b , and Tnfa expression in vitro in murine macrophages. We detect immunomodulatory sulfonolipids (SoLs) in the active fraction, which are also increased in the blood of A. timonensis -colonized mice; and we identify other putative bioactive lipids in the A. timonensis OMVs. Thus, A. timonensis OMVs represent a potential mechanism for Alistipes -mediated delay of colitis progression in Il10 -deficient mice through the delivery of immunomodulatory lipids, including SoLs, and modulation of the host plasma lipidome.

Molecular Mechanisms of Biofilm Formation in Helicobacter pylori

BACKGROUND

Biofilm formation in Helicobacter pylori (H. pylori) helps bacteria survive antibiotic exposure and supports bacterial colonization and persistence in the stomach. Most of the published articles have focused on one aspect of the biofilm. Therefore, we conducted the current study to better understand the mechanism of biofilm formation, how the biofilm contributes to antibiotic resistance, and how the biofilm modifies the medication delivery mechanism.

METHODS

We conducted a literature review analysis of the published articles on the Helicobacter pylori biofilm between 1998 and 2024 from the PubMed database to retrieve eligible articles. After applying the inclusion and exclusion criteria, two hundred and seventy-three articles were eligible for our study.

RESULTS

The results showed that biofilm formation starts as adhesion and progresses through micro-colonies, maturation, and dispersion in a planktonic form. Moreover, specific genes modulate each phase of biofilm formation. Few studies have shown that mechanisms, such as quorum sensing and diffusible signal factors, enhance coordination among bacteria when switching from biofilm to planktonic states. Different protein expressions were also observed between planktonic and biofilm strains, and the biofilm architecture was supported by exopolysaccharides, extracellular DNA, and outer membrane vesicles.

CONCLUSIONS

This infrastructure is responsible for the increased survival of bacteria, especially in harsh environments or in the presence of antibiotics. Therefore, understanding the biofilm formation for H. pylori is crucial. This study illustrates biofilm formation in H. pylori to help improve the treatment of H. pylori infection.

Outer Membrane Vesicles Formed by Clinical Proteus mirabilis Strains May Be Incorporated into the Outer Membrane of Other P. mirabilis Cells and Demonstrate Lytic Properties

Outer membrane vesicles (OMVs) are extracellular structures, ranging in size from 10 to 300 nm, produced by Gram-negative bacteria. They can be incorporated into the outer membrane of a recipient's cells, which may enable the transfer of substances with lytic properties. Due to the scarce information regarding the OMVs produced by Proteus mirabilis, the aim of this study was to test the blebbing abilities of the clinical P. mirabilis O77 and O78 strains and to determine the blebs' interactions with bacterial cells, including their possible bactericidal activities. The production of OMVs was visualised by Transmission electron microscopy (TEM). The presence of OMVs in the obtained samples as well as the phenomenon of OMV fusion to recipient cells were confirmed by Enzyme-Linked ImmunoSorbent Assay (ELISA) and Western blotting assays. The bacteriolytic activity of the OMVs was examined against P. mirabilis clinical strains and reference Staphylococcus aureus and Escherichia coli strains. It was shown that each of the two tested P. mirabilis strains could produce OMVs which were able to fuse into the cells of the other strain. The lytic properties of the O78 OMVs against another P. mirabilis O78 strain were also demonstrated. This promising result may help in the future to better understand the mechanisms of the pathogenesis and to treat the infections caused by P. mirabilis.