bims-bac4me Biomed News
on Microbiome and trained immunity
Issue of 2025–09–07
eighteen papers selected by
Chun-Chi Chang, Lunds universitet



  1. Elife. 2025 Sep 02. pii: e106443. [Epub ahead of print]14
      The long-term functional adaptation of innate immune cells following an initial stimulation, referred to as trained immunity or innate immune memory, enhances responsiveness and protection against secondary infections. Toll-like receptors (TLRs), an evolutionarily conserved family, recognize microbial-associated molecular patterns, initiating innate and adaptive immune responses. TLR signaling cascades induce the production of pro-inflammatory cytokines, antimicrobial peptides, and interferons, promoting pathogen clearance, while also driving epigenetic and metabolic reprogramming that enhances immune responses and protection to subsequent challenges. However, TLRs also recognize endogenous ligands contributing to chronic inflammation and autoimmune diseases. This review examines the role of TLRs and their various agonists in mediating trained immunity across diverse immune cell types, with an emphasis on their dual role in protecting against infections and chronic inflammation. It highlights recent clinical trials of TLR agonists as immunomodulatory agents and their therapeutic potential in infectious diseases and cancer. By providing an in-depth analysis of TLR-driven trained immunity, this review highlights the extensive influence of TLRs on immune cell populations and their implications for the development of novel, broad-spectrum immunotherapies.
    Keywords:  Toll-like receptors; chronic inflammation; immunology; inflammation; innate immunity; microbial infection; trained immunity
    DOI:  https://doi.org/10.7554/eLife.106443
  2. Clin Immunol. 2025 Aug 29. pii: S1521-6616(25)00168-8. [Epub ahead of print] 110593
      Staphylococcus aureus nasal colonisation is commonplace among healthy individuals, yet the immune mechanisms enabling bacterial persistence remain unclear. S. aureus drives local immunosuppression during nasal colonisation to facilitate persistence. This study reveals that S. aureus subverts microRNA-21 activity to promote IL-10 production within nasal tissue, while simultaneously impeding local pro-inflammatory responses. MiR-21 activity helps establish a S. aureus-induced immunosuppressive microenvironment which supports S. aureus persistence. Macrophages, which are key IL-10 producers, rapidly upregulate miR-21 upon S. aureus exposure.MiR-21 expression also coincides with an increase in intracellular survival of S. aureus within macrophages. Furthermore, S. aureus represses macrophage glycolysis to promote intracellular survival, which is dependent upon miR-21. Upon S. aureus colonisation, miR-21-/- mice demonstrate an overall improved bacterial clearance compared to their WT counterparts. These findings place the targeting of miR-21, which controls glycolytic activity in macrophages, as a potential avenue to reducing bacterial persistence during S. aureus colonisation.
    Keywords:  Bacterial persistence; Glycolysis; Nasal colonisation; Staphylococcus aureus; miR-21
    DOI:  https://doi.org/10.1016/j.clim.2025.110593
  3. Elife. 2025 Sep 04. pii: e106610. [Epub ahead of print]14
      Human and murine studies reveal that innate immune cells are able to mount enhanced responses to pathogens after primary inflammatory exposure. Innate immune memory has been shown to last for months to years, longer than the lifespan of most innate immune cells. Indeed, long-lived hematopoietic stem and progenitor cells (HSPCs) serve as a cellular reservoir for innate immune memory. In this review, we summarize the evidence that innate immune memory is epigenetically encoded in HSPCs, and we consider whether HSPC subpopulations with differentiation bias, cell autonomous epigenetic reprogramming, or both features underlie the phenomenon of central trained immunity. We further profile the significant implications of central trained immunity in stem cell transplant, aging, inflammatory diseases, and vaccination strategies for the future.
    Keywords:  epigenetics; hematopoietic progenitor cells; hematopoietic stem cells; immunology; inflammation; innate immune memory; metabolism; trained immunity
    DOI:  https://doi.org/10.7554/eLife.106610
  4. J Leukoc Biol. 2025 Aug 29. pii: qiaf123. [Epub ahead of print]
      Trained immunity amplifies innate immune responses in an antigen-independent manner. This study explored the ability of trained human primary macrophages to modulate the phenotype and function of T cells. Macrophages play an important role in antigen presentation, resulting in T-cell activation and antigen-specific clonal expansion; however, few studies have investigated whether trained immunity induction in macrophages modulates T cell activation. Here, through surface marker analysis of naive, β-glucan-, and BCG-trained macrophages, we identified eight distinct macrophage clusters following trained immunity induction. One of these populations showed an increase in surface activation markers CD40 and CD86, as well as MHC molecules. In vitro co-culture of T cells with autologous BCG-trained macrophages resulted in a skewing towards TH17 cells. We also observed an increase in TH17 percentage after BCG vaccination of human subjects. The bias towards TH17 triggered by trained macrophages required direct T cell to macrophage contact. Trained macrophages potentiated TH17 skewing independently of the antigen presented. While co-cultures of T cells and BCG-trained macrophages responded with higher production of interferon (IFN)-γ and interleukin (IL)-17 after stimulation, no clear shifts towards effector or memory T cells were observed. In conclusion, this study provides evidence that BCG-trained macrophages can modulate T cell function towards a TH17 phenotype, suggesting that BCG-induced trained immunity has the potential to enhance not only innate immune responses but also to modify adaptive T cell immunity.
    Keywords:  BCG; T cells; Trained Immunity; macrophages; vaccination
    DOI:  https://doi.org/10.1093/jleuko/qiaf123
  5. J Clin Invest. 2025 Sep 02. pii: e192469. [Epub ahead of print]135(17):
      Trained immunity (TRIM) is a form of long-lasting functional reprogramming of innate immune cells and their progenitors that enhances responsiveness to subsequent stimuli. Although first characterized in myeloid cells, TRIM was recently extended to nonmyeloid cell types, including endothelial and glial cells, which also exhibit stimulus-driven, memory-like behavior. While initially recognized as a protective mechanism, particularly in the context of vaccines and acute infections, TRIM can also become maladaptive, promoting chronic inflammation, immune dysfunction, and disease. This Review focuses on virus-induced TRIM while also addressing microbial, metabolic, and endogenous inducers. We examine key ligands and receptors that initiate TRIM and dissect the associated signaling and epigenetic pathways. Importantly, we argue that maladaptive TRIM arises not from a specific ligand, receptor, or molecular event, but from contextual factors such as stimulus persistence, dose, tissue microenvironment, and preexisting inflammation. The nature of the secondary challenge also shapes whether a trained response is adaptive or maladaptive. We further discuss TRIM induction in the bone marrow, involvement of both myeloid and nonmyeloid cells, and the role of lipid rafts in sustaining TRIM. We review maladaptive TRIM's potential contribution to systemic diseases, such as atherosclerosis, diabetes, sepsis, cancer, and autoimmunity, along with its influence on viral vaccine responses. Finally, we outline potential strategies to redirect maladaptive TRIM and propose key outstanding questions for future research.
    DOI:  https://doi.org/10.1172/JCI192469
  6. Virulence. 2025 Dec;16(1): 2553789
      Staphylococcus aureus, traditionally viewed as an extracellular pathogen, is increasingly recognized for its ability to persist intracellularly, particularly within macrophages. This intracellular lifestyle is central to osteomyelitis, a chronic bone infection characterized by persistent inflammation, bone destruction, and impaired repair. Within bone, S. aureus exploits macrophage plasticity by driving a shift from pro-inflammatory, bactericidal M1-like states to anti-inflammatory, tissue-reparative M2-like phenotypes. This polarization suppresses immune clearance and promotes an environment conducive to bacterial survival and dissemination. Additional strategies - including biofilm formation, small colony variants, and inhibition of phagolysosomal killing - further enhance persistence and immune evasion. While these mechanisms are well studied in extracellular infections, their role in intracellular survival is increasingly evident. This review synthesizes emerging insights into how S. aureus manipulates macrophage function to establish chronic bone infection and highlights therapeutic opportunities targeting macrophage polarization to improve immune-mediated clearance and bone repair in osteomyelitis.
    Keywords:  Staphylococcus aureus; intracellular infection; macrophage polarization; osteomyelitis; pathogenesis; phagocytosis
    DOI:  https://doi.org/10.1080/21505594.2025.2553789
  7. Mol Biol Rep. 2025 Aug 29. 52(1): 855
       BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) pneumonia is a severe infection with high mortality, where alveolar macrophages (AMs) play a critical role in host defense through M1 polarization. MicroRNA-155 (miR-155) is known to modulate immune responses, but its specific role in AM polarization during MRSA pneumonia remains unclear. This study investigates how miR-155 regulates M1 macrophage polarization and MRSA pneumonia.
    METHODS: The experiments were performed in both vitro and in miR-155 knockout mice. The activity of miR-155 and polarization of AMs were evaluated using scanning electron microscopy, immunofluorescence, enzyme-linked immunosorbent assay (ELISA), and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Lung pathology, inflammatory markers, and potential signaling pathways (particularly AKT/mTOR) were analyzed.
    RESULTS: miR-155 expression was significantly upregualted in MRSA infection, while miR-155 promoted M1 macrophage polarization as demonstrated by distinct morphological changes, elevated CD86 levels, and increased IL-6 production. miR-155 deficiency attenuated this response, reducing inflammatory cytokine release and lung pathology while impairing AKT/mTOR pathway activation, indicating that miR-155 exacerbates MRSA-induced pneumonia by driving M1 polarization through AKT/mTOR signaling.
    CONCLUSIONS: Our findings reveal that miR-155 modulates M1 macrophage polarization and aggrevates MRSA-induced pneumonia by activating the AKT/mTOR pathway. This study provides new insights into host-pathogen interactions in MRSA infection, suggesting miR-155 as a potential therapeutic target.
    Keywords:  Acute pneumonia; Macrophage; Methicillin resistant staphylococcus aureus; MicroRNA 155; Polarization
    DOI:  https://doi.org/10.1007/s11033-025-10934-0
  8. J Hazard Mater. 2025 Aug 29. pii: S0304-3894(25)02615-9. [Epub ahead of print]497 139696
      Microplastics (MPs) are ubiquitous environmental pollutants posing serious concerns owing to their potential health implications. MPs exert detrimental effects via the plastic particles, MP-bound chemicals, and MP-carrying pathogens. Streptococcus pneumoniae (pneumococcus) is a major pathogen causing bacterial pneumonia and respiratory inflammation. However, specific immune responses of macrophages to pneumococcus under MP exposure remain unclear. In this study, we aimed to investigate the mechanisms by which MPs inhibit macrophage functions, bacterial clearance, and inflammation during pneumococcal infection. Our results showed that MP exposure significantly impaired macrophage phagocytosis and inhibited pneumococcal engulfment. Furthermore, MPs synergistically enhanced C-C motif chemokine ligand 2 (CCL2) production via the phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) and mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) pathways, promoting M1 macrophage polarization and activating the ferroptosis pathway upon pneumococcal infection. Understanding the roles of MPs in the exacerbation of macrophage-driven inflammation will facilitate the development of new strategies to manage and treat pneumococcus-induced pulmonary diseases.
    Keywords:  CCL2; Ferroptosis; Inflammatory response; Macrophage; Microplastics; Pneumococcus
    DOI:  https://doi.org/10.1016/j.jhazmat.2025.139696
  9. Microbiol Spectr. 2025 Sep 02. e0077325
      Current treatments fall short in managing allergic rhinitis (AR), emphasizing the need for additional strategies. Beneficial bacteria application shows promise in AR; however, most studies focus on oral probiotic administration without monitoring the applied strains in the upper respiratory tract (URT) and their local effects. In this randomized, double-blind, placebo-controlled trial, the probiotic Lacticaseibacillus rhamnosus GG was administered via chewable tablets in seasonal AR patients, randomized to probiotic (n = 33) or placebo (n = 31) groups. Per-protocol analysis of the URT microbiome, immune markers, and AR symptoms was performed. L. rhamnosus GG trafficked from chewables to the oropharynx (77%, P = 0.02) and nasopharynx (41%, P < 0.0001). Control of self-reported AR symptoms via validated questionnaires under grass pollen exposure was observed after 2 weeks of probiotic administration and not upon placebo. A local decrease in salivary interleukin-4 (P < 0.05) and nasal IL-13 (P < 0.0001) was observed in the probiotic group. These data indicate that L. rhamnosus GG chewables can target the URT and exert local effects on key allergy cytokines after temporal probiotic engraftment.IMPORTANCEAllergic rhinitis (AR) or hay fever is a highly prevalent condition, impacting nearly half the population in some countries. Supplementation of beneficial bacteria or probiotics has gained increasing attention in AR, and a key innovative way to do this is direct administration to the upper airways. Our study shows for the first time that the model probiotic strain Lacticaseibacillus rhamnosus GG can traffic to the nose in AR patients when administered via a slow-releasing chewable tablet. This trafficking is associated with local benefits in the airways, including on grass pollen-induced nasal symptoms and allergy-related cytokines.
    Keywords:  Lacticaseibacillus; allergy; human microbiome; probiotics
    DOI:  https://doi.org/10.1128/spectrum.00773-25
  10. Science. 2025 Sep 04. 389(6764): eadp6252
      Revealing insights into the function of microbial communities requires moving beyond measuring bulk taxonomic composition to detecting interactions between subpopulations. Following the transformative impact of single-cell gene expression profiling techniques on numerous fields of human biology, recent years have seen increased application to microbes. We review progress in the development of these techniques and discuss challenges in applying them to microbial communities. We highlight applications for dissecting the microbiome in human health and disease that reveal functional heterogeneity within gut communities, antibiotic responses, and the dynamics of mobile genetic elements. As single-cell gene expression technologies continue to develop, they are becoming ever more essential for examining and modulating the role of microbial communities in clinical and wider environments.
    DOI:  https://doi.org/10.1126/science.adp6252
  11. Commun Biol. 2025 Aug 30. 8(1): 1314
      Shrimp aquaculture is critically important for global food security, but viral diseases like white spot syndrome virus (WSSV) cause devastating economic losses, highlighting the urgent need for effective disease control strategies. While trained immunity has been observed in invertebrates like shrimp after exposure to pathogens, the underlying molecular mechanisms remain elusive. Here we reveal that lysine acetyltransferase KAT8-mediated histone H3K27ac is critical for antiviral defense in shrimp Marsupenaeus japonicus. We demonstrate that ultraviolet-inactivated WSSV (UV-WSSV) induces antiviral trained immunity in the shrimp via KAT8-dependent H3K27ac. UV-WSSV training enhances glycolysis and the tricarboxylic acid (TCA) cycle, increasing acetyl-CoA production. This acetyl-CoA fuels KAT8 activity, depositing H3K27ac marks at the promoter of the NF-κB-like transcription factor Dorsal. This epigenetic modification upregulates Dorsal expression, leading to the enhanced production of the antiviral cytokine Vago5 and antimicrobial peptides (AMPs) upon subsequent WSSV challenge. Furthermore, H3K27ac directly activates key glycolytic genes (Hk2, Pk, Ldh), creating a feedforward loop that sustains metabolic reprogramming. Our work reveals a conserved KAT8-H3K27ac axis driving trained immunity in invertebrates through integrated metabolic-epigenetic crosstalk, analogous to mammalian systems. These findings provide a crucial theoretical foundation for developing antiviral vaccines and sustainable immunostimulants to control disease in shrimp aquaculture.
    DOI:  https://doi.org/10.1038/s42003-025-08767-5
  12. Food Sci Nutr. 2025 Sep;13(9): e70871
      Radiotherapy, a common method for treating pelvic and abdominal cancer, can easily result in radiation enteritis (RE). The gut microbiota and its metabolites have a crucial role in regulating macrophage polarization and maintaining immune homeostasis. Lactobacillus reuteri FN041, derived from human milk, can promote M2 polarization while attenuating RE. After FN041 treatment, the crypt depth and goblet cell numbers were significantly improved in RE mice. The levels of Muc2, ZO-1, and Occludin were significantly higher in the FN041 group than in the RE group. FN041 stimulated the polarization of macrophages toward M2 and inhibited the expression of IL-6 and TNF-α in RE mice. Mechanically, FN041 regulated the gut microbiota and metabolites, including key intermediates in phospholipid synthesis such as CDP-DG, prostaglandins, and their phospholipid derivatives (including PI, PE, PA, and PS), which were linked to M2 macrophage polarization. Collectively, FN041 exerts a protective effect against RE by modulating macrophage polarization based on gut microbiota and its metabolites.
    Keywords:  M2 macrophages polarization; fatty acid oxidation; gut microbiota; inflammation; radiation enteritis
    DOI:  https://doi.org/10.1002/fsn3.70871
  13. Folia Microbiol (Praha). 2025 Sep 03.
      Inflammatory bowel disease (IBD) is a chronic condition that leads to inflammation and damage to the gastrointestinal tract. Since dysregulation of the immune system is one of the triggers for IBD, taking probiotics as an immunomodulator in the gut could help control inflammation and IBD by influencing signaling pathways. The present research applied in vitro models to explore the effectiveness of our native probiotic Lactobacillus spp. in regulating MAPK and MYD88-independent inflammatory signaling pathways. We exposed HT-29 cells to Gram-negative bacteria to assess changes in inflammation-related pathways. Treatments were performed before, after, and simultaneously with a cocktail of Lactobacillus spp. (Lactiplantibacillus plantarum PR 365, Lactiplantibacillus plantarum PR 42, Lacticaseibacillus rhamnosus PR 195, Levilactobacillus brevis PR 205, Limosilactobacillus reuteri PR 100). This assessment was conducted using the quantitative real-time PCR method. According to our research, the expression of MAPK and MYD88-independent signaling pathways genes increased after exposure to Gram-negative components; however, using of our probiotic strains resulted in a significant reduction in the expression levels of MAPK genes in all treatments and phases. The expression levels of MYD88-independent genes were different following treatment with our selected Lactobacillus strain. The Lactobacillus spp. strains demonstrated anti-inflammatory effects on HT-29 cells by modulating MAPK and MYD88-independent signaling pathways. Our results indicate that these native potential probiotic strains exhibited beneficial effects in all three treatment phases. Therefore, it can be inferred that these probiotic strains, as beneficial agents, may be considered for the prevention and treatment of inflammation-related diseases such as IBD.
    Keywords:   Lactobacillus spp.; IBD; Inflammation; MAPK; MYD88-independent; Signaling pathways
    DOI:  https://doi.org/10.1007/s12223-025-01321-0
  14. Life Sci. 2025 Aug 30. pii: S0024-3205(25)00567-3. [Epub ahead of print] 123932
      Sepsis, a critical lethal critical illness, involves glucose and lipid metabolism disorders. However, the specific mechanisms underlying these alterations require further investigation. Acute lung injury (ALI), one of the most serious complications of sepsis, has a high mortality rate. Fibroblast growth factor 21 (FGF21), a key metabolic regulator, can regulate glucose metabolism. However, the short half-life (t½) of FGF21 limits its clinical application. In this study, we designed FGF21-loaded M2 macrophage-derived exosomes, named FGF21-M2-Exos, for the treatment of sepsis-induced ALI. We demonstrated that FGF21-M2-Exos were able to release FGF21 in a controlled and sustained manner. In addition, FGF21-M2-Exos were present in the lungs of mice at 24 h. Importantly, our results suggest that FGF21-M2-Exos alleviate sepsis-induced lung damage. Moreover, the RNA sequencing results revealed that FGF21-M2-Exos regulate immune function via several inflammatory signalling pathways. Furthermore, we found that FGF21-M2-Exo administration protects against sepsis-induced lung injury by downregulating inflammation-related protein expression, promoting M2 macrophage polarization, inhibiting glycolysis and reducing cellular apoptosis. Overall, the use of FGF21-M2-Exos, which regulate inflammatory and metabolic processes, may be a promising strategy for treating sepsis-induced ALI.
    Keywords:  FGF21; Glycolysis; M2 macrophage-derived exosomes; Macrophage polarization; Sepsis-induced lung injury
    DOI:  https://doi.org/10.1016/j.lfs.2025.123932
  15. Histol Histopathol. 2025 Sep 05. 18980
      Lactate, as an end-product of glycolysis, has been considered as a metabolic waste that participates in a few physiological functions. Recently, a novel study by Zhao's laboratory reported that lactate can serve as an epigenetic modification substrate, causing histone or nonhistone lysine residues to undergo lactylation, which then regulates gene transcription, translation, and protein function. Subsequent studies confirmed that lactylation plays an important role in a series of physiological and pathological processes, such as inflammation, cancer, and other biological processes. In this review, we summarize advanced achievements on the effects of lactylation in various diseases and potential treatment targets, providing a reference and direction for future research.
    DOI:  https://doi.org/10.14670/HH-18-980
  16. Adv Exp Med Biol. 2025 ;1478 573-613
      Lactate (La-) is a ubiquitous carbohydrate-derived metabolite and a major player in the coordination of whole-body metabolism. As the redox-balanced end-product of glycolysis, La- forms the conceptual node linking glycolysis, a process that does not require oxygen, and which occurs in the cytosol, to the TCA cycle and aerobic bioenergetics in the mitochondria. Through rapid multisystem exchange involving membrane monocarboxylate transporters, lactate concentration ([La-]) in the blood offers a "snapshot" of relative rates of glycolytic La- production and its mitochondrial consumption. Thus, while strenuous physical activity elicits a transient La- accumulation, adaptations to exercise training often include attenuated [La-]s for a given submaximal work rate, as well as lower [La-]s at rest. Conversely, elevated resting [La-] in the fasted state can reflect an often-ortentous metabolic scenario involving multisystem metabolic (dys)function characteristic of acute and chronic health issues. At the cellular level, tumors often exhibit augmented glucose uptake and preferential production of La-, even in the presence of oxygen (i.e., the Warburg effect). From coordination of whole-body metabolism during exercise to signaling in cancer cells, the role of La- in metabolism continues to expand and holds potential for multiple clinical and sub-clinical applications.
    Keywords:  Cancer; Cardiometabolic disease; Diabetes; Oxygen; Pyruvate; Sepsis
    DOI:  https://doi.org/10.1007/978-3-031-88361-3_24