The innate immune system serves as a first line of defense by utilizing a variety of pattern recognition receptors (PRRs) that detect various nucleic acids generated during virus infection, many of which activate the STING pathway, leading to interferon production. One family of PRRs, the Aim2-like receptors (ALRs), is thought to contribute to innate immunity by this mechanism. However, the Alr locus is highly polymorphic at the sequence and copy number level. We found that at least one member in mice, IFI207, contributes to innate immunity by preventing the degradation of STING that normally occurs after its activation, defining a novel mechanism for sustaining immune response. Several ALRs have been implicated in adipogenesis, autoimmune disease, and inflammation, and identification of the pressures that shaped the genes in the locus is thus important for understanding the biological processes in which the ALRs function.

Fungal cell walls are dynamic extracellular structures essential for growth and morphogenesis, making them prime targets for antifungal drugs and the host immune system. Although many protein families involved in the synthesis, crosslinking, and degradation of cell wall polymers are known, the molecular functions and structural evolution of most cell wall proteins remain poorly understood. Our in-depth structural, functional, and phylogenetic analysis of the fungal SUN domain protein family sheds light on a central question: how specific protein families have evolved structurally to enable dynamic cell wall remodeling during growth and division. Moreover, this work identifies precise structural targets within the fungal cell wall that could guide the development of novel diagnostics and therapeutics against life-threatening fungal infections.

Fungal balls (aspergillomas) are a debilitating complication of chronic pulmonary aspergillosis, but their functional biology as multi-kingdom ecosystems is poorly understood. Through integrated multi-omics analysis of 61 patient-derived fungal balls, we reveal their complex ecology. While Aspergillus fumigatus dominates the fungal niche (59% of patients), bacterial co-colonization is ubiquitous, primarily by Pseudomonas aeruginosa and Haemophilus influenzae. Metabolomics and metatranscriptomics unveil a structured division of labor and active warfare, including metabolic cross-feeding, competition for iron, and reciprocal antagonism via secondary metabolites, such as fumagillin and fumigaclavine C produced by A. fumigatus. Host metabolomics and transcriptomics revealed a potent but dysregulated human immune response, characterized by neutrophil activation and failed resolution. Our findings redefine aspergilloma not as a mere fungal aggregate, but as a resilient polymicrobial biofilm across kingdoms, in which synergistic and antagonistic inter-kingdom interactions drive pathogenesis and chronicity, suggesting new therapeutic strategies targeting the pathogenic consortium.IMPORTANCEChronic pulmonary aspergillosis (CPA) and its hallmark fungal balls (aspergillomas) represent a debilitating and difficult-to-treat respiratory disease, affecting millions worldwide. Here, we provide the first integrated multi-omics profile of surgically resected fungal balls from 61 CPA patients, revealing these structures not as mere fungal colonies, but as resilient, cross-kingdom biofilms teeming with bacterial co-colonizers, particularly Pseudomonas aeruginosa and Haemophilus influenzae. Our findings uncover a dynamic battlefield where fungi and bacteria engage in metabolic cross-feeding, chemical warfare, and competition for nutrients such as iron. We demonstrate that the host mounts a potent but dysregulated immune response characterized by chronic neutrophilic inflammation and failed resolution, driving tissue damage and disease persistence. Our data provide a foundation for novel therapeutic strategies aimed at disrupting microbial synergy, modulating host inflammation, and breaking the cycle of chronic infection, an approach that could significantly improve outcomes for patients with this refractory disease.

Interferon epsilon (IFNε) is a unique type I IFN that, unlike other family members, is not induced by infection but is constitutively expressed in epithelial tissues. In this manuscript, we define the epithelial cell types that constitutively express IFNε in the uterus and small intestine at a single-cell resolution. We show that mice lacking IFNε lose key antiviral defenses in a tissue-dependent manner; uterine epithelial cells have diminished basal ISG expression, and key populations of cytokine-expressing enterocytes are absent from the small intestine. In the intestine, this correlates with increased susceptibility to infection with an enteric virus in mice. These findings establish IFNε as a key contributor to mucosal immunity, sustaining antiviral defenses within tissue-specific epithelial cells of both the female reproductive tract and intestine, and broaden our understanding of its role beyond traditional pathogen-induced interferon responses.

Vancomycin is a widely prescribed antibiotic used in the treatment of gram-positive bacterial infections. We previously showed that this antibiotic disrupted protective antifungal immune responses via microbiome dysbiosis, enhancing susceptibility to invasive candidiasis. Antibiotics are an independent risk factor for developing this life-threatening fungal infection, but whether microbiota-independent mechanisms also drive this association is not clear. Here, we show that vancomycin directly impairs macrophage responses to Candida albicans, the main causative agent of invasive candidiasis. Vancomycin-treated macrophages were less able to kill C. albicans despite normal phagocytosis rates and were hyper-inflammatory and more likely to die during infection. Using a fluorescently labeled vancomycin, we observed vancomycin uptake by macrophages in vivo and within close proximity to the mitochondrial outer membrane. Vancomycin treatment led to a significant depolarization, reduced respiratory capacity, and a hyper-fragmented morphology of mitochondria, as well as increased cellular ROS production. Taken together, this work demonstrates direct effects of vancomycin on mammalian immune cells, helping us to understand the pro-inflammatory effects of this drug and how it promotes susceptibility to life-threatening fungal infection.IMPORTANCEAntibiotics are widely prescribed drugs used to treat bacterial infections; however, their use may increase the likelihood of developing life-threatening fungal infections in vulnerable patients. Candida albicans is a commensal fungus in humans but may cause serious disease in patients with defined risk factors, including antibiotic exposure. We find that the antibiotic vancomycin significantly impairs the ability of macrophages to kill C. albicans yeast. Vancomycin-induced defects in fungal killing were associated with changes to mitochondria in antibiotic-exposed macrophages, which also exhibited enhanced oxidative stress and reduced survival during fungal infection. This work identifies a direct mechanism by which antibiotics may impair antifungal immunity.

Legionella pneumophila is the main cause of Legionnaires' disease, an increasingly prevalent pneumonia. Prior studies indicated that L. pneumophila expresses type IV pili, a common form of pili that is mainly known for mediating DNA uptake, twitching motility, and attachment to biotic and abiotic surfaces. By utilizing a variety of in silico and experimental approaches, wehave helped redefine the major structural component (pilin) of the L. pneumophila pili. More significantly, we uncovered a heretofore unknown and seemingly novel role for the pilin in L. pneumophila growth in low-iron conditions and iron acquisition/assimilation. These findings have broad implications for understanding other bacteria and infectious diseases, as well as offering fresh insight into the roles of pilins in bacterial physiology and the mechanisms of iron assimilation.

Streptomyces coelicolor A3(2) is a highly potent model antibiotic producer, with a chromosome harboring at least 20 secondary metabolite biosynthetic gene clusters (BGCs). Precise control of these multiple pathways is provided by a complex network of regulatory proteins and small signaling molecules. In this work, we show that coelimycin (CPK) and actinorhodin (ACT) production are exclusive processes. Induction of CPK synthesis by γ-butyrolactones inhibited ACT production when we simultaneously overexpressed the ACT upper activator protein AtrA; yet, this effect was not observed under overexpression of ActII-orf4-the direct activator of the ACT BGC and the direct AtrA target. We conclude that CPK intermediates inhibit the cascade of ACT induction at the level of AtrA pleiotropic regulator activity. Our proteomic data reveal that, besides being an ACT inducer, AtrA is a high-level regulator that activates arsenopolyketide synthesis but inhibits the production of undecylprodigiosin and calcium-dependent antibiotic. AtrA also downregulates primary metabolism of carbohydrates, lipids, and amino acids, along with the tricarboxylic acid cycle.IMPORTANCEBacteria from the genus Streptomyces possess one of the most complex gene regulation machineries in the bacterial kingdom, allowing them to coordinate production of multiple compounds at discrete timing. Navigating through these regulatory networks to unlock the biosynthetic potential is challenging. Expression of silent biosynthetic gene clusters (BGCs) often occurs only under strict culture conditions and, as in the case of coelimycin, can be coordinated via quorum sensing. Here, we have investigated the interplay between coelimycin and actinorhodin production in the model organism Streptomyces coelicolor A3(2). We show that even the products of BGCs can have a regulatory function. The richness of potentially competing biosynthetic pathways may hinder high-yield biosynthesis of the desired product under fermentation conditions. Our results show the importance of designing host organisms with lowered background regulation by γ-butyrolactones for the desired biosynthetic pathway activation.

The rising prevalence of invasive fungal infections, particularly among immunocompromised individuals, has become a critical public health concern. However, antifungal drug development has not kept pace with this growing need, and treatment options remain limited to a small number of drug classes. The emergence of multidrug-resistant fungal pathogens, such as Candida auris, further exacerbates this crisis by reducing the efficacy of existing therapeutics and increasing the risk of treatment failure. In this study, we evaluate the antifungal potential of FK20, a random peptide mixture (RPM) composed of L-phenylalanine and L-lysine. FK20 displays potent activity against C. auris and other clinically relevant Candida species, impairs biofilm formation, and exhibits synergy with caspofungin. Importantly, FK20 limits the emergence of resistance and demonstrates therapeutic efficacy in a murine model of systemic candidiasis. These findings establish RPMs as a promising new class of antifungals with broad-spectrum activity and clinical potential against drug-resistant fungal infections.

Although therapeutic antibodies had success in protecting vulnerable individuals from severe COVID-19 during the early stages of the pandemic, many lost effectiveness as SARS-CoV-2 accumulated mutations that compromised neutralizing activity. Our experiments show that antibody protection against SARS-CoV-2 strains can be enhanced by genetically engineering the Fc region or altering its N-linked glycosylation to improve interactions with FcγRs on host immune cells. Modified versions of S309, the parent of the clinically used sotrovimab antibody, more effectively reduce viral burden and inflammation in the lung and shape protective transcriptional responses, which, together, result in improved lung ventilatory function and outcome after SARS-CoV-2 infection. Thus, antibody engineering can serve as a strategy to enhance therapeutic activity against rapidly evolving viruses with the potential to escape neutralization.