Cell Host & Microbe

Sialic acids are abundant components of host- and diet-derived glycans in the human gut and serve as important nutrients that shape microbial fitness and interspecies competition. Excess free sialic acids are also linked to inflammation and pathogen susceptibility. While well-studied gut bacteria such as E. coli and Bacteroides spp. catabolize sialic acids via the NanAKE or NanLE-RokA pathways, the metabolic capacity of many microbiome members remains undefined. To identify sialic acid catabolizing bacteria, we cultured fecal samples from healthy human donors. The gut anaerobe Hungatella hathewayi was selected under sialic acid-supplemented conditions. H. hathewayi is a poorly characterized gram-positive Lachnospiraceae associated with long-lived individuals and purine metabolism. Here we establish that H. hathewayi grows robustly on sialic acids as a sole carbon source using a pathway homologous to the canonical NanAKE system of E. coli, despite the species phylogenetic distance. We functionally validated these orthologs through growth assays and heterologous complementation in E. coli knockout strains. Comparative analyses further showed that key catalytic residues in H. hathewayi NanA are conserved despite overall sequence divergence from E. coli. Additionally, we find that colocalized sialic acid transporters and regulatory proteins are not orthologous to E. coli proteins and instead are related to proteins from other gut anaerobes. Together, these findings expand our understanding of sialic acid utilization within the human gut microbiome. We identify H. hathewayi as an overlooked but capable sialic acid degrader that can contribute to modulation of gut sialic acid levels and related inflammation. ImportanceSialic acids play an important role in mammalian and microbial signalling. Excess free sialic acids increase susceptibility to gut pathogens and induce inflammation. Gut bacteria can both generate and consume free sialic acids, and these pathways are conserved across diverse bacteria. E. coli and B. fragilis consume sialic acids as a carbon source, decreasing free sialic acid levels. We identify H. hathewayi as another bacteria capable of sialic acid consumption and define the enzymes responsible. H. hathewayi is a prevalent member of the human gut microbiome, but it is not genetically tractable, limiting enzymatic characterization. H. hathewayi is enriched in the gut microbiomes of long-lived individuals and expected to be an important contributor to purine degradation to limit gout risk. Defining sialic acid catabolism in non-model species is essential to understanding the evolution and conservation of this pathway as well as how nutrient competition shapes gut microbiome composition.

Plants are colonized by a diverse microbiome, with microorganisms residing inside and outside of plant tissues. Plants can harness the protective traits of their microbial inhabitants to ward off insect pests and fungal pathogens. However, current understanding of the role of commensal interactions on activating the desired microbial genomic traits remains limited. Here we show that biosynthesis of the antifungal 2,5-dihydro-L-phenylalanine (DHP) by the endophytic Streptomyces sp. PG2 is strongly induced upon colonization of Arabidopsis thaliana. DHP production protects the plant from infection by the fungal root pathogen Rhizoctonia solani, both in vitro and in vivo.. We identified the DHP biosynthetic gene cluster (BGC) and showed that heterologous expression of the BGC in the DHP non-producer Streptomyces coelicolor also conferred plant-inducible DHP production. The BGC was also found in plant-associated Gram-negative bacteria, and in Pseudomonas syringae FF5 we again observed strongly enhanced DHP production upon plant colonization. An ecology-inspired elicitor screen showed that L-valine and brassinosteroid hormones elicit DHP biosynthesis in the plant-beneficial Streptomyces sp. PG2, while L-valine also elicited DHP biosynthesis in S. coelicolor. In vivo experiments confirmed the stimulation of antifungal activity in Streptomyces sp. PG2 by L-valine, while brassinolide mutant plants showed reduced DHP induction. Conversely, neither L-valine nor brassinolide elicited the expression of the DHP BGC in the pathogenic P. syringae, revealing important divergence in the responses to plant signaling, which may reflect selectivity in how endosymbionts and pathogens respond to host cues. Collectively, our data demonstrate that plant colonization can elicit the biosynthetic potential of root-associated microbes, thereby enhancing plant resilience.

Antibiotic tolerance paves the way for acquired resistance in bacterial pathogens. However, the mechanisms of tolerance and its evolutionary role in acquired resistance in pathogenic fungi, particularly molds, remains elusive. Here, we identified an Inhibitor of Growth domain protein (IngB) as a novel epigenetic regulator of azole tolerance in Aspergillus fumigatus. The loss of ingB promotes supra-MIC growth on agar surface despite susceptible MICs in standardized assays. Moreover, established {Delta}ingB biofilms are less susceptible to azoles in vitro and in vivo. Subsequent exposure of the tolerant strain to high azole concentrations resulted in rapid acquired resistance, most notably a frameshift mutation in a putative 20S proteasome maturation protein, UmpA, while the susceptible wildtype strain failed to acquire adaptive mutations. The data suggest that IngB-mediated tolerance provides an epistatic background for the emergence of azole resistance. Our work shows drug tolerance facilitates resistance emergence in a critical fungal pathogen. ImportanceWhile antimicrobial drug resistance causes a significant adverse effect on human health, drug tolerance can also lead to insufficient pathogen clearance, resulting in infection relapse. However, the mechanisms of antifungal drug tolerance and its evolutionary role in acquired drug resistance in pathogenic fungi, particularly the molds, remains elusive. We identified IngB as a novel regulator of azole tolerance in Aspergillus fumigatus. Importantly, loss of IngB leads to rapid azole drug resistance under azole-selective pressure. Our work identifies a novel regulator of antifungal tolerance and suggests antifungal drug tolerance can pave the way for resistance emergence in a critical fungal pathogen.

Candidozyma auris is an emerging multi-drug resistant fungal pathogen characterized by high mortality and rapid transmission in healthcare settings, but the genetic drivers of phenotypic variation between strains and the landscape of gene essentiality in this organism remain undercharacterized. Here, we integrate pangenomic analysis with global essentiality screening to establish a foundational understanding of the C. auris genome and identify potential therapeutic targets. We performed pangenome analysis on 695 outbreak strains of C. auris selected to be genetically representative of publicly sequenced genomes. After using BLAST to refine the pangenome, we found that 96.8% of gene families were core, with the remaining high-confidence accessory gene families primarily consisting of gene loss events or clade-specific genes. The high proportion of core genes emphasizes the clonal nature of these outbreak strains, but comparative analysis with the closely related C. haemuli species complex suggested that most of these core genes are functionally dispensible. To examine this hypothesis, we developed a novel insertional mutagenesis approach that leverages the promiscuous integration of linear DNA in the C. auris genome. This global analysis identified 614 high-confidence essential genes. Crucially, nearly one-third of these genes, including the conserved translation initiation factor Sui1, exhibit divergent essentiality patterns compared to the model yeasts Candida albicans and Saccharomyces cerevisiae. These findings highlight organism-specific biology that would be overlooked by orthology alone. By combining pangenomic diversity with functional essentiality, this study provides a comprehensive resource for identifying species-specific determinants of virulence and prioritizing novel targets for antifungal drug development.

How the microaerophilic Campylobacter jejuni grows in the inflamed gut is poorly understood, hampering our ability to identify novel targets for controlling infections by this pathogen. Our prior ferret study indicated that C. jejuni growth during infection is driven by intestinal inflammation. Without manipulating microbiota or introducing pro-inflammatory genetic lesions (or both), conventional mice are naturally resistant to C. jejuni colonization and infection. To test the impact of inflammation per se on C. jejuni infection, we induced transient intestinal inflammation in mice using short-term dextran sodium sulfate (DSS) treatment. The resulting colitis disrupted colonization resistance, enabling rapid C. jejuni growth in the murine colon within three days of infection, accompanied by exacerbated intestinal inflammation. DSS-induced colitis led to enrichment of mucin-degrading bacteria and depletion of taxa producing short-chain fatty acids and indole; metabolomic profiling confirmed a marked reduction in colonic indole levels in both DSS-treated and infected mice. At physiological concentrations, indole inhibited C. jejuni growth in vitro and resulted in reduced transcript levels from key energy-generating pathways, including nitrate respiration (napA), aerobic respiration (ccoN), lactate utilization (lctP), and the acetate switch (ackA/ptaA); consistent with this, mutations in these pathways led to fitness defects in DSS-treated mice, highlighting their importance for C. jejuni colonization in the inflamed gut. Moreover, treatment with indole or the indole-producing probiotic Escherichia coli Nissle 1917 significantly reduced C. jejuni colonization in vivo. Our findings show how C. jejuni establishes and grows in the inflamed gut and demonstrate that microbiota-derived metabolites play a key role in regulating C. jejuni pathogenicity. SignificanceThe mechanisms by which the microaerophilic pathogen C. jejuni proliferates in the inflamed intestine remain poorly understood. Using a DSS-induced colitis mouse model, we identify host physiological changes, microbiota alterations, and metabolic factors that promote C. jejuni colonization during intestinal inflammation. These findings provide mechanistic insight into why Campylobacter species are frequently detected in patients with Inflammatory Bowel Disease (IBD) and how infection can exacerbate intestinal inflammation and worsen disease symptoms. We further identify the microbiota-derived metabolite indole as a potent inhibitor of C. jejuni colonization, highlighting a potential metabolite-based therapeutic strategy to combat emerging multidrug-resistant C. jejuni infections.

The ocular surface is a mucosal tissue that is constantly exposed to environmental antigens and potential pathogens. Human microbiomes play a critical role in the balance of surveillance and inflammation at sites of colonization. Historically, the investigation of the ocular microbiome has been difficult due to its paucibacterial nature and the inhospitable environment of the ocular surface. Despite this, Corynebacterium mastitidis (C. mast) developed a unique ability to colonize the eye and elicit a protective immune response characterized by induction of IL-17 from {gamma}{delta} T cells and protection from corneal infection. Therefore, we sought to understand the unique bacterial machinery that C. mast utilizes to colonize the eye and how it affects the induction of an eye-specific immune signature. Using a C. mast transposon mutant library, we identified a mutant that completely lacked an ability to form biofilm, colonize the eye, and induce in vivo immunity. Whole genome sequencing revealed a disruption in the sortase F gene, which anchors proteins to the cell wall of C. mast, governing biofilm formation and tethering of adhesins to the cell surface. Additionally, we show that mutation in individual C. mast adhesins does not affect ocular colonization or immune induction. By understanding the molecular mechanism of ocular microbial colonization, this work advances our understanding of how bacteria colonize and induce immune responses on the eye, providing a foundation for developing novel therapeutic strategies against ocular infections.

Plant-associated microbial communities play a critical role in plant health and disease resistance, but the mechanisms which reshape these communities during pathogen infection are poorly understood. In this study, we investigated how infection of maize by the smut fungus Ustilago maydis is functionally linked with the bacterial phyllosphere microbiome and explored the role of an antimicrobial effector GH25 in fungal infection. Using a combination of culture-dependent and culture-independent approaches, we compared the leaf microbiomes of infected and uninfected plants. We observed a significant increase in microbial abundance and pronounced shifts in community composition and identified distinct health-associated (HCom) and disease-associated (DCom) bacterial communities. To assess whether U. maydis directly manipulates the microbiome, we tested the antimicrobial activity of the antimicrobial effector GH25 against isolated strains. Notably, all HCom bacteria were sensitive to GH25 and co-inoculation of HCom bacteria with a U. maydis {Delta}gh25 knockout mutant significantly reduced fungal virulence. In contrast, DCom exhibited minimal sensitivity to U. maydis and did not affect the virulence of U. maydis {Delta}gh25. Functional profiling revealed infection-associated shifts in predicted metabolic potential, consistent with U. maydis induced leaf tumors being strong sink tissues. Together, the data shows that U. maydis infection reshapes the maize phyllosphere microbiome through a combination of effector-mediated antimicrobial activity and host metabolic reprogramming.

Secreted mucins are the major component of the mucus layer that protects intestinal epithelial surfaces by blocking excessive interactions with the microbiota. Mucins are complex glycoproteins decorated with over 100 different O-glycans. Some bacteria can utilize mucins and excessive degradation has been associated with disruption of the mucus barrier and inflammation. Despite the importance of mucins, a detailed enzymatic pathway by which gut bacteria degrade colonic mucin O-glycans and the impact of this process on gut colonization are unknown. Here, we identified >100 genes that are expressed by the symbiont Bacteroides thetaiotaomicron during growth on different O-glycan substrates, revealing effects of glycan structure on gene expression. The characterization of 33 glycoside hydrolase enzymes revealed the pathway for colonic O-glycan degradation by this bacterium. In vivo competition experiments show that multiple exo-acting enzymes targeting mucin capping structures are central to gut colonization and may provide targets to inhibit bacterial mucin degradation.

The skin microbiome regulates key skin processes, yet the functional diversity of a dominant genus, Staphylococcus, remains poorly resolved at the strain level for multiple species across its pathogenic and commensal continuum. It is likely that Staphylococcus effects on skin are diverse at these finest taxonomic resolutions, but current skin models lack the physiological relevance and scalability needed to profile this diversity. Using an organotypic 3D human skin model (reconstructed human epidermis, RHE), we profiled skin responses to 187 Staphylococcus strains across seven dominant species. Canonically pathogenic species (e.g., S. aureus) induced broad inflammatory responses, whereas prototypical commensal species (e.g., S. hominis) elicited more nuanced effects on innate immune and skin barrier responses. Strikingly, S. epidermidis displayed pronounced strain-level heterogeneity, with subsets inducing either commensal or pathogen-like responses despite lacking canonical virulence factors, suggesting pleiotropic effects. Comparative genomics, dual-transcriptomics, untargeted metabolomics, and growth phenotyping revealed species- and strain-specific traits underlying these differential effects on RHE, including the presence of select cell surface proteins and differential arginine metabolism. Together, our study provides the first high-throughput, species- and strain-resolved analysis of skin-Staphylococcus interactions, offering mechanistic insights and a platform for microbiome-based strategies to modulate skin inflammation and diseases. One-line summaryHigh-throughput profiling of Staphylococcus in a human skin model shows that species- and strain-level diversity underlies a continuum of host barrier and immune responses.

The gut microbiome is essential for human health. Although the gut microbiota is largely stable at the species level in healthy individuals, strain-level variation remains less understood. Many bacterial strains encode toxin delivery systems that may shape competition within the gut. Here, we investigate how contact-dependent growth inhibition (CDI) and colicins influence intestinal colonization by a competitive murine Escherichia coli isolate, R12. We show that R12 can colonize an intact mouse gut microbiota by displacing resident Enterobacteriaceae, but success depends on multiple interacting factors. CDI systems and colicins provide a competitive advantage against resident E. coli, particularly during early colonization, while metabolic flexibility and access to alternative carbon sources support long-term persistence. Colonization outcomes vary between hosts and are shaped by resident microbiota composition, strain-level competition, and the initial invader-to-resident ratio. Overall, successful gut invasion is determined by the combined effects of bacterial antagonistic systems, metabolic capacity, and ecological context.

Candida glabrata is a leading cause of invasive candidiasis. The gut serves as its primary reservoir, yet factors governing colonization and pathogenic potential remain poorly defined. Here, we identify immunoglobulin A (IgA) as a key regulator of C. glabrata within the intestinal microbiome. We found that C. glabrata induces an IgA response in a strain-specific manner. Comparative transcriptional and proteomic analyses of IgA-inducing and non-inducing strains identified a putative adhesin, Awp11, whose expression correlated with IgA induction. Awp11 is directly targeted by IgA and is required for inducing C. glabrata-specific IgA and Th17 responses in vivo. Functionally, Awp11 promotes colonization of a complex intestinal microbiome, and intestinal IgA limits this advantage. In most strains, AWP11 transcription is dynamic and limited by IgA in the gut. This identifies Awp11 as a key determinant of strain-dependent immunogenicity and gut colonization that C. glabrata may dynamically regulate to balance colonization and immune evasion.

The role of the microbiota in facilitating infection is increasingly recognized, though the underlying mechanisms remain under investigation. In this study, we demonstrate that the gut microbiome, particularly Lactiplantibacillus plantarum, promotes enteric infection in Drosophila melanogaster by reshaping host physiology and immune responses. Upon gut colonization, L. plantarum enhances fatty acid (FA) production in the gut. Reducing FA synthesis improves host survival, and pathogen mutants deficient in FA utilization exhibit reduced virulence. FAs support pathogen growth, increase virulence, and enhance resistance to antimicrobial effectors, ultimately facilitating pathogen persistence in the gut. Persisting pathogens consequently overstimulate the immune system, leading to excessive production of antimicrobial peptides (AMPs). Flies lacking AMPs, particularly Metchnikowin and Attacin D mutants, show better survival during infection, implicating AMPs in immunopathology. Our findings identify a mechanism whereby microbiota-induced release of host FAs stimulates pathogen virulence and persistence, ultimately driving AMP-mediated immunopathology.

WD40 domains are major protein-protein interaction (PPI) scaffolds, yet their contributions to fungal pathogenicity remain poorly defined. We systematically analysed 94 canonical WD40 proteins in Cryptococcus neoformans. Conditional knockdown and sporulation identified 36 essential WD40 proteins, while in vitro and in vivo profiling of 103 signature-tagged deletion strains spanning 52 genes uncovered 31 pathogenicity-related WD40 proteins, including epigenetic and post-transcriptional regulators. We identified Wcp1, a dual-domain protein whose WD40-repeat and cyclophilin domains are required for growth at 37{degrees}C under 5% CO2. Its WD40 scaffold and PPIase domain supported CO2/heat tolerance and virulence. Notably, Wcp1 couples these functions to acidic pH adaptation: wcp1{Delta} failed to grow under elevated temperature and CO2 at acidic pH, exhibited enhanced intracellular acidification, reduced macrophage survival and attenuated virulence in Drosophila and mice. Integrated transcriptomic and proteomic analyses place Wcp1 at the centre of intracellular pH homeostasis, coordinating proton transport, metabolic adaptation and stress-buffering networks.

Candida albicans is a major opportunistic pathogen in humans that is capable of breaching mucosal barriers and causing severe systemic infections with high mortality. How the host controls mucosal infection and prevents dissemination remains unclear but is essential for improving disease outcomes. Here, we demonstrate that C. albicans induces specific IL-1 family members, which are critical for initiating mucosal protection by controlling antimicrobial peptides, IL-17, and neutrophil responses. Loss of combined IL-1 family signalling led to severe mucosal C. albicans infection, which was eventually resolved by a potent neutrophil response. However, in neutropenic conditions (a key risk patient factor) abolishing IL-1 family signalling resulted in C. albicans dissemination, predominantly to the liver, mirroring clinical disease and leading to mortality. This study highlights the IL-1 family as a key initiator of mucosal immunity, restricting mucosal invasion and cooperating with neutrophils to prevent life- threatening systemic infections.

MDA5 is a cytosolic pattern-recognition receptor (PRR) that binds to double-stranded RNA (dsRNA) and subsequently interacts with the signaling adaptor protein MAVS to initiate the antiviral interferon (IFN) response. Our group previously demonstrated that MDA5 is essential for host resistance against the fungal pathogen, Aspergillus fumigatus. Although fungal dsRNA was sufficient to activate MDA5 signaling, the precise source of A. fumigatus dsRNA responsible for this MDA5-stimulating function remains unknown. Here, we demonstrate that the magnitude of the IFN-dependent antifungal response is A. fumigatus strain dependent. Unexpectedly, we found that A. fumigatus isolates infected with dsRNA mycoviruses triggered a more robust MAVS-dependent inflammatory response within alveolar macrophages. Furthermore, dsRNA mycovirus infection increased fungal susceptibility to antifungal killing without altering other A. fumigatus growth characteristics. Although dsRNA mycovirus infection did not alter virulence in an acute bronchopneumonia model of A. fumigatus infection, it significantly impaired virulence and improved disease parameters in a chronic model of allergic bronchopulmonary aspergillosis (ABPA). Collectively, these findings reveal a novel role for trans-kingdom interactions in driving the host antifungal IFN response and modulating virulence in chronic aspergillosis models.

Hospital outbreaks caused by the fungal pathogen Candida parapsilosis are of growing concern due to their increased drug resistance and high mortality rates. However, the genetic bases of clinically-relevant traits in this species remain poorly explored. Here, we mapped genotype-phenotype relationships across 189 isolates from a multi-hospital Candida parapsilosis outbreak, for which we measured 61 diverse clinical phenotypes and generated complete genome sequences. As variation in previously-known genes explained little of the observed phenotypic diversity, we leveraged convergence genome-wide association studies and interpretable machine-learning models that predict phenotypes from genetic variants. These approaches identified candidate drivers of virulence and antifungal resistance, confirming expected mechanisms while uncovering novel ones. Predictive models were accurate for key traits, including azole resistance and clinical features of infected patients. Our results shed light on the genetic bases of clinically-relevant traits in a major fungal pathogen, and pave the way towards sequence-based diagnostics for improved patient outcomes.

The tuft cell-ILC2 amplification circuit has emerged as a central paradigm of anti-helminth immunity in laboratory animals, driving the so-called weep and sweep response, required for parasite expulsion. Yet soil-transmitted helminths (STHs) commonly establish chronic infections in humans. Whether tuft cell expansion is required for parasite clearance under naturalistic conditions remains unknown. Here, using wildlings, a naturalized mouse model exposed from birth to complex microbial communities and pathogens, we re-investigated anti-STH immunity in the context of ecological realism. Following infection with Nippostrongylus brasiliensis, specific pathogen-free (SPF) mice mounted markedly amplified type 2 responses in both lung and intestine compared to wildlings. In the intestine, SPF mice mounted robust tuft cell expansion, IL-25 production, ILC2 accumulation, and goblet cell hyperplasia. In contrast, infected wildlings exhibited delayed parasite expulsion, limited tuft cell expansion, reduced IL-25 and ILC2 responses, and attenuated goblet cell expansion. Wildling tuft cells, but not goblet cells, displayed markedly reduced expansion in response to succinate or exogenous IL-13, indicating selective hypo-responsiveness of the epithelial sensory compartment. Microbial transfer into adult SPF mice selectively conferred tuft cell hypo-responsiveness without impairing ILC2 accumulation or goblet cell expansion. Tuft cell hypo-responsiveness in wildlings and FMT recipients was associated with enrichment of fermentative bacteria and increased levels of the short chain fatty acids acetate and propionate. Together, these findings indicate that ecological microbial exposure imprints systemic type 2 immunity during early-life, whereas epithelial responsiveness remains plastic and microbiome-dependent, thereby revealing regulatory constraints not evident under SPF conditions. One Sentence SummaryOur findings reveal that in a naturalized immune-microbiome context, intestinal tuft cells are surprisingly hypo-responsive, highlighting how environmental microbial exposure can calibrate type 2 immunity and helminth resistance.

Clostridioides difficile infection (CDI) susceptibility and severity are strongly associated with preexisting colonic inflammation. However, chronic inflammatory conditions such as cystic fibrosis rarely progress to symptomatic CDI despite high rates of C. difficile colonization, suggesting that inflammation alone is insufficient to explain disease vulnerability. Notably, populations relatively protected from symptomatic CDI exhibit impaired regenerative capacity within the colon epithelium. Here, we used single cell RNA sequencing of human colonoid monolayers to map markers of CDI susceptibility and severity to cell populations associated with inflammation and epithelial repair. We identified an inducible microfold-like (M-like) population that is largely absent from the healthy colon but emerges during inflammation and regeneration. These cells were enriched for markers of severe CDI, C. difficile toxin interaction genes, and elevated CCL20 and CFTR expression. Spatial imaging localized CCL20-producing cells to wound-like gaps in mock and CDI-treated colonoids, identifying a repair-associated niche active independent of infection. Following exposure to C. difficile, wound-healing transcription within the M-like lineage declined while tuft-like populations expanded and upregulated genes associated with immune cell recruitment. These findings demonstrate that epithelial regeneration shapes host CDI vulnerability. IMPORTANCEClostridioides difficile infection can lead to severe illness and death in vulnerable populations despite available treatments. Clinical signs of inflammation during active Clostridioides difficile infection are strongly associated with disease outcome, yet these responses primarily reflect tissue damage already underway, limiting opportunities to prevent progression. In contrast, conditions linked to severe disease, including inflammatory bowel disease and antibiotic exposure, are associated with colonic inflammation before infection or at the time of diagnosis, highlighting an opportunity for earlier identification of high-risk individuals. Using human colonoid single cell transcriptomics and spatial imaging, we identified a microfold-like cell population enriched for inflammatory mediators and Clostridioides difficile toxin interaction genes linked to severe disease. This population was active even in the absence of infection, suggesting that repair-associated populations within the inflamed colon may help identify susceptibility to severe CDI before clinical progression occurs.

Bacteriophages are key drivers of microbial ecology and evolution, and the rapid expansion of phage sequencing has created sustained demand for curated reference genome databases. We released the INfrastructure for a PHAge REference Database (INPHARED) in January 2021 to provide quality-controlled metadata for complete phage genomes from cultured isolates. Here, we compare the 2021 and 2026 snapshots, spanning a five-year period that included a substantial overhaul of bacterial virus taxonomy by the ICTV. The database has approximately doubled, from 14,244 to 28,777 genomes, yet the proportion representing novel species-level diversity has declined, indicating that redundant sequencing is outpacing new discovery. Host bias persists despite the addition of 97 new host genera. We have incorporated genome quality assessments, lifestyle predictions, and defence and anti-defence system annotations, providing an updated resource and a snapshot of the current state of phage genomics.

The Streptococcus pneumoniae capsule is a major determinant of virulence, yet whether bacteria actively remodel it during infection remains unclear. Studying Swiss and South African clinical isolates (serotypes 1, 6B, 8, 12F, 19F, and 35B), we identified a rapid, tissue-specific response: capsule thickness increased within hours upon co-exposure to host cells and tissues. Only two 12F strains failed to thicken. Thickening was greatest in brain tissue, moderate in serum, and absent on the epithelium. This adaptation occurred independently of cod locus phase variation and nutritional factors, and was instead driven by a soluble, thermostable host signal (<3 kDa). Thickening correlated with neuroinflammation but did not require it, as it also occurred in contact with resting brain immune cells. It exacerbated meningitis in mice and enhanced bacteremia. Once induced, capsule thickening dampened inflammatory responses, coinciding with downregulation of pneumolysin, a major pro-inflammatory toxin. Genetic analysis of the non-thickening 12F isolates, together with targeted mutagenesis, identified two independent determinants of capsule-thickness modulation: a specific promoter-proximal element and SPD_0642, a conserved putative transporter encoded outside the capsule operon. Both contributed to the host-induced thickening phenotype. Pneumococci therefore rapidly remodel their surface in response to tissue-specific cues within the host, in a manner distinct from stochastic phase variation outside it. ImportanceMany bacteria are covered by a slimy outer layer, known as a capsule, that helps them evade the immune system. The amount of this layer can influence how easily harmful bacteria cause disease. Until now, scientists knew that bacteria can turn capsule production on or off through changes in their DNA. In this study, we show that Streptococcus pneumoniae, a common cause of serious infections, can also adjust its capsule in another way. It senses soluble signals from the tissues it enters, allowing it to recognize where it is in the body and to gradually change the thickness of its protective outer layer. This finding offers a new way of understanding how bacterial infections develop and may point to new treatment strategies.