Cell Host & Microbe

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.

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 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.

Dysbiosis and bacterial pathobionts contribute to inflammation in IBD and CRC, yet the molecular drivers of this process remain unclear. We identify the Klebsiella pneumoniae type VI secretion system (T6SS) as a key promoter of intestinal inflammation and tumor progression. Metagenomic analyses revealed enrichment of T6SS encoding genes in the gut microbiota of IBD patients during inflammatory flares. In zebrafish and mouse models, K. pneumoniae T6SS activity exacerbated inflammation and promoted colorectal tumor growth. Mechanistically, T6SS firing enhanced the secretion of LPS via outer membrane vesicles (OMVs), driving NF-{kappa}B activation and interferon signalling in host cells. In vivo, T6SS-dependent inflammation was associated with the expansion of regulatory T-cell subsets and an immunosuppressive tumor microenvironment. These findings redefine the T6SS as a microbial determinant of host inflammation and cancer progression, highlighting T6SS inhibition as a potential therapeutic approach for IBD and CRC. HighlightsO_LIT6SS-encoding Enterobacteria are enriched in the gut microbiota of IBD patients C_LIO_LIKlebsiella pneumoniae T6SS exacerbates colitis in mice C_LIO_LIT6SS activity enhances outer membrane vesicle secretion and LPS release C_LIO_LIT6SS promotes colorectal tumorigenesis and immune dysregulation C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/715367v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1c99341org.highwire.dtl.DTLVardef@e2d0eborg.highwire.dtl.DTLVardef@1021387org.highwire.dtl.DTLVardef@1502c97_HPS_FORMAT_FIGEXP M_FIG C_FIG

Root-knot nematodes are obligate plant parasites that cause substantial agricultural losses worldwide. They induce highly specialized, metabolically hyperactive feeding sites within host roots, which serve as their sole source of nutrients throughout their life cycle. The formation and maintenance of these feeding sites depend on the manipulation of host developmental pathways by nematode-derived secretions. Phytosulfokines (PSKs) are small plant peptide hormones that regulate cell division, tissue expansion, and growth responses, processes essential for feeding site development. Here, we identify root-knot nematode genes predicted to encode peptides with a conserved PSK functional motif. These genes are predominantly expressed during the early stages of infection and localize to secretory glands, suggesting a role in early parasitism. Moreover, silencing PSK-like gene expression reduces root gall formation and nematode reproduction. Together, these findings reveal that root-knot nematodes deploy PSK-like peptides as virulence factors to promote successful parasitism, providing the first report of PSK peptide mimicry in any plant pathogen.

During evolution, bacteria have developed the ability to interact intimately with eukaryotic hosts. These interactions span a dynamic continuum ranging from pathogenicity to mutualism, along which bacteria can rapidly evolve and shift their lifestyles. However, the molecular mechanisms that enable bacteria to adapt to new hosts and to transition between distinct interaction modes remain poorly understood. Here, using a unique combination of two independent evolution experiments, we identified and characterized parallel adaptive mutations in spoT, which encodes the bifunctional (p)ppGpp synthetase-hydrolase. These mutations promote the adaptation of the plant pathogen Ralstonia pseudosolanacearum to two distinct plant-associated environments and two distinct lifestyles, the xylem of both susceptible and tolerant host plants as a pathogen and the root nodules of a legume as a symbiont, without compromising virulence on susceptible hosts. These mutations enhance the utilization of multiple carbon and nitrogen sources, including substrates known to be abundant in xylem sap, and increase bacterial exponential growth rate in minimal medium, suggesting reduced basal (p)ppGpp levels. Assessment of a strain deficient in SpoT synthetase activity confirmed that lowering basal (p)ppGpp levels is adaptive in both plant environments. Together, our findings reveal that fine-tuning intracellular (p)ppGpp concentrations represents an efficient strategy for optimizing bacterial adaptation to complex host-associated environments.

Monosaccharides support Salmonella enterica serovar Typhimurium colonization of the gut, yet the role of their oxidized derivatives remains understudied. Sugar acids are largely diet-independent carbon sources generated by host-driven oxidative processes, but their contribution during infection - particularly that of less oxidized aldonic and uronic acids - has not been defined. Here, we systematically assess the role of sugar acids derived from D-glucose and D-galactose in S. Typhimurium SL1344 colonization. Among D-glucose-derived acids, D-gluconate accumulated to the highest levels and was the dominant substrate supporting luminal expansion in streptomycin-pretreated mice, exceeding the more oxidized acids D-glucuronate and D-glucarate. During chronic infection, D-glucose-derived sugar acids became increasingly important for pathogen persistence. Ecological niche invasion assays identified these compounds as a principal metabolic niche, whereas D-galactose-derived acids contributed minimally. Consistent with a transient, inflammation-linked nutrient niche, sugar acid utilization pathways were similarly prevalent in Escherichia coli from individuals with and without inflammatory bowel disease. Together, these findings identify D-gluconate as a key inflammation-dependent nutrient source that fuels Enterobacteriaceae expansion in the inflamed gut.

Aspergillus fumigatus, an opportunistic human fungal pathogen, encodes numerous secondary metabolite biosynthetic gene clusters (BGCs) that are tightly regulated and often remain silent under standard conditions. Co-cultivation with Streptomyces rapamycinicus or treatment with the secondary metabolite from this species, the arginoketide azalomycin F, induce the otherwise silent fumicycline (fcc) BGC of A. fumigatus. To elucidate the underlying regulatory circuitry, we performed transcriptome analyses of A. fumigatus exposed to azalomycin F or co-cultured with S. rapamycinicus. Both conditions triggered a coordinated antibacterial response, characterized by induction of specific secondary metabolites and antibacterial effectors, alongside repression of other BGCs, including those for fusarinine C, pyripyropene A, and fumagillin. Among the most strongly induced genes was a zinc cluster transcription factor, designated SmpR for secondary metabolite multiple pathway regulator, which is conserved within Ascomycota. SmpR expression was selectively induced by azalomycin F, specific Streptomyces species and other bacteria isolated from soil such as Kribbella spp. and Arthrobacter spp.. Functional analyses revealed that SmpR is required for activation of the fumicycline BGC: its deletion reduced, whereas its overexpression enhanced fumicycline production independently of external stimuli. We further demonstrate that SmpR acts upstream of the pathway-specific regulator FccR and additionally controls multiple antibacterial BGCs, including those for hexadehydroastechrome, helvolic acid and xanthocillin. Together, our data identify SmpR as a key regulator coordinating antibacterial secondary metabolism in response to bacterial signals in A. fumigatus.

Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterium with high intrinsic antibiotic resistance, requiring innovative therapeutics. During infection, smooth and rough colony morphotypes can coexist in the human body, participating in the pathogenesis. Despite its increasing clinical importance and phage therapy being a last resort treatment recently, the genetic basis of phage interaction in M. abscessus remains poorly understood. Previous work has focused largely on rough strains or the surrogate host Mycobacterium smegmatis. Here, we isolated novel phages that efficiently infect both morphotypes, allowing us to characterize phage-resistant mutants from paired smooth and rough clinical isolates to determine the genetic basis of the infectivity. Integrating whole-genome sequencing, transcriptomics, and phage susceptibility and adsorption assays, we deeply analyzed 30 phage-resistant variants and found that resistance trajectories were shaped primarily by host morphotype rather than by the selecting phage. We confirmed the TPP locus as a conserved determinant of phage infection in both morphotypes and identified previously undescribed hotspot mutations in furB and nrnA, together with a multi-gene deletion, in smooth-derived resistant variants. Whereas the TPP locus and the multi-gene deletion represent stable genomic changes affecting lipid-associated loci, frameshift mutations in furB and nrnA, not previously linked to lipid metabolism, were accompanied by broad transcriptional rewiring of lipid-related genes. Resistance was mutation-dependent and consistently associated with impaired phage adsorption, indicating an early block in infection. Together, these findings show that phage recognition in M. abscessus is shaped by mycomembrane lipid architecture rather than a single dedicated receptor and uncover regulatory and metabolic pathways with implications for more durable phage-based therapies.

During chronic lung infections, Pseudomonas aeruginosa diversifies under selection from antibiotics, metabolic constraints, and host defenses. Macrophages are key sentinels of the innate immune system and play a central role in clearing airway pathogens. Yet, how they process heterogeneous bacterial populations remains poorly understood. Here, we investigate how P. aeruginosa evades phagocytosis under conditions that mimic chronic infection. We use an attenuated mutant lacking a functional type III secretion system (T3SS), which reduces macrophage killing, allowing us to isolate determinants of bacterial susceptibility to phagocytosis. Using transposon insertion sequencing (Tn-seq), we identify bacterial fitness factors under phagocytic selection. Our screen reveals that disruption of genes involved in swimming and twitching motility reduces uptake by macrophages. We find that motility defects interfere with the physical interactions between bacteria and macrophages. Live-cell imaging shows that motility-deficient bacteria exhibit reduced surface exploration and unstable attachment to macrophages, limiting their internalization. Clinical isolates with reduced swimming or twitching motility display similarly impaired uptake. Restoring T3SS activity in these motility mutants rescues cytotoxicity toward macrophages, with one notable exception: flagellum-less, hyper-piliated P. aeruginosa remains avirulent and resistant to phagocytosis due to their lack of engagement with macrophages. Together, these results support two distinct immune evasion strategies: during chronic infection, reduced motility promotes a "freeze"-like state that limits detection and engulfment, whereas during acute infection, P. aeruginosa adopts a "fight"-like strategy by activating its T3SS to eliminate macrophages. SummaryHow immune cells recognize and eliminate bacteria is typically explained by molecular signaling, yet the role of physical interactions remains unclear. We show that bacterial motility is a key determinant of phagocytosis by macrophages. Using functional genomics and live imaging, we find that swimming and twitching motility promote bacterial uptake by enabling effective surface exploration and stable physical engagement with macrophages. Loss of motility commonly observed in chronic P. aeruginosa infections reduces these interactions and allows bacteria to evade engulfment. In contrast, during acute infection, bacteria rely on T3SS-mediated killing of macrophages, independently of motility. These findings reveal that phagocytosis is governed not only by immune recognition but also by bacterial mechanical behavior, and identify a shift in host-pathogen interactions associated with chronic versus acute infection. More broadly, this work establishes mechanics as an important dimension of immune evasion.

The liver receives microbe and host signals from the intestine via the portal vein, and thus connects the gut to systemic physiology. Homeostatic control of the timing of systemic responses is critical to prevent the expansion and dissemination of gut microbes and to mitigate untoward effects from prolonged systemic inflammation, however these mechanisms remain enigmatic. Here, to determine the role of the liver in coordinating systemic immune responses to enteric infection, matched measurements of global gene expression profiles were collected from the murine liver and intestinal epithelium throughout the course of enteric infection and clearance of Citrobacter rodentium, a mouse model of infectious colitis. These data revealed metabolic suppression in the liver during the peak of infection and a long-lived immune signaling pattern in the colon associated with CD4 and CD8 T cell infiltration that persisted beyond the clearance of infection. Furthermore, an early inflammatory signal was detected in the liver that resolved before the peak of disease and pathogen colonization. This self-limited, early signal depended on the pathogens virulence program and correlated with the timing of a corresponding systemic response, including circulating TNF- and IL-6, key mediators of acute-phase proteins. These results uncover the temporal pattern of hepatic changes in response to the course of intestinal infection and provide correlative evidence that an early pulse of gene expression in the liver coordinates and limits the duration of the systemic acute-phase protein response. Author summaryLocalized infections can trigger systemic inflammatory responses that help limit infection. However, prolonged systemic inflammation risks tissue damage and disease. Thus, the timing of systemic immune reactions is critical to the balance between immunity and damage. Yet, knowledge of the pathways that link gut-localized infections to systemic immune tone is limited. Since the liver is anatomically central to the connection between the gut and circulatory systems, we hypothesized that monitoring the kinetics of liver gene expression throughout the natural course of an intestinal bacterial infection would provide a valuable resource and yield insight into the control of systemic immune tone. Critically, we identified a burst of liver cytokine signaling that occurred and resolved before peak pathogen burden and disease in the colon and predicted the circulating inflammatory response. We propose that this early and self-limited signal from the liver coordinates the timing of the systemic response, ensuring it occurs early enough to promote immunity and resolve before causing tissue damage.

T helper 17 (Th17) cells are a critical T lymphocyte subset involved in mucosal immunity and host defense against enteric pathogens. Although ketogenic diets (KD) and the major ketone body {beta}-hydroxybutyrate (BHB) reshape gut microbiota and suppress Th17 responses under defined diet conditions, it remains unclear whether elevation of BHB alone, independent of dietary macronutrient composition and systematic metabolic shift, is sufficient to remodel Th17-inducing commensals and alter host susceptibility to enteric infection. Here, we used 1,3-butanediol (BD), a precursor metabolized to BHB independently of KD, to elevate systemic BHB levels in mice. BD treatment significantly reduced the frequency of ileal Th17 cells, as assessed by flow cytometry for Th17 markers IL-17A and ROR{gamma}t. 16S rRNA gene sequencing revealed that BD altered gut microbial community structure, as indicated by beta-diversity analysis based on Bray-Curtis dissimilarity, and reduced Shannon diversity and evenness. Linear discriminant analysis effect size identified segmented filamentous bacteria (SFB) as significantly decreased in the ileum following BD treatment, and SFB abundance positively correlated with Th17 markers. Microbiota transplantation demonstrated that BD-shaped microbiota was sufficient to suppress Th17 responses in recipient mice, accompanied by reduced SFB abundance. In a Citrobacter rodentium infection model, BD treatment was associated with increased pathogen burden, and fecal C. rodentium levels were negatively correlated with SFB abundance. Together, these results indicate that BD-induced elevation of BHB reshapes commensal microbiota, including decreasing SFB levels, resulting in dampened Th17 responses and increased susceptibility to enteric infection. IMPORTANCEDiet is a key determinant of gut microbial composition and mucosal immune function, yet the microbial mechanisms linking how diet-mediated changes to metabolism regulate immune responses remain incompletely understood. Th17 cells play central roles in both protective mucosal immunity and inflammatory pathology, making them a critical target of immunometabolic regulation. In this study, we show that {beta}-hydroxybutyrate (BHB), generated independently of diet, suppresses intestinal Th17 responses by reshaping the gut microbiota, reducing SFB levels, a potent Th17-inducing murine commensal. We further demonstrate that BHB-associated microbiota changes are linked to increased susceptibility to enteric infection. This work provides a mechanistic framework illustrating how metabolic state can influence host immunity through selective effects on commensal microbes. These findings inform future studies of microbiota-mediated immune regulation.

Successful gastrointestinal colonization (GI) by bacterial pathogens requires adaptation to nutrient competition and host-derived stresses in the gut, with adaptation via the bacterial stringent stress response playing a critical role. Epidemiological data suggest that the GI tract serves as a reservoir from where K. pneumoniae can spread and cause invasive disease or transmit to another host. DksA is a conserved stringent response transcriptional regulator that was identified in an in vivo transposon mutagenesis screen as an important K. pneumoniae gut determinant. However, its role in K. pneumoniae pathogenesis and gut colonization remains uncharacterized. Here, we demonstrate that DksA is required for survival against membrane-targeting antibiotics, consistent with a role in cell envelope stress tolerance. In addition, DksA positively regulates capsule biosynthesis gene expression and hypermucoviscosity and is essential for robust biofilm formation. Using a murine model, we show that DksA functions as a determinant of GI colonization independently of the resident gut microbiota. Furthermore, we demonstrate that DksA is important for environmental survival and transmission by regulating RpoS, thereby providing a mechanistic link between the stringent stress response, environmental survival, and subsequent transmission. Together, these findings establish DksA as a central integrator of the stringent response, coordinating membrane stress resistance, virulence traits, and gastrointestinal colonization in K. pneumoniae. ImportanceK. pneumoniae, a pathobiont, is responsible for multidrug-resistant infections and poses a major threat in hospital settings as well as community-acquired invasive infections. The bacterium tightly coordinates its virulence-associated traits to adapt to diverse environmental conditions and survive; however, the regulatory mechanisms remain poorly understood. In this study, we demonstrated that the conserved stringent response regulator DksA contributes to bacterial membrane stability, thereby affecting antibiotic resistance, inherent virulence, and persistence traits of K. pneumoniae. Additionally, DksA was identified as required for gut colonization, environmental survival through dysregulation of RpoS, and transmission to a naive host. These results enhance our overall understanding of the K. pneumoniae stringent response and will provide new avenues for controlling K. pneumoniae infections.

Bacteria encode diverse antiphage defense systems, yet mechanisms that target RNA phages remain comparatively underexplored. Here, we used a cDNA-based functional selection strategy to systematically identify genes that confer resistance to RNA phage infection independently of receptor variation in Pseudomonas aeruginosa. This approach uncovered previously uncharacterized antiphage defense systems, most of which are located within genomic islands, consistent with their being bona fide components of bacterial immune systems. Several systems conferred selective resistance to RNA phages and their carriage was associated with pilin variability, suggesting layered anti-phage immunity. Among these systems, Zws is the most prevalent RNA phage defense system and functions as a multidomain effector. Structural modeling and in vitro cleavage assays showed that ZwsA is an RNA endonuclease that selectively cleaves RNA phage genomes through a predicted NERD domain. Together, these findings expand the current framework of bacterial antiphage immunity and highlight the power of functional genomics to uncover cryptic components of the bacterial antiviral arsenal. IMPORTANCEBacteria harbor a broad repertoire of antiphage defense systems, but our understanding of mechanisms that target RNA phages remains limited, being heavily biased toward defenses against DNA phages. By applying a cDNA-based functional selection strategy, this study overcomes a major obstacle in defense-gene discovery and uncovers previously uncharacterized genes that represent bona fide components of the bacterial immune arsenal against RNA phages. The identification and characterization of Zowangsin (ZwsA), a NERD-domain RNA endonuclease that selectively cleaves specific signatures within RNA phage genomes, establish targeted RNA degradation as a central principle of bacterial defense against RNA phages. More broadly, this work expands the conceptual framework of bacterial antiviral immunity and illustrates the utility of functional selection for uncovering cryptic immune systems with implications for phage biology, RNA biology, and biotechnology. HIGHLIGTHSO_LIcDNA-based functional screen identifies six defense systems that restrict RNA phages C_LIO_LIThese defense systems are enriched within genomic islands of Pseudomonas aeruginosa C_LIO_LIZws, Szs, and Mws systems confer selective defense against RNA phages C_LIO_LIZwsA is a signature-selective RNA endonuclease that targets phage genomic RNA C_LI

Limited resource availability in the gut promotes competitive interactions between bacteria, which drive adaptive within-host evolution (1-3). While adaptive evolution of bacterial communities has been increasingly studied in the recent years (4-7), its functional implications for host physiology remain unknown. Here, we show that within-host evolution of the human commensal Enterococcus faecalis boosts colonization resistance to enteric Salmonella enterica serovar Typhimurium (S. Typhimurium) infection. During gut colonization, E. faecalis evolves the ability to metabolize fructoselysine, an abundant Amadori rearrangement product generated by thermal food processing. The depletion of this diet-derived nutrient prevents S. Typhimurium colonization by restricting an essential resource. This protective mechanism was conserved across independent mouse colonies and arises via diverse evolutionary trajectories, including nucleotide polymorphisms, gene amplifications, and a horizontal gene transfer event. Additionally, analysis of E. faecalis isolates from human infants revealed that adaptation to fructoselysine availability occurs in a diet-dependent manner. Isolates from infants fed with fructoselysine-rich formula were able to utilize fructoselysine, whereas those from infants fed with fructoselysine-poor breast milk were not. Conclusively, our results identify an inherent microbiome-driven self-healing mechanism, wherein bacterial evolution restores colonization resistance against enteric pathogens through evolved nutrient depletion. Understanding these evolutionary dynamics will inform microbiome-targeted approaches to prevent and treat infectious diseases by harnessing adaptive bacterial metabolism.

Mycoviruses are widespread in fungi, yet their diversity and host associations remain poorly explored in many lineages, including smut fungi. Here, we report the discovery of the first eight novel RNA viruses infecting the Brassicaceae-associated smut fungus Thecaphora thlaspeos. Using transcriptomic datasets derived from fungal mycelium and host plant controls, we identified dsRNA viral genomes supported by consistent read abundance, high genome coverage, and codon usage patterns closely matching those of the fungal host. All genomes are monosegmented and bicistronic, encoding capsid protein and polymerase genes in compact arrangements. Genome annotation and phylogenetic analyses based on the predicted RNA polymerase classified these viruses within the genera Totivirus and Eimeriavirus. Comparative analyses across fungal strains revealed intraspecific variation in virome composition, suggesting that host genetic background may influence viral community structure and that multiple dsRNA infection is common. Together, these findings expand the known diversity of mycoviruses in Ustilaginomycotina and identify T. thlaspeos as a host of a complex RNA virome. This work establishes a foundation for future studies on virus prevalence, transmission, and potential impacts on fungal biology and plant pathogenesis.

Despite the established association between the gut microbiome and colorectal cancer (CRC), the functional distinction between microbial passengers and drivers of CRC progression remains unresolved. Here, we collected stool, blood, as well as paired tumor, and normal mucosa tissues from seventy-seven CRC patients to characterize the systemic and localized impact of the gut microbiome on early- and late-stage CRC. By deep shotgun metagenomic sequencing, we identified distinct bacterial species and functions residing in tumor versus normal mucosa, highlighting an enrichment of oral-associated bacteria in tumor tissues. Several of these species remained undetected in the stool microbiome analysis. We further combined bacterial culturing with untargeted metabolomics of bacteria enriched in tumor and normal mucosa tissues, revealing distinct clusters of metabolic potential. Functional testing of multiple members from one cluster comprising both tumor- and mucosa-enriched species revealed Leptotrichia wadei as a pro-tumorigenic bacterium in a murine CRC model. Single-nucleus RNA sequencing and in vitro experiments further demonstrated that L. wadei and its secretome induces M2 macrophage polarization to promote tumor growth. Overall, our study shows that metabolic specialization structures microbial colonization niches, while species-specific metabolic outputs identify functional drivers of CRC progression, and uncovers L. wadei as an oncogenic bacterium in CRC.

Allergic diseases are heterogeneous conditions shaped by immune pathways and environmental influences, including the gut microbiome. Using cross-sectional data from 508 adults in the KORA FF4 cohort (275 with IgE sensitization, 233 without), we provide a multimodal statistical analysis of deep IgE profiles and concomitant gut microbial amplicon sequencing variant (ASV) data. We identified three latent allergy components in the cohorts IgE profiles that reflects food, pollen, and house dust mite markers and enables interpretable stratification of the cohort. Contrary to prior studies, microbial diversity did not differ between sensitized and non-sensitized individuals across all cohort strata. Differential abundance analysis identified 61 ASVs, with enrichment in Bacteroidaceae, Oscillospiraceae, and Veillonellaceae families, and depletion in the Lachnospiraceae family. Microbial network analysis further identified altered family-level associations in pollen- and food-sensitized individuals. Taxon set enrichment highlighted folic acid- and vitamin A-producing taxa, with consistent signals from Prevotella copri (depleted) and Bacteroides massiliensis (enriched). Together, our analysis points toward specific microbial families and metabolic groups as correlates of IgE sensitization in an adult population. HIGHLIGHTSO_LIIgE sensitization clusters reflect allergen sources and cross-reactive proteins C_LIO_LIThree latent allergy components capture the IgE profile structure of the entire cohort C_LIO_LIDistinct IgE patterns are linked to changes in taxa compositions and associations C_LIO_LIFolic acid- and vitamin A-producing taxa are enriched in IgE-sensitized individuals C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/714318v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1d1c8fborg.highwire.dtl.DTLVardef@1e1fea7org.highwire.dtl.DTLVardef@1589fcorg.highwire.dtl.DTLVardef@160282_HPS_FORMAT_FIGEXP M_FIG C_FIG

RumC1 is a structurally unique bacteriocin with broad-spectrum efficacy, including against multidrug-resistant pathogens, yet acting by an undefined mechanism. By integrating genetics, biochemistry, computational modeling and single-cell fluorescence microscopy, we demonstrate that RumC1 is a distinct cell-wall-targeting toxin. First, all RumC1-resistant mutants isolated through a high-rate, genome-wide mutagenic screening exhibited specific impairments in peptidoglycan homeostasis regulation, pinpointing this pathway as critical for RumC1 activity. Second, RumC1 selectively accumulates within neosynthesized peptidoglycan, leading to cell growth arrest and death in a dose-dependent manner. Third, we characterize the RumIc1 immunity protein of the RumC1 biosynthetic cluster as a peptidase acting at the cell surface to protect the cells by trimming the stem peptide crucial for cell-wall assembly. As such, RumIc1 provides cross-protection against vancomycin, while RumC1 is demonstrated to act differently from this glycopeptide antibiotic. Collectively, these findings establish RumC1 as a toxin targeting a key peptidoglycan intermediate of cell wall maturation.