npj Biofilms and Microbiomes最新文献

Viruses are integral yet underexplored components of coral holobionts, with their roles in shaping microbial diversity, modulating symbioses, and contributing to Darwin's paradox remaining largely unresolved. Here, we present the Global Coral Holobiont Virome Database (GCHVD), encompassing 76,755 viral contigs and 36,860 unique viral operational taxonomic units (vOTUs) identified from 36 coral species across 18 regions worldwide. The virome is dominated by Uroviricota, Nucleocytoviricota, Preplasmiviricota, and Artverviricota, with lytic lifestyles prevailing. Host identity emerged as the primary determinant of viral community structure, exerting a stronger influence than geographic factors. Extensive virus-microbe interaction networks revealed that viruses enhance biogeochemical cycling by augmenting host metabolic processes. Functional profiling uncovered a diverse repertoire of auxiliary metabolic genes (AMGs) associated with P, Fe, S, N, and CH₄ metabolism. Moreover, controlled microcosm experiments demonstrated that viral addition reshapes microbial community composition, enhances diversity, and drives elemental cycling within the holobiont. Together, these findings establish viruses as previously overlooked regulators of coral symbioses, orchestrating microbial dynamics, fueling nutrient fluxes, and sustaining reef productivity. Our work provides new insights into resolving Darwin's paradox from a viral ecological perspective.

Polymicrobial diseases, such as periodontitis, are shaped by microbial interactions and nutrient‑responsive metabolic adaptations. Here, we identify novel porphyrin pigments produced by Porphyromonas gingivalis in response to haemoglobin concentrations resembling those found in the gingival sulcus and periodontal pocket. Under these conditions, P. gingivalis develops a distinctive pink, highly fluorescent phenotype. Spectroscopic and mass‑spectrometric analyses revealed the accumulation of protoporphyrin IX (PPIX), manganese‑substituted PPIX (Mn‑PPIX), and haem. Deletion of the haemin‑binding protein gene fetB greatly reduced Mn‑PPIX production and fluorescence, whereas complementation restored both. Structural and biochemical characterisation demonstrated that FetB shares homology with bacterial metal chelatases and catalyses the insertion of metal ions into tetrapyrrole rings. Mn‑PPIX exhibited selective antimicrobial activity against several oral bacteria, including Streptococcus mitis, Streptococcus salivarius, Enterococcus faecalis, and oral Lactobacillus species, while other streptococci were resistant. These findings indicate that P. gingivalis modulates porphyrin metabolism in response to host‑derived haemoglobin, producing extracellular pigments with selective antimicrobial properties that may shape the oral community and promote dysbiosis. Targeting Mn‑PPIX production or limiting haemoglobin availability may offer new strategies to restore microbial balance and mitigate disease progression.

The oral microbiota plays a vital role in human health, yet most studies have focused on individual bacterial taxa. To provide a more comprehensive understanding, we analyzed tongue microbiota data from 729 Japanese individuals and classified samples into three types (orotypes): Neisseria-dominant (N), Prevotella-dominant (P), and Streptococcus-dominant (S) types. Each orotype exhibited distinct co-occurrence network structures and was associated with lifestyle factors such as oral care, diet, and smoking. The S type was associated with higher odds of abnormal oral health and metabolic syndrome-related outcomes compared to the N type. In addition, we developed a robust classification model (ROC-AUC > 0.95) to predict orotypes, which showed temporal stability in nearly half of individuals over a 6-year period. These findings highlight the value of orotype classification for monitoring tongue microbial communities and suggest its potential in health risk assessment.

The sustainability of poultry farming faces significant challenges due to rising feed costs and competition with human food sources. Dietary fibre offers a promising, cost-effective alternative due to its beneficial impact on gut health. We utilised a multi-omics approach to understand the influence of soluble inulin and insoluble cellulose dietary fibres on the composition and function of caecal microbiota in broilers. High inulin supplementation (4%) significantly altered caecal microbial composition and promoted broader microbial metabolic adaptations, indicating a strong fermentative response to this soluble fibre source. In contrast, high cellulose (4%) had a minimal impact, reflecting its limited fermentability and structural complexity. These findings provide valuable insights into how different fibre types and quantities shape gut microbial communities and their functional potential. A deeper understanding of these interactions will aid in formulating targeted dietary strategies to optimise gut health, nutrient utilisation, and overall poultry performance.

Socioeconomic status (SES) correlates with adverse health outcomes, but the underlying biological mechanisms remain unclear. We examined how area-level deprivation (Townsend Deprivation Index) influences gut microbiome composition and function and whether the gut microbiome mediates the effects of deprivation on metabolic and mental health. A total of 1390 females from TwinsUK with shotgun metagenomes were included in this study. We found that higher Townsend deprivation was associated with reduced alpha diversity (Beta [95% CI] = -1.60 [-3.00, -0.21]) and distinct microbial composition shifts (PERMANOVA P = 0.001). Twelve species and 22 functional pathways were linked to deprivation, distinguishing between deprivation groups (AUC = 0.725-0.744), with altered energy metabolism in deprived individuals. Townsend deprivation was associated with anxiety (OR [95%CI] = 1.09 [1.01, 1.18]) and diabetes (OR [95% CI] = 1.16 [1.03, 1.30]). Importantly, Intestinimonas massiliensis and Lawsonibacter sp_NSJ_51 partially mediate the effect of anxiety. Lawsonibacter sp_NSJ_51 also mediated the deprivation-diabetes association. These findings suggest that socioeconomic deprivation influences microbiome composition and function, mediating disparities in metabolic and mental health.

Marine animal epidermal surfaces act as a transitional viral habitat-an epidermal ecotone-between tissues and the environment, supporting diverse tripartite relationships between animals, microbes, and viruses, which have yet to be investigated. In this review, we synthesize the viral ecology of marine animal epidermal tissues, surfaces, and aura biomes to identify knowledge gaps and highlight the value of marine animal epidermis as a novel model system for microbiome research.

Intestinal pH influences microbiota composition and activity, yet its impact on microbial metabolite production remains elusive. Gut bacterial tryptophan catabolism yields metabolites with opposing health effects. Indole, a precursor of indoxyl sulfate (IS), is linked to chronic kidney disease (CKD), while indolelactic acid (ILA) and indolepropionic acid (IPA) have positive health effects. Analysis of fecal pH and tryptophan metabolites in two human cohorts revealed positive correlations between fecal pH, indole, and urinary IS, and negative correlations with ILA and IPA. Fecal indole and pH showed no correlation with fecal tryptophanase (tnaA) gene abundance. In vitro fermentations showed that low pH (5.5) inhibited indole production by E. coli, enhancing tryptophan availability for C. sporogenes to produce beneficial metabolites. Human fecal cultures confirmed pH-dependent tnaA gene repression and indole suppression. These findings highlight the role of pH as a key regulator of gut bacterial tryptophan metabolism with therapeutic relevance for CKD.

Maternal gut dysbiosis caused by inflammatory bowel disease during pregnancy can affect the gut health of the offspring by altering the composition of the gut microbiota, as well as immune function; however, the underlying mechanisms and potential for therapeutic intervention remain unclear. This study investigated the impact of maternal colitis on the gut health of offspring, and assessed the therapeutic potential of microbial manipulation. Offspring born to mothers with colitis exhibited gut microbial dysbiosis characterized by Lactobacillus spp. depletion, impaired barrier function, low-grade intestinal inflammation, compromised Wnt signaling, reduced crypt cell proliferation and diminished organoid-forming capacity, all of which increased their susceptibility to colitis in adulthood. Notably, early-life interventions such as fecal microbiota transplantation (FMT), targeted supplementation with Lactobacillus and cross-fostering during the postnatal period effectively reshaped the gut microbiota and reduced the risk of developing colitis later in life. These findings underscore the critical impact of the prenatal maternal gut microbial community on programming offspring intestinal barrier function and immune homeostasis, thereby influencing lifelong disease susceptibility. Moreover, the early-postnatal period represents a crucial therapeutic window in which microbial interventions like FMT can effectively mitigate gut dysbiosis and confer long-term protection against colitis.

Lactobacillus crispatus is a dominant member of the healthy vaginal microbiota, yet the mechanisms by which it modulates host immunity remain poorly defined, in part due to the lack of tractable in vivo models. Here, we integrate bacterial genetics, in vitro epithelial systems, human-derived data and proteomic approach (Olink®) to uncover a critical role for L. crispatus exopolysaccharides (EPS) in shaping the bacteria-vagina interactions. Comparative genomics identified a conserved EPS biosynthetic locus, with the priming glycosyltransferase gene epsE emerging as a regulatory node, in line with its distinct expression in human vaginal samples. Functional disruption of epsE abrogated L. crispatus EPS production and revealed its role for immune modulation. In human vaginal epithelial monolayers, EPS presence enhanced immune-regulatory (LAP TGF-beta-1) and anti-inflammatory (CST5) responses, whereas its absence triggered elevated pro-inflammatory cytokines (IL1β, IL6, IL8) and matrix metalloproteinase (MMP10). In a 3D vaginal organotypic model, EPS increased chemokines (CXCL5, CXCL6) linked to immune surveillance and the presence of the markers was validated in vaginal samples of healthy volunteers. These findings position EPS as a key immunomodulatory structure of L. crispatus, advancing our mechanistic understanding of host-commensal interactions and informing microbiome-based strategies to promote vaginal health.

The gut microbiota plays a vital role in host reproduction, yet its contribution to semen quality in boars remains unclear. In this study, we analyzed 556 boars from three commercial breeds and identified Muribaculaceae as a key microbial taxon positively associated with sperm quality, with the effect mediated by short-chain fatty acids (SCFAs). This association was validated in Yorkshire boars with extreme semen phenotypes. Fecal microbiota transplantation in mice confirmed that enrichment of Muribaculaceae improved semen quality, likely through enhanced SCFA production and reduced inflammation in the gut and reproductive tract. Furthermore, in vitro fermentation and mouse experiments demonstrated that a designed functional fiber selectively promoted Muribaculaceae, increased SCFA levels, and improved sperm quality. These findings suggest a functionally supported and potentially translational association between gut microbiota and boar fertility, suggesting that targeted dietary modulation of Muribaculaceae may represent a novel strategy to enhance reproductive performance in livestock.