npj Biofilms and Microbiomes最新文献

The gut microbiota influences host metabolism, immunity, and organ physiology, making it an attractive therapeutic target. However, clinical probiotic trials often produce inconsistent results, reflecting context-dependent effects shaped by metabolic, ecological, dietary, and host-specific factors. We critically synthesized the literature on hyperoxaluria, a condition of elevated urinary oxalate associated with kidney stones and chronic kidney disease, as a mechanistically tractable model for probiotic development. We examined evidence from clinical studies, microbiome analyses, and mechanistic experiments to identify factors influencing efficacy, with a focus on Oxalobacter formigenes, a specialist oxalate-degrading anaerobe. Across trials, probiotic success depended less on dose, strain identity, or persistence, and more on the ecological context - particularly the baseline abundance of oxalate-degrading genes (oxc, frc) in the native microbiota. Efficacy was highest when these metabolic niches were vacant. Diet, delivery format, and broader microbial community structure also shaped outcomes. A taxon-centric approach is insufficient for predicting probiotic efficacy. We propose a three-phase framework for rational design: (1) case-control microbiome studies to identify metabolically relevant deficits; (2) mechanistic in vivo and in vitro validation to establish causality; and (3) complex systems modeling to predict context-specific responses. This metabolism-first, ecology-grounded strategy is generalizable to other microbiota-linked conditions and supports precision microbial therapeutics.

Given the increasing demand for sustainable agricultural solutions utilizing the microbiome, particularly the use of biofertilizer (BF), it is essential to understand the mode of action and the role of predatory protists, along with their interactions with biocontrol strains and resident community members. We therefore examined these interactions through a long-term field experiment and a series of greenhouse and pot experiments. In field and greenhouse studies, we observed that Bacillus significantly stimulated the growth of Cercomonas, a genus of predatory protists, in the soil. In turn, these protists promoted the growth of Bacillus, leading to increased detection of polyketide synthase (PKS) genes and the inhibition of bacterial wilt pathogen Ralstonia solanacearum. We here reveal a positive feedback loop between the biocontrol agent Bacillus and predatory protists, which explains the biofertilizer-induced reduction of plant pathogens. These findings highlight the significance of synergistic interactions between functional microbes and predatory protists in suppressing soil-borne diseases. Moreover, it underscores the potential of incorporating predator-prey interactions into agricultural practices to foster more sustainable ecosystem development.

Rhizosphere microbiomes play an essential role in promoting plant growth and health. Although host genotype is known to shape rhizosphere microbial communities, it remains unclear whether core microbial taxa can persist across genetically diverse hosts and contribute to plant performance. Here, we conducted a large-scale analysis of 1005 rhizosphere samples from 335 maize populations to investigate the effects of host genetic variation on rhizosphere microbiota. We observed significant genotype-dependent variation in both bacterial and fungal community diversity and composition. However, community assembly was predominantly governed by stochastic processes, suggesting an evolutionary conservation of rhizosphere microbiota across genotypes. Based on the hypothesis that core microbes may consistently associate with maize independent of genotypes, we identified a core bacterial taxon, ASV245 (Pseudomonas sp.), which was consistently enriched across all maize genotypes. The corresponding strain, designated as WY16, was isolated from maize roots and significantly promoted both stem and root growth by activating maize hormone signaling pathways. These findings highlight the persistence and functional roles of genotype-independent core microbes, deepening our understanding of plant-microbiome interactions and providing new insights for microbiome-based strategies in sustainable agriculture.

Very early onset inflammatory bowel disease (VEO-IBD) is a clinically distinct form of IBD manifesting in children before the age of six years. Disease in these children is especially severe and often refractory to treatment. While previous studies have investigated changes in the fecal microbiome and metabolome in adult and pediatric IBD, insights in VEO-IBD remain limited. This multi-omics analysis reveals changes in the fecal microbiome and metabolome in children diagnosed with VEO-IBD compared with age- and sexmatched healthy controls. Untargeted metabolomics analysis identified a depletion of short-chain N-acyl lipids and an enrichment of dipeptides, tripeptides, and oxo bile acids in children with VEO-IBD. Differential abundance analysis of 16S rRNA sequencing data showed lower abundance of beneficial bacteria such as Bifidobacterium and Blautia, and higher abundance of Lachnospira, Veillonella, and Bacteroides in VEO-IBD. Multi-omics integration revealed associations between the altered gut microbiome composition and metabolic dysregulation, specifically for the N-acyl lipids. This study offers unique insight into fecal microbial and metabolic signatures in VEO-IBD, paving the way for a better understanding of disease patterns and thereby more effective treatment strategies.

Peripartum dairy cows are highly susceptible to metabolic disorders, with ketosis being the most prevalent postpartum disease associated with rumen microbial dysbiosis and systemic inflammation. However, the mechanisms by which microbial alterations compromise rumen epithelial integrity remain poorly understood. Using peripartum cows with ketosis as a model, we demonstrated that perturbations of rumen microbiota disrupt tryptophan metabolism, resulting in pronounced depletion of indole-3-acetic acid (IAA). The loss of IAA-producing taxa (Lactobacillus and Bifidobacterium) contributed to reduced IAA levels and epithelial barrier dysfunction, whereas enrichment of proinflammatory taxa (Candidatus Saccharimonas and Mycoplasma) was associated with exacerbated epithelial inflammation. In vitro, IAA supplementation activated the AhR/IL-22 signaling pathway, promoting bovine rumen epithelial cells (BRECs) regeneration and restoring barrier integrity. These findings identify the microbiota-IAA-AhR/IL-22 axis as a key regulator of rumen epithelial homeostasis and suggest that targeting this pathway represents a promising strategy to prevent metabolic disorders in dairy cows.

The quorum-sensing molecule 3,5-dimethylpyrazine-2-ol (DPO), known for regulating biofilm formation in Vibrio cholerae, has unknown distribution among commensal bacteria. We screened 37 bacterial strains using a validated biosensor and found widespread production. Inoculating mice with high producers elevated gut DPO levels, highlighting DPO's potential influence on gut microbiota. These findings expand DPO's ecological relevance and underscore quorum sensing as a potentially critical influence on microbiome function and host-microbe interactions.

The rise of multidrug-resistant bacteria, particularly biofilm-forming pathogens such as Staphylococcus epidermidis, highlights the urgent need for alternative antimicrobial strategies. Phage therapy, which uses phages to selectively infect and lyse bacterial cells, offers a promising solution. In this study, we evolved the lytic phage vB_Sep_Steph1 under both biofilm and planktonic conditions, using varying initial phage inoculum titers. Whole-genome sequencing of evolved populations revealed recurrent condition-dependent mutations in holins and structural genes with putative depolymerase activity-critical for host recognition and biofilm degradation. Phenotypic improvements in traits such as antibacterial efficacy and replicative fitness were observed to be highly dependent on both the presence of biofilm and the initial phage titer during evolution. Furthermore, some evolved phage lineages could delay bacterial resistance better than the ancestral strain. These findings support the utility of directed phage evolution to improve therapeutic efficacy and robustness, particularly against biofilm-associated infections.

Microplastic biofilms, known as the "plastisphere", harbor diverse microbial communities and serve as reservoirs for antibiotic resistance genes (ARGs). This review discussed the mechanisms driving bacterial community alteration on microplastics and delineated the pathways through which ARGs transfer within microplastic biofilms. We expected to provide a comprehensive understanding of the ecological and human health impacts associated with microplastic biofilms and ARGs, thereby informing strategies to mitigate plastic pollution and its risks.

AML often relapses due to chemotherapy resistance, increasingly linked to gut microbiome dysbiosis. Microbial drug modification, immune modulation, and metabolite-driven survival/epigenetic changes (e.g., SCFAs, kynurenine) promote resistance. Clinical data associate reduced diversity, loss of Faecalibacterium, and Enterococcus overgrowth with poorer outcomes. Microbiome interventions (FMT, probiotics, diet) show promise; priorities are standardizing methods and defining microbe-metabolite mechanisms to guide trials.

Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.