npj Biofilms and Microbiomes最新文献

Plant Growth-Promoting Rhizobacteria (PGPR) are key bio-agents for sustainable agriculture. This review conceptualizes PGPR as rhizosphere engineers that enhance soil nutrients, restructure microbial networks, and boost plant stress tolerance. While their mechanisms are well-understood in the lab, a significant translational gap limits field efficacy due to inconsistent colonization and environmental context-dependency. We critically analyze this gap and propose integrated strategies-from advanced formulations to synthetic consortia-to unlock the reliable application of PGPR for global food security.

The interactions between hosts and their microbiomes are driven in part by chemical communication, which influences immune responses, metabolism, and microbial community structure. Neuroendocrine signals are central to this bidirectional communication, forming the basis of microbial endocrinology. Although host-derived hormones, including catecholamines, are known to affect microbial physiology, much of the existing literature focuses on a limited number of model organisms or complex in vivo systems, where disentangling direct microbial responses from host-mediated effects is challenging. As a result, systematic comparative analyses of direct bacterial responses under controlled conditions remain scarce. Here, we performed a systematic in vitro screen under anaerobic conditions to assess catecholamine effects on the growth dynamics of phylogenetically diverse human gut bacteria. Catecholamines altered multiple growth parameters in a species-specific manner, with effects detectable at nanogram concentrations. Multivariate analyses, including principal component analysis and non-metric multidimensional scaling, revealed lineage-associated response patterns across taxa. Although derived from monoculture experiments, these intrinsic responses provide a comparative framework for understanding how direct hormone-microbe interactions may contribute to microbiome dynamics under host stress. Overall, this study provides a quantitative cross-species dataset to inform future systems-level investigations in microbial endocrinology.

Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder with elusive pathogenesis and lack of targeted therapies. While exercise can ameliorate ASD-like behaviors, its underlying mechanisms remain unclear. Recent studies have identified dysbiosis of gut microbiota and altered levels of short-chain fatty acids (SCFAs), as critical contributors to ASD-associated behavioral abnormalities. This study investigated the potential role of the gut-brain axis, specifically the vagal pathway, in mediating the therapeutic effects of voluntary wheel running exercise in a valproic acid (VPA)-induced ASD-like rat models. We demonstrated that six weeks of voluntary wheel running exercise attenuated ASD-like behavioral deficits. Exercise restructured gut microbial communities and elevated SCFA levels, notably butyrate, in feces and plasma. Concurrently, exercise normalized imbalances of neuroactive substances in the hippocampus and prefrontal cortex and suppressed neuroinflammation, evidenced by reduced microglial/astrocytic reactivity and a shift in microglial polarization toward an anti-inflammatory phenotype. Critically, subdiaphragmatic vagotomy attenuated these exercise-induced improvements, including the restoration of neuroactive substance homeostasis, resolution of neuroinflammation, and the amelioration of behavioral deficits. Our findings suggest that intact vagal signaling plays a critical role in coordinating gut-derived microbial and metabolic signals with central neuroadaptations to mediate the benefits of voluntary exercise on ASD-like behaviors.

Continental shelves are important areas for global biogeochemical cycling, yet the roles of sediment viruses in these areas remain poorly understood. Here, 48 surface sediment samples from the Chinese continental shelf were analyzed, and 12,540 viral operational taxonomic units (vOTUs) were identified. Taxonomic classification found that 93.6% of the vOTUs could not be assigned at the family level, and protein-sharing networks showed that 60.4% were singletons. Viral community structure was shaped primarily by temperature and water depth. A total of 557 auxiliary metabolic genes (AMGs) were identified, including those involved in sulfur reduction and phosphorus acquisition (Pho-family proteins). Additionally, diverse antibiotic resistance genes (ARGs) were detected, suggesting anthropogenic influence. This study reveals the diversity, ecological function, and environmental drivers of viral communities in continental shelf sediments, providing new insights into viral contributions to microbial ecology and biogeochemical processes.

Global nitrogen (N) deposition, a major consequence of climate change, has profound impacts on soil microbes, yet comparative studies investigating the effects of different N types and levels on diverse soil microorganisms and their ecological functions remain scarce. Here, we conducted a 7-year simulated N deposition with multiple levels (Low, Medium, High) and multiple forms (NH₄NO₃, NH₄Cl, KNO₃), combining amplicon sequencing, QMEC chips and ¹⁵N isotope tracing to analyze their impacts on soil microbial communities of prokaryotes, fungi and Cercozoa, elemental cycling, and N transformation. The results showed that N forms dominated Cercozoa and prokaryote community structures (P < 0.05) but not fungi. High NH₄⁺-N deposition significantly reduced microbial resistance (P < 0.05), while NO₃^--N deposition enhanced prokaryote-Cercozoa bipartite network stability and linearly increased community resistance (P < 0.05), supporting the ecological phenomenon of "Interdependence Leading to Enhanced Resilience". Elevated N deposition increased microbial diversity but inhibited key C / N cycling genes (e.g., pmoA, hzsB, nirK2, and nirS1) and N transformation (P < 0.05), raising CH₄ emission and soil N enrichment risks. In conclusion, this study provides scientific support for mitigating N deposition impacts and advancing environmental sustainability.

Labor induction failure increases the risk of unplanned cesarean delivery and maternal-neonatal complications. However, the determinants of induction sensitivity remain poorly understood. In this prospective cohort of 85 term pregnant women undergoing labor induction with Propess® (prostaglandin E2), we combined full-length 16S rRNA sequencing of the vaginal microbiota, untargeted metabolomics of vaginal secretions, and transcriptomic analysis of cervical stromal cells exposed to Lactobacillus crispatus supernatant to identify predictive factors and underlying mechanisms. We found that women with a poor induction response exhibited higher vaginal microbiota α-diversity and a significant reduction in L. crispatus abundance. The relative abundance of L. crispatus predicted induction success with an area under the curve (AUC) of 0.80 (95% CI: 0.70-0.90). Metabolomic analysis revealed distinct vaginal metabolic alterations in induction-insensitive women. Importantly, in vitro experiments showed that L. crispatus supernatant directly modulates the transcriptome of cervical stromal cells, upregulating genes involved in uterine contraction, tissue remodeling, and immune regulation. Our results identify vaginal L. crispatus as a key biomarker for labor induction sensitivity and elucidate a potential mechanism by which it primes the cervix for prostaglandin response. These findings provide a novel microbiota-host interaction framework for personalizing induction strategies in precision obstetrics.

Long-term farming practices leave an imprint on soil microbiomes, but how these changes influence crop drought resilience remains poorly understood. Here, we examined avocado orchards managed organically or conventionally for two decades and recurrently exposed to drought, to assess how management history shapes the rhizosphere microbiota and its contribution to plant stress tolerance. Organic and conventional systems resulted in distinct soil physicochemical profiles that were associated with shifts in rhizosphere microbial community composition. Organic management was characterized by higher soil pH, phosphorus availability, water content, and C:N ratio, together with a consistent enrichment of spore-forming bacteria, especially members of the Bacillaceae family. We established a culture collection from the organic rhizosphere, dominated by Bacillaceae, and identified three top-performing strains: Bacillus halotolerans B19 and B21, and Bacillus subtilis B26. In greenhouse assays, B. halotolerans strains mitigated drought stress by preserving biomass and reducing leaf proline accumulation, while B. subtilis provided partial protection. Gene expression analysis revealed strain-specific responses that nonetheless converged on bdh (2,3-butanediol dehydrogenase) induction, highlighting a common mechanism for drought mitigation. Together, these findings establish a mechanistic link between long-term organic farming and microbial functions underpinning drought resilience in perennial agroecosystems, paving the way for climate-smart farming strategies.

The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.

Atopic dermatitis (AD) is characterized by cutaneous dysbiosis marked by Staphylococcus aureus overgrowth, reduced commensal diversity, barrier dysfunction, and chronic inflammation. We investigated acacia gum (AG) as a topical prebiotic to modulate staphylococcal community structure and biofilm ecology in AD. Using both in vitro and in vivo approaches, we examined how AG reshaped microbial interactions and host responses. In coculture systems, AG selectively promoted Staphylococcus epidermidis while suppressing S. aureus. The S. aureus growth inhibition by AG involved direct antibacterial activity and commensal-mediated effects. We found that AG-upregulated glutamyl endopeptidase in S. epidermidis played a role in suppressing S. aureus colonization. AG disrupted both developing and established S. aureus biofilms and reduced intracellular persistence within macrophages, indicating activity across extracellular and host-associated niches. Beyond microbiota modulation, AG attenuated keratinocyte and macrophage activation via downregulation of proinflammatory cytokines and chemokines. In an AD-like mouse model, topical AG reduced S. aureus burden by three orders of magnitude, improved microbial diversity, partially restored barrier integrity, and decreased inflammatory cell infiltration without detectable toxicity. Collectively, AG reprograms staphylococcal dysbiosis and biofilm stability, supporting microbiota-directed prebiotic modulation as a mechanistically defined strategy for AD.

Miscarriage occurs in approximately 15% of all pregnancies, and recent studies have suggested a potential role of the microbiome. A nested case-control study from the Swedish Maternal Microbiome cohort was conducted, including 34 participants who sent at least one vaginal or fecal microbiome sample and questionnaire data before miscarrying (n = 34), and matched controls (n = 105 for regression models, n = 27 for machine learning models). Non-vaccine type HPV (aOR 3.95, 95%CI 1.04-15.06) and vaginal microbiome with community state type (CST) II (aOR 6.52, 95%CI 1.58-26.98) or CST-IVB (aOR 4.18, 95%CI 1.08-16.18) in early pregnancy were associated with an increased risk of miscarriage. Furthermore, we explored six machine learning algorithms using 70% of the cohort for training and 30% for testing, for the prediction of miscarriage using vaginal (AUROC 85%), fecal (AUROC 81%) and questionnaire (AUROC 82%) data separately and combined (AUROC 82%). Our results highlight the urgency of HPV screening and vaccine development for women's reproductive health. Despite limitations, including a small number of miscarriage cases, our results indicate the potential for both vaginal and fecal microbiomes in the prediction of miscarriage.