Frontiers in microbiomes最新文献

Alzheimer's disease (AD) is one of the most diagnosed neurodegenerative disorders worldwide and presents a significant challenge for both affected individuals and their caregivers. Alzheimer's disease is characterized by the accumulation of amyloid plaques and dysfunctional tau protein in the brain, along with the final development of dementia. Recently, in addition to the strongly developing ischemic etiology of AD, it is suggested that the gut and oral microbiota may also participate in the development of this disease. This involvement may stem from an unbalanced diet and the consumption of foods containing harmful chemical additives. An unhealthy diet can compromise the integrity of the gut barrier, facilitating the translocation of bacterial pathogens and leading to a pro-inflammatory T-cell response mediated by innate immune cells. This inflammatory response can disrupt systemic homeostasis and may contribute to neuroinflammation. The brain and gut interact through a complex network known as the "gut-brain-microbiota axis," and emerging studies suggest that the intestinal microbiota and their metabolites may play a significant role in the pathogenesis of Alzheimer's disease. Moreover, these inflammatory mediators and microbial metabolites can reach the brain via the gut-brain axis, potentially exacerbating neurodegenerative processes. Preclinical and limited clinical evidence indicates that low-fiber diets are associated with alterations in intestinal microbiota composition, which may contribute to the onset and progression of Alzheimer's disease. This review aims to explore the potential connections between AD and the gut microbiome, emphasizing the significance of dietary factors in shaping these relationships. A comprehensive understanding of the interactions between the human microbiome and the brain, particularly in the context of diet and its ingredients, may enhance our understanding of AD etiology and inform the development of preventative strategies, through dietary modifications or therapeutic interventions. This area of research holds promise for identifying novel approaches to prevent or slow the progression of AD.

Endophytic bacteria contribute to plant growth, stress tolerance, and pathogen resistance. Their effective use in agriculture requires the identification of strains that combine multiple beneficial traits with consistent performance across different field conditions. Accordingly, this study examines Bacillus and Pseudomonas endophytes isolated from Cannabis sativa L. and Chelidonium majus L. for plant growth promotion, abiotic stress tolerance, and biocontrol properties. Plant growth-promotion traits included indole, siderophore, and organic acid production, phosphate and zinc solubilization, and biofilm formation. Results showed that all the tested bacterial isolates produced indoles, with the highest levels recorded in Pseudomonas strain PPW-26, whereas several Pseudomonas strains exhibited strong siderophore production. Strain PPW-26 tested positive for methyl-red, indicating organic acid production, whereas other Pseudomonas strains tested negative. Moderate to high nutrient solubilization profiles were observed across all Pseudomonas strains. Bacillus strains, particularly BS-114, exhibited higher biofilm formation relative to Pseudomonas. Assessment of abiotic stress tolerance included proline accumulation, superoxide dismutase activity, and growth under varying temperature, salinity, and drought conditions. All strains displayed tolerance to the tested stresses, with Bacillus strains showing stronger resilience to high temperature and salinity, accompanied by elevated proline accumulation and superoxide dismutase activity in selected strains. Biocontrol potential was evaluated through biosurfactant production and antifungal activity. Bacillus strains showed high biosurfactant activity and strong inhibition of fungal pathogens. Strain BS-120 exhibited broad-spectrum inhibition against Fusarium oxysporum, Fusarium graminearum, and Rhizoctonia solani-AG3. Analysis of genome sequences identified biosynthetic gene clusters encoding antifungal metabolites, including fengycin and surfactin, consistent with the observed inhibition. Genome-wide similarity analysis and ANI-based clustering revealed the presence of highly similar and genetically distant strains within each genus. For Bacillus spp., ANI values ranged from 87.62% to 98.83%, whereas for Pseudomonas spp. they ranged between 83.91% and 99.99%, confirming the presence of substantial intra-genus diversity. Phylogenetic analysis showed well-supported clades consistent with ANI clustering. Overall, this study demonstrates that endophytic Bacillus and Pseudomonas strains exhibit complementary and strain-dependent traits associated with plant growth promotion, stress tolerance, and pathogen suppression, supporting their further evaluation as potential bioinoculants for sustainable agriculture.

Introduction: The gut microbiome influences cardiovascular health through metabolite production and immune modulation. Gut microbial dynamics and cardiovascular outcomes are also shaped by biological sex. However, sex-specific responses to myocardial infarction (MI) that involve the gut microbiome and intestinal milieu remain poorly defined, particularly in older hosts. Here, we characterize gut microbiome structure and function alongside physiological and immune responses to MI across multiple tissues in aging male and female mice.

Methods: MI was induced by permanent LAD ligation and confirmed by echocardiography in C57BL/6N retired breeder mice. Sham surgery (SH) and no surgery (NoSx) groups served as controls. Gut microbiota and the cecal metabolome were characterized using 16S rRNA sequencing and untargeted UPLC-MS, respectively. Immune cells in the small intestine, heart, bone marrow, and spleen were quantified by flow cytometry, and small intestinal morphology was assessed on H&E-stained sections.

Results: Sex-specific differences were evident at baseline. Following MI, pronounced time- and sex-specific differences in gut microbial and immune cell populations were observed, peaking on day 3 (D3) and absent in SH and NoSx controls. Early increases in Bacteroidaceae, Tannerellaceae, and Marinifilaceae were present in both sexes, with sex-specific enrichment of Bacteroidaceae in males and Akkermansiaceae in females. Metabolomic analyses identified increased secondary bile acid derivatives, including cholylvaline in males and 12-oxo-lithocholic acid in females. Integration of microbiota-metabolome data revealed MI-responsive and homeostatic taxa with opposing metabolite signatures, while functional analyses indicated enrichment of propanoate and amino acid metabolism pathways. These changes were temporally aligned with acute MI-induced expansion of intestinal MHCII⁺CD11c⁺ dendritic cells and TCRαβ⁺CD4⁺, TCRαβ⁺CD8αβ⁺, and CD25⁺FoxP3⁺ regulatory T cells on D3 in both sexes. Males alone exhibited marked increases in intestinal TCRγδ⁺ T cells, while females showed increased accumulation of innate immune cells.

Discussion: Convergence of peak physiological, immunological, and microbial responses on day 3 after MI reveals coordinated responses across the gut-heart axis that are fundamentally influenced by sex. Our findings highlight the need for personalized, sex-specific perioperative strategies and identify the gut microbiome as a potential therapeutic target to improve outcomes after MI.

Introduction: Hematopoietic stem cell transplantation (HSCT) profoundly disrupts the gut microbiome and may contribute to adverse post-transplant outcomes. Fecal microbiota transplantation (FMT) has emerged as a strategy to restore microbial diversity; however, data in pediatric HSCT recipients remain limited.

Methods: We conducted a longitudinal analysis of 17 pediatric HSCT recipients who received FMT. Fecal samples were collected before FMT and at days 7, 14, and 30 after treatment. Gut microbiome composition was analyzed using 16S rRNA gene sequencing.

Results: Baseline samples showed reduced microbial diversity and a dysbiotic microbial profile. Following FMT, microbial diversity increased progressively, with recovery evident from day 7 and stabilization by day 30. Taxonomic analyses demonstrated depletion of dysbiosis-associated genera and enrichment of beneficial short-chain fatty acid-producing taxa, including Faecalibacterium, Blautia, Subdoligranulum, and Akkermansia. Distinct microbial configurations were observed according to gastrointestinal involvement by acute graft-versus-host disease.

Conclusions: FMT was associated with progressive restoration of gut microbiome diversity and structure in pediatric HSCT recipients, supporting its potential role as a microbiota-based strategy to promote ecological recovery after HSCT.

Introduction: Eczema and food allergy commonly emerge during infancy and are linked to changes in the gut microbiome, yet it remains unclear when microbiome differences associated with allergic disease first appear during development.

Methods: We analyzed age-stratified shotgun metagenomic data from 97 children aged 4-36 months, including physician-confirmed cases of eczema or food allergy and non-allergic controls, excluding recent antibiotic or probiotic exposure. Microbial taxa, functional pathways, and composite microbiome metrics were evaluated across three developmental stages: early infancy (4-6 months), mid-infancy (6-12 months), and toddlerhood (12-36 months).

Results: Differences between allergic and non-allergic children were minimal before 6 months of age but became more apparent during mid-infancy and persisted into toddlerhood. Allergic conditions were associated with reduced abundance of fiber-fermenting and butyrate-producing taxa, enrichment of facultative and inflammation-associated microbes, lower microbiome maturation scores, and shifts in metabolic and inflammatory functional capacity.

Discussion: These findings suggest that gut microbiome divergence associated with allergic disease becomes more apparent during mid-infancy, highlighting a developmentally relevant period for understanding early immune disruption. The results support further longitudinal and interventional studies aimed at clarifying whether earlier microbiome-targeted strategies may help modify progression along the atopic march.

Background: Pulmonary arterial hypertension is a progressive disease involving the pulmonary vasculature and is defined as a mean pulmonary arterial pressure (mPAP) >20 mmHg at rest. Pulmonary arterial hypertension during pregnancy is associated with increased maternal mortality and adverse fetal outcomes. The present study aimed to investigate differences in the initial meconium microbiota between neonates born to mothers with congenital heart disease-associated pulmonary arterial hypertension (CHD-PAH) and those born to mothers with congenital heart disease (CHD) alone, thereby elucidating the potential influence of pulmonary arterial hypertension on the establishment of the early-life gut microbiome.

Methods: We collected first-pass meconium samples from neonates in the pulmonary hypertension group (PH group, n = 23) and the control group without pulmonary hypertension (NC group, n = 17) and characterized microbial profiles using 16S rRNA sequencing.

Results: The PH group showed lower alpha diversity, with reduced Shannon and observed features indices (both P < 0.05), whereas Bray-Curtis beta diversity showed substantial overlap between groups. At the phylum level, the overall gut microbial structure was broadly comparable between the PH and NC groups, with no statistically significant differences in the relative abundance of dominant taxa. At the genus level, the mean relative abundance of Streptococcus was significantly lower in the PH group than in the NC group (0.20% vs. 2.09%, P = 0.0072). Predicted functional profiling suggested potential differences in dominant metabolic pathways between groups, including enrichment of ubiquinone biosynthesis and aromatic amino acid/chorismate biosynthesis pathways in the PH group.

Conclusion: Collectively, these findings extend current evidence on PAH-related alterations in early-life microbial ecosystems and provide a plausible microbiome-based basis for investigating the biological mechanisms underlying adverse maternal-fetal outcomes associated with pulmonary arterial hypertension.

The gut microbiota and bile acids (BAs) exist in a tightly regulated, bidirectional relationship that influences host metabolism, immune function, and disease. Primary BAs synthesized in the liver are chemically transformed by intestinal microbes into a diverse pool of secondary BAs, which exert antimicrobial effects and activate host signaling pathways including Farnesoid X Receptor (FXR), Takeda G protein-coupled receptor 5 (TGR5), and sphingosine-1-phosphate receptor 2 (S1PR2). These pathways regulate BA homeostasis, epithelial barrier integrity, inflammation, and carcinogenesis. Disruption of this BA-microbiome axis has been implicated in biliary tract cancers (BTCs), a group of aggressive malignancies with rising global incidence and limited therapeutic options. Secondary BAs and BA receptor signaling contribute to tumor initiation and progression through NF-κB activation, oxidative stress, and altered cell survival, whereas reduced FXR signaling and obstructed enterohepatic circulation further promote inflammatory dysregulation. Emerging evidence demonstrates that microbial dysbiosis and altered BA metabolism are associated with distinct BTC microbial profiles, enriched in taxa such as Fusobacterium, Salmonella, Prevotella, and Actinomyces, alongside depletion of commensals including Lactobacillus. These taxa influence inflammatory signaling, BA transformation, and epithelial injury, contributing to carcinogenesis. Microbiome-BA interactions also shape anti-tumor immunity and responses to immune checkpoint inhibitors (ICIs). Specific microbial signatures-particularly enrichment of Lachnospiraceae, Erysipelotrichaceae, Bacteroidetes, and Alistipes-correlate with enhanced immune activation and improved clinical outcomes in hepatobiliary cancers. Modulation of gut microbiota through antibiotics, probiotics, or fecal microbiota transplantation can influence BA composition, immune surveillance, and therapeutic efficacy. Collectively, these data highlight the central role of the BA-microbiome axis in BTC pathogenesis and treatment response. Microbial and BA metabolite profiling represent promising avenues for biomarker development, while targeted manipulation of BA signaling and microbial ecology offers potential therapeutic strategies to improve BTC outcomes.

Integrating perennial forage seed crops into annual cropping sequences can diversify the rotations and improve soil health, yet their effects on the soil microbial communities and functions are not yet fully elucidated on the Canadian prairies. Using a 10-year field experiment with eight cropping sequences under varying supplemental nitrogen (N) fertilization levels, we evaluated the impacts of integrating perennial seed crops and annual crops on soil microbial biomass carbon (MBC), the composition and diversity of prokaryotic and fungal communities, and the activities of key enzymes involved in carbon (C), N, phosphorus (P), and sulfur (S) cycling, namely β-glucosidase, N-acetyl-β-glucosaminidase, acid phosphomonoesterase and arylsulfatase. The crop sequences containing intermittent succession of perennial and annual crops had 17% greater soil MBC, higher fungal richness (e.g., Chao1 indices of 92.8 vs. 87.6) and 22% greater β-glucosidase activity than annual-only sequences. The relative abundances of the two most abundant prokaryotic phyla - Actinobacteriota and Proteobacteria - as well as the second most abundant fungal class, Dothideomycetes, followed the same trend. The soils with more frequent recurrence of grassy perennials in the sequences exhibited greater MBC (34%), higher prokaryotic Shannon diversity, greater fungal richness, and higher arylsulfatase activity (68%) than soils with more frequent recurrence of perennial legumes, although the predominant prokaryotic phylum, Actinobacteriota was more abundant in legume-based systems. The cropping sequences dominated by creeping red fescue grass seed crops exhibited the greatest improvement in most of the soil microbial metrics studied. Nitrogen fertilizer increased the relative abundance of the copiotrophic Actinobacteriota but decreased that of the oligotrophic Acidobacteriota. Prokaryotes were associated with C, N, P and S cycling, whereas fungi were primarily linked to C cycling. Overall, diversifying annual grain cropping systems with perennial forage seed crops, particularly creeping red fescue, enhanced key indicators of biological soil health.

Introduction: Non-Western diets are increasingly studied for their relationship to gut microbiota composition and diversity, although most research in this area has focused on plant-based, fiber-rich diets. Here, we present a single-participant longitudinal study investigating gut microbiota dynamics during a transition from a Western diet to a 12-week Indigenous Arctic animal-based diet composed of minimally processed raw, dried, and fermented animal-source foods. During one month of this period, the participant consumed dried whole fish (ammassak), including intestinal contents, representing a form of gastrophagy, a practice common to the Arctic diet, that may increase exposure to food-associated microbes.

Methods: Fecal samples (n = 29) were collected before, during, and after the Arctic diet phase. 16S rRNA gene sequencing of the V3-V4 region was used to profile bacterial communities. Diversity metrics, Firmicutes/Bacteroidota (F/B) ratios, and taxonomic composition analyses were performed to assess compositional shifts across diet phases.

Results: Alpha diversity remained relatively steady throughout the study, with a tendency toward higher values during the Arctic diet. The F/B ratio increased from 1.31 to 2.12 during the Arctic diet phase and remained elevated (2.38) after returning to a Western diet. Beta diversity analysis revealed significant restructuring of the gut microbiota at the onset of the Arctic diet, followed by partial reversibility upon returning to a Western diet. Fiber-associated taxa like Prevotella 9 disappeared, and Bifidobacterium declined, while protein- and fat-associated taxa, including Bacteroides, Lachnoclostridium, and Alistipes, increased. Several genera appeared during the Arctic diet phase that were absent during the preceding Western diet phase, consistent with altered microbial exposure. Among those, Photobacterium was also detected in the ammassak, suggesting potential microbial exposure during the gastrophagy period.

Discussion: These results provide preliminary evidence that the gut microbiota can shift substantially during an Indigenous Arctic dietary transition. Because the Arctic diet also substantially overlapped with sustained high physical activity, the observed changes should be interpreted in the context of a combined dietary and lifestyle transition. These findings highlight the need for a better understanding of underrepresented dietary patterns, such as those of Arctic Indigenous communities, and their relationship with the gut microbiota.

The rhizosphere and root-associated microbiomes play a crucial role in nutrient acquisition, stress tolerance, and overall plant performance. However, little is known about how microbial communities assemble and shift across environments in pecan (Carya illinoinensis). In this study, we compared the bacterial and fungal community compositions in the roots and rhizosphere of four pecan clonal rootstocks (NMU03, NMU04, NMU05, and NMU155) cultivated under greenhouse conditions, as well as their subsets that were subsequently transplanted to the field. Amplicon sequencing of 16S rRNA and ITS regions revealed significant differences in microbial diversity and taxonomic composition across environments and genotypes. Bacterial assemblages in greenhouse roots were typically dominated by a few families (e.g., Burkholderiaceae, Rhodanobacteraceae, and unclassified taxa). In contrast, field samples exhibited broader taxonomic distributions, with families such as Xanthobacteraceae, Haliangiaceae, and Geminicoccaceae emerging as dominant members. Fungal OTU abundance was consistently higher than bacterial abundance across all genotypes, likely reflecting mutualistic associations with mycorrhizal fungi, such as those in the Elaphomycetaceae family. Interestingly, Aspergillaceae dominated greenhouse and field fungal communities, suggesting ecological adaptability and potential contributions to plant stress tolerance. Comparisons with earlier greenhouse studies revealed that while some signature core microbiome members were retained following transplantation from the greenhouse to the field, the abundance of others decreased, highlighting successional shifts in community structure driven by environmental transitions. Together, these findings demonstrate the dynamic, genotype and environment-specific structuring of pecan microbiomes and highlight the importance of microbiome-informed breeding strategies to improve plant-microbe associations under variable growth conditions among pecan breeders.