Search Results (129)

Coptotermes formosanus is an economically significant termite species with a highly organised caste system, in which division of labour underpins colony function. Although gut microbiota is widely recognised for its roles in host nutrition and adaptation, much less is known about how these microbial communities are structured across castes. To explore caste-related gut bacterial variation in C. formosanus, we analysed the community structure of both workers and soldiers using high-throughput amplicon sequencing targeting the bacterial 16S rRNA gene. Although both castes were dominated by Bacteroidota and Spirochaetota, which together accounted for 78.87% to 85.78% in workers and 63.31% to 84.38% in soldiers, significant caste-associated differences were evident. Workers showed significantly higher bacterial richness, as indicated by observed ASVs, Chao1 indices, and Faith’s PD. Further clear caste-associated bacterial community was revealed by beta-diversity analysis. Differential taxonomic analysis revealed distinct caste-associated enrichment patterns. In addition, co-occurrence network analysis indicated a caste-associated interaction structure, with soldier-biased taxa forming a dense, highly connected module while worker-biased taxa contributed to local structure and bridging positions. Furthermore, chemoheterotrophy and fermentation were predicted to be enriched in workers, whereas nitrate reduction, aerobic chemoheterotrophy, aromatic compound degradation, and phenotypes related to biofilm formation, stress tolerance, and mobile elements were predicted to be relatively enriched in soldiers. Moreover, qPCR analysis further showed caste-associated differences in dominant gut protists, with Pseudotrichonympha in workers significantly higher than in soldiers and positively correlated with Azobacteroides. These results provide clear evidence of caste-associated differentiation in gut microbial composition and offer a foundation for identifying novel microbial targets for termite pest management. Full article

Background: Lung cancer (LC) remains a leading cause of cancer-related mortality, often compounded by suboptimal chemotherapy efficacy and systemic toxicity. Emerging evidence implicates the gut microbiota in modulating tumor progression, immune function, and treatment outcomes. Methods: We evaluated Zowell, a novel live bacterial therapeutic (LBT) developed via LiveBiom^® co-fermentation, as an adjunct to cisplatin in a murine LC model harboring humanized microbiota. Mice were assigned to treatment groups: Zowell alone, cisplatin alone, their combination, and fecal microbiota transplantation (FMT) as a benchmark. Results: Zowell monotherapy significantly reduced tumor burden, and its combination with cisplatin produced synergistic anti-tumor effects. 16S rRNA sequencing revealed enrichment of beneficial taxa (Bifidobacterium, Lactobacillus, and Allobaculum) and suppression of contextual genera (Clostridium and Akkermansia). Treatment rebalanced gut ecology, evidenced by a lowered Firmicutes/Bacteroidetes ratio and increased alpha diversity. Zowell outperformed FMT in reducing tumor volume and inflammatory indices. Lipidomic profiling of tumor tissues identified elevated levels of immunomodulatory lipid mediators, including resolvins and prostanoids, suggesting remodeling of the tumor microenvironment toward inflammation resolution and immune activation. Conclusions: These findings support Zowell as a precision microbiome therapeutic that potentiates chemotherapy through gut microbial reprogramming and tumor lipid signaling modulation, offering translational promise for enhancing immunotherapeutic response and mitigating chemotherapy-induced toxicity. Full article

Background: Carotid plaque rupture is a critical event in ischemic stroke, yet the potential involvement of the intraplaque microbiota across disease stages remains unclear. Methods: We performed dual-omics profiling by analyzing host transcriptomes and PathSeq-derived microbiomes from 48 human carotid RNA-seq specimens spanning early lesions (intimal thickening; n = 10), stable plaques (n = 20), and unstable plaques (n = 18). Host transcriptomes were profiled alongside intraplaque microbiomes extracted via the GATK PathSeq pipeline with rigorous in silico decontamination. We integrated differential expression analysis, microbial diversity metrics, and functional inference. Furthermore, an integrated machine learning approach (incorporating Boruta feature selection) was employed to identify exploratory cross-kingdom diagnostic biomarkers. Results: Microbial beta diversity diverged significantly across disease stages, accompanied by the progressive upregulation of 54 host genes critical for extracellular matrix remodeling and immune chemotaxis. Strikingly, despite the inherent noise and artifacts associated with low-biomass sequencing, we computationally detected the distinct enrichment of 21 bacterial taxa in unstable plaques, predominantly oral and gut mucosal pathobionts. Computationally inferred functional profiling revealed that these unstable plaque-associated microbiota were significantly linked to predicted cell death, IL-17, and HIF-1 signaling pathways and exhibited strong positive correlations with host matrix-degrading transcripts. Statistical modeling suggested associative links among specific microbial enrichment, host transcriptomic dysregulation, and plaque instability, highlighting concurrent biological cross-talk. Importantly, our integrated machine learning pipeline established a 14-feature cross-kingdom biomarker panel (10 host genes and 4 bacteria) that discriminated stable from unstable plaques (cross-validated AUC = 0.869). Conclusions: Intraplaque microbiome dynamics computationally associate with host transcriptomic alterations during carotid plaque evolution. This synergistic host–microbiome association provides a hypothesis-generating framework linking microbial dysbiosis to plaque destabilization, offering novel mechanistic insights and highlighting the exploratory cross-kingdom biomarker panel as a highly promising foundation for future experimental validation and stage-tailored clinical diagnostics. Full article

Hypersaline soils are poly-extreme terrestrial habitats characterized by high salinity, in some cases heavy-metal contamination, temperature fluctuations, and nutrient limitation. These conditions impose strong selective pressures, and many prokaryotic inhabitants still remain uncultured. Here, we conducted an extensive culturomics study of 549 isolates from the hypersaline soils of the Odiel Saltmarshes Natural Area (Southwest Spain) and compared the results with previously generated shotgun metagenomic datasets from the same environment in order to evaluate taxonomic composition, functional potential, and ecological representativeness. Cultivation across media containing 7.5%, 15%, and 25% (w/v) total salts yielded microorganisms belonging to three major phyla: Pseudomonadota, Bacillota (Bacteria) and Halobacteriota (Archaea). At the genus level, bacterial isolates were dominated by Marinobacter, Halomonas, and Aquibacillus at 7.5% (w/v) salinity, whereas extremely halophilic archaea, including Halorubrum, Halogeometricum, and Haloarcula, were predominantly recovered from media containing 25% (w/v) salts. Among the isolates, 57 strains displayed identity values < 98.65% for 16S rRNA gene sequence comparison, suggesting their putative status as new taxa. Comparison with metagenomic datasets showed that culture-dependent approaches successfully recovered the dominant haloarchaeal groups but missed some abundant bacterial phyla, such as Gemmatimonadota. Conversely, culturomics enabled the isolation of unknown species from the rare biosphere, including representatives of the novel genus Terrihalobacillus, which are typically detected at low abundance in metagenomic datasets. Together, these results demonstrate the complementarity of culturomics and metagenomics and provide an insight into the microbial communities inhabiting the hypersaline soils of the Odiel Saltmarshes. Full article

The gut microbiome has emerged as a critical determinant of health and disease across virtually all organ systems. In the context of chronic kidney disease (CKD) and renal transplantation, mounting evidence reveals a complex bidirectional relationship between the intestinal microbiota and kidney function—commonly referred to as the gut–kidney axis. Patients with CKD harbor a profoundly altered gut microbial ecosystem characterized by reduced diversity, depletion of beneficial commensal organisms, and expansion of pathobiont taxa capable of generating uremic toxins and pro-inflammatory mediators. These perturbations are further compounded by the uremic milieu itself, dietary restrictions, frequent antibiotic exposure, and the use of immunosuppressive agents following transplantation. The gut–liver–kidney axis adds an additional layer of complexity, linking hepatic metabolism, bile acid signaling, endotoxemia, and systemic immune activation to the progression of renal disease. Gut-derived metabolites—including short-chain fatty acids (SCFAs), bile acids, trimethylamine N-oxide (TMAO), and tryptophan-derived uremic solutes such as indoxyl sulfate and p-cresyl sulfate—serve as molecular mediators of inter-organ crosstalk and have been identified as both biomarkers and therapeutic targets. A growing body of literature supports the diagnostic and prognostic utility of microbiome composition and its metabolic signatures in patients with CKD and those undergoing renal replacement therapy. Therapeutic strategies aimed at restoring microbial homeostasis—encompassing dietary interventions, prebiotics, probiotics, synbiotics, fecal microbiota transplantation (FMT), bile acid–based therapies, and novel pharmacological approaches—hold considerable promise for improving outcomes in CKD and transplant recipients. Importantly, the bidirectional relationship between immunosuppressive drugs and the gut microbiota has emerged as a clinically significant determinant of both microbial ecology and drug pharmacokinetics: each major immunosuppressive agent class—corticosteroids, calcineurin inhibitors, mycophenolate mofetil, and mTOR inhibitors—induces characteristic dysbiotic patterns, while in turn, the microbiota modulates drug bioavailability through enzymatic biotransformation (notably bacterial beta-glucuronidase activity affecting mycophenolic acid enterohepatic recirculation) and modulation of host drug-metabolizing enzymes. This narrative review provides a comprehensive overview of the current understanding of microbiome dysbiosis in the setting of renal disease and transplantation, examines the mechanistic underpinnings of the gut–liver–kidney axis, details the multifaceted impact of dysbiosis on transplant outcomes—including allograft function and rejection, infection, post-transplant diabetes, and cardiovascular complications—and critically appraises the translational potential of microbiome-targeted interventions. We conclude by highlighting ongoing challenges and future directions toward personalized, microbiome-informed clinical care. Full article

Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide, largely due to late-stage diagnosis and the limited sensitivity of current screening approaches for early lesions. In recent years, the gut microbiota has emerged as a key factor in colorectal carcinogenesis, offering promising opportunities for the development of novel, non-invasive diagnostic and therapeutic strategies. Specific bacterial species and microbial metabolites have been implicated in colorectal carcinogenesis and are under investigation as potential biomarkers for CRC detection. However, despite growing evidence of association, most remain investigational and require further clinical validation before routine implementation. Among the proposed bacterial biomarkers, Fusobacterium nucleatum is one of the most promising candidates for clinical implementation, with encouraging evidence supporting its use in non-invasive stool-based CRC detection. Streptococcus gallolyticus subsp. gallolyticus and Clostridium septicum currently serve primarily as clinical warning markers due to their well-established association with occult colorectal malignancy rather than as screening biomarkers. In contrast, pks⁺Escherichia coli, enterotoxigenic Bacteroides fragilis, Enterococcus faecalis, and Peptostreptococcus anaerobius remain investigational. Helicobacter pylori has limited value for CRC detection because of its inconsistent association and low specificity. Overall, this review summarizes the most extensively studied bacterial species and microbial metabolites involved in colorectal cancer development, with particular emphasis on their underlying pathogenic mechanisms and highlighting their potential value as diagnostic biomarkers and therapeutic targets. It also highlights emerging bacterial taxa and microbial signatures that have been associated with early tumorigenesis in recent studies. Full article

The Azores are characterized by intense volcanic activity, creating unique environments such as fumarole sites, where geothermal gases and high temperatures drive distinct chemical and biological processes. To investigate small-scale heterogeneity within such a site, six visually distinct samples were collected within a 30 cm radius at an active fumarole on São Miguel Island. The samples were analyzed for elemental and mineralogical composition, bacterial lipid biomarkers (PLFAs), and microbial community structure using a novel DNA separation technique to specifically target the living microbiome. Despite mineralogical similarities across all samples—predominantly composed of alunite, alkali-feldspar, and quartz—significant microbial heterogeneity was observed. Both PLFA and bacterial iDNA analyses revealed distinct microbial communities associated with specific conditions indicated by the specific colors: red and brown samples were dominated by Proteobacteria and Actinobacteriota, yellow and green by Thermoplasmatota and Actinobacteriota, and white and gray by Crenarchaeota. Interestingly, the gray samples exhibited a broader microbial composition, sharing some taxa with all other samples. These striking color variations are likely driven by differences in both specific mineral composition and microbial pigmentation, reflecting localized biogeochemical processes. Our findings demonstrate that extreme microbial heterogeneity can occur over remarkably small spatial scales within fumarolic systems, underscoring the complex interplay between chemical and biological factors in these dynamic volcanic habitats. Full article

Sustainable agriculture increasingly relies on organic amendments that integrate circular economy principles. Municipal Solid Waste (MSW)-derived compost (MSW-compost) represents a promising candidate as soil amendment in viticulture, yet its impact on soil microbiota remains poorly investigated. This study assessed the effects of MSW-compost application on the bacterial microbiota of a Mediterranean vineyard soil over a twelve-month period, comparing two application methods (surface mulching and tillage incorporation). Soil DNA was analyzed by 16S rRNA gene metabarcoding, complemented by functional prediction (Picrust2) and the Tea Bag Index to assess soil decomposition activity. MSW-compost significantly increased alpha-diversity and affected beta-diversity (p = 0.001) of the microbiota, regardless of the application method, with significant effects persisting throughout the entire observation period despite a clearly diminishing trend. Devosia emerged as the hub taxon of the co-occurrence network and was increased by compost addition. MSW-compost application mode remarkably affected the microbial network, with mulched treatment leading to a more complex, denser, and more interconnected network. While a similar number of taxa were increased or decreased, functional prediction revealed a notable enrichment of metabolic pathways, both synthetic and degradative, in the MSW-compost amended samples; this finding was supported by the enhanced red tea decomposition data (p = 0.007). Our results indicate that MSW-compost acts as a beneficial soil amendment, simultaneously enhancing microbial diversity and soil decomposition activity. This study provides novel evidence supporting the use of MSW-compost as a sustainable tool for improving soil microbiological quality in productive vineyards. Full article

The human gut microbiome is essential for immune regulation and mucosal homeostasis, functions that are profoundly disrupted during HIV infection. Early viral replication in the gut-associated lymphoid tissue (GALT) triggers a self-reinforcing cycle of CD4⁺ T-cell depletion, epithelial barrier breakdown, and increased microbial translocation. This persistent immune activation continues even under effective antiretroviral therapy (ART). A growing body of evidence indicates that HIV infection is consistently associated with alterations in gut microbial communities. This dysbiosis is typically characterized by fewer beneficial butyrate-producing commensal bacteria and an enrichment of pro-inflammatory microbial taxa. It also involves disturbances in key microbial metabolites, including short-chain fatty acids (SCFAs) and tryptophan catabolites. Such changes not only exacerbate systemic inflammation but may also contribute to incomplete immune reconstitution and the persistence of latent viral reservoirs despite long-term ART. In this review, we summarize current knowledge of microbiome–HIV interactions, with particular emphasis on the mechanisms through which gut dysbiosis contributes to immune dysfunction and viral persistence. We discuss recent advances in multi-omics technologies, as well as experimental systems such as gnotobiotic and humanized mouse models and intestinal organoid platforms that are helping to elucidate these complex interactions. Furthermore, we evaluate emerging microbiome-targeted interventions—including probiotics, prebiotics, fecal microbiota transplantation, and engineered bacterial therapeutics—and consider their potential role as adjunctive strategies in HIV treatment and cure research. By integrating microbiological, immunological, and clinical perspectives, this review highlights key knowledge gaps and outlines future research directions aimed at harnessing the gut microbiome as a novel therapeutic avenue in HIV management and eradication. Full article

The Gastrodia elata Blume (GE) life cycle is unique, since its successful germination and growth rely on symbiosis with specific fungi (e.g., Armillaria mellea). However, the community succession, tissue specificity and functional potential of endophytic and rhizosphere bacterial communities during the seed formation stage of GE remain unclear. Here, we used high-throughput 16S rRNA gene sequencing to systematically explore the composition, diversity, and dynamic succession of bacterial communities across different stages of seed formation and among various tissues. Our results revealed that the endophytic community remained relatively stable across most developmental stages and tissue types (ANOSIM R = 0.4568, p = 0.001), with significant compositional shifts only occurring at the fruiting stage in specific tissues (stems and seeds). In contrast, the rhizosphere soil bacterial community showed stronger developmental succession (ANOSIM R = 0.7037, p = 0.001), with progressive divergence and the strongest segregation observed between the initial planting and fruiting stages. Alpha diversity peaked at the flowering stage for endophytic bacteria (Shannon index) and at the bud formation stage for rhizosphere soil bacteria, with persistent core taxa (Bacteroides in endophytic bacteria, Pseudarthrobacter in rhizosphere soil bacteria) dominating across stages. Functional predictions revealed stable core metabolic pathways, with stage-specific enrichments of glycolysis or gluconeogenesis at late developmental stages. These results provide novel ecological insights into the spatiotemporal dynamics of bacterial communities across different stages of GE seed formation, highlighting the distinct ecological strategies of endophytic and rhizosphere soil bacteria during the reproductive development of the plant. Full article

Sea buckthorn (Hippophae rhamnoides L.) leaves are rich in nutrients and bioactive constituents, with great potential for fermented tea development. It has been demonstrated that Fuzhuan brick tea processing can improve sea buckthorn leaf tea flavor, but the underlying microbial succession remains unexplored. Therefore, we characterized the dynamic succession and interrelationships of bacterial and fungal communities via Illumina NovaSeq 6000 sequencing. β-diversity analysis revealed successive shifts in microbial community structure, with fungal communities changing mainly in the early stage and bacterial communities varying more in the late stage of fermentation. The relative abundance of Pseudomonas, a genus frequently associated with flavor formation and tea quality, increased steadily. Fungal taxonomic analysis revealed that the genus Aspergillus, particularly the species Aspergillus chevalieri, remained dominant throughout the fermentation process. Linear discriminant analysis effect size indicated an enrichment of microbial taxa typical of fermentation, accompanied by a relative reduction in putative opportunistic microbes. Additionally, Aspergillus exhibited significant negative correlations with five key differentially abundant bacterial genera. Interestingly, microbial co-occurrence networks suggested an overall tendency toward coexistence rather than mutual exclusion between the bacterial and fungal communities. This work provides a theoretical foundation for the development of novel fermented sea buckthorn leaf tea products. Full article

Post-traumatic stress disorder (PTSD) is a debilitating psychiatric condition that impairs psychological functioning and increases susceptibility to various chronic illnesses, including inflammatory, metabolic, and cognitive disorders. Recent advances in neuroscience and microbiology have identified the brain–gut–microbiota axis as a key mediator of neuroimmune and neuroendocrine regulations, providing new insight into the pathophysiology of PTSD. This review synthesizes current findings from preclinical and clinical studies on gut microbiome alterations in PTSD, highlighting the underlying mechanistic pathways. Dysbiosis in PTSD is associated with immune dysregulation, altered neuroendocrine signaling, and neurotransmitter imbalances. Animal models, particularly those using the single prolonged stress paradigm, have demonstrated behavioral and microbial changes that mirror the characteristics of human PTSD. Human studies have revealed reduced abundance of beneficial bacterial taxa and increased inflammation-associated genera in patients with PTSD. Although emerging evidence supports the role of gut microbiota in PTSD, further research is needed to establish causal relationships and optimize microbiome-targeted therapies. Overall, the gut microbiome offers a novel and potentially modifiable target for the prevention and treatment of PTSD. Full article

The gastrointestinal (GI) barrier is a highly coordinated, multilayered defence system that maintains intestinal homeostasis by separating the luminal microbiota from the internal milieu. In liver cirrhosis, this barrier undergoes profound structural and functional disruption, emerging as a central driver of bacterial translocation and infection-related complications. Among these, spontaneous bacterial peritonitis (SBP) represents a major determinant of morbidity, mortality, and disease progression. Barrier failure in cirrhosis is not attributable to a single defect but results from the convergence of multiple interconnected mechanisms. Structural alterations include disruption of epithelial tight junctions and deterioration of the mucus layer, leading to increased intestinal permeability and loss of spatial compartmentalisation. These changes are compounded by microbial dysbiosis, characterised by reduced diversity, depletion of short-chain fatty acid-producing taxa, and expansion of pathobionts. In parallel, cirrhosis-associated immune dysfunction impairs both mucosal and systemic antimicrobial defences, while gut–vascular barrier disruption facilitates systemic dissemination of bacteria and microbial products. The resulting increase in bacterial translocation plays a pivotal role in the pathogenesis of SBP and contributes to systemic inflammation, circulatory dysfunction, and acute decompensation. Importantly, this process establishes a self-amplifying pathogenic loop in which barrier dysfunction, dysbiosis, and immune dysregulation mutually reinforce each other. Recent advances have identified key molecular pathways involved in barrier regulation, including bile acid–FXR signalling and microbiome-derived metabolites, providing novel targets for therapeutic intervention. While current management relies largely on antibiotics and supportive care, emerging strategies aim to restore barrier integrity and modulate the gut–liver axis. A deeper understanding of GI barrier dysfunction offers new opportunities to prevent bacterial translocation and improve clinical outcomes in patients with liver cirrhosis. Full article

(1) Airborne fine particulate matter (PM_2.5) poses a growing threat to poultry production by impairing intestinal health, disturbing microbial balance, and reducing growth performance. Rosmarinic acid (RA), a natural polyphenol with antioxidant, anti-inflammatory, and gut microbiota-regulating properties, can effectively maintain intestinal homeostasis. To date, its protective effects against PM_2.5-induced intestinal injury in broilers remain largely unclear. This study investigated whether dietary RA supplementation mitigates intestinal damage and microbiota dysbiosis caused by PM_2.5 in broilers and explored the related mechanisms. (2) A total of 144 21-day-old broilers were randomly allocated to three groups, control (CON), PM_2.5 exposure (PM), and PM_2.5 exposure plus rosmarinic acid (RA), with six replicates of eight broilers each. (3) Results indicated that PM_2.5 exposure severely impaired growth performance, whereas dietary RA significantly increased average daily feed intake and average daily gain, decreased the feed-to-gain ratio, and elevated final body weight in broilers. RA significantly attenuated PM_2.5-induced intestinal inflammation, as evidenced by reduced expression of inflammatory cytokines (IL-6 and IFN-γ) and downregulation of key components in the TLR4 signaling pathway (TLR4, MyD88, and NF-κB). Inhaled PM_2.5 exposure impaired the intestinal epithelial barrier, marked by decreased mRNA levels of MUC2 and CLDN1 and increased caspase3 expression. Dietary RA treatment effectively restored these indicators, suggesting its role in maintaining epithelial integrity. Furthermore, RA reshaped the gut microbiota structure, altering both α- and β-diversity. Notably, RA led to a higher proportion of potentially health-promoting bacterial taxa, including Lactobacillus, V9D2013_group, and Oscillospirales, while reducing opportunistic pathogens like Shuttleworthia. (4) In conclusion, RA alleviates PM_2.5-induced intestinal inflammation, reinforces the epithelial barrier, and modulates the intestinal microbiota in broilers, likely through inhibition of the TLR4/NF-κB signaling. These findings reveal a novel mechanism by which RA mitigates pollutant-induced intestinal injury via gut microbiota modulation and TLR4/NF-κB suppression, offering new insights into the gut–lung axis in avian species. Full article

To improve the degradation rate of sulfamethoxazole (SMX) under hypoxic conditions in paddy fields during the flooding period, a laboratory microcosm experiment was established in this study to investigate the regulatory effect of straw return on the hypoxic degradation of SMX and its underlying microbial mechanisms. The results demonstrated that straw addition significantly promoted the hypoxic degradation of SMX. By the 10th day of the experiment, the residual SMX content in the straw-amended group was only 11.3% of that in the non-straw control group, and the average degradation rate throughout the experimental period was increased by 85.7%. Straw provided complex carbon sources, including organic carbon (e.g., starch, sugars, and humus) and cellulose, which not only reshaped the microbial community structure and created new ecological niches but also increased the microbial network density under SMX stress from 0.010 to 0.024. Acinetobacter, Bacillus, and Pseudomonas, which possess both straw decomposition and SMX degradation capabilities, sequentially became the dominant bacterial taxa. These dominant taxa can adapt to hypoxic fermentation in the flooded environment and co-metabolize SMX by activating the metabolic pathways of aromatic compounds and sugars. This study is expected to open up a novel approach for the remediation of SMX-contaminated flooded paddy fields and provide valuable innovative insights for technological breakthroughs and practical applications in related fields. Full article