Search Results (927)

Boron (B) is increasingly recognized as more than a trace dietary element, emerging as a context-dependent organizer of molecular interactions at the host–microbiome interface. B exhibits reversible covalent chemistry driven by Lewis’ acidity and selective affinity for cis-diol-rich biomolecules, enabling dynamic complexation with polyols, glycans, and phenolic ligands that dominate the intestinal mucus environment and shape microbial ecology. We synthesize evidence supporting an architecture-based framework in which B modulates biological function by conditioning the physicochemical context of microbial communication rather than acting as a single-pathway effector. Central to this model is spatial bioavailability, distinguishing plasma-accessible boron from microbiota-accessible boron (MAB), species that persist in the lumen and mucus layer long enough to influence interface-level processes. We propose that insufficient or altered MAB availability may contribute to dysbiosis (DYS) by destabilizing quorum-associated coordination, signal persistence, and mucosal microstructure, thereby promoting barrier dysfunction and inflammaging. Particular attention is given to B-mediated symbiotaxis, a hypothesis-driven concept describing how B-containing molecular assemblies may bias microbial communities toward cooperative, barrier-supportive configurations and reduce ecological volatility. We identify key knowledge gaps and experimental priorities (speciation-aware measurements, signal-centric readouts) necessary to determine when, where, and how B-mediated molecular architecture may counteract DYS and support healthspan. Full article

The rectal mucosa houses a large number of viruses with important roles in shaping the local microbial communities and modulating immune responses, which could influence host susceptibility to infection and other diseases. Unique composition of the gut microbiome, including the predominance of clinically significant eukaryotic viruses like herpesviruses, cytomegalovirus, and human papillomavirus, has been described in both people with HIV (PWH) and men who have sex with men (MSM) vulnerable to HIV. Despite these insights, the rectal virome and the clinical implications of virome–bacteriome–immune interactions in the rectal mucosa remain poorly understood. In this review, we synthesize existing data on the composition of the rectal virome, its interactions with the bacteriome and the immune system, and implications on clinical outcomes in people living with or vulnerable to HIV. We also highlight the gaps and research needed to further explore and unravel these relationships. Full article

Antimicrobial resistance (AMR) represents a major global health threat, largely driven by antibiotic overuse and the protective role of bacterial biofilms. Quorum sensing (QS), a bacterial communication system regulating virulence and biofilm formation, has emerged as a promising therapeutic target. Quorum quenching (QQ), which disrupts QS without directly inhibiting bacterial growth, is considered a potential anti-virulence strategy that may reduce selective pressure for resistance. This review critically evaluates recent advances in QQ research, focusing on its clinical applicability, limitations, and risks. We analyzed studies from the last five years involving natural compounds, synthetic molecules, nanoparticles (NPs), and combination therapies targeting key pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus in models of lung diseases, mainly cystic fibrosis, chronic wounds, burns, and implant-associated infections. While numerous compounds demonstrate significant in vitro anti-biofilm and anti-virulence activity, major challenges remain, including limited in vivo validation, pharmacokinetic constraints, toxicity concerns, microbiome disruption, and the potential development of tolerance or functional resistance. Although QQ offers a promising adjunctive approach to conventional antibiotics, its long-term clinical feasibility requires comprehensive evaluation of evolutionary dynamics, host–microbe interactions, and safety profiles. Full article

Over the past several decades, the gut microbiome (GM) has been the focus of extensive investigation. In recent years, major discoveries such as the role of maternal breastfeeding in infant GM development and mode of delivery on infant GM health have expanded scientific knowledge on this topic. As this is a rapidly expanding field of research, substantial work remains to further elucidate and integrate the existing evidence on its role in allergic response and immunological development. This comprehensive review will examine the latest discoveries in GM research and its role in the development of food allergies across the lifespan. Examining the existing literature may identify knowledge gaps regarding precise mechanisms through which the development of GM influences the maturation of the immune system. Given the abundance of the literature, we conducted a database search for articles published within the past 10 years. A total of 56 original research articles were retrieved, analyzed, and included in our review. This review article aims to integrate the current evidence on understanding how the development of GM impacts the immune system and food allergy response throughout the lifespan. We aim to uncover microbial mechanisms of allergy response, host and microbe interactions, and opportunities for therapeutic intervention. Additionally, we aim to reveal gaps in the current knowledge of the GM’s influence on allergy development, offering directions for future research. Full article

Subterranean termites, particularly Odontotermes obesus, cause severe damage to forest nurseries and plantations in arid and semi-arid ecosystems. This study demonstrates the dual functional role of endophytic entomopathogenic fungi, Metarhizium anisopliae and Beauveria bassiana, in termite suppression and induction of plant defense responses. Laboratory bioassays revealed significantly higher virulence of M. anisopliae, with a lower LT₅₀ (lethal time required to cause 50% mortality) of 33.1 h compared to B. bassiana (46.7 h), a steeper probit slope (5.4 ± 0.3), and strong model fit (R² = 0.95), indicating rapid and synchronized mortality. Endophytic colonization varied across host species and application methods, with soil incorporation consistently outperforming foliar inoculation. Maximum colonization (82.5%) was recorded in Tecomella undulata and exceeded 80% in Azadirachta indica under M. anisopliae. Biochemical analyses revealed significant increases in protein (up to 3.5 mg g⁻¹), phenols (3.7 mg g⁻¹), and tannins (2.7 mg g⁻¹). Activity of defense enzymes was significantly enhanced, with catalase reaching 263.5 U mL⁻¹, while Phenylalanine ammonia-lyase and Tyrosine ammonia-lyase exceeded 170 and 198 U mL⁻¹, respectively, indicating activation of antioxidant and phenylpropanoid pathways. Molecular docking analysis further revealed strong interactions between fungal metabolites and termite cellulase, with Bassianin (−8.4 kcal mol⁻¹) and Tenellin (−8.1 kcal mol⁻¹) showing the highest binding affinities. These findings highlight the combined biochemical and molecular mechanisms underlying fungal-mediated termite suppression and plant defense induction, and future research should prioritize transcriptomic validation, rhizosphere microbiome interactions, formulation optimization, and long-term multi-location field evaluation to support sustainable termite management strategies. Full article

Triplophysa yarkandensis (Cypriniformes: Nemacheilidae), a rare endemic fish in the Tarim River Basin, Xinjiang, China, plays a pivotal role in maintaining the stability of plateau saline–alkaline aquatic ecosystems, yet its survival is increasingly threatened by habitat salinization. However, the multi-dimensional synergistic adaptation mechanisms linking its phenotypic variation, intestinal structure, and associated microbial communities to extreme saline–alkaline stress remain poorly understood. In this study, we innovatively integrated morphological/intestinal histological characterization, 16S rRNA gene sequencing, and microbial ecological analyses (co-occurrence networks and assembly processes) to systematically decode its adaptive strategies. Results revealed that T. yarkandensis exhibits a streamlined body shape, morphological variability, and elongated intestinal villi that may support locomotion and nutrient/ion uptake under osmotic stress. Its gut exerts a stringent selective filter, driving distinct differentiation between water and gut microbial communities—with gut-enriched core taxa (Aurantimicrobium and Aestuariivirga) and functional pathways (unsaturated fatty acid biosynthesis and ABC transporters) specialized for osmoregulation. Notably, the water microbial assembly is dominated by stochastic processes, while the gut assembly relies on host-driven deterministic selection, forming a habitat-specific adaptive pattern. These findings uncover the synergistic adaptation system of host phenotype and gut microbiota for survival in extreme saline–alkaline habitats, advancing our understanding of fish–microbe co-evolution in extreme ecosystems and providing critical theoretical support for the conservation of rare plateau fish, as well as guidance for the utilization of saline–alkaline water resources in aquaculture. Full article

Thismia species are non-photosynthetic plants entirely dependent on fungal partners for carbon and nutrients. While their arbuscular mycorrhizal associations are well-documented, bacterial symbiont roles remain unexplored. Using 16S rRNA gene amplicon sequencing, we investigated endophytic bacterial communities in T. gardneriana, T. javanica, and T. mirabilis from geographically distinct locations in Thailand. Despite geographic separation, Thismia spp. consistently harbored bacterial compositions taxonomically and functionally distinct from surrounding soil microbiomes. Root endospheres were significantly enriched in Pseudomonadota and Bacteroidota, particularly Puia, while showing reduced compositional dynamics of Acidobacteriota and Planctomycetota. Bacterial communities in Thismia roots were markedly distinct from surrounding soil, while root endosphere communities from geographically distinct habitats clustered together regardless of spatial separation. Mantel and partial Mantel tests confirmed that host species identity, not geographical location, was the primary predictor of root bacterial community structure. Functional prediction analyses suggested root-associated communities were enriched for nitrogen cycling pathways, particularly nitrogen fixation and nitrate reduction. The selective enrichment of Bacteroidota, known for nitrogen fixation and phosphate mobilization, suggests these bacteria provide critical nutritional support in nutrient-poor forest floor environments. Isolated root strains belonged exclusively to Bacillota, including Neobacillus with plant growth-promoting traits. Our findings highlight the importance of tripartite plant–fungal–bacterial interactions in Thismia nutritional ecology. Full article

Spaceflight exposes astronauts to multiple environmental stressors that promote oxidative stress, including ionizing radiation, microgravity, circadian rhythm disruption, and psychological stress. These factors increase the production of reactive oxygen species (ROS) and disturb redox homeostasis, potentially affecting multiple physiological systems during long-duration missions. In addition to environmental challenges, nutritional factors may further influence oxidative balance in space. Space food systems rely on long-term storage and processing, which can lead to degradation of antioxidant nutrients and alterations in dietary composition. Furthermore, spaceflight conditions may modify eating behaviors and disrupt gut microbiome composition, both of which are closely linked to host redox regulation. This review examines current knowledge on oxidative stress during spaceflight and discusses how space food systems, dietary composition, and microbiome alterations interact with spaceflight stressors to influence redox homeostasis. Potential strategies to mitigate oxidative stress are also discussed, including preservation of antioxidant nutrients, optimization of dietary composition, reduction in pro-oxidant exposures, and microbiome-targeted approaches to support astronaut health during long-duration missions. Full article

Increasing evidence suggests pancreatic cancer develops within a host–microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome–tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes. Full article

Campylobacter (C.) jejuni and C. coli are common zoonotic bacteria in pigs, which typically act as asymptomatic carriers. However, the effects of Campylobacter colonisation on the porcine intestinal microbiota and metabolome remain poorly understood. This study investigated microbiome and metabolome alterations associated with co-colonisation by C. jejuni and C. coli in the different intestinal segments of pigs. Thirty-two weaned piglets were assigned to a control group and a group inoculated with C. coli ST5777/CT828 and C. jejuni ST122/CT206. Four weeks post inoculation, jejunal and caecal contents were analysed for Campylobacter counts, metabolite profiles and microbial composition. All animals remained clinically healthy. Both Campylobacter species colonised the jejunum and caecum, with higher C. coli counts in the caecum. Campylobacter-colonised pigs showed significantly altered metabolite profiles, including reduced cysteine and urea and increased glycine in the jejunum, as well as elevated 3-hydroxybutyrate levels in the caecum. In contrast, short-chain fatty acid concentrations in the caecum were unaffected by infection. Microbiota analysis revealed a significant reduction in caecal alpha diversity, whereas jejunal diversity remained unchanged. Infected pigs exhibited increased relative abundances of Lactobacillaceae and Bifidobacteriaceae and a decreased abundance of Pseudomonadota, including Enterobacteriaceae. In conclusion, Campylobacter co-colonisation induces distinct microbiome and metabolome alterations in pigs despite the absence of clinical disease. These findings highlight complex host-microbiota–pathogen interactions that may be relevant for future Campylobacter control strategies in pig production. Full article

Background and Objectives: Gastric cancer remains a leading cause of cancer-related mortality worldwide and develops through complex interactions between environmental factors, microbial dysbiosis, and host molecular pathways. Although Helicobacter pylori infection is a well-established risk factor, emerging evidence suggests that broader alterations in the gastric microbiome may also contribute to carcinogenesis. However, the associations between gastric cancer-associated microbial taxa and host gene expression profiles remain insufficiently characterized. This study aimed to identify host gene signatures associated with gastric cancer-related microbial taxa through a descriptive analysis integrating microbiome-derived taxa with transcriptome data. Materials and Methods: Microbial taxa associated with gastric cancer were systematically retrieved from the Disbiome database. Taxon set enrichment analysis (TSEA) was performed using the MicrobiomeAnalyst platform to identify host genes associated with gastric cancer-associated taxa. Importantly, TSEA relies on healthy reference data from the Human Microbiome Project and does not establish gastric cancer-specific interactions or causal relationships. Gene expression levels were subsequently evaluated using The Cancer Genome Atlas (TCGA) PanCancer stomach adenocarcinoma (STAD) dataset by comparing tumor and matched normal gastric tissues. Gene interaction network and transcription factor (TF) enrichment analyses were conducted to explore predicted regulatory relationships. Results: Among 64 microbial taxa associated with gastric cancer, 43 were reported as elevated. After removing overlapping taxa across studies, 37 elevated and 21 reduced taxa were retained for analysis. TSEA identified 11 host genes associated with gastric cancer-related microbial taxa. Transcriptomic analysis demonstrated significant downregulation of DPP6 and DLG2, while KDM4D, USP34, and VDR were significantly upregulated in gastric cancer tissues compared with normal controls. Network and TF enrichment analyses revealed predicted co-expression and co-localization patterns among these genes, suggesting their potential involvement in immune-related processes, epigenetic regulation, and cellular organization. Conclusions: This descriptive study identifies distinct host gene expression signatures associated with gastric cancer-associated microbial dysbiosis. This study is purely associative and hypothesis-generating; no causal or mechanistic inferences are made. TSEA used healthy reference data and therefore does not reflect gastric cancer-specific host–microbe interactions. The findings provide a basis for future hypothesis-driven research but require validation in independent cohorts. Full article

The human gut microbiota represents a complex and dynamic ecosystem of trillions of microorganisms that play a fundamental role in maintaining physiological homeostasis, regulating metabolism, and modulating the immune system. This narrative review explores the biochemical intricacies of the gut microbiome, focusing on the dominant phyla (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Fusobacteria) and their specific contributions to host health. A critical emphasis is placed on the metabolic outputs of these microorganisms, such as short-chain fatty acids (SCFAs) like butyrate, which serve as vital energy sources and anti-inflammatory signaling molecules. Conversely, the review examines how dysbiosis, the disruption of microbial balance, is mechanistically linked to the pathogenesis of diverse conditions, including obesity, diabetes mellitus, inflammatory bowel disease (IBD), and gout. Furthermore, it highlights the profound impact of dietary interventions on microbial architecture, notably, how non-digestible carbohydrates promote beneficial taxa and eubiosis, while high-fat and high-sugar diets drive metabolic endotoxemia and systemic inflammation. By synthesizing current knowledge on microbial biotransformations of proteins and polyphenols, this work underscores the bidirectional relationship between nutrition and the microbiome. Ultimately, understanding these biochemical interactions is essential for developing targeted probiotic, prebiotic, and nutritional strategies to prevent and manage chronic metabolic and inflammatory disorders. Full article

Background/Objectives: The human gastrointestinal tract is a dynamic and interactive micro-ecosystem, with its distinct microbial population residing in the gut. The healthy condition of the gut is integrated into the normal functioning of all physiological activities. The gut microbiome is critical for the functioning of metabolism via several gut-axis connections with different systems in the human body; thus, it affects the status of health and general well-being. The fundamental physiology and homeostatic shifts are associated with specific diseases caused by a disrupted balance in the diversity of the gut microbiome, which could be due to a condition of dysbiosis in a host, instigated by several reasons. Some studies have been conducted on the selective isolation of probiotic species from dairy and other food sources to obtain effective probiotic strains, which have been studied and used by dietary intake strategies to restore gut microbial diversity, which is disturbed by some disease/s. Methods: Our search strategy included specific keywords—gut, microbiota, microbiome, disease, dysbiosis, probiotic bacteria and yeast—and was based on a timeframe of 15 years in the web-based electronic databases of PubMed, Scopus, and Web of Science. Among the few hundred results, a secondary screening was conducted to select references on probiotics studied for disease management with preclinical evidence and some reports on clinically validated outcomes; we excluded the search results for screening fermented foods for taxonomy studies of isolated probiotics. Results: The summarised information using two figures and two tables has been presented in this article from the review of 137 selected references: >75% have been published in the last 10 years. Conclusions: Further advances in modelling and analysis of the gut microbiota are required to understand their influence on the occurrence of certain diseases; this approach will allow us to establish research strategies for filling knowledge gaps, inconsistencies in clinical evidence, or limitations in translating probiotic effects from experimental models to humans. Full article

Background/Objectives: Glyphosate-based formulations are globally pervasive pollutants increasingly recognized as potential contributors to antimicrobial resistance (AMR) in environmental microbiomes. Although glyphosate is designed to inhibit plant 5-enolpyruvylshikimate-3-phosphate synthase, it also affects microbial metabolism, stress response, and genetic exchange. This review synthesizes the pathways through which glyphosate, its metabolite aminomethylphosphonic acid (AMPA), and commercial mixtures influence resistance-associated phenotypes and the dissemination of antibiotic resistance (ABR). Methods: A critical synthesis of the literature was conducted to evaluate the mechanistic and ecological interactions between glyphosate exposure and bacterial resistance in soil, aquatic, and host-associated microbiomes. Results: Experimental evidence showed that sublethal glyphosate exposure induced oxidative stress, altered membrane permeability, activated multidrug efflux pumps, and promoted tolerance phenotypes that could modify antibiotic susceptibility. It also enhances mutation rates and horizontal gene transfer processes associated with the emergence of resistance under controlled conditions. At the community level, glyphosate exposure is associated with microbiome restructuring and enrichment of resistance determinants, often without major shifts in overall diversity of the microbiome. These effects have been reported at environmentally relevant concentrations, although the evidence remains largely derived from laboratory and mesocosm studies. Conclusions: Glyphosate acts as both a biochemical modulator of resistance-related phenotypes and an environmental selective pressure that shapes microbial communities. Its widespread use and environmental persistence position it as a context-dependent contributor to the emergence and dissemination of AMR through interacting mechanistic and ecological pathways. Integrating AMR endpoints into pesticide risk assessments and surveillance frameworks is warranted, in addition to expanded field-based validation. Full article

Antibiotic-associated diarrhea (AAD) is primarily driven by disruption of the gut microbiota accompanied by intestinal mucosal injury. Although multiherb formulations are widely used in East Asian medicine, their collective ecological effects and integrated microbiome–host mechanisms have not been systematically synthesized. This systematic review included 17 preclinical studies that investigated multiherbal formulations in AAD models. Given the substantial heterogeneity in the formulation composition, experimental design, and analytical platforms, a descriptive synthesis was performed. The included formulations were categorized into four clusters based on their shared herbal composition: Qiwei Baizhu San (QWBZP), Lizhong Tang (LZT), Gegen Qinlian Tang (GQT), and other supportive multiherbal formulations. The cluster-based synthesis revealed distinct convergent therapeutic strategies. The QWBZP and LZT clusters primarily supported the restoration of host metabolic and digestive functions, whereas the GQT cluster exhibited potent pathogen control effects with the suppression of opportunistic taxa. Across all clusters, a convergent microbiome–host response emerged, characterized by enrichment of commensal bacteria (e.g., Lactobacillus), upregulation of tight junction proteins (e.g., ZO-1, occludin), and attenuation of pro-inflammatory mediators (e.g., TNF-α, myeloperoxidase). Multiherb formulations in AAD models not only act as microbial modulators but also function as host-directed modulators that stabilize the intestinal homeostatic niche. Botanical interventions may facilitate endogenous microbiome recovery by reinforcing mucosal integrity and reducing environmental resistance. This ecological framework provides a rationale for future translational studies evaluating integrated herbal–probiotic strategies and precise microbiome management for patients with AAD, while further clinical validation is warranted. Full article