@article {pmid42103282,
year = {2026},
author = {Cissé, M and Moullé, V and Brossaud, R and Oullier, T and Neunlist, M},
title = {Microbiota-Gut-Brain Axis in Neurodegenerative Diseases: The Role of Bacterial Amyloids.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101802},
doi = {10.1016/j.jcmgh.2026.101802},
pmid = {42103282},
issn = {2352-345X},
abstract = {Neurodegenerative diseases are proteinopathies, characterized by misfolded protein aggregation in the brain that drives neuronal dysfunctions. Neurodegenerative diseases are also increasingly recognized as multi-organ disorders in which the gut plays a pivotal role. Indeed, recent advances in the research field of neurodegenerative diseases suggest that the gut is not merely a passive bystander, given the high prevalence of gastrointestinal symptoms, but a critical contributor to disease etiology, with evidence supporting a direct role in initiating and driving disease progression. Among environmental factors increasingly recognized as modulators of neurodegenerative disease progression, the gut microbiota has gained prominence. Beyond the impact of altered bacterial metabolites, growing evidence indicate a potential role of gut microbiota-derived amyloids in neurodegenerative diseases. For instance, gut microbial amyloids such as curli can cross-seed host proteins like α-synuclein and β-amyloid promoting aggregation, gut-to-brain propagation, and exacerbating neurodegeneration, revealing a novel mechanism linking the microbiome to neurodegenerative diseases. This conceptual shift opens promising avenues for strategies targeting the gut microbiota, including therapeutic and preventive interventions aimed at reshaping microbial communities or limiting exposure to pathogenic amyloids to reduce risk of neurodegenerative diseases. Here, we review recent discoveries to elucidate the complex interplay between gut microbiota and host amyloids, offering insights for enhancing gut and brain health and potentially preventing or reversing neurodegenerative disease progression.},
}

@article {pmid42164666,
year = {2026},
author = {Wu, X and Li, M and Xu, Y and Liu, X and Gao, Z and Jiang, X and He, J and Wu, Y and Wu, C},
title = {Axillary and gut microbiota characteristics in axillary bromhidrosis patients and the effect of microwave therapy: a case-control study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1769465},
pmid = {42164666},
issn = {1664-302X},
abstract = {INTRODUCTION: Axillary bromhidrosis is characterized by excessive sweat gland activity and foul body odor, significantly affecting patients' psychological well-being and social interactions.

METHODS: This study recruited 30 axillary bromhidrosis patients and 30 healthy controls, collecting sweat and stool samples for microbiome analysis. Among the patients, 8 patients received microwave therapy, collecting pre- and post-treatment samples for microbiome analysis.

RESULTS: The axillary microbiota of patients showed significant differences compared to healthy controls, particularly with increased abundance of odor-causing bacteria such as Staphylococcus and related species (Staphylococcus hominis, Staphylococcus haemolyticus) (LDA > 3, p < 0.05). While the gut microbiota composition showed no significant changes, but LEfSe analysis revealed that SCFAs-producing bacteria (Bacteroides stercoris, Phocaeicola massiliensis, and Phocaeicola vulgatus) was significantly elevated (LDA > 3, p < 0.05), indicating that the abundance changes of SCFAs-producing bacteria may be associated with axillary odor production through the regulation of metabolic processes. Correlation analysis revealed positive correlations between axillary odor-producing genera (Staphylococcus, Peptoniphilus, Anaerococcus) and gut SCFAs-producing genera (Roseburia, Blautia, Clostridium), suggesting a bidirectional microbiota network through gut-derived butyrate production and immune modulation (p < 0.05). However, further experimentals are required to confirm the causal relationship. Furthermore, microwave therapy significantly altered axillary microbiota diversity, potentially alleviating axillary odor by inhibiting odor-producing bacteria (Staphylococcus) (LDA > 3, p < 0.05), while exerting minimal impact on the gut microbiota. KEGG pathway enrichment analysis revealed significant metabolic activity changes in lipid, carbohydrate, sulfur, and amino acid metabolism pathways.

CONCLUSION: This study is the first to demonstrate the interrelationship between the axillary and gut microbiota in axillary bromhidrosis patients, showing a link between gut-derived butyrate production and axillary odor. These findings offer new insights into the microbiological mechanisms underlying axillary bromhidrosis and identify potential microbial targets for future gut-based systemic treatments.},
}

@article {pmid42164667,
year = {2026},
author = {Ma, H and Li, J and BanMa, C and Yuan, F and Chen, Y and Yang, X and Yang, X and Wang, T and Zhou, G},
title = {Analysis of microbial diversity in Lagotis brevituba Maxim. from different production areas on the Qinghai-Xizang Plateau and its correlation with secondary metabolic products.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797784},
pmid = {42164667},
issn = {1664-302X},
abstract = {Lagotis brevituba Maxim. (Lagotis brevituba), belonging to the genus Lagotis within the family Scrophulariaceae. The content of its secondary metabolites exhibits significant variation across different provenances, yet the underlying mechanisms linking these variations to microbial associations remain unclear. In this study, 12 samples of rhizosphere soil, root systems, and plant specimens of Lagotis brevituba were collected from various locations on the Qinghai-Xizang Plateau, and the physicochemical properties of the soil were systematically determined. Using high-throughput 16S and ITS rRNA sequencing technologies, the diversity and composition of bacterial and fungal communities were analyzed; simultaneously, the concentrations of 10 key secondary metabolites were quantitatively determined using high-performance liquid chromatography (HPLC). Furthermore, correlation network analysis and redundancy analysis were used to investigate the relationships among soil physicochemical factors, microbial communities, and secondary metabolites. The results indicate that an elevation of 4500 m serves as a critical threshold, marked by significant changes in soil physicochemical properties. Specifically, compared to the HA group (3500-4500 m), the EA group (elevation > 4500 m) exhibited significantly lower soil organic matter and available phosphorus content, while pH and total nitrogen content were significantly higher. These soil changes indicate the presence of nutrient-poor and alkaline stress conditions, which in turn led to the differentiation of rhizosphere bacterial communities and stimulated the synthesis of more antioxidant metabolites (e.g., significantly elevated β-Sitosterol, Quercetin, and Plantamajoside) in the EA group. Microbial community analysis revealed that bacterial community structure exhibited a significant response to changes in elevation, whereas fungal communities showed no significant differences. Soil physicochemical properties (particularly pH, SOM, and AP) are key mediating factors driving microbial community differentiation and the accumulation of secondary metabolites. A combined analysis of correlation networks and Zi-Pi values identified 19 key OTUs (Operational Taxonomic Units) mediating the relationships between microorganisms and metabolites. Notably, Aquabacterium exhibited significant negative correlations with Luteolin and Acteoside, while Streptomyces showed significant positive correlations with Hyperoside (P < 0.05). This study demonstrates that soil environmental factors structure microbial communities, which in turn play a crucial role in regulating the secondary metabolites of medicinal plants. These findings provide theoretical foundations for elucidating the environment-microbiome-metabolite nexus in Lagotis brevituba.},
}

@article {pmid42164668,
year = {2026},
author = {Moro, MS and Ludwig, TD and Scaketti, M and Francisconi, AF and Mendes, LW and Pinheiro, JB and Zucchi, MI},
title = {Host genetics and environment shape the gut microbiome of Euschistus heros and Piezodorus guildinii and potentially influencing their adaptation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1782301},
pmid = {42164668},
issn = {1664-302X},
abstract = {BACKGROUND: Euschistus heros and Piezodorus guildinii are major soybean pests across the Americas. Gut-associated bacteria influence insect nutrition, detoxification, and stress tolerance, potentially enhancing adaptation to diverse hosts and management regimes. We investigated how host genetics and environment shape gut microbiome structure and functional potential in these species.

RESULTS: We sequenced the 16S rRNA V4 region from 189 insects collected across Brazil and the United States. Microbiomes were dominated by Proteobacteria and Firmicutes, exhibiting high intra- and interpopulation variability. Diversity and community structure varied significantly among lineages and locations; while environment explained a larger share of overall variance, host genetics provided a more distinct statistical signal for group differentiation. In E. heros, genera linked to nutrient acquisition and detoxification (e.g., Pantoea, Wolbachia) were more prevalent. In P. guildinii, Candidatus Benitsuchiphilus-associated with diapause and uric-acid metabolism-predominated. Predicted functions included chemoheterotrophy, nitrogen fixation, and degradation of aromatic compounds, with distinct patterns across species and geographic lineages.

CONCLUSION: Both genetic and environmental factors shape the composition and functional capacity of stink bug gut microbiomes, potentially contributing to host adaptation across different agricultural landscapes. These insights open avenues for microbiome-informed strategies to improve the sustainability and efficacy of soybean pest management.},
}

@article {pmid42164669,
year = {2026},
author = {Yuan, B and Li, C and Wang, Q and Yao, Q and Guo, X and Wang, Z},
title = {Maize stover mulching combined with an optimized fertilization strategy reshapes rhizosphere microbial communities and functions in greenhouse potato.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1670904},
pmid = {42164669},
issn = {1664-302X},
abstract = {Protected cultivation systems offer opportunities for improving potato productivity but are often constrained by inefficient maize stover utilization and suboptimal fertilization practices. In this study, a 4 × 4 factorial experiment was conducted using the potato cultivar 'Jishu No. 1' to decode the rhizosphere microbial mechanisms underpinning plant growth and yield enhancement under greenhouse conditions. We hypothesized that integrated management (the synergy between stover mulching and fertilization) would modify the soil microenvironment, thereby reshaping microbial community assembly patterns and functional gene distributions. The results showed that while split fertilization combined with moderate stover mulching (F2S2, 8,500 kg·hm[-2] stover mulching) was most effective in enhancing plant physiological status, full topdressing combined with the same mulching level (F3S2) achieved the highest agronomic productivity, increasing total yield to 42.33 t·hm[-2]. Metagenomic analysis revealed that the F3S2 strategy significantly reshaped the rhizosphere microbiome, characterized by higher α-diversity and the enrichment of pathways related to carbon metabolism and carbohydrate processing. Notably, F3S2 promoted the recruitment of copiotrophic taxa, particularly Actinobacteriota, whose relative abundance was significantly and positively correlated with soil organic phosphorus (r = 0.623, p < 0.05). In contrast, oligotrophic groups like Acidobacteriota were relatively less abundant in nutrient-rich treatments. These findings demonstrate that moderate stover mulching combined with dynamic fertilization provides a high-resource niche that favors functional microbial groups, thereby driving rhizosphere nutrient cycling to support potato performance. This study underscores the importance of optimized stover and fertilizer management strategies in protected cultivation.},
}

@article {pmid42164770,
year = {2026},
author = {Botia Carreño, EO and Elghandour, MMMY and De Palo, P and Maggiolino, A and De Angelis, M and Salem, AZM},
title = {Nano/microencapsulation of feed additives for ruminal microbiome modulation and enteric methane mitigation in ruminants: a critical review.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1798669},
pmid = {42164770},
issn = {2297-1769},
abstract = {The latest advances in nutrition, microbiology, and omics sciences are redefining strategies to improve health indices and productivity in livestock. A novel strategy focuses on the deliberate modulation of rumen and intestinal microbiome ecosystems, which, besides being complex, are crucial for animal performance. The use of feed additives, such as bioactive compounds derived from plants and probiotics, has a long tradition supported by their known antioxidant, anti-inflammatory, and antimicrobial properties, among others. However, their practical efficacy is often compromised by their high susceptibility to degradation. Environmental factors such as light, temperature, and harsh conditions like extreme pH and enzymatic and microbiota activity in the gastrointestinal tract of livestock can inactivate these compounds before they reach their site of action to exert the beneficial effects mentioned above. To solve this challenge, nanotechnology, specifically micro- and nanoencapsulation techniques, presents an innovative solution. These strategies can protect bioactive compounds, providing controlled release and targeted delivery to specific absorption sites. This design not only optimizes probiotic survival and bioavailability of bioactive compounds but also facilitates more effective modulation of ruminal and intestinal microbial communities. Recent evidence indicates that this modulation translates into tangible productive benefits, such as better nutrient absorption and higher energy efficiency, positively impacting parameters like milk production. Additionally, these encapsulation techniques improve the efficiency of these bioactive compounds to mitigate enteric methane emissions by altering ruminal fermentation patterns. This review critically analyzes the mechanisms, applications, and potential of encapsulation technologies in ruminant production. Special emphasis is placed on how these delivery systems represent a significant advance toward precision nutrition. Indeed, the efficacy of encapsulation for microbiota manipulation and toxicological challenges for safe and sustainable implementation is discussed. This critical review addresses the following questions: (1) Under what conditions could encapsulation offer real advantages over traditional additives in ruminant livestock? (2) Are there biologically significant differences between nano- and microencapsulation in the ruminal environment? (3) How are changes in the ruminal microbiota translated into productive performance and environmental impact? (4) What is the balance between productive and environmental sustainability benefits versus the toxicological risks of nanomaterials?},
}

@article {pmid42164832,
year = {2026},
author = {Kumar, A and Krishan, B and Dhiman, S and Sharma, A and Thadiyan, V and Azmi, W},
title = {Beyond antibiotics: innovative and translational strategies to overcome antimicrobial resistance.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {201},
pmid = {42164832},
issn = {2190-572X},
abstract = {The rapid rise of antimicrobial resistance demands therapeutic strategies that extend beyond conventional antibiotics. However, most existing reviews describe emerging alternatives without systematically linking their mechanistic advances to translational readiness and clinical implementation barriers. This review addresses this gap by integrating evidence across multiple beyond-antibiotic approaches, including antimicrobial peptides, bacteriophage therapy, CRISPR-based antimicrobials, nanotechnology-enabled delivery systems, anti-virulence agents, host-directed immunotherapies, microbiome modulation (engineered probiotics and fecal microbiota transplantation), and drug-repurposing or combination therapies. The principal contribution of this synthesis is a comparative framework that maps mechanisms of action, engineering innovations, and translational evidence across these diverse strategies. Advances such as peptidomimetics, engineered phages, and nanoparticle carriers that enhance stability, targeting, and therapeutic efficacy are highlighted, along with synergistic strategies including phage-antibiotic and CRISPR-nanocarrier combinations. The review further identifies major barriers limiting clinical translation, including delivery efficiency, toxicity and ecological concerns, large-scale production challenges, cost, inconsistent clinical outcomes, and regulatory fragmentation for biologics and live therapeutics. To facilitate clinical implementation, the study proposes a translational roadmap emphasizing standardized evaluation assays, physiologically relevant infection models, integrated rapid diagnostics, and regulatory frameworks tailored for emerging antimicrobial platforms, thereby supporting the development of sustainable therapies for the post-antibiotic era.},
}

@article {pmid42164875,
year = {2026},
author = {Lei, C and Liang, R and Cheng, B and Cao, X and Zhang, J and Wang, C and Wang, Z},
title = {Foodborne Carbon Dots Trigger Appetite Suppression: Mechanistic Insights from the Microbiota-Gut-Brain Axis.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {5},
pages = {965-977},
pmid = {42164875},
issn = {2833-8278},
abstract = {Foodborne carbon dots (FCDs) are an overlooked ingestible nanoscale food substance, and the potential ingestion risks associated with persistent dietary preferences need to be clearly articulated. In this study, the effects of FCDs and glucose CDs on feeding behavior in mice were elucidated from the perspectives of gut microbiome, metabolic flow monitoring, and metabolomics. The results demonstrated that persistent intake of FCDs (25 mg/kg/day) for 30 days significantly caused diminished appetite. Mechanistic findings suggested that FCDs were involved in the regulation of appetite reduction through the microbiota-gut-brain axis. FCDs induce perturbations in the gut microbiota, leading to increased levels of intestinal inflammation. In addition, the intake of FCDs was directly involved in microbial metabolism to generate SCFAs, activate intestinal GPR-41/43, promote the release of glucagon-like peptide, and further stimulate the hypothalamus to significantly downregulate the expression of AGRP and upregulate the expression of POMC, ultimately leading to the reduction of appetite. Moreover, intake of FCDs regulates intestinal fatty acid metabolism, amino acid metabolism, and other factors affecting the level of health of the organism. The present work highlights the impact of dietary intake of source FCDs on ingestion, providing unique perspectives on the potential health threats of FCDs.},
}

@article {pmid42164883,
year = {2026},
author = {Gai, S and Li, G and Xu, W and Nan, X and Qu, G and Peng, G and Jiang, G},
title = {From Microbial Dysbiosis to Host Pathogenesis: Unraveling the Gut Microbiome's Role in Environmental Toxicology.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {5},
pages = {800-803},
pmid = {42164883},
issn = {2833-8278},
}

@article {pmid42164891,
year = {2026},
author = {Zhang, Y and Meng, X and Gong, J and Xu, Y and Hua, Q and Chen, W and Wang, T and He, X and Xu, R and Gao, Y and Ye, C and Wu, C and Fan, Y and Zu, L and Zhu, T},
title = {Short-Term High-Altitude Exposure Alters Pharyngeal and Gut Microbiome.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {5},
pages = {1002-1011},
pmid = {42164891},
issn = {2833-8278},
abstract = {High-altitude exposure poses significant health challenges, where microbial communities may serve as important contributors to host acclimatization. We conducted a longitudinal study to investigate the dynamic changes in pharyngeal and gut microbiota before, during, and after acclimatization to the Mount Qomolangma region (high-altitude, 4300-5200 m above sea level, m.a.s.l.). Twenty healthy participants underwent four health visits: at baseline level (Beijing, 50 m.a.s.l.), upon arrival at the high altitude, after a week of acclimatization, and upon return to the baseline level. Throat swabs and fecal samples were collected for 16S rRNA amplicon sequencing to assess microbial composition and diversity. Linear mixed-effects models were employed to estimate the altitude-associated variations in pharyngeal and gut microbes compared to the baseline. Pharyngeal microbial diversity showed statistically significant alterations after 1 week at high altitude, with the Shannon index decreasing by 12.0% (95% CI: -21.8 to -2.9%) and the Simpson index increasing by 2.6% (1.3 to 4.0%). In contrast, gut microbial diversity decreased upon initial high-altitude exposure but tended to revert to baseline after 1 week of acclimatization. Beta diversity analyses revealed significant differences in pharyngeal microbiota across visits, while gut microbiota differences were less pronounced. Using the linear discriminant analysis effect size (LEfSe) method, we identified 11 pharyngeal and four gut microbes that were differentially abundant across visits, which could shape the host's resilience to high-altitude challenges. Our study reveals that high-altitude exposure disrupts pharyngeal and gut microbial diversity over time and modulates the abundance of some opportunistic pathogens. These shifts may mediate host responses to hypoxic environments, underscoring the microbiomes' role in physiological acclimatization.},
}

@article {pmid42165017,
year = {2026},
author = {Hansson, P and Myhrstad, MCW and Costantini, L},
title = {Editorial: Impact of dietary factors on human gut microbiota and gastrointestinal endocrinology.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1858858},
doi = {10.3389/fendo.2026.1858858},
pmid = {42165017},
issn = {1664-2392},
}

@article {pmid42165190,
year = {2026},
author = {Iqbal, T},
title = {Gut microbiota and disease.},
journal = {Essays in biochemistry},
volume = {69},
number = {6},
pages = {},
doi = {10.1042/EBC20250046},
pmid = {42165190},
issn = {1744-1358},
support = {N/A//NIHR | Birmingham Biomedical Research Centre (Birmingham BRC)/ ; N/A//NIHR | Efficacy and Mechanism Evaluation Programme (EME)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Neoplasms/microbiology/drug therapy/metabolism ; *Neurodegenerative Diseases/microbiology/metabolism ; },
abstract = {The human gut microbiome-predominantly in the colon-comprises vastly more genetic material than that contained in human cells. Three papers in this journal highlight the functional consequences of imbalance (dysbiosis) of the gut microbiome regarding neurodegenerative conditions, cancer chemotherapy, and the wide-reaching consequences of aberrant metabolism of complex carbohydrates and amino acids in the gut.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Neoplasms/microbiology/drug therapy/metabolism
*Neurodegenerative Diseases/microbiology/metabolism

@article {pmid42165232,
year = {2026},
author = {Nap, B and Thinnes, CC and Thiele, I},
title = {Whole-body metabolic modelling and its prospects in precision nutrition.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-19},
doi = {10.1017/S0029665126103061},
pmid = {42165232},
issn = {1475-2719},
abstract = {Nutrition has long been investigated with respect to its influence on human health. With the availability of various omics data, such as metagenomics and metabolomics, novel insights have been obtained into the influence of nutrition, particularly concerning the gut microbiome. The gut microbiome plays an important role in the breakdown of food-derived compounds and in producing essential bioactive metabolites required for human health. However, this wealth of information made the interactions between nutrition and human health increasingly intricate, and unravelling these links is complex. This review covers the concepts of genome-scale metabolic modelling as a tool to understand the links between nutrition, the gut microbiome and human metabolism and its applications. Genome-scale metabolic modelling treats metabolism as a mathematical problem which was used to develop models of human metabolism that incorporate physiology and organ-specific metabolism, known as whole-body metabolic models (WBMs). WBMs can incorporate physiological data, such as sex, weight, and body fat percentage, as well as nutrition in the form of its metabolite constituents. Finally, the gut microbiome can also be incorporated through a mathematical representation of the species present, based on stool metagenomics. WBMs have already been applied to understand gut microbiome-host co-metabolism in various non-communicable diseases. However, challenges remain, as metabolites measured in food items in public databases typically cover only common metabolites, and engagement with end-users such as nutritionists and policymakers is limited. Nevertheless, WBMs represent a promising step towards digital metabolic twins and thus personalised nutrition and medicine.},
}

@article {pmid42165244,
year = {2026},
author = {Kouraki, A and McWilliams, D and Valdes, AM},
title = {Interactions between nutrition, GLP-1 secretion, and composition of the gut microbiome.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
pmid = {42165244},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: Glucagon-like peptide-1 (GLP-1) is a key incretin hormone regulating insulin secretion, appetite, and energy balance. Recent research highlights complex interactions between dietary composition, gut microbiome metabolism and GLP-1 secretion. Understanding these relationships is increasingly important given the widespread clinical use of GLP-1 receptor agonists for obesity and type 2 diabetes and the growing interest in microbiome-targeted nutritional strategies.

RECENT FINDINGS: Recent studies demonstrate that microbial metabolites mediate many nutritional effects on GLP-1 secretion. Fermentation of dietary fibres generates short-chain fatty acids (SCFAs) that stimulate GLP-1 secretion through FFAR2/FFAR3 signalling. Additional microbial metabolites can regulate enteroendocrine signalling, including indole derivatives, N-acyl glycines and bile acid metabolites. Human and preclinical studies show that dietary interventions such as β-glucan supplementation, fermentable carbohydrate diets, probiotics, polyphenols and plant polysaccharides can influence GLP-1 secretion through microbiome-dependent mechanisms.

SUMMARY: Evidence supports an interaction between nutrition, the gut microbiome and GLP-1 signalling. Microbial metabolites link dietary substrates to GLP-1 secretion and diet shapes the microbial communities producing them. Integrating microbiome profiling with dietary interventions may help optimise metabolic therapies and explain variability in responses to GLP-1-based treatments.},
}

@article {pmid42165302,
year = {2026},
author = {Tian, L and Ren, W and Li, Y and Ding, L and Yu, Z and Yu, Y and Li, S and Zhang, T and Du, Z},
title = {Nanocarriers enhance oral bioavailability: from absorption mechanisms to design strategies.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/10408398.2026.2672547},
pmid = {42165302},
issn = {1549-7852},
abstract = {Gastrointestinal barriers (acidic environment, mucus barrier, tight junctions, and microbiota metabolism) have long constrained the oral bioavailability of food-derived bioactives, especially lipophilic constituents. Recent advances in functionalized nanoparticle strategies offer sophisticated techniques to address these challenges. Specifically, precise control of particle size, morphology and surface functionalization enhances mucus penetration and cellular uptake of nanocarriers. Advanced nanocarrier strategies, such as mucosal adhesion, receptor-mediated targeting, and co-delivery with permeation enhancers, facilitate efficient absorption by opening intercellular gaps and activating specific endocytosis pathways. Intelligent designs for pH, enzyme, redox, and microbiome responses resulted in precise protection and targeted release of cargoes in various gastrointestinal segments. This review summarizes critical strategies for absorption-optimized oral nanoplatforms, including absorption mechanisms, mucosal retention, receptor-mediated endocytosis, co-delivery with absorption enhancers, and multi-strategy coupling. We emphasize strategic orientations for maximizing oral absorption efficiency of bioactive ingredients, offering a transformative framework for architecting next-generation oral nanocarrier platforms of food-derived components.},
}

@article {pmid42165387,
year = {2026},
author = {Sekiya, S and Masuda, M and Mizuno, Y and Naka, H and Goto, C and Imai, H and Umezaki, M},
title = {Interindividual Variation in Adult Gut Microbiome Composition in Two Rural Communities in Japan: Associations With Energy and Nutrient Intakes.},
journal = {American journal of human biology : the official journal of the Human Biology Council},
volume = {38},
number = {5},
pages = {e70274},
doi = {10.1002/ajhb.70274},
pmid = {42165387},
issn = {1520-6300},
support = {24H00575//JSPS KAKENHI/ ; 19H03315//JSPS KAKENHI/ ; 23K21790//JSPS KAKENHI/ ; 20K21443//JSPS KAKENHI/ ; 23K17525//JSPS KAKENHI/ ; 20H05127//JSPS KAKENHI/ ; 22003//Cooperative Research Program of the Institute of Nature and Environmental Technology, Kanazawa University/ ; 23003//Cooperative Research Program of the Institute of Nature and Environmental Technology, Kanazawa University/ ; JPMJSP2108//JST SPRING/ ; //The Kyoto University Center for Maritime Asian and Pacific Studies (MAPS)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Japan ; Rural Population/statistics & numerical data ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; *Energy Intake ; *Diet/statistics & numerical data ; *Nutrients ; Aged ; Young Adult ; RNA, Ribosomal, 16S/analysis ; },
abstract = {OBJECTIVES: The "Japanese diet" has long been regarded as a key factor contributing to the remarkable life expectancy of the Japanese population. Given that the gut microbiome is thought to mediate the link between diet and health, this study investigated energy and nutrient intake among rural populations in Japan, who are presumed to adhere closely to the traditional "Japanese diet," and examined their association with gut microbiome diversity and composition.

METHODS: A cross-sectional study of 263 individuals aged ≥ 20 years was conducted in two rural communities in Japan, in July and August 2022. Participants completed a food frequency questionnaire, and we measured weight and height and collected fecal samples. The diversity and composition of the gut microbiome were assessed using 16S ribosomal RNA analysis. The associations between energy and nutrient intakes and alpha diversity metrics, beta diversity metrics, and the relative abundance of bacteria at the genus level were assessed.

RESULTS: Individuals who consumed more nutrients characteristic of seafood, rice, and vegetables (vitamin D, omega-3 highly unsaturated fatty acids, carbohydrates, total dietary fiber, and insoluble dietary fiber) had significantly higher gut microbiome diversity, while those who consumed more alcohol and fat had significantly lower microbiome diversity. Energy intake from alcohol, as well as intakes of cholesterol, iron, vitamin B1, vitamin C, carbohydrates, soluble dietary fiber, omega-3 highly unsaturated fatty acids, and calcium were significantly associated with beta diversity metrics (p < 0.05), indicating that gut microbiome composition varied with these nutrient intakes.

CONCLUSION: Nutrient intakes may influence the interindividual variation in the gut microbiome seen in two rural populations in Japan. Future research should focus on elucidating the interactive effects between the "Japanese diet" and the gut microbiome.},
}

Humans
*Gastrointestinal Microbiome
Japan
Rural Population/statistics & numerical data
Male
Female
Adult
Cross-Sectional Studies
Middle Aged
*Energy Intake
*Diet/statistics & numerical data
*Nutrients
Aged
Young Adult
RNA, Ribosomal, 16S/analysis

@article {pmid42165419,
year = {2026},
author = {Green, ET and Carbone, I and Mitchell, CE},
title = {Seasonal Assembly of the Phyllosphere Fungal Microbiome of a Perennial Grass is Robust to Nutrient Addition.},
journal = {Molecular ecology},
volume = {35},
number = {10},
pages = {e70384},
doi = {10.1111/mec.70384},
pmid = {42165419},
issn = {1365-294X},
support = {2016-67013-25762//U.S. Department of Agriculture/ ; DEB-2308472//National Science Foundation/ ; },
mesh = {Seasons ; *Plant Leaves/microbiology ; *Fungi/genetics/classification ; Nutrients ; *Mycobiome/genetics ; *Microbiota/genetics ; Phylogeny ; Soil Microbiology ; *Poaceae/microbiology ; Soil/chemistry ; *Lolium/microbiology ; Biodiversity ; },
abstract = {The leaf microbiome plays an important role in plant health and defence. Despite its importance, how the assembly of the leaf microbial community is modified by environmental conditions such as nutrient availability remains relatively uninvestigated. Soil nutrient availability may shift the outcome of microbial interactions within a host individual or influence the pool of microbes across the plant community. We hypothesised that leaf microbial diversity would increase across the season as leaves collect additional taxa, and that this seasonal assembly would be sensitive to nutrient addition. To assess this, we tracked the assembly of the fungal phyllosphere microbiome of the grass tall fescue (Lolium arundinaceum) in old-field vegetation over the growing season and experimentally tested whether the seasonality of the microbiome was modified by experimental addition of soil nutrients. Fungal diversity (Shannon diversity index, richness, and evenness) increased early in the season, with most metrics saturating before the end of the season. Community composition as measured by Bray-Curtis dissimilarity also shifted over the early and mid-growing season. Phylogeny-based machine-learning identified fungal lineages that were abundant in different seasons, linking seasonal community shifts to their evolutionary context. Nutrient addition was less important than time of season, but still significantly altered community composition and interacted with time to influence richness, with lowest richness in the low nutrient addition plots early in the season. The clear seasonality of the microbiome provides support for a dynamic phyllosphere microbiome, suggesting further studies manipulating fungal recruitment over the season. Furthermore, it highlights the robustness of seasonal assembly to variation in nutrient availability.},
}

Seasons
*Plant Leaves/microbiology
*Fungi/genetics/classification
Nutrients
*Mycobiome/genetics
*Microbiota/genetics
Phylogeny
Soil Microbiology
*Poaceae/microbiology
Soil/chemistry
*Lolium/microbiology
Biodiversity

@article {pmid42165584,
year = {2026},
author = {Lee, S and Dobes, P and Mascellani Bergo, A and Killer, J and Marciniak, J and Hurychova, J and Sreibr, S and Kamler, M and Purnoch, V and Hlinakova, L and Titera, D and Cinek, O and Carolan, JC and Hyrsl, P and Havlik, J},
title = {Bacterial supplementation shapes honey bee gut microbiota and host metabolism under controlled and field conditions.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0028326},
doi = {10.1128/msystems.00283-26},
pmid = {42165584},
issn = {2379-5077},
abstract = {Gut bacteria are essential to honey bee (Apis mellifera) health, supporting digestion, immunity, and resilience against stressors. Probiotic-based strategies have been proposed to enhance core gut symbionts, yet the underlying mechanisms and influences of environmental context on these effects are not fully understood. This study examined the influence of gut-derived bacterial supplementation on the honey bee gut microbiome, proteome, and metabolome across three conditions: (i) controlled cages, (ii) semi-controlled cages allowing contact with nestmates, and (iii) field conditions. Treatment groups received a bacterial supplement containing Lactobacillus helsingborgensis, Lactobacillus apis, Bifidobacterium choladohabitans, and Bifidobacterium polysaccharolyticum, while control groups received only a sucrose solution. Gut samples from 10-day-old bees were analyzed. Supplemented bees showed strong gut colonization by Bifidobacterium and Lactobacillus, especially under controlled and semi-controlled conditions. In the field, L. helsingborgensis remained significantly enriched in the treatment group, demonstrating short-term ecological resilience in the natural hive environment. Proteomic changes in supplemented bees included an increased abundance of major royal jelly protein precursors and mitochondrial-associated proteins, together with reduced abundance of several ribosomal and translation-related proteins involved in peptide biosynthesis and cellular protein quality control. Metabolomic analysis revealed reproducible shifts across all three conditions. Treatment groups showed higher concentrations of microbial fermentation products (acetate, succinate) and potential neuromodulatory metabolites (ornithine, γ-aminobutyrate), while sucrose, N-acetylglucosamine, and uridine were constantly lower compared to controls. These findings highlight reproducible, context-dependent effects of bacterial supplementation on honey bee gut physiology and provide a framework for interpreting microbiome-based interventions in pollinator health.IMPORTANCEHoney bees are essential pollinators whose health is influenced by their gut microbiome. Probiotic applications aimed at improving gut health have been proposed, yet outcomes remain inconsistent and vary across settings. Results from laboratory experiments often differ from those observed under field conditions, making it difficult to understand the complex dynamics of eusocial insect colonies. Here, we evaluate honey bee gut-derived bacterial supplementation across controlled, semi-controlled, and field settings using bacterial profiling, proteomic, and metabolomic analyses. We demonstrate that bacterial-supplemented groups consistently reshape gut community composition and modulate host physiological processes, but in a context-dependent manner. These results provide a unified understanding of how microbial interventions function at colony and individual levels, guiding the rational design of probiotic strategies to support honey bee health under realistic conditions.},
}

@article {pmid42165805,
year = {2026},
author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM},
title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42165805},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/physiology ; *Colon/microbiology/virology ; Escherichia coli/virology/genetics ; Bacteria/genetics/virology/classification ; Phage Therapy ; Feces/microbiology ; },
abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteriophages/genetics/physiology
*Colon/microbiology/virology
Escherichia coli/virology/genetics
Bacteria/genetics/virology/classification
Phage Therapy
Feces/microbiology

@article {pmid42165911,
year = {2026},
author = {Chen, H and Chen, H and Xie, L and Jiang, K and Xia, E and Mao, J and Liu, Z and Li, X and Xiao, Y and Qian, X and Jin, Z},
title = {Novel salivary biomarkers of Alzheimer's disease identified by integrated metabolomics and microbiomics analysis.},
journal = {Clinical oral investigations},
volume = {30},
number = {6},
pages = {},
pmid = {42165911},
issn = {1436-3771},
support = {LGF22H100005 and LTGY24H100005//the Natural Science Foundation of Zhejiang Province/ ; 2023YFF0611002//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology/diagnosis ; *Saliva/microbiology/chemistry/metabolism ; Biomarkers/metabolism/analysis ; Male ; *Metabolomics/methods ; Female ; Aged ; *Cognitive Dysfunction/metabolism/microbiology ; Case-Control Studies ; Microbiota ; Aged, 80 and over ; },
abstract = {OBJECTIVES: Alzheimer's disease (AD) and mild cognitive impairment (MCI) represent significant health challenges, with identification of biomarkers from non-invasive biofluid critical for large-scale screening and effective intervention.

MATERIAL AND METHODS: In this study, we performed a comprehensive analysis integrating non-targeted metabolomics and 16S rDNA sequencing of saliva samples from 3 age and sex-matched groups containing 18 AD patients, 15 MCI individuals and 19 healthy controls (HC).

RESULTS: Salivary metabolites including histamine (biogenic amine), carveol (monoterpene), and 2-phosphoglycerate (glycolytic intermediate) were significantly altered in AD patients. In addition, L-glutamic acid (excitatory neurotransmitter) levels were notably reduced in MCI patients, suggesting its potential as a biomarker for MCI. Microbial analysis revealed a decrease in the abundance of Actinomyces and Stomatobaculum in AD patients. In contrast, MCI patients exhibited a reduction in Atopobium and Actinomyces, along with an increase in Gemella and Peptostreptococcus compared to HC. An integrated analysis of microbiota and metabolites uncovered significant correlations, such as a positive correlation between Lactobacillus crispatus and GABA in AD patients, and an association between Klebsiella pneumoniae and multiple metabolites in AD patients. Additionally, MCI patients exhibited a higher abundance of "potentially pathogenic" microbiota species, highlighting a distinct microbiome profile.

CONCLUSIONS: Our findings revealed distinct metabolic and microbiomic alterations across the groups.

CLINICAL RELEVANCE: These findings suggest that saliva may harbor valuable biomarkers for the early diagnosis of AD and MCI. Moreover, our results underscore the involvement of the "oral-brain axis" in the pathogenesis of neurodegenerative diseases, offering new insights into potential therapeutic targets.},
}

Humans
*Alzheimer Disease/metabolism/microbiology/diagnosis
*Saliva/microbiology/chemistry/metabolism
Biomarkers/metabolism/analysis
Male
*Metabolomics/methods
Female
Aged
*Cognitive Dysfunction/metabolism/microbiology
Case-Control Studies
Microbiota
Aged, 80 and over

@article {pmid42165922,
year = {2026},
author = {Xiao, L and Zhao, F},
title = {Microbiome research beyond description and association.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42165922},
issn = {1869-1889},
}

@article {pmid42165942,
year = {2026},
author = {Tamahane, V and Shah, N and Kajale, N and Khadilkar, A and Khadilkar, V and Gondhalekar, K and Shouche, Y and Mylari, G},
title = {Effect of prebiotic intervention on glycemic control and gut microbiome profile in Indian children with type 1 diabetes mellitus (T1DM): a pilot randomised control trial.},
journal = {Endocrine},
volume = {91},
number = {1},
pages = {},
pmid = {42165942},
issn = {1559-0100},
mesh = {Humans ; *Prebiotics/administration & dosage ; Child ; *Diabetes Mellitus, Type 1/microbiology/blood/diet therapy ; *Gastrointestinal Microbiome/drug effects/physiology ; Pilot Projects ; Male ; Female ; Adolescent ; *Oligosaccharides/administration & dosage/therapeutic use/pharmacology ; Double-Blind Method ; India ; *Glycemic Control ; Inulin/administration & dosage ; Glycated Hemoglobin/analysis ; Blood Glucose ; },
abstract = {BACKGROUND: Type 1 diabetes mellitus (T1DM) is increasingly associated with gut microbial dysbiosis. Emerging evidence suggests that short-chain fatty acids(SCFA) producing bacteria play a role in glucose regulation and immune modulation. However, interventional data in children remain limited.

OBJECTIVE: To evaluate the effect of an oligofructose-enriched inulin intervention on glycemic control and gut microbiome composition in Indian children with T1DM.

METHODS: In double-blind, randomised, placebo-controlled pilot trial, 68-children (8-18years) with established T1DM were allocated to receive either 8 g/day of oligofructose-enriched inulin or an isocaloric maltodextrin placebo for 12 weeks. Anthropometry, glycated-hemoglobin (HbA1c), and stool-microbiome-profiles (16SrRNA sequencing) were assessed at baseline and endline. Alpha and beta-diversity indices, differential abundance analyses(DESeq2), were compared between groups.

RESULTS: Sixty-one participants (32 prebiotic, 29 placebo) completed the study with a mean compliance of 80%. Baseline characteristics and HbA1c levels were comparable between groups. No significant difference in HbA1c was observed after intervention (prebiotic 9.8 ± 1.4% vs. placebo 10.6 ± 2.5%; p > 0.05). However, the prebiotic group demonstrated a significant enrichment of SCFA-producing taxa, including Intestinibacter, Lachnospiraceae_UCG004, Megasphaera, Prevotella_2, and Agathobacter(p < 0.05). Families such as Lachnospiraceae, Bifidobacteriaceae, Ruminococcaceae, Atopobiaceae and Akkermensiaceae were increased significantly, while alpha- and beta-diversity indices remained stable. No significant adverse events were reported apart from isolated mild hypoglycemic episodes.

CONCLUSIONS: Prebiotics intervention modulated beneficial gut bacteria(SCFA-producing) without any change in glycemic control, suggesting possible long-term metabolic and anti-inflammatory benefits in T1DM. Larger studies are needed. Adding natural prebiotic-rich foods to daily diets of children with T1DM could be a simple, affordable.},
}

Humans
*Prebiotics/administration & dosage
Child
*Diabetes Mellitus, Type 1/microbiology/blood/diet therapy
*Gastrointestinal Microbiome/drug effects/physiology
Pilot Projects
Male
Female
Adolescent
*Oligosaccharides/administration & dosage/therapeutic use/pharmacology
Double-Blind Method
India
*Glycemic Control
Inulin/administration & dosage
Glycated Hemoglobin/analysis
Blood Glucose

@article {pmid42165961,
year = {2026},
author = {Sammad, A and Khan, S and Zhang, YY and Bai, XL and Zhu, X and Yin, K},
title = {Gut Microbial Dysbiosis in Type 2 Diabetes Patients with Concurrent Atherosclerosis.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {},
pmid = {42165961},
issn = {1534-6242},
support = {2022GXNSFBA035664//the Regional Science Fund project grants/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome ; *Atherosclerosis/microbiology/complications/epidemiology ; *Diabetes Mellitus, Type 2/complications/microbiology ; },
abstract = {PURPOSE OF REVIEW: The association of the gut microbiome with T2DM has been conflicting due to the disease's inherent complexity-a challenge that is further exacerbated in T2DM-related atherosclerotic cardiovascular diseases (ASCVD). Even when individual microbial species are associated with T2DM or ASCVD, mechanisms remain elusive-highlighting a pressing need for gut microbiota profiling in T2DM-related ASCVD. This perspective review examines gut microbial dysbiosis in T2DM with atherosclerosis (T2DM-AS), focusing on population-specific profiles from southern China and microbial biomarkers to predict disease progression.

RECENT FINDINGS: T2DM-AS patients exhibit reduced Firmicutes-to-Bacteriodota ratio, with reduced Clostridia, Oscillospirales, Ruminococcaceae, and Faecalibacterium. Dysbiosis includes increased pro-inflammatory Enterobacteriaceae, Enterococcaceae, and Streptococcaceae, with higher abundances of Escherichia-Shigella, Klebsiella, Streptococcus, and Alloprevotella. Beneficial butyrate-producing genera Faecalibacterium, Dialister, and Butyricicoccus are markedly depleted. Enterobacteriaceae/Escherichia-Shigella abundance strongly correlates with the Gensini score, serum zonulin (a gut permeability marker), cholesterol, triglyceride, and alanine aminotransferase. Mechanistically, the bacterial type III secretion system primarily drives a pathogenic cascade involving: (1) ferroptosis-mediated intestinal damage, (2) gut barrier disruption, (3) abnormal glycerophospholipid metabolism with phosphatidylcholine upregulation, and (4) macrophage activation and systemic inflammation that aggravates atherosclerosis. Pathogenic gut microbial signatures-enrichment of type III secretion system-harboring Enterobacteriaceae and depletion of butyrate-producing taxa-represent potential biomarkers for T2DM-AS progression. The type III secretion system-ferroptosis-lipid metabolism axis critically links gut dysbiosis to accelerated atherosclerosis, suggesting interventions targeting gut barrier integrity or lipid metabolism as therapeutic avenues. Population-specific profiling is essential for microbiome-based approaches to T2DM-AS management.},
}

Humans
*Dysbiosis/microbiology/complications
*Gastrointestinal Microbiome
*Atherosclerosis/microbiology/complications/epidemiology
*Diabetes Mellitus, Type 2/complications/microbiology

@article {pmid42165973,
year = {2026},
author = {Shaffer, M and North, D and Bibby, K},
title = {Correction: Evaluating Nanotrap Microbiome Particles as A Wastewater Viral Concentration Method.},
journal = {Food and environmental virology},
volume = {18},
number = {2},
pages = {},
doi = {10.1007/s12560-026-09697-z},
pmid = {42165973},
issn = {1867-0342},
}

@article {pmid42166037,
year = {2026},
author = {Sasse, R and Mejias-Beck, J},
title = {Nitric Oxide in the Intestinal Stem Cell Niche: A Spatial Model of Nitrosative Stress and Clonal Evolution in Colitis-Associated Colorectal Cancer.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42166037},
issn = {1573-2568},
abstract = {PURPOSE: Chronic colitis is a major risk factor for colitis-associated colorectal cancer (CAC), but the mechanisms linking recurrent inflammation to crypt-level dysplasia remain incompletely defined. This review examines whether spatially heterogeneous nitric oxide (NO) and reactive nitrogen species (RNS) exposure within the intestinal stem cell (ISC) niche may connect inflammation, DNA damage, stemness, and clonal evolution in CAC.

METHODS: This narrative, mechanistic review synthesized peer-reviewed English-language studies identified through PubMed/MEDLINE, Web of Science, and Google Scholar through 1 May 2026. Included literature addressed NO/NOS biology, ISC and crypt niche regulation, colitis-associated carcinogenesis, nitrosative DNA damage, cancer stem-like traits, and epithelial, stromal, immune, vascular, lymphatic, microbial, neural, and glial NO sources.

RESULTS: Constitutive NOS-derived NO supports mucosal perfusion, barrier integrity, and homeostasis, whereas colitis-associated NOS upregulation can generate high-flux NO, peroxynitrite, epithelial injury, and mutagenic nitrosative stress. The reviewed evidence supports a spatial NO/RNS-field model in which recurrent crypt-level nitrosative microdomains influence DNA damage, repair stress, Wnt/stemness signaling, immune selection, microbiome-redox interactions, and cancer stem-like programs. However, direct causal evidence in human colitic ISCs remains limited.

CONCLUSION: Chronic colitis may create recurring NO/RNS-rich crypt microenvironments that favor survival and expansion of damaged or NO-tolerant stem/progenitor clones. This model may guide crypt-resolved biomarker development and locally restricted prevention strategies, but prospective validation is required.},
}

@article {pmid42166056,
year = {2026},
author = {Jayaneththi, U and Sneddon, NW and Burkitt, LL and Jeyakumar, P and Anderson, CWN and Fermin, LM and Donaghy, DJ},
title = {Host Filtering Shapes the Soil-gut Microbiome Linkages in Pastoral Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02791-6},
pmid = {42166056},
issn = {1432-184X},
abstract = {Soil and ruminant gut microbiomes are linked within grazing pastoral systems, yet the strength and direction of these connections under different pasture management systems remain poorly understood. This study characterised bacterial communities in soil and faeces from cattle and sheep grazing standard and diverse pastures managed under contemporary and regenerative practices using 16 S rRNA gene sequencing. Shared bacterial taxa between soil and gut were identified, and their dominance patterns and soil-gut diversity relationships were evaluated using Spearman correlations and Procrustes analyses. Several taxa, including Prevotella copri, Faecalibacterium prausnitzii, Akkermansia muciniphila, Bacteroides uniformis, Clostridium perfringens and Fibrobacter succinogenes were commonly shared between soil and gut but were usually more prevalent in the gut, indicating predominant host‑associated dominance. Soil exhibited significantly greater bacterial alpha diversity than the gut across all treatments, and neither pasture diversity nor management significantly affected soil-gut alpha diversity differences or the contributions of shared taxa. Correlations between soil and gut alpha diversity were weak and non-significant, and correlations for beta diversity between soil and gut varied through time and among treatments without reaching significance. These findings indicate that, although soil-gut microbial connectivity exists, gut communities are primarily shaped by host-related ecological processes and internal filtering, with soil acting mainly as a diverse reservoir and sink for gut-derived taxa. This highlights that host-driven gut microbiomes primarily shape the soil-gut microbiome link, limiting the strong direct influence of pasture diversity or management.},
}

@article {pmid42166181,
year = {2026},
author = {Hijri, M and Aliyat, FZ and Legeay, J and Lee, SJ and Idbella, M and Anwar, AF and Errafii, K and Marasco, R and Biswas, MK and Venturi, V and Zézé, A and Gemeda, M and Eziuzor, SC and Makhalanyane, T and Ahmed, B},
title = {Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag132},
pmid = {42166181},
issn = {1751-7370},
abstract = {Microbial ecology and microbiome science are increasingly central to global "One Health" efforts, a framework that recognizes the interconnected health of humans, animals, and the environment. In Africa, these fields are particularly important for addressing interconnected challenges in public health, agriculture, and ecosystem resilience. Discussions at the ISME-Africa Morocco 2025 regional meeting highlighted both progress and persistent gaps in African microbiome research. Initiatives such as the African BioGenome Project and Human Heredity and Health in Africa demonstrate the feasibility of population-representative studies, regional training, networking, and open-science frameworks; however, the research landscape remains fragmented, with limited intra-African collaboration and continued reliance on external funding and leadership. The development of Africa-specific reference genomes, population-based microbiome datasets, is essential to address these gaps and ensure global representation. This perspective synthesizes current evidence and outlines strategic priorities to transition from toward coordinated pan-African research networks and flagship programs. Key recommendations include developing Africa-specific genome reference datasets, establishing pan-continental consortia, fostering equitable African-non-African partnerships, integrating microbiome science into policy frameworks, and adopting FAIR open-science practices. Strengthening bioinformatics and computational capacity will be essential to transform fragmented data into high-impact, coordinated insights. Advancing these priorities will accelerate translation into One Health outcomes, including antimicrobial resistance surveillance, food security, climate-resilient agriculture, and precision medicine. Africa's rich microbial diversity offers significant potential for antibiotic discovery, improved crop productivity, and sustainable agricultural systems. Collectively, strengthening Africa-led, collaborative microbiome research will enable the continent's microbial diversity to drive impactful solutions with regional and global relevance.},
}

@article {pmid42166227,
year = {2026},
author = {Kaushik, K and Sharma, M and Sharma, R and Reza, A and Sharma, G and Panwar, S and Nagraik, R and Negi, P and Sharma, A},
title = {Gut microbiota: The hidden hallmark of aging.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02808},
pmid = {42166227},
issn = {1588-2640},
abstract = {Aging is the natural process of changes that are accumulated over time and are responsible for the ever-increasing susceptibility to diseases and death. Extensive research has been done to understand the role of gut microbiota in aging, however, limited progress has been made. Thus, considering the need of the hour we have tried to give a new perspective to this body of research by delving deep into all major factors that are associated with gut microbiome and aging. This review presents a holistic view of the relation between gut microbiome and aging starting from hallmarks of aging and evolution of gut microbiome over lifespan to intricate mechanisms like inflammaging, immunosenescence, gut-brain axis, mitochondrial dysfunction, nutrient imbalance and cardiac implications. In addition, it highlights different therapies like fecal microbiota transplantation, omics and metabolomics studies, and gut modulation therapies that show a promising future towards regulation of gut microbiota for aging interventions. More importantly, this review is an addition to the existing literature which advocates gut microbiome as an additional hallmark of aging, summarising the known status of the research in this field, contributing to developing gut microbiota targeted healthy aging.},
}

@article {pmid42166232,
year = {2026},
author = {Rettschlag, S and Barrantes, I and Hahn, A and Bull, J and Raschke, U and Mlynski, R and Kreikemeyer, B and Warnke, P and Skusa, R},
title = {Microbiome of the Eustachian tube in patients with chronic obstructive Eustachian tube dysfunction and healthy individuals.},
journal = {European journal of microbiology & immunology},
volume = {},
number = {},
pages = {},
doi = {10.1556/1886.2026.00015},
pmid = {42166232},
issn = {2062-509X},
abstract = {OBJECTIVE: The Eustachian tube (ET) is essential for middle ear ventilation. Chronic obstructive ET dysfunction may lead to chronic otitis media and cholesteatoma, but its pathophysiology remains unclear. Commensal bacterial colonization of the ET has not previously been studied in healthy individuals or affected patients.

STUDY DESIGN AND PATIENTS: Prospective cohort study was conducted at a tertiary academic referral center including 13 patients with chronic obstructive ET dysfunction and 37 controls. Between 2017 and 2020, intraoperative tissue samples and swabs were collected using a contamination-minimized Yankauer suction technique. Samples underwent conventional culture diagnostics, microbiome analysis via 16S rDNA sequencing, and histopathological examination.

RESULTS: Culture identified 552 bacterial strains, with greater diversity in controls (34 genera) than in patients (19 genera). Microbiome analysis confirmed a larger core microbiome in controls. Rothia was more abundant in patients, whereas Veillonella predominated in controls. Genera such as Rothia and Gemella may be linked to microbial alterations in chronic ET dysfunction.

CONCLUSION: This first combined culture-based and molecular analysis using a novel sampling-technique demonstrated reduced bacterial diversity in chronic ET dysfunction patients, resembling patterns seen in other chronic respiratory morbidities. Future studies should incorporate complementary sampling approaches and cutting-edge sequencing technologies, additionally assessing viral etiologies.},
}

@article {pmid42166336,
year = {2026},
author = {Lv, C and Xia, Q and Yan, S},
title = {Symbiont-mediated mechanisms of insecticide resistance in insects.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {3},
pages = {},
pmid = {42166336},
issn = {1536-2442},
mesh = {Animals ; *Insecticide Resistance/genetics ; *Symbiosis ; *Insecta/microbiology/genetics/drug effects ; *Insecticides/pharmacology ; },
abstract = {Insecticide resistance threatens sustainable agricultural intensification worldwide. Once regarded solely as a host-encoded evolutionary response, resistance is now known to be strongly influenced by microbial symbionts. Here, we synthesize recent advances showing that vertically and horizontally transmitted bacteria, fungi, and viruses modulate insect-toxicant interactions through 3 intertwined mechanisms: (i) direct enzymatic degradation of the active ingredient inside the gut lumen or hemocoel, (ii) transcriptional or posttranscriptional up-regulation of host detoxification gene networks (cytochrome P450s, carboxylesterases, and glutathione S-transferases), and (iii) epigenetic or immune-mediated priming that accelerates metabolic clearance while dampening insecticide-induced oxidative stress. Symbiont-mediated shifts in toxicity thresholds are context-dependent, varying with host genotype, symbiont strain, insecticide chemistry, and route of exposure. Symbionts may synergize with classical resistance mutations to produce super-resistant phenotypes, or conversely sensitize insects through pro-toxicant bioactivation. We propose an integrative "symbiont-insecticide-host" triangulation framework combining gnotobiotic manipulation, spatial metabolomics, and CRISPR-based microbial genetics to identify causal loci. Microbiome engineering through symbiont replacement, phage therapy or engineered plasmids offers a green resistance-management tool that lowers selection pressure on synthetic chemistries while preserving biocontrol compatibility. Clarifying these microbe-centered pathways is essential for predicting resistance trajectories and for designing durable, next-generation pest-control strategies aligned with food-security and environmental-quality goals.},
}

Animals
*Insecticide Resistance/genetics
*Symbiosis
*Insecta/microbiology/genetics/drug effects
*Insecticides/pharmacology

@article {pmid42166504,
year = {2026},
author = {Seo, SH and Lee, JW and Oh, S and Hong, JS and Lee, BS and Kwon, SJ and Kim, KS and Park, JS and Heo, JS and Ahn, KH and Lee, HJ and Park, KU},
title = {Machine learning reveals microbiome differences by periodontitis severity.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0349686},
pmid = {42166504},
issn = {1932-6203},
mesh = {Humans ; *Machine Learning ; *Periodontitis/microbiology/pathology ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Severity of Illness Index ; Dysbiosis/microbiology ; Aged ; },
abstract = {Periodontitis is a chronic inflammatory disease driven by microbial dysbiosis, yet the microbial signatures associated with severity remain incompletely understood. This study investigated changes in subgingival microbial composition across clinically defined severity groups and evaluated the performance of microbiome-based machine-learning models for classifying periodontitis severity. Subgingival plaque samples from 84 patients were analyzed using 16S rRNA gene sequencing. Microbial diversity showed a modest decreasing trend with increasing severity, although differences were not statistically significant. Five machine learning models were applied to classify periodontitis. Random Forest and XGBoost achieved AUC values of 0.98, indicating statistically significant classification performance (p < 0.05) after feature selection. Validation using three external cohorts demonstrated substantial performance variability across populations, reflecting differences in oral microbiome composition, sample type, and periodontal status definitions. Feature importance analysis identified Fusobacterium, Campylobacter, Stomatobaculum, Leptotrichia and Segatella as key contributors to periodontitis severity classification, consistent with their established roles in periodontal dysbiosis. These findings highlight the potential of microbiome-based models for classifying periodontitis severity while underscoring the need to incorporate diverse populations and robust feature-selection strategies to enhance generalizability.},
}

Humans
*Machine Learning
*Periodontitis/microbiology/pathology
*Microbiota/genetics
Male
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Adult
Severity of Illness Index
Dysbiosis/microbiology
Aged

@article {pmid42166641,
year = {2026},
author = {Nodehi, M and Veisi Malekshahi, Z and Rahimnia, R and Verdi, J and Vousooghi, N and Seyhoun, I},
title = {Immunometabolism crosstalk between regulatory T cells and glucose homeostasis of type 1 diabetes.},
journal = {Clinical and experimental immunology},
volume = {220},
number = {1},
pages = {},
pmid = {42166641},
issn = {1365-2249},
mesh = {*Diabetes Mellitus, Type 1/immunology/metabolism/therapy ; Humans ; *T-Lymphocytes, Regulatory/immunology/metabolism ; Homeostasis/immunology ; Animals ; Hyperglycemia/immunology ; Immune Tolerance ; *Glucose/metabolism ; Forkhead Transcription Factors/genetics ; },
abstract = {Type 1 diabetes mellitus (T1D) is an autoimmune disease that is associated with the loss of pancreatic β cells. Regulatory T cells (Tregs) play a critical role in the maintenance of immune tolerance; however, the number and function of Tregs have been found to be compromised in T1D. Genetic changes in FOXP3, as well as the role of hyperglycaemia and the accumulation of advanced glycation end products, have been proposed as potential mechanisms for the dysfunction of Tregs. However, the current understanding suggests that the role of the metabolic reprogramming associated with hyperglycaemia is more likely to be a potential mechanism for the instability of Tregs rather than a well-established primary mechanism for the development of T1D. Several therapeutic strategies have been explored in experimental models for the management of autoimmune diseases associated with Tregs dysfunction. These include the administration of low-dose interleukin-2, metformin, and dietary or microbiome-based therapies. These therapies have been found to modulate the immune system; however, the efficacy of these therapies for the management of T1D is to be established. In the present review article, the current understanding of the role of the interrelationship between hyperglycaemia, metabolic reprogramming, and Tregs-mediated immune tolerance in the pathogenesis of type 1 diabetes is reviewed.},
}

*Diabetes Mellitus, Type 1/immunology/metabolism/therapy
Humans
*T-Lymphocytes, Regulatory/immunology/metabolism
Homeostasis/immunology
Animals
Hyperglycemia/immunology
Immune Tolerance
*Glucose/metabolism
Forkhead Transcription Factors/genetics

@article {pmid42166933,
year = {2026},
author = {Penalba-Iglesias, D and Robas-Mora, M and González-Reguero, D and Fernández-Pastrana, VM and Lobo, AP and Jiménez-Gómez, PA},
title = {A novel Bacillaceae bacterium enhances phytoprotection and mercury detoxification in contaminated soils.},
journal = {Ecotoxicology and environmental safety},
volume = {319},
number = {},
pages = {120261},
doi = {10.1016/j.ecoenv.2026.120261},
pmid = {42166933},
issn = {1090-2414},
abstract = {Environmental pollution due to heavy metals has become a global issue over the latest decades, affecting environmental, animal, and human health. This research conducted a phenotypic, genomic, and functional characterization of Methalobacillus radiculiexplorans C204, a bacterial strain isolated from highly mercury-contaminated soils in the Almadén mining district (Ciudad Real, Spain). The main objective was to evaluate its potential as a bioremediation agent and plant growth-promoting bacterium (PGPB) for application in the recovery of heavy metal-degraded soils. Morphological and biochemical analyses revealed typical adaptations of bacteria resistant to abiotic stress. Genomic analysis identified a broad repertoire of genes associated with PGPB functions, as well as key operons conferring resistance to mercury (merA, merB), copper (copA, copB), and zinc/cadmium (czc), along with multiple antibiotic resistance mechanisms. Additionally, species-level genomic divergence from the closest validated relatives (ANI = 83%, dDDH = 28.8%), together with AAI-based differentiation, phylogenomic placement and the partial absence of conserved signature indels characteristic of Neobacillus, support the recognition of this strain as a distinct genus-level lineage within the Bacillaceae family. In plant assays using Lupinus albus grown in soils with varying Hg concentrations, the bacterial inoculation significantly enhanced plant growth, stabilized nutritional profiles, improved physiological indicators, and reduced mercury accumulation in plant tissues by up to 93%. Positive effects were also observed on the soil microbiome, with the strain contributing to the recovery of microbial metabolic activity and the maintenance of functional diversity under toxic conditions. Overall, the results position M. radiculiexplorans C204 as a native, multifunctional bacterial strain of high biotechnological interest and a promising candidate for assisted phytoremediation strategies aimed at restoration of mercury-contaminated soils.},
}

@article {pmid42166940,
year = {2026},
author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM},
title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.},
journal = {Pathology, research and practice},
volume = {285},
number = {},
pages = {156543},
doi = {10.1016/j.prp.2026.156543},
pmid = {42166940},
issn = {1618-0631},
abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.},
}

@article {pmid42167019,
year = {2026},
author = {Abdullaeva, Y and Rochau, S and Löwe, M and Holert, J and Philipp, B},
title = {Occurrence and metabolic properties of bacteria from the genus Novosphingobium indicate their use as model organisms for studying biodegradation processes in activated carbon filters in advanced wastewater purification.},
journal = {Water research},
volume = {302},
number = {},
pages = {126123},
doi = {10.1016/j.watres.2026.126123},
pmid = {42167019},
issn = {1879-2448},
abstract = {Activated carbon filters are increasingly being installed in sewage treatment plants to adsorb organic micropollutants from purified wastewater. Biodegradation also contributes to micropollutant removal in the filters, but the respective microorganisms and underlying processes are largely unexplored. Particularly, it is unknown to which extent active desorption of micropollutants takes place and which molecular mechanisms are involved. For addressing these questions microbial model organisms are required. In this study, the prokaryotic microbiome of a newly installed activated carbon filter in a fourth clarification stage of a municipal wastewater treatment plant was analyzed over 12 months by 16S rRNA gene amplicon sequencing. Bacterial families with relative abundancies above 1% stabilized after 2 months and included the potential micropollutant degraders Hyphomonadaceae and Sphingomonadaceae. Among the latter, members of the genus Novosphingobium were frequently found and closely related to the type strain N. aromaticivorans DSM 12444, which is known to degrade synthetic chemicals. Strain DSM 12444 and the Pseudomonadaceae strains Teo15 and Salic, which were isolated from enrichment cultures with filter material but not detected in the microbiome, were selected as model organisms for laboratory growth experiments with granulated activated carbon loaded with benzoate and salicylate. Strain DSM 12444 reached a significantly higher final optical density when grown on granular activated carbon pre-loaded with either benzoate or salicylate compared to strains Teo15 and Salic, respectively. Extraction of residual benzoate and salicylate from activated carbon granules indicated that >95% of the aromatic compounds had been depleted by strain DSM 12444 compared to about 70% and 50% by strains Teo15 and Salic, respectively. Transcriptomic analysis indicated differential gene expression of strain DSM 12444 during growth with benzoate in the presence and absence of GAC. These results qualify N. aromaticivorans as a feasible model organism to study the mechanisms of bacterial growth with organic substrates adsorbed to activated carbon which could support the design of bioaugmentation strategies for enhancing micropollutant removal.},
}

@article {pmid42167245,
year = {2026},
author = {Sun, H and Noya-Alarcon, O and Wang, J and Daniel, SG and Bittinger, K and Mohamed, W and Scanlan, PD and Shah, C and Kundu, T and Blaser, MJ and Mueller, NT and Lander, O and Bevilaqua, M and Robles, DV and Contreras, M and Dominguez-Bello, MG},
title = {Rapid microbiome restructuring associated with medical exposure in remote Amazonian Indigenous communities.},
journal = {Cell reports},
volume = {},
number = {},
pages = {117343},
doi = {10.1016/j.celrep.2026.117343},
pmid = {42167245},
issn = {2211-1247},
abstract = {Many factors contribute to reduced microbial diversity associated with Westernization, complicating efforts to identify early drivers of microbiome change. Here, we examine microbiome variation during the introduction of a sustained medical program into previously low-exposure remote Indigenous villages. We analyze fecal samples and body-site swabs from 335 Amerindians across multiple villages before and during repeated program visits, prior to major dietary or lifestyle transitions. Low-exposure villages show higher baseline gut microbiota diversity than the medium-exposure village, and microbiota diversity declines over time in association with repeated exposure, particularly in children. Changes include loss of specific gut taxa, reduced bacterial network connectivity, and shifts in functional gene profiles toward those reported in urban populations. Oral microbiota diversity decreases, while skin and nasal diversity show modest changes. These findings indicate that repeated exposure to basic medical interventions coincides with rapid microbiome restructuring during early stages of ecological transition.},
}

@article {pmid42167251,
year = {2026},
author = {Zheng, X and Wang, J and Sun, Y and Zhang, H and Tang, Y and Kuang, J and Jiao, F and Zhou, C and Xia, M and Ren, J and Cai, Y and Yao, C and Zhao, A and Qu, C and Liu, L and Yang, Y and Guan, Q and Jiang, R and Ren, Z and Chen, T and Li, M and Xia, X and Xia, L and Zhao, M and Li, Y and Ding, K and Zhou, Z and Shi, Y and Wan, X and Sun, B and Xie, G and Gao, F and Zhou, J and Hu, C and He, Y and Jia, W and Xie, RH and Jia, W},
title = {Hyocholic acids shape neonatal immune tolerance and microbiota assembly.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2026.04.016},
pmid = {42167251},
issn = {1932-7420},
abstract = {Bile acids (BAs) are essential for regulating metabolism, immune responses, and host immunity-gut microbiome interactions. Here, we report that in human newborns, hyocholic acid (HCA) species constitute 51.03% of total BAs in meconium and 13.74% in infant serum, declining to <5% in adults. HCAs drive CD4[+] T cell differentiation toward regulatory T cells while suppressing pro-inflammatory T helper (Th)17 cells, facilitating healthy microbiome colonization. Neonates with high HCA levels show a reduced incidence of infections and gastrointestinal disorders during the first year of life. Mechanistically, HCAs are produced by the fetal-specific enzyme CYP3A7, creating a transient metabolic window that coordinates the gut-immune axis during early development. These findings reveal HCAs as primary BAs and critical mediators of immune programming, with implications for preventing early-life inflammatory diseases.},
}

@article {pmid42167294,
year = {2027},
author = {Zeng, S and Almeida, A and Mu, D and Wang, S},
title = {Temporal variations of the gut microbiome in human health.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101388},
doi = {10.1016/j.lanmic.2026.101388},
pmid = {42167294},
issn = {2666-5247},
abstract = {The colonisation of the human gut microbiome commences at birth and continues to evolve throughout the lifespan. A balanced symbiotic relationship between the host and gut microbiome is essential for maintaining overall health. This two-part Series presents a comprehensive overview of the gut microbiome across temporal and spatial dimensions, considering diurnal, seasonal, and lifespan variations while covering the entire gastrointestinal tract. We also discuss the extrinsic and intrinsic factors that shape the microbial ecosystem and affect host homoeostasis, health, and disease susceptibility. In this first Series paper, we summarise current knowledge on the microbial succession and evolutionary trajectory of the gut microbiome from neonates to adults aged 100 years and older, subsequently focusing on diurnal rhythms and seasonal patterns. We then discuss how these temporal variations in the gut microbiome are determined and how they contribute to beneficial or detrimental health outcomes in the host. Overall, elucidating the multiscale temporal dynamics of the human gut microbiome will open crucial opportunities to expand knowledge of host-microbiome interactions and their biological and clinical implications.},
}

@article {pmid42167295,
year = {2027},
author = {Wang, S and Almeida, A and Mu, D and Zeng, S},
title = {Spatially resolved architecture of the human gut microbiome and its health implications.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101389},
doi = {10.1016/j.lanmic.2026.101389},
pmid = {42167295},
issn = {2666-5247},
abstract = {The human gut microbiome shows dynamic variation throughout the lifespan and remarkable spatial organisation within the gastrointestinal tract. Complementing the focus of the first paper of this Series on the human microbiome dynamics and health, which focused on the temporal dynamics of the human gut microbiome, this second Series paper explores its biogeographical signatures, which often reflect distinct physiological niches in gastrointestinal tract regions. The spatial architecture of the gut microbiome is shaped by various factors and has important clinical implications for host homoeostasis, health, and disease. In this Series paper, we discuss current knowledge on the microbial biogeography along the gastrointestinal tract, the factors governing these spatial patterns, and their functional consequences for the host. We further focus on host-microbe interactions mediated by microbial metabolites and their impact on host health. Finally, we summarise the methodological advances that are enabling in-situ high-resolution spatial mapping of the gut microbiome as crucial tools for unravelling the detailed mechanisms of host-microbiome crosstalk. Overall, understanding the principles that govern the spatial ecology of the gut microbiome can inform the development of novel therapies designed to precisely manipulate microbial niches and restore homoeostasis along the gastrointestinal tract, thereby improving human health.},
}

@article {pmid42167365,
year = {2026},
author = {Hu, X and Huang, J and Dong, S and Xu, K and Zheng, M and Cai, J and Chen, Y and Wang, T and Zhang, Y},
title = {Functionalized nanoparticles for the precise treatment and prevention of bacterial infections.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {115035},
doi = {10.1016/j.jconrel.2026.115035},
pmid = {42167365},
issn = {1873-4995},
abstract = {Multidrug-resistant (MDR) bacterial infections are an escalating health issue, and their rise poses a major threat worldwide. Inappropriate antibiotic use, including unnecessary prophylaxis, and nonpathogen-directed therapy, accelerates resistance, diminishing the effectiveness of conventional antibiotics. Consequently, novel antimicrobial strategies are urgently required to achieve precise prevention and treatment of bacterial infections while minimizing selective pressure for resistance. Nanotechnology-based antimicrobials are promising candidates because of their unique advantages: payload concentration at infection sites, biofilm penetration and disruption, synergism with conventional antibiotics, and modulation of host immunity via innate/adaptive immune activation (e.g., macrophage polarization, dendritic cell maturation, and immunogenic cell death induction). This review describes the current classifications and antibacterial mechanisms of nanoantibacterial agents and summarizes strategies for targeted antibacterial and immunoregulatory nanoparticle therapies. We also identify key translational challenges, including safety and immunotoxicity, biodistribution and clearance, microbiome and environmental impacts, scalable manufacturing, assay standardization, regulatory issues, and clinical validation. Finally, we outline future directions, such as rational design of stimulus-responsive nanocarriers, data-driven optimization, theranostics, and clinically aligned evaluation. These efforts aim to advance nanoantibacterials that complement antibiotics, enabling precise MDR infection management, thereby bridging the gap between prevention and treatment to address the global antimicrobial resistance crisis.},
}

@article {pmid42167424,
year = {2026},
author = {Fan, J and Li, Y and Jin, H and Yu, X and Wang, D and Lin, Y and Wang, Y and Wei, F},
title = {Comprehensive review on Cistanche polysaccharides: Structure, gut microbiota and processing characteristics.},
journal = {International journal of biological macromolecules},
volume = {367},
number = {},
pages = {152634},
doi = {10.1016/j.ijbiomac.2026.152634},
pmid = {42167424},
issn = {1879-0003},
abstract = {Cistanche deserticolaY.C.Ma and Cistanche tubulosa (Schenk) Wight are Cistanche Hoffmg. Et Link medicinal plants with a long traditional medicine history. Polysaccharides, the primary bioactive components, exhibit diverse pharmacological effects. Recently, research on the interaction between herbal polysaccharides and the gut microbiota has gained significant attention. Cistanche polysaccharides modulate the intestinal microbiome, and processing techniques significantly affect the content, structure, and function of these polysaccharides. Systematic reviews on structural characterization, bioactivities, gut microbiota interactions, and processing effects of Cistanche polysaccharides remain scarce. This review examines Cistanche polysaccharide research advances, including extraction, structural characterization, bioactivities and quality control. It emphasizes the link between bioactivities and gut microbiota, and how processing techniques influence them. Key findings show Cistanche polysaccharides have multiple bioactivities, including regulating gut microbiota and intestinal barrier. By modulating gut microbiota and metabolites, they confer health benefits such as relieving constipation and treating alcoholic fatty liver. Processing techniques alter their properties via physical-chemical changes, affecting herbal quality. Integration with advanced disciplines expands their biomedical applications. This review provides insights for deepening Cistanche polysaccharide research, improving herbal quality, promoting standardized production, and facilitating their development.},
}

@article {pmid42167440,
year = {2026},
author = {Kuttiappan, A and Vanangamudi, M and Ashique, S and Mishra, N},
title = {Pharmacomicrobiomics and the gut-brain axis: microbial modulation of drug response in brain disorders.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {104700},
doi = {10.1016/j.drudis.2026.104700},
pmid = {42167440},
issn = {1878-5832},
abstract = {Pharmacomicrobiomics is the study of how the gut microbiota affects the metabolism, efficacy, and safety of drugs. Gut microbes play a key role in neurochemical communication along the gut-brain axis and can alter responses to neuroactive medications. Dysbiosis alters pharmacodynamics by modulating the synthesis of neurotransmitters, immune function and neuroinflammation. Concurrently, it alters pharmacokinetics through microbial biotransformation, which directly changes drug bioavailability, activation, and clearance {AuQ: Edit OK?}.
Increasing evidence shown an association between variations in microbiome and differences in response to treatment in brain disorders. By integrating pharmacomicrobiomics into neuropharmacology, there are opportunities to achieve precision medicine by optimising therapy selection. This review emphasizes the importance of the gut microbiome in controlling drug response and highlights emerging microbiome-targeted approaches aiming to improve therapeutic efficacy and reduce adverse effects in neuropsychiatric and neurodegenerative disorders.},
}

@article {pmid42167558,
year = {2026},
author = {Shafiq, M and Ali, S and Zeb, L},
title = {Antimicrobial Peptides in Shrimp Aquaculture: Mechanisms, Translational Applications, and Future Perspectives.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111428},
doi = {10.1016/j.fsi.2026.111428},
pmid = {42167558},
issn = {1095-9947},
abstract = {Shrimp aquaculture is a cornerstone of global seafood production but continues to face recurrent disease outbreaks and increasing restrictions on antibiotic use. The declining efficacy of conventional antibiotics and rising antimicrobial resistance (AMR) underscore the urgent need for novel, immune-based strategies. Antimicrobial peptides (AMPs) are small, bioactive molecules integral to the shrimp innate immune system that exhibit broad-spectrum antimicrobial activity and immunomodulatory potential. This review highlights recent mechanistic and applied advances in AMPs as sustainable, antibiotic-sparing alternatives for disease management. This review synthesizes current knowledge on endogenous shrimp AMPs and evaluates exogenous AMPs applications, delivery technologies, and regulatory considerations. Particular attention is given to limitations related to peptide stability, production scalability, delivery efficiency, and potential resistance development. A structured translational framework is proposed to guide the development of AMP-based disease management strategies for shrimp aquaculture, linking peptide discovery and engineering with formulation, farm validation, environmental assessment, and regulatory implementation. This framework leverages AI-assisted peptide discovery, host immune priming, microbiome-informed formulations, and scalable biomanufacturing to achieve farm-ready solutions that enhance shrimp health and sustainability.},
}

@article {pmid42167664,
year = {2026},
author = {Getange, D and Mukaratirwa, S and Khogali, R and Yuko, E and Kabii, J and Bargul, JL and Villinger, J},
title = {Tissue-specific and sex-dependent microbiome structure in east African cattle ticks (Amblyomma gemma and Rhipicephalus pulchellus) and their bovine hosts.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105961},
doi = {10.1016/j.meegid.2026.105961},
pmid = {42167664},
issn = {1567-7257},
abstract = {Ticks and their vertebrate hosts share intimate ecological interactions that shape microbial community composition, with implications for tick fitness and pathogen transmission. However, the extent and specificity of tick-host microbial interactions remain poorly understood, particularly in East African tick species. Here, we characterised microbial communities across multiple tissue types from two economically important tick species (Amblyomma gemma and Rhipicephalus pulchellus) and their shared bovine host using 16S rRNA V1-V2 gene sequencing. We profiled haemolymph, midgut, salivary glands, and gonads from individual ticks (25 Am. gemma and 8 Rh. pulchellus), alongside 12 bovine blood samples. Microbiota were dominated by Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota, with Coxiella, Rickettsia, and Acinetobacter as the most abundant genera. Despite substantial taxonomic overlap, Am. gemma harboured more unique bacterial genera than Rh. pulchellus, suggesting species-specific microbial associations. Alpha and beta diversity analyses indicated distinct community structures between tick species and host blood. Tissue-level analyses revealed striking sexual dimorphism in both species: males exhibited stable microbial communities across tissues, whereas females showed strong tissue-dependent variation in richness, diversity, and composition. Co-occurrence network analyses, restricted to Am. gemma due to limited Rh. pulchellus sample size, identified sex- and tissue-specific putative keystone taxa, including Georgenia in male midguts, Serratia in female salivary glands, Enhydrobacter in ovaries, and Gemmatimonas in testes, suggesting roles in community stability. These findings highlight tissue-specific and sex-dependent factors as key determinants of tick microbial community composition, with implications for pathogen maintenance and transmission in East African livestock systems.},
}

@article {pmid42167755,
year = {2026},
author = {Goerlich, K and Solis, NV and Filler, SG and Mitchell, AP},
title = {Shared anti-biofilm targets of biofilm regulators Wor3 and Bcr1 in Candida albicans.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyag129},
pmid = {42167755},
issn = {1943-2631},
abstract = {Candida albicans is an opportunistic fungal pathogen and a component of the human microbiome. C. albicans virulence traits include biofilm production, which is governed by a large transcriptional network. Mutations of some biofilm regulators cause the same severe biofilm-defective phenotype in multiple clinical isolates. Mutations of others, such as Wor3, Bcr1, Ndt80, and Ume6, have mild or variable phenotypes among clinical isolates. We hypothesized that Wor3 may share functions with another variable-phenotype biofilm regulator. This hypothesis predicts that a double mutant lacking Wor3 and the shared-function regulator will have a severe biofilm defect in all clinical isolates. We observed that a wor3Δ/Δ bcr1Δ/Δ double mutant has a severe biofilm defect in vitro in 5 strain backgrounds tested. It also has a severe oral biofilm defect in a mouse oropharyngeal candidiasis model in the SC5314 strain background. RNA-seq data indicate that 5 genes encoding cell surface/secreted proteins are upregulated in wor3Δ/Δ, bcr1Δ/Δ, and wor3Δ/Δ bcr1Δ/Δ strains: CWH8, DAG7, JEN2, PGA6, and YWP1. Deletion mutations of CWH8, DAG7, PGA6, or YWP1 enable biofilm formation in vitro in an SC5314-derived wor3Δ/Δ bcr1Δ/Δ strain, and deletion of YWP1 enables biofilm formation in vitro in wor3Δ/Δ bcr1Δ/Δ strains from 4 other genetic backgrounds. YWP1 has been shown to have anti-biofilm activity previously, but CWH8, DAG7, and PGA6 are newly described anti-biofilm genes. Our study illustrates the value of strain variation considerations for gene function analysis and the importance of repression targets of biofilm regulators. In addition, our results expand the number of anti-biofilm genes.},
}

@article {pmid42167838,
year = {2026},
author = {Opatoyinbo, JO and Akanbi, CA and Ojo, AB and Ogunlakin, AD and Molehin, OR and Ojo, OA},
title = {Emerging trends in cancer biomarkers and their clinical effect on personalized treatment.},
journal = {Advances in cancer research},
volume = {170},
number = {},
pages = {139-173},
doi = {10.1016/bs.acr.2025.12.002},
pmid = {42167838},
issn = {2162-5557},
mesh = {Humans ; *Precision Medicine/methods/trends ; *Biomarkers, Tumor/genetics/metabolism ; *Neoplasms/therapy/diagnosis/genetics/metabolism ; },
abstract = {One of the most difficult global health issues is cancer, whose incidence and mortality rates are expected to rise significantly over the next several decades. This increasing burden highlights the need for early diagnosis, accurate prognostic tools, and predictive markers for individualized treatment plans. Biomarkers, which are measurable indicators of disease states or therapeutic responses, have become essential to modern oncology and are driving the precision medicine revolution by improving patient stratification, directing therapy choices, and facilitating disease monitoring. This review explores the development of cancer biomarkers, tracing their progression from early histopathological and serum markers to advanced molecular and immunological tools. The key biomarker categories discussed include genomic alterations such as somatic mutations, gene fusions, and copy number variations, all of which offer actionable insights for targeted therapies. Epigenetic markers, which include noncoding RNAs, histone modifications, and DNA methylation, are notable for their regulatory functions and hold promise as noninvasive diagnostic instruments. Proteomic and metabolomic methods offer useful insights into tumor biology, while circulating biomarkers, including circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and exosomes, allow real-time, noninvasive monitoring of disease progression and minimal residual disease. Immunological biomarkers such as the tumor mutational burden (TMB) and programmed cell death ligand-1 (PD-L1) expression are becoming increasingly important in guiding immunotherapy choices. This study also highlights how emerging technologies, including next-generation sequencing, liquid biopsy platforms, and artificial intelligence-based analytics, have accelerated biomarker discovery and integration into clinical workflows. The observable advantages of biomarker-driven care are demonstrated by case studies and real-world applications in a variety of cancer types. Despite tremendous advancements, obstacles such as tumor heterogeneity, intertest variability, high costs, inconsistent regulations, and differences in healthcare infrastructure prevent widespread adoption, particularly in low- and middle-income nations where access to biomarker technologies is still unequal and could exacerbate global disparities in cancer outcomes. Future directions include the use of multiplex biomarker panels, the integration of digital pathology, and the exploration of novel biomarker domains such as the tumor microenvironment and microbiome. Personalized neoantigen-based vaccines and immunotherapies also represent promising frontiers. Overall, this review underscores the transformative potential of biomarkers in reshaping cancer diagnostics and therapeutics and calls for sustained collaborative research, technological advancements, and equitable policy frameworks to realize their full global impact.},
}

Humans
*Precision Medicine/methods/trends
*Biomarkers, Tumor/genetics/metabolism
*Neoplasms/therapy/diagnosis/genetics/metabolism

@article {pmid42167887,
year = {2026},
author = {Cui, D and Zhou, Y and Zhou, Y and Ge, R and Mao, H and Mathesh, M and Han, L and Yang, W and Yan, F},
title = {Gut microbiota dysbiosis and metabolic alterations in rheumatoid arthritis: a barrier to periodontal repair.},
journal = {RMD open},
volume = {12},
number = {2},
pages = {},
doi = {10.1136/rmdopen-2026-006931},
pmid = {42167887},
issn = {2056-5933},
mesh = {Animals ; *Dysbiosis/metabolism/etiology ; *Arthritis, Rheumatoid/metabolism/etiology/microbiology/pathology ; *Gastrointestinal Microbiome ; Rats ; Male ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Arthritis, Experimental/metabolism ; Rats, Sprague-Dawley ; Metabolomics/methods ; X-Ray Microtomography ; RNA, Ribosomal, 16S/genetics ; Bone Regeneration ; Biomarkers ; },
abstract = {OBJECTIVE: To investigate the impact of rheumatoid arthritis (RA) on periodontal healing and the underlying mechanisms.

METHODS: Mandibular periodontal bone defect (PBD) and collagen-induced arthritis (CIA) models were established in male Sprague-Dawley rats aged 6 weeks, assigned to four groups: control (CON), CIA, PBD and CIA+PBD. Periodontal repair was evaluated at 1, 3 and 6 weeks. To examine the contribution of gut microbiota, pseudo-germ-free rats with PBD received 3-week faecal microbiota transplantation (FMT) from either healthy or CIA donors. Arthritis severity was assessed by paw thickness and arthritis index, while bone microarchitecture was examined by micro-CT and histology. Gut microbiota and metabolites were analysed using 16S ribosomal RNA high-throughput sequencing and untargeted metabolomics.

RESULTS: CIA was found to significantly impair periodontal bone healing and suppress osteogenesis-related markers, including runt-related transcription factor 2 and alkaline phosphatase. Compared with CON rats, CIA and PBD, CIA+PBD groups exhibited gut microbial dysbiosis and metabolic alterations, particularly in arachidonic acid and tryptophan pathways. FMT from CIA donors further increased osteoclast numbers and delayed bone regeneration. Furthermore, gut-derived factors from CIA animals were associated with increased macrophage expression of pro-inflammatory cytokines, including tumour necrosis factor-alpha and interleukin-1 beta.

CONCLUSION: Overall, RA-related gut microbiota dysbiosis and metabolic disturbances are linked to impaired periodontal healing, potentially through enhanced inflammatory responses. This study highlights a microbiome-immune-metabolic axis that may influence periodontal regeneration in RA.},
}

Animals
*Dysbiosis/metabolism/etiology
*Arthritis, Rheumatoid/metabolism/etiology/microbiology/pathology
*Gastrointestinal Microbiome
Rats
Male
Disease Models, Animal
Fecal Microbiota Transplantation
Arthritis, Experimental/metabolism
Rats, Sprague-Dawley
Metabolomics/methods
X-Ray Microtomography
RNA, Ribosomal, 16S/genetics
Bone Regeneration
Biomarkers

@article {pmid42167986,
year = {2026},
author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S},
title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.},
journal = {Journal of the World federation of orthodontists},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ejwf.2026.03.003},
pmid = {42167986},
issn = {2212-4438},
abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.

METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.

RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri‑implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).

CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri‑implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.},
}

@article {pmid42168143,
year = {2026},
author = {Verma, AK and Narwal, A and Kamboj, M and Devi, A and Tewari, S and Bhardwaj, R},
title = {Oral microbiome dysbiosis of Porphyromonas gingivalis in oral leukoplakia, oral squamous cell carcinoma and radiation-induced oral mucositis: a qPCR-based cross-sectional study.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/17460913.2026.2678151},
pmid = {42168143},
issn = {1746-0921},
abstract = {BACKGROUND: Porphyromonas gingivalis is a key periodontal pathogen increasingly implicated in periodontitis and oral carcinogenesis. Among its virulence determinants, fimbriae encoded by the fimA gene exhibit pathogenic potential. While previous studies have mainly focused on fimA II and IV genotypes in periodontitis, limited data exist on the role of fimA I in oral squamous cell carcinoma (OSCC), and radiation-induced oral mucositis (RIOM). The present study aimed to evaluate the relative abundance of the fimA I genotype across different oral disease conditions and to assess its potential role as a biomarker of disease associated microbial dysbiosis.

METHODS: In total, 96 oral swab samples were collected from six groups: healthy nonsmokers, healthy smokers, periodontitis, OL, OSCC, and RIOM. Quantitative real-time PCR was performed to assess the relative abundance of the genotype using genotype-specific primers.

RESULTS: FimA I expression was highest in RIOM, followed by OSCC and periodontitis, and lowest in OL and healthy groups. A statistically significant increase was observed in RIOM and OSCC compared to controls (p < 0.05).

CONCLUSION: The fimA I genotype shows higher abundance in OSCC and RIOM, suggesting its potential role as a microbial biomarker in disease monitoring and therapeutic targeting.},
}

@article {pmid42168337,
year = {2026},
author = {Tao, M and Liu, Y and Guo, H and Gao, S and Wang, Y and Yan, X and Zhu, Y},
title = {The role of the gut microbiota in radiation enteritis: from mechanistic insights to therapeutic applications.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42168337},
issn = {2399-3642},
support = {BK20250559//Natural Science Foundation of Jiangsu Province (Jiangsu Provincial Natural Science Foundation)/ ; 82403008//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M762749//China Postdoctoral Science Foundation/ ; },
mesh = {*Gastrointestinal Microbiome/radiation effects ; Humans ; *Enteritis/microbiology/therapy/etiology ; *Radiation Injuries/microbiology/therapy ; Dysbiosis/microbiology ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Radiotherapy/adverse effects ; },
abstract = {Radiation enteritis (RE) is a severe adverse reaction after abdominal and pelvic radiotherapy, with a complicated pathogenesis and no effective treatment. Although gut microbiota dysbiosis was reported to play a critical role in RE, related molecular characteristics and intervention strategies have not been extensively summarized. In this review, the mechanisms of RE, including injury to intestinal stem cells, damage to the vascular endothelium, reshaped immune microenvironment, and mucosal barrier dysfunction, are discussed. In addition, radiation-induced gut microbiota dysbiosis is characterized by decreased abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Bifidobacterium bifidum, and increased abundance of detrimental bacteria such as Escherichia-Shigella and Enterococcus. Beneficial and detrimental bacteria affect the development of RE by regulating inflammatory signaling pathways such as NF-κB and JAK/STAT3, and through their metabolites such as bile acids and short-chain fatty acids. Accordingly, several microbiome-targeted therapeutic strategies, including antibiotic administration, dietary interventions, fecal microbiota transplantation, probiotic administration and engineered bacteria, have been developed to mitigate RE. However, some challenges still remain for these therapeutic strategies. The goal of this review is to highlight the crucial role of gut microbiota dysbiosis in the pathogenesis of RE, thereby accelerating the development of individualized microbial therapies against this disease.},
}

*Gastrointestinal Microbiome/radiation effects
Humans
*Enteritis/microbiology/therapy/etiology
*Radiation Injuries/microbiology/therapy
Dysbiosis/microbiology
Animals
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Radiotherapy/adverse effects

@article {pmid42168404,
year = {2026},
author = {Huang, L and Liu, X and Huang, F and Chen, L and Yue, J},
title = {Berberine reshapes gut microbiota and attenuates bone loss in estrogen-deficient osteoporosis via the gut-bone axis.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42168404},
issn = {1432-1912},
support = {LGF22H060014//the Basic Public Welfare Research Project of Zhejiang Natural Science Foundation of China/ ; },
abstract = {Postmenopausal osteoporosis (PMO) is a metabolic bone disorder characterized by estrogen deficiency-induced bone loss, deterioration of bone microstructure, and increased fracture risk. Current therapeutic agents are limited in efficacy and may have adverse effects. Berberine, a traditional Chinese medicinal compound, exhibits multitarget regulatory potential. However, its mechanism of action in alleviating PMO through modulation of the gut microbiota remains unclear. The objectives of this study are to assess the potential of berberine in mitigating estrogen deficiency-induced osteoporosis through modulation of the gut microbiota and to elucidate its underlying mechanisms. An ovariectomy (OVX)-induced PMO mouse model was established and divided into control, model, and berberine-treated (100 mg/kg/day) groups. Bone microstructure was examined using micro-CT, gut microbiota composition was analyzed through 16S rRNA sequencing; inflammatory factors and bone metabolism markers were evaluated using immunofluorescence; western blotting, qRT-PCR, and serum cytokine levels were quantified using ELISA. Berberine effectively reversed the OVX-induced gut dysbiosis by restoring the diminished levels of norank_f_Muribaculaceae and mitigating the elevated abundance of Lachnospiraceae_NK4A136_group, norank_f_Lachnospiraceae, and Roseburia. This modulation led to the suppression of intestinal inflammation, evidenced by decreased expression of IL-1β, IL-6, IL-8, and TNF-α, and an enhancement in gut barrier integrity, as indicated by increased levels of occludin and ZO-1. These changes collectively reduced the translocation of LPS into circulation. Consequently, berberine attenuated systemic and local release of pro-inflammatory cytokines and the activation of osteoclasts, resulting in the amelioration of PMO. Berberine mitigates PMO by reshaping the gut microbiota, improving intestinal barrier function, and suppressing systemic inflammation, thereby inhibiting bone resorption and restoring bone metabolic balance. This study offers a novel microbiome-targeted therapeutic approach for PMO.},
}

@article {pmid42168503,
year = {2026},
author = {Yang, X and Huang, B and Ren, J and Fang, L and He, W and Mei, Y},
title = {Synergistic Consortia with Bacillus megaterium A14 Enhance Cadmium Immobilization in the Arachis hypogaea Rhizosphere.},
journal = {Current microbiology},
volume = {83},
number = {7},
pages = {},
pmid = {42168503},
issn = {1432-0991},
mesh = {*Cadmium/metabolism ; *Rhizosphere ; *Arachis/microbiology/metabolism ; *Bacillus megaterium/metabolism/physiology ; Soil Microbiology ; *Microbial Consortia ; *Soil Pollutants/metabolism ; Plant Roots/microbiology/metabolism ; Soil/chemistry ; },
abstract = {The microbial immobilization of cadmium bioavailability in peanut-growing soils is crucial for food safety. This study investigated the effects of exogenously applied Bacillus megaterium A14 on the indigenous rhizosphere microbiome of peanut plants and its role in modulating cadmium uptake and bioavailability. Shake-flask experiments revealed that co-culture of A14 with two native rhizosphere strains, Microbacterium S3 and Paenibacillus S22, synergistically enhanced cadmium immobilization. Non-invasive micro-test technology (NMT) further demonstrated that A14 promoted the Cd[2+] uptake capacity of S22 in co-inoculation. Pot experiments showed that inoculation with the three-strain consortium SD6 (A14, S3, and S22) reduced cadmium (Cd) content in peanut stems and roots by 51.34% and 29.14%, respectively. Additionally, the consortium altered Cd speciation in rhizosphere soil, decreasing the exchangeable fraction from 41% to 23% while increasing the residual fraction from 10% to 30%. B. megaterium A14 attracted cooperative strains S3 and S22 via metabolic secretions, and their close biofilm-based association facilitated metabolite exchange and functional synergy. The consortium immobilized Cd[2+] through intracellular uptake and extracellular adsorption, thereby reducing soil Cd bioavailability and alleviating Cd-induced oxidative stress in plants. This study proposes an ecological strategy using synergistic microbial consortia to mitigate cadmium bioavailability and uptake in crops, providing new insights into rhizosphere microbial interactions and a theoretical basis for developing composite microbial inoculants in sustainable agriculture.},
}

*Cadmium/metabolism
*Rhizosphere
*Arachis/microbiology/metabolism
*Bacillus megaterium/metabolism/physiology
Soil Microbiology
*Microbial Consortia
*Soil Pollutants/metabolism
Plant Roots/microbiology/metabolism
Soil/chemistry

@article {pmid42168524,
year = {2026},
author = {Akagi, S and Sato, Y and Sakamoto, T and Minamisawa, M},
title = {Sequential co-extraction of gut microbial DNA and fecal polyamines enables integrated microbiome-metabolite profiling in an Alzheimer's disease mouse model.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-54312-7},
pmid = {42168524},
issn = {2045-2322},
support = {FTR-156//Translational Research Grant from Fujita Health University/ ; FTR-156//Translational Research Grant from Fujita Health University/ ; },
abstract = {Early, non-invasive biomarkers for Alzheimer's disease (AD) are urgently needed. Impaired polyamine metabolism, regulated by intracellular pathways and the gut microbiota, has been reported in postmortem brains of AD patients. Here, we developed a sequential co-extraction workflow (Method 10) that enables recovery of gut bacterial DNA and fecal free polyamines-putrescine, spermidine, and spermine-from the same small mouse fecal sample, allowing paired microbiome and metabolite profiling. Applying this workflow to an AD knock-in mouse model and age-matched controls at 8, 32, and 56 weeks revealed an early decrease in Lactobacillus abundance at 8 weeks accompanied by elevated spermidine levels (p < 0.05), while total fecal polyamine concentrations increased further in AD mice at 56 weeks. These findings suggest that integrated fecal microbiome-polyamine profiling may provide exploratory microbiota-polyamine signatures associated with AD progression.},
}

@article {pmid42163620,
year = {2026},
author = {Lu, D and Lu, J and Yang, P and Lou, L and Li, W and Zhou, Y},
title = {Microbiome and Lipidomics Reveal the Mechanism of Eight Zhes Decoction on MAFLD.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113862073460107260407065758},
pmid = {42163620},
issn = {1875-5402},
abstract = {INTRODUCTION: The therapeutic potential of Eight Zhes Decoction (EZD) against metabolic dysfunction-associated fatty liver disease (MAFLD) is well-recognized; however, the underlying biological pathways are not well understood. To address this gap, an integrated investigation using both lipidomics and metagenomics was conducted to reveal the mechanistic rationale behind the effects of EZD.

METHODS: A MAFLD mouse model was established using a Methionine-Choline-Deficient (MCD) diet combined with CCl₁. The mice were treated with EZD for four weeks. Hepatic injury was assessed via H&E, Oil Red O, and Masson staining. Untargeted hepatic lipidomics and shotgun metagenomics were employed to profile lipid species and the gut microbiota composition, respectively.

RESULTS: Histopathological analysis confirmed that EZD significantly alleviated hepatic steatosis, ballooning degeneration, and fibrosis. Lipidomics identified 277 differential lipids; EZD treatment notably downregulated 24 TGs and modulated pathways related to arachidonic acid metabolism and bile secretion. Metagenomics revealed that EZD reshaped the gut microbiota, significantly increasing the abundance of Alistipes sp. while reducing the abundance of Faecalibaculum rodentium.

DISCUSSION: Correlation analysis demonstrated that the restored Alistipes sp. was negatively correlated with multiple hepatic TGs, whereas Faecalibaculum rodentium was positively correlated with lipid accumulation.

CONCLUSION: EZD mitigates MAFLD in mice by synergistically regulating hepatic lipid metabolism and gut microbiota. Specifically, the therapeutic effect involves restoring Alistipes sp. and modulating the gut-liver axis, providing experimental evidence for the clinical application of EZD.},
}

@article {pmid42163680,
year = {2026},
author = {Yan, Q and Liu, Y and Liu, X and Zhou, S and Zhang, Y},
title = {From the Gut to the Mind: Elucidating the Microbiome-chronobiology Axis in the Context of Depressive Illness.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X433342260331161438},
pmid = {42163680},
issn = {1875-6190},
abstract = {INTRODUCTION: Depression is a highly prevalent mood disorder and is often comorbid with gastrointestinal dysfunction and circadian disturbances. Many studies suggest that gut microbiota (GM) dysbiosis and circadian rhythm disruption may contribute to depressive pathophysiology; however, the mechanistic interactions between these systems remain incompletely defined. Deciphering these interactions may provide insights into prospective therapeutic targets or biomarkers for depression, although further mechanistic studies are needed to validate these findings.

METHODS: The PubMed, Web of Science, Embase, and the Cochrane Library for articles published between January 2000 and December 2024 served as the basis of this review for analyzing, which covers original research, meta-analyses, high-impact reviews published in English, and excluding conference abstracts, case reports, and studies focusing solely on animal models without potential translational implications. After independently screening all retrieved articles and resolving discrepancies, a narrative synthesis approach was adopted to integrate data on mechanistic pathways, clinical associations, and translational potential.

RESULTS: In this review, we focused on the dynamic interaction network between the GM and circadian rhythms, considering a new pathway by which they participate in the occurrence and development of depressive symptoms through bidirectional regulation: significant abnormalities in the GM structure of depressed patients are specifically associated with disruption of the circadian rhythm, and this association is dysbiosis-misalignment.

DISCUSSION: Deciphering the molecular mechanisms of the regulatory loop may provide valuable information that can help screen specific therapeutic targets and biomarkers for depression, which may promote the transformation of depression diagnosis and treatment models from symptomatic treatment to precision-targeted intervention.

CONCLUSION: Studies have confirmed dysbiosis-misalignment between the GM and circadian rhythms: dysbiosis can reshape the regulatory system underlying circadian rhythm, and disruption of the circadian rhythm in turn exacerbates dysbiosis. This interaction imbalance may drive the pathophysiological processes of depression. In this review, we highlighted that a comprehensive assessment of the interaction mechanism of the microbiome-chronobiology axis may help overcome the current bottleneck in treating depression and may provide a theoretical basis for developing novel intervention strategies with both timeliness and targeting.},
}

@article {pmid42163696,
year = {2026},
author = {Seneff, S and Nigh, G and Kyriakopoulos, AM},
title = {Melatonin in Health and Disease and its Metabolism by the Gut Microbes: Implications for Deuterium Homeostasis?.},
journal = {Current medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298673468554260508041733},
pmid = {42163696},
issn = {1875-533X},
abstract = {Deuterium (2H), a heavy isotope of protium (1H), is a naturally occurring element with a significant impact on human metabolism. Despite its natural presence, deuterium can impair mitochondrial function by damaging ATPase pumps; consequently, biological organisms have evolved sophisticated strategies to mitigate the risks of deuterium overload and protect mitochondrial integrity. Multiple enzymes have evolved to prefer hydrogen over deuterium in their reactions to protect these pumps. One class of enzymes is the cytochrome P450 (CYP) enzymes, which oxidize many substrates, mainly in the Endoplasmic Reticulum (ER), often producing water as a by-product. Furthermore, hydrogen peroxide (H2O2), produced in the ER by ERO1, can travel via the cytoplasm to the mitochondria, where it is reduced to two molecules of water via glutathione peroxidase. Melatonin is an ancient antioxidant molecule that first appeared in photosynthetic bacteria billions of years ago to protect against oxygen produced by respiration. In this paper, we present a hypothesis that melatonin metabolism in the gut provides deuterium- depleted protons to the enterocyte mitochondria. Few are aware that melatonin, known mainly as the hormone produced by the pineal gland to regulate circadian rhythms, is produced in the gut at 400 times the amount produced by the pineal gland. In the gut lining, melatonin is synthesized from N-acetylserotonin through the addition of a methyl group from S-adenosylmethionine. This methyl group, which we argue is severely deuterium-depleted due to its gut microbial source, is then fully metabolized by CYP2C19 in the ER of enterocytes in the small intestine, producing four molecules of water, which we argue would also be depleted in deuterium. Melatonin is recycled from the gut to the liver multiple times via the bile acids, and it is repeatedly converted back to N-acetylserotonin and regenerated, each time producing four water molecules derived from its methyl group. Butyrate, another nutrient supplied by gut microbes, stimulates the synthesis of serotonin and melatonin from tryptophan in the gut. Melatonin is a powerful antioxidant in mitochondria and promotes a healthy microbiome. Melatonin deficiency is associated with the severity of long COVID, and melatonin supplementation can help minimize side effects.},
}

@article {pmid42163722,
year = {2026},
author = {Hackmann, TJ and Parris, JP and Seshadri, R and Lingga, C},
title = {Microbe Decoder uncovers functional traits of microbes in microbiome datasets.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag515},
pmid = {42163722},
issn = {1362-4962},
support = {2018-67015-27495//National Institute of Food and Agriculture/ ; 1019985//National Institute of Food and Agriculture/ ; //University of California, Davis Small Grant in Aid of Research/ ; },
abstract = {Microbe Decoder is a web server that predicts functional traits of microbes in microbiome sequencing datasets. Sequencing has revealed thousands of organisms in most ecosystems, but the functional traits of many organisms remain unclear. Existing tools can predict names of organisms or their genes, but they rarely predict concrete biological functions (e.g. fermentation or anaerobic growth). Microbe Decoder fills this gap using three complementary tools relying on taxonomy, metabolic networks, or machine learning. These tools accept either names or gene functions as inputs and are integrated into an easy-to-use web app. When tested against data for microbial isolates, Microbe Decoder showed good predictive performance (e.g. balanced accuracy of 0.85). When applied to datasets from the gut, sediment, and sea, it predicted shifts in functional traits over space and time. Microbe Decoder is designed for use with prokaryotes, with the goal of including eukaryotes in the future. By revealing functional traits of microbes in biological systems, Microbe Decoder will advance biology, medicine, and environmental science. Microbe Decoder is available at https://www.microbe-decoder.org/.},
}

@article {pmid42163806,
year = {2026},
author = {Devi, S and Debnath, N and Yadav, P and Satyavolu, S and Yadav, AK and Tyagi, N},
title = {Dynamic Modulation of the Gut Microbiome in Neurodegenerative Diseases: Mechanisms, Therapeutic Potential, and Clinical Perspective.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70165},
doi = {10.1002/cph4.70165},
pmid = {42163806},
issn = {2040-4603},
support = {TPA-971566//American Heart Association/ ; 24TPA1304527//American Heart Association/ ; 25TPA1481771//American Heart Association/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neurodegenerative Diseases/microbiology/metabolism/therapy ; Animals ; Brain-Gut Axis/physiology ; Brain/metabolism ; },
abstract = {The gut and brain communicate bidirectionally through the gut microbiota, forming a complex network often referred to as the "microbiota-gut-brain axis." The gastrointestinal microbiome produces various metabolites, including short-chain fatty acids (SCFAs), tryptophan-derived compounds, and secondary bile acids. Research indicates that disruptions in the intestinal microbiota (dysbiosis) and impaired gut-brain axis are associated with various neurological conditions. The central nervous system (CNS) influences digestive processes via the hypothalamic-pituitary-adrenal (HPA) axis and autonomic nervous system (ANS). On the other hand, the gut reciprocally affects brain function through microbial metabolites, neuroactive substances, and intestinal hormones via multiple pathways, including neural (vagal), immune, and endocrine signaling; however, only a subset of metabolites can directly access the CNS due to blood-brain barrier (BBB) selectivity. These microbial metabolites can directly or indirectly influence the CNS and modulate neuro-immune signaling by activating receptors, such as the aryl hydrocarbon receptor (AhR) and G protein-coupled receptors (GPCRs). By acting as ligands for these receptors, metabolites modulate neural signaling and exert neuroprotective effects. This review discusses how probiotic-derived metabolites modulate the gut-brain axis and provide neuroprotective effects, focusing on the receptors they activate and their downstream signaling pathways involved in neuroprotection.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Neurodegenerative Diseases/microbiology/metabolism/therapy
Animals
Brain-Gut Axis/physiology
Brain/metabolism

@article {pmid42164043,
year = {2026},
author = {Ng, MK and Jacofsky, D and Barsoum, W and Mont, MA},
title = {Calcium montmorillonite clay: a clinically oriented narrative review of emerging perioperative and supportive applications.},
journal = {Annals of translational medicine},
volume = {14},
number = {2},
pages = {18},
pmid = {42164043},
issn = {2305-5839},
abstract = {Calcium montmorillonite (CMM) clay, a naturally occurring mineral-rich volcanic clay has garnered scientific attention for its detoxification properties, gastrointestinal (GI) support, skin benefits, and potential metabolic modulation. Recent advances in pharmaceutical-grade formulation and mechanistic understanding have renewed clinical interest in CMM as a low-risk, non-systemic adjunct in modern medical practice. General practitioners and surgeons may find it particularly useful as a safe adjunct in gut health, topical recovery, and inflammatory modulation. With supporting data from preclinical and clinical research, including studies on aflatoxin binding, microbiome modulation, and treatment of radiation enteritis and pediatric diarrhea, CMM represents a promising natural therapeutic mineral for integration into modern health protocols. This narrative review summarizes the biological properties, clinical safety, indications, and emerging efficacy data surrounding CMM, with a focus on potential perioperative and wellness applications.},
}

@article {pmid42164238,
year = {2026},
author = {Garrido-Martín, EM and Kontic, M and Rooney, C and Mansouri, N},
title = {Immune checkpoints in lung cancer.},
journal = {Breathe (Sheffield, England)},
volume = {22},
number = {2},
pages = {250244},
pmid = {42164238},
issn = {1810-6838},
abstract = {The advent of immune checkpoint inhibitors (ICIs) has revolutionised the management of lung cancer, transforming it from a historically immune-resistant malignancy into a paradigm for durable immunotherapy response. This review provides a comprehensive overview of the biological and clinical foundations of checkpoint regulation in the lung and their implications for patient care. We first explore the unique pulmonary immune environment, where continuous exposure to environmental antigens necessitates a delicate balance between tolerance and defence. Within this context, immune checkpoints, such as programmed cell death protein 1 (PD-1) and its ligand PD-L1 as well as cytotoxic T-lymphocyte-associated protein 4, maintain physiological self-tolerance but can be subverted by tumour cells to evade immune surveillance. Emerging inhibitory receptors, including LAG-3, TIGIT and TIM-3, contribute additional layers of immune regulation and resistance, highlighting opportunities for combinatorial therapeutic strategies. The clinical section summarises pivotal trials establishing ICIs as the standard of care across metastatic, locally advanced and early-stage lung cancer. These agents now span the full disease continuum, from neoadjuvant and adjuvant to perioperative and consolidation settings. We also address the management of immune-related adverse events and the need for precision in patient selection through biomarkers, such as PD-L1 expression, tumour mutational burden and circulating immune signatures. Finally, we discuss ongoing challenges, including mechanisms of primary and acquired resistance, and emerging approaches integrating spatial multi-omics, dynamic immune monitoring and microbiome profiling. Together, these advances are reshaping lung cancer immunotherapy towards a more precise, adaptive and durable model of care.},
}

@article {pmid42164255,
year = {2026},
author = {Ma, D and Xu, Y and Liang, R and Meng, Q and Liu, Y and Hu, D and Zhu, B and Zheng, Y and Luo, Q},
title = {Chlorogenic acid modulates gut microbiota and metabolites to alleviate intrahepatic cholestasis of pregnancy: Insights from 16S rRNA sequencing and metabolomics.},
journal = {Biochemistry and biophysics reports},
volume = {46},
number = {},
pages = {102619},
pmid = {42164255},
issn = {2405-5808},
abstract = {Intrahepatic cholestasis of pregnancy (ICP) is a liver disorder marked by impaired bile flow, elevated serum bile acids, and pruritus, posing significant risks to maternal and fetal health. Current treatments, including ursodeoxycholic acid, have shown limited efficacy, underscoring the need for more effective therapies. Chlorogenic acid (CGA), a polyphenolic compound with antioxidant, anti-inflammatory, and hepatoprotective properties, has shown promise in managing liver diseases, but its role in ICP remains poorly understood. This study investigated the therapeutic effects of CGA in a rat model of ICP induced by 17α-ethinylestradiol. CGA treatment significantly reduced liver enzyme levels, total bile acids, and bilirubin, while improving histopathological liver damage. CGA also modulated key proteins involved in bile acid synthesis and transport, including FXR, CYP7A1, NTCP, and BSEP. Additionally, CGA treatment improved intestinal barrier function by upregulating tight junction proteins, including ZO-1. Metabolomics and 16S rRNA gene sequencing revealed that CGA treatment restored gut microbiota balance in ICP rats. CGA demonstrated a dose-dependent response, with higher doses providing more pronounced therapeutic effects. These findings suggest that CGA alleviates ICP by regulating bile acid metabolism, improving liver function, and modulating the gut microbiome, highlighting its potential as an effective therapeutic option for managing ICP.},
}

@article {pmid42164260,
year = {2026},
author = {Shi, H and Jiang, L and Cai, Y and Chen, Z and Hu, Y and Zhou, Y and Li, J and Zhang, D and Cao, Z and Wang, S},
title = {Regulatory Effects of a Lipid-Lowering Strain Lactobacillus plantarum 58 Isolated From Dregs Vinegar on Metabolism-Related Gene Expression, Gut Microbiota, and Metabolic Biomarkers of Hybrid Grouper Under High-Fat Diets.},
journal = {Aquaculture nutrition},
volume = {2026},
number = {},
pages = {4888310},
pmid = {42164260},
issn = {1365-2095},
abstract = {Lactobacillus plantarum 58 (lactic acid bacteria [LAB] 58), isolated from vinegar dregs, was incorporated at 1 × 10[8] CFU/g diet into the feeds of hybrid groupers to assess its lipid-lowering efficacy under normal (7.52 % lipid) or high-fat (14.83 % lipid) regimens. A 2 × 2 factorial design generated four diets: C (normal), H (high-fat), C58 (normal + LAB 58), and H58 (high-fat + LAB 58). Serum biochemical parameters tests, histological section, and Oil Red O staining results indicated that in both LAB 58-supplemented groups (C58 and H58), serum triglycerides and total cholesterol (T-CHO) declined regardless of basal lipid content, and hepatic fat vacuolation and lipid-droplet accumulation were markedly curtailed. The qPCR data revealed that LAB 58 elevated the levels of hepatic lipolysis genes (adipose triglyceride lipase [ATGL], carnitine palmitoyltransferase 1 [CPT-1], farnesoid X receptor [FXR], and lipoprotein lipase [LPL]) while simultaneously suppressing lipid synthesis gene expressions (fatty acid synthase [FAS] and stearoyl-CoA desaturase 1 [SCD-1]) in the H58 group compared with the H group. Gut-microbiota profiling showed a pronounced Firmicutes-to-Bacteroidetes shift, driven by increased Bacteroides, Faecalibacterium, and Lachnospiraceae-UCG-004; the relative abundance of Lactobacillus spp. surged, especially in the H58 group. Metabolomic analysis of intestinal contents further disclosed elevated levels of beneficial fatty acids-linoleic and α-linolenic acids in H58 group. In conclusion, these findings demonstrate that LAB 58 alleviates lipid metabolic disorders by modulating hepatic gene expression, restructuring the gut microbiota, and enhancing beneficial metabolites.},
}

@article {pmid42164266,
year = {2026},
author = {Lin, SH and Lin, RJ and Chang, RY and Huang, YF and Hsu, YY and Chu, CL and Chen, YL and Lin, CY and Fu, SC},
title = {Heterogeneity in the association between gut microbiota and insomnia moderated by Parkinson's disease status.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1691665},
pmid = {42164266},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Parkinson Disease/complications/microbiology ; *Sleep Initiation and Maintenance Disorders/microbiology/etiology/complications ; Male ; RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics/chemistry ; },
abstract = {INTRODUCTION: Parkinson's disease (PD) is frequently accompanied by insomnia, and emerging evidence suggests the gut microbiome may play a role. This study investigates gut microbiome differences associated with insomnia in PD patients compared to non-PD individuals.

METHODS: We analyzed 310 participants (185 PD patients, 125 controls) categorized by insomnia status. Gut microbiome profiles were obtained using 16S rRNA sequencing and processed with DADA2 using the SILVA database for taxonomic assignment. Alpha and beta diversity analyses and differential abundance analysis were conducted, and functional prediction was performed using PICRUSt2, adjusting for relevant confounders.

RESULTS: Insomnia was linked to higher alpha diversity in non-PD individuals but lower alpha diversity in PD patients. Interaction analysis confirmed distinct associations between insomnia and microbial diversity in the two groups. Differential abundance analysis identified unique insomnia-associated bacterial genera, with differing insomnia-risk-reducing and insomnia-risk-increasing taxa. Functional analysis showed six enriched pathways in controls but only two in PD patients, with no overlap.

DISCUSSION: These findings suggest that insomnia in PD is associated with distinct gut microbiome profiles compared with non-PD individuals. The results highlight the importance of considering disease context when examining microbiome-sleep relationships and may inform future research on microbiome-based approaches for sleep disturbances in PD.},
}

Humans
*Gastrointestinal Microbiome
*Parkinson Disease/complications/microbiology
*Sleep Initiation and Maintenance Disorders/microbiology/etiology/complications
Male
RNA, Ribosomal, 16S/genetics
Female
Aged
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Biodiversity
DNA, Bacterial/genetics/chemistry

@article {pmid42164272,
year = {2026},
author = {Yaghi, M and Gonzalez, T and Vecin, N and Pastar, I and Lev-Tov, H},
title = {A bioelectric dressing improves postderoofing outcomes in hidradenitis suppurativa by microbiome modulation: A split-body, randomized clinical trial.},
journal = {JID innovations : skin science from molecules to population health},
volume = {6},
number = {4},
pages = {100461},
pmid = {42164272},
issn = {2667-0267},
abstract = {UNLABELLED: Hidradenitis suppurativa tunnels represent treatment-resistant disease compartment that perpetuates inflammation, microbial dysbiosis, and relapse. Surgical deroofing remains the standard intervention, yet optimal postoperative wound management strategies are lacking.

OBJECTIVES: We aimed to evaluate the efficacy of a wireless bioelectric wound dressing compared with that of standard of care in modulating tunnel-associated microbiota and preventing surgical site recurrence after hidradenitis suppurativa deroofing.

METHODS: In this randomized, single-center, split-body trial, patients with bilateral Hurley stages II-III axillary disease underwent tunnel deroofing, with 1 side randomized to bioelectric wound dressing or standard of care (petrolatum and gauze dressing). Subjects (n = 12) were followed for 8 weeks to assess primary outcomes: healing rates. Secondary outcomes included disease recurrence at week 8, change in bacterial load, microbiome composition, and QOL.

RESULTS: Bioelectric wound dressing-treated sites showed a significant reduction in bacterial load at weeks 2 and 4 after excision, with enrichment of commensals and a shift away from anaerobic taxa, which were not observed in standard of care-treated sites. Minimal recurrences were observed on bioelectric wound dressing-treated sides alone compared with multiple recurrences on standard of care-treated sites, with trends of improved healing trajectories.

CONCLUSIONS: Optimized wound care holds a potential to reduce surgical site recurrence and reverse hidradenitis suppurativa dysbiosis. Our data emphasize the importance of postsurgical care to improve outcomes in patients with hidradenitis suppurativa. This trial was registered at ClinicalTrials.gov with NCT05057429. Study registration was submitted on September 15, 2021.},
}

@article {pmid42164318,
year = {2026},
author = {Aizpurua, O and Brenner, E and Martin-Bideguren, G and Garin-Barrio, I and Cabido, C and Alberdi, A},
title = {Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag106},
pmid = {42164318},
issn = {2730-6151},
abstract = {Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (Calotriton asper) inhabiting two distinct environments: Pyrenean subalpine brooks and Atlantic montane streams. From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes, respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. Although alpha diversity remained similar across environments, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community-shared across environments and accounting for over 85% of reads-that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not associated with broad-scale dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.},
}

@article {pmid42164491,
year = {2026},
author = {Green, M and Cleary, S and Kwiecien-Delaney, B and Foster, JA},
title = {Compositional maturation of the microbiome and adaptive immunity in the postnatal period.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1772425},
pmid = {42164491},
issn = {1664-3224},
mesh = {Animals ; *Adaptive Immunity ; *Gastrointestinal Microbiome/immunology ; Mice ; Mice, Inbred C57BL ; T-Lymphocyte Subsets/immunology ; T-Lymphocytes/immunology ; },
abstract = {INTRODUCTION: Recent research has highlighted the role of the gut microbiome in shaping the development and function of the mammalian immune system. Interactions between these complex networks of microbes and host cells serve not only to train major aspects of adaptive and innate immunity but also to establish commensal host-microbe relationships and symbiosis throughout the lifespan. T-cells are a critical aspect of this paradigm, acting as intermediates between the microbiome and many aspects of host health and disease. Despite a large body of literature examining these interactions, we have yet to completely understand how the ontogeny of these systems co-evolves across the lifespan and how the emergence of specific T-cell-microbe signals relates to key developmental milestones.

METHODS: To answer this question, this work conducted a compositional integrative analysis on deep immune and microbiome profiling of wild-type C57Bl/6 mice across the first two weeks of life, post-weaning, and young adulthood.

RESULTS: The results show that T-cell ontogeny follows different developmental trends in mucosal and peripheral immune compartments and that temporal trends in microbial community abundance creates a modular network of associations between specific taxa and functional T-cell subsets.

DISCUSSION: These results provide insight into the longitudinal development of microbiota-immune system interactions throughout the lifespan, as well as the mechanistic relevance of microbiota-derived signals at key developmental milestones.},
}

Animals
*Adaptive Immunity
*Gastrointestinal Microbiome/immunology
Mice
Mice, Inbred C57BL
T-Lymphocyte Subsets/immunology
T-Lymphocytes/immunology

@article {pmid42164500,
year = {2026},
author = {Mao, Q and Lin, B and Xia, W and Zhang, Y and Lei, Y and Cao, Q and Xu, M},
title = {Melatonin-induced restoration of the intestinal mucosal barrier in inflammatory bowel disease via activation of the SIRT1-LKB1-pAMPK axis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1811583},
pmid = {42164500},
issn = {1664-3224},
mesh = {Animals ; *Sirtuin 1/metabolism ; *Melatonin/pharmacology/metabolism ; *Intestinal Mucosa/drug effects/metabolism/pathology/microbiology ; *AMP-Activated Protein Kinases/metabolism ; Mice ; *Inflammatory Bowel Diseases/metabolism/drug therapy/pathology ; Humans ; Male ; AMP-Activated Protein Kinase Kinases ; *Protein Serine-Threonine Kinases/metabolism ; Disease Models, Animal ; Signal Transduction/drug effects ; Gastrointestinal Microbiome/drug effects ; Female ; Mice, Inbred C57BL ; Colitis ; },
abstract = {BACKGROUND: Numerous studies indicated inflammatory bowel disease (IBD) patients suffered from sleep disturbances. Although melatonin (MT) exerts positive effects on maintaining circadian rhythms and anti-inflammation, its impact on the gut microbiome and its function in mediating gut health remain largely unexplored. To evaluate the efficacy and investigate the mechanisms of MT in repairing the intestinal mucosal barrier in IBD.

METHODS: Fecal MT and its metabolites in IBD patients were detected. A DSS-induced colitis mice model and a LPS-stimulated NCM460 cell inflammation model were used to explore the mechanism of melatonin in IBD.

RESULTS: IBD patients had lower levels of serum MT and fecal 2-oxomelatonin. Furthermore, MT enhances intestinal antimicrobial peptides and effectively alleviates colitis. Mechanistically, MT restored the abundance of the probiotic Akkermansia and decreased the conditional pathogen Desulfovibrio. MT upregulates the SIRT1 (Sirtuin 1) and pAMPK (phosphorylated AMP-Activated Protein Kinase) in mouse colonic tissues. Whereas Ex-527 (the SIRT1 inhibitor) and Compound C (the pAMPK inhibitor) abolished the protective effects of MT in DSS mice. In LPS-stimulated cells, the inhibitor blocked the regulation of MT on proinflammatory factors, antimicrobial peptides and tight junctions. Mechanistically, MT was associated with activation of the SIRT1-LKB1-pAMPK pathway, suggesting its potential involvement in regulating the above changes.

CONCLUSION: Our findings suggest that MT may ameliorate colitis by regulating gut microbiota, modulating antimicrobial peptide secretion, and reinforcing intestinal epithelial barrier integrity potentially via activation of the SIRT1-LKB1-pAMPK axis.},
}

Animals
*Sirtuin 1/metabolism
*Melatonin/pharmacology/metabolism
*Intestinal Mucosa/drug effects/metabolism/pathology/microbiology
*AMP-Activated Protein Kinases/metabolism
Mice
*Inflammatory Bowel Diseases/metabolism/drug therapy/pathology
Humans
Male
AMP-Activated Protein Kinase Kinases
*Protein Serine-Threonine Kinases/metabolism
Disease Models, Animal
Signal Transduction/drug effects
Gastrointestinal Microbiome/drug effects
Female
Mice, Inbred C57BL
Colitis

@article {pmid42164501,
year = {2026},
author = {Yu, J and Li, Q and Zou, S and Rong, Y and Zhang, Y and Chen, C},
title = {Antibiotic use and immune-related adverse events in patients treated with immune checkpoint inhibitors: analysis of the FAERS database.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1733373},
pmid = {42164501},
issn = {1664-3224},
mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; Aged ; Databases, Factual ; *Neoplasms/drug therapy/immunology ; *Drug-Related Side Effects and Adverse Reactions/etiology/epidemiology ; Gastrointestinal Microbiome/drug effects ; Aged, 80 and over ; Adult ; Adverse Drug Reaction Reporting Systems ; Risk Factors ; },
abstract = {BACKGROUND: The use of antibiotics may influence the efficacy and toxicity of immune checkpoint inhibitors (ICIs) by altering the gut microbiota. However, current evidence on the link between antibiotic use and immune-related adverse events (irAEs) is limited. This study aims to evaluate whether antibiotics increase the risk of irAEs in ICI-treated patients and to examine their relationship to the timing of irAEs onset.

METHODS: We analyzed data from the FAERS database from 2014 to the fourth quarter of 2024. Using multivariable logistic regression and descriptive statistical analyses, we evaluated the association between antibiotic co-reporting and irAE reporting frequency and the timing across different antibiotic categories and ICIs regimens.

RESULTS: Our study included 155,157 patients treated with ICIs, of whom 9,518 (6.1%) received antibiotic therapy. Patients who used antibiotics had a significantly higher reported frequency risk of irAEs (OR = 1.17; 95%CI: 1.12-1.23; FDR<0.001) compared to those who did not. The strongest associations were observed in patients receiving fluoroquinolones, sulfonamides, penicillin, macrolides, cephalosporins, and monobactams. Co-reporting was associated with a higher reported frequency of irAEs in patients receiving PD-L1 inhibitors (OR = 1.51; 95% CI: 1.39-1.65; FDR<0.001). In exploratory descriptive analysis restricted to patients who reported irAEs, the median time to first reported irAE was shorter in the antibiotic co-reporting group than in the non-co-reporting group (31 days (IQR: 9-105) vs. 42 days (IQR: 14-122), Wilcoxon rank-sum test P < 0.001). Stratified analysis by ICI type showed that this pattern was most evident in patients receiving PD-1 inhibitors.

CONCLUSIONS: Analysis of the FAERS database suggests that antibiotic co-reporting during ICIs therapy is associated with a higher reported frequency of irAEs and a shorter median time to first reported irAE among patients who experienced irAEs. These findings are subject to the inherent limitations of the FAERS database, including the inability to determine the temporal sequence of antibiotic and ICI exposure, unmeasured confounding, reporting artifacts, and the unsuitability of spontaneous reporting data for formal time-to-event analysis. Prospective cohort studies with detailed medication timing, clinical phenotyping, and microbiome profiling are needed to validate these signals.},
}

Humans
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
*Anti-Bacterial Agents/adverse effects/therapeutic use
Male
Female
Middle Aged
Aged
Databases, Factual
*Neoplasms/drug therapy/immunology
*Drug-Related Side Effects and Adverse Reactions/etiology/epidemiology
Gastrointestinal Microbiome/drug effects
Aged, 80 and over
Adult
Adverse Drug Reaction Reporting Systems
Risk Factors

@article {pmid42164510,
year = {2026},
author = {Yin, X and Peng, H and Li, Y and Song, Y and Yao, N and Shen, Z and Chen, H and Huang, L and Li, P and He, Z and Chen, Q},
title = {Ankylosing spondylitis and the gut microbiome: future research hotspots and trends.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1784757},
pmid = {42164510},
issn = {1664-3224},
mesh = {*Spondylitis, Ankylosing/microbiology/immunology/etiology ; Humans ; *Gastrointestinal Microbiome/immunology ; Bibliometrics ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: Ankylosing spondylitis (AS) is an autoimmune disease. Its exact cause remains unclear. It is generally believed to result from a combination of genetic and environmental factors, as well as immune disorders. However, growing evidence suggests that the gut microbiota plays a key role in the pathogenesis of AS. Therefore, this study aims to systematically analyze the current state of research on AS and the gut microbiome. It also explores future research hotspots.

METHODS: We searched the Web of Science Core Collection (WoSCC) and PubMed databases, including relevant literature on AS and the gut microbiome published up to January 1, 2026. We then performed a visualized bibliometric analysis using CiteSpace, VOSviewer, and Bibliometrix software.

RESULTS: The WoSCC dataset included 165 articles. Both the annual publication volume and citation counts showed an upward trend. Brown, Ma, and Liu B were the most productive authors. Regarding country output, China ranked first with 60 articles, followed by the USA with 36. Major contributing institutions were also primarily located in China and the USA. Current research hotspots focus on inflammation, Mendelian randomization, HLA-B27, probiotics, and short-chain fatty acids. A validation analysis using the PubMed database (115 articles) yielded results consistent with the WoSCC findings.

CONCLUSION: Our study provides key insights into the relationship between the gut microbiota and AS. It clarifies current research hotspots and development trends. Future researchers should conduct prospective studies to confirm causality and combine multi-omics analysis to reveal underlying molecular mechanisms.},
}

*Spondylitis, Ankylosing/microbiology/immunology/etiology
Humans
*Gastrointestinal Microbiome/immunology
Bibliometrics
*Biomedical Research/trends

@article {pmid42164524,
year = {2026},
author = {Hu, S and He, C and Sun, K and Zhou, H and Liu, X and Wang, H and Li, S and Yu, H and Xu, K and Li, W},
title = {The gut-liver/bile axis: Gut microbiota and bacterial extracellular vesicles remodeling hepatobiliary pathogenesis.},
journal = {iScience},
volume = {29},
number = {5},
pages = {115623},
pmid = {42164524},
issn = {2589-0042},
abstract = {Global hepatobiliary disease burden is increasing, prompting gut-liver axis research. Gut microbiota-secreted bacterial extracellular vesicles (BEVs) carry bioactive molecules affecting host immunity, inflammation, and metabolism. Whether BEVs actively or passively cause liver damage is unclear. This review suggests gut-derived BEVs trigger hepatic innate immunity and sterile inflammation. By combining current findings on how gut microbes, their BEVs, and hepatobiliary diseases interact, we improve the "gut-liver/bile axis" idea. Acknowledging BEVs' active part in disease offers new ways to use them as diagnostic markers and treatment targets, likely better managing hepatobiliary disorders.},
}

@article {pmid42164586,
year = {2026},
author = {Unuvar, GK and Mese, EA and Rello, J},
title = {Strategies to prevent cross-transmission of multidrug-resistant microorganisms in intensive care units: A narrative review.},
journal = {Journal of intensive medicine},
volume = {6},
number = {3},
pages = {221-228},
pmid = {42164586},
issn = {2667-100X},
abstract = {Organisms' transmission in intensive care units (ICUs) should be addressed by modulation of the skin and gut microbiome (endogenous) or by acquisition of the environment (exogenous). The microbiome has recently been reported as a reservoir of organisms, modulating the immune host response. Interventions on the gut microbiome are a promising way to prevent the development of hospital-acquired infections in the ICU and reduce the risk of cross-transmission of multidrug-resistant microorganisms. Maintaining the cleanliness of patient care areas is a safety strategy for preventing healthcare-associated infections and recent insights on microbiome modulation to reduce the risk for cross-infection. Evidence indicates that regular cleanliness monitoring can positively influence patient outcomes. The development of standardized cleaning checklists is strongly recommended. Key procedural strategies include preliminary site evaluations to determine the extent of contamination or surface damage, cleaning from low-touch to high-touch areas, and progressing from clean to contaminated regions. Chemical agents such as quaternary ammonium compounds, sodium hypochlorite, and hydrogen peroxide are effective for decontamination. Studies demonstrate a positive correlation between the number of touches a surface receives and its bacterial load, emphasizing the importance of assessing contamination levels and cleaning quality. Such evaluations inform the development of environmental cleaning protocols, guide facility policies, and improve program effectiveness. Cleanliness evaluation monitoring should measure the assessment of cleaning practices and cleanliness levels. Using probiotics, prebiotics, and synbiotics is an innovative strategy to reduce dysbiosis and improve host immunity. Lastly, strengthening staff education is essential to enhancing environmental infection control.},
}

@article {pmid42164663,
year = {2026},
author = {Glapa-Nowak, A and Nowak, JK and Kurek, S and Walkowiak, J},
title = {What a pickle-a metagenomic perspective on the cucumber fermentation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809866},
pmid = {42164663},
issn = {1664-302X},
abstract = {Food fermentation involves an interplay between multiple strains and species. This delicate composition during fermentation has been investigated so far using both classical and molecular methods; however, the results remain difficult to interpret. In this perspective article, we discuss the spontaneous fermentation of cucumber from organic and commercial cultivation (from 1st day to 90th day) based on our preliminary data from a nanopore sequencing study. The present study is the first to report the occurrence of coagulase-negative cocci in cucumber fermentation [Staphylococcus saprophyticus (0.01%) and Staphylococcus schleiferi (0.03%)]. Furthermore, we conclude that own-cultivation cucumbers may exhibit a lower incidence and diversity of phages, which have practical implications for designing future studies as well as for direct consumers. Our data also show that, even in the absence of phages (own-cultivation cucumbers <1%), lactic acid bacteria dominance occurs, which contrasts with previous conclusions and contributes to the discussion on the role of phages in maintaining the balance between Enterobacteriaceae and lactic acid bacteria in plant fermentation. The powerful metagenomic approach provides a broader understanding of the day-to-day and sample-to-sample diversity within microbiome communities. The maturity of the fermentation product may play a significant role in exerting specific biological actions. This should be accounted for before planning an intervention study.},
}

@article {pmid42153004,
year = {2026},
author = {Bogatyrenko, E and Dunkai, T and Kim, A},
title = {Core Bacterial Microbiome in Wild Sea Cucumbers (Apostichopus japonicus) from the Sea of Japan.},
journal = {Indian journal of microbiology},
volume = {66},
number = {2},
pages = {441-451},
pmid = {42153004},
issn = {0046-8991},
abstract = {UNLABELLED: The taxonomic composition of gut bacterial communities in wild Japanese sea cucumbers, Apostichopus japonicus, from coastal waters of the Russian part of the Sea of Japan was identified by high-throughput sequencing. The bacterial communities were comprised mainly of the phyla Proteobacteria (38.33-57.22%), Actinobacteriota (24.24-29.93%), Firmicutes (12.01-25.12%), and Bacteroidota (1.6-2.17%) that made up a total of 94.5% of the samples studied. As the results showed, the region and habitat have a significant effect on the bacterial structure of the gut microbiome in A. japonicus. The invertebrates from each of the water bodies under study were characterized by their unique sets of symbiotic microorganisms. However, 32 bacterial genera were found in the animals from all of the water bodies. Of these, nine bacterial genera were the dominant taxa in terms of percentage of their representation in the samples: Stappia (15.89-34.68%), Stenotrophomonas (3.45-11.44%), Bacillus (1.05-7.71%), Staphylococcus (4.64-11.76%), Rhodococcus (3.07-11.08%), Corynebacterium (2.55-7.77%), Cutibacterium (15.89-34.68%), Pseudomonas (1.2-1.7%), and Streptococcus (1.09-1.57%). The discovery of bacterial genera common across all samples indicates the existence of a core microbiome potentially essential for the host's health and functions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01493-w.},
}

@article {pmid42153502,
year = {2026},
author = {Kumar, S and Jindal, A and Mainuddin, and Rastogi, H and Kumar, A},
title = {Unraveling the Multifunctional and Translational Paradigm of Nanoparticulate Systems against Colorectal Cancer.},
journal = {ACS applied bio materials},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsabm.5c02297},
pmid = {42153502},
issn = {2576-6422},
abstract = {Colorectal cancer (CRC) is a health burden due to its high mortality rate, recurrence rate, and drug resistance. The limitations of traditional methodologies (such as radiotherapy, chemotherapy, surgery, and targeted active ingredients) include inefficient delivery to tumor tissue, systemic toxicity, drug resistance, and poor specificity. Hence, drug delivery through micro- and nanoparticulate systems offers innovations and can address these obstacles successfully. The design, functionality, and translational potential of particulate systems specifically designed for CRC treatment are reviewed in this study. Next, this review discusses various primary aspects, including the types of carriers (polymeric, solid lipid, inorganic, and hybrid nanoparticles/NP), their particulate physical attributes (size, shape, surface charge, composition), and factors affecting drug encapsulation and release kinetics that affect the basic design principles. Additionally, this review unfolds a discussion over targeting approaches, such as active ligand-mediated targeting, passive EPR-based accumulation, and stimulus-responsive systems activated by external stimuli, pH, enzymes, redox, or even the microbiome. Furthermore, conventional chemotherapeutics, phytochemicals and nutraceuticals, gene-based therapies (siRNA, miRNA), and combinatorial modalities (chemo and immunotherapy, photothermal, photodynamic) are included in the therapeutic payloads. Moreover, in vitro, in vivo, and clinical-stage nanoparticulate systems are highlighted with translational advancements. Specifically, this review emphasizes the benefits offered, including enhanced solubility, stability, targeted distribution, and multifunctionality (imaging, triggered release). In addition, primary challenges to translation, such as regulatory, scalability, reproducibility, biological processes, and long-term safety issues, are also discussed. Conclusively, innovative approaches like regulatory frameworks, microbiome-driven delivery designs, aspects of artificial intelligence/machine learning (AI/ML)-guided optimization, and stealth and biomimetic hybrid particulates can be beneficial from futuristic aspects. Suggestively, to expedite the transition from NP invention to effective CRC therapeutics, a translational roadmap is required that encourages the combination of modern materials science, computational design, and clinical validation.},
}

@article {pmid42153538,
year = {2026},
author = {Julanon, N and Unhapipatpong, C and Wongjirattikarn, R and Anutraungkool, T and Chaowattanapanit, S and Choonhakarn, C and Sawanyawisuth, K and Shantavasinkul, PC and Zouboulis, CC and Piguet, V},
title = {Role of Probiotics in Managing Acne Vulgaris: A Systematic Review and Meta-Analysis of Clinical Trials.},
journal = {Journal of cutaneous medicine and surgery},
volume = {},
number = {},
pages = {12034754261445880},
doi = {10.1177/12034754261445880},
pmid = {42153538},
issn = {1615-7109},
abstract = {BACKGROUND: Dysregulation of the skin microbiome is implicated in acne pathogenesis.

OBJECTIVE: To evaluate the efficacy of probiotics in the management of acne.

METHODS: Searches were conducted in 3 databases through June 30, 2024. Clinical trials that compared probiotics with controls and investigated their efficacy in acne were included. Primary outcomes were standardized mean differences (SMDs) for the change from baseline to posttreatment in total lesion count (TLC), noninflammatory lesion count (NILC), and inflammatory lesion count (ILC). Secondary outcomes included Global Acne Grading System (GAGS) scores, Investigator's Global Assessment, erythema, and sebum levels.

RESULTS: Thirteen studies comprising 18 study arms and 1453 participants were included. There were no significant reductions in TLC (SMD, -0.22; 95% confidence interval [CI]: -0.50 to 0.07; I[2] = 75%), NILC (SMD, -0.20; 95% CI: -0.48 to 0.08; I[2] = 72%), or ILC (SMD, -0.13; 95% CI: -0.34 to 0.09; I[2] = 52%) with probiotics compared with controls. However, oral probiotics were associated with a significant reduction in GAGS scores (SMD, -0.47; 95% CI: -0.81 to -0.13; I[2] = 67%) versus controls. Subgroup analyses indicated that this effect was most prominent in mild-to-moderate acne patients who received oral probiotics containing Lactobacillus species combined with other strains for a minimum of 12 weeks.

CONCLUSIONS: Probiotics did not demonstrate a significant reduction in acne lesion counts. However, they were associated with improvements in acne severity as measured by GAGS scores. These findings should be interpreted with caution given the heterogeneity across studies and the fluctuating natural course of acne.},
}

@article {pmid42153569,
year = {2026},
author = {Zhang, Q and Li, Y and Han, Y and Zhou, W and Li, X and Sun, J and Bai, W},
title = {Correction to "Lactiplantibacillus plantarum FEED8 Biosynthesis of Pyranoanthocyanin (Cyanidin-3-glucoside-4-vinylcatechol) Improves Oxidative Stress and Inflammation of the Gut Microbiome in Cadmium-Exposed Mice".},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c06010},
pmid = {42153569},
issn = {1520-5118},
}

@article {pmid42153643,
year = {2026},
author = {Jeilu, O and Simachew, A and Hartmann, EM and Alexandersson, E and Johansson, E},
title = {CAZyme fold architecture is conserved between disparate environments despite extreme sequence divergence.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0048526},
doi = {10.1128/msystems.00485-26},
pmid = {42153643},
issn = {2379-5077},
abstract = {Microbial carbohydrate-active enzymes (CAZymes) underpin carbon cycling across Earth's ecosystems; however, how contrasting environments shape CAZyme diversity and structural conservation remains poorly understood. Here, we applied shotgun metagenomics to compare the carbohydrate-degradation potential of two functionally prolific but physicochemically opposed ecosystems: the alkaline-saline soda lakes of the East African Rift Valley and the anaerobic ruminant gut. From 34 metagenomes (12 soda lake and 22 rumen), we recovered 371 quality-filtered metagenome-assembled genomes, of which 84% of soda lake and 52% of rumen MAGs represented novel species. Rumen communities, dominated by Bacteroidota, Fibrobacterota, and Bacillota, exhibited significantly higher taxonomic diversity and were enriched in carbohydrate catabolism and fermentation pathways. Soda lake communities, dominated by Pseudomonadota, displayed greater evolutionary divergence (lower RED scores) and were enriched in pH homeostasis, oxidative and osmotic stress, sulfur cycling, and carbon fixation pathways. To assess whether structural conservation persists despite extreme sequence divergence, we predicted three-dimensional structures for 12 representative enzymes from six glycoside hydrolase families (GH1, GH3, GH5_11, GH9, GH10, and GH28) using AlphaFold 3. All 12 structures adopted canonical GH family folds with high confidence (pTM 0.75-0.97). These results demonstrate that environmental selection drives distinct taxonomic and functional strategies for carbon processing while preserving three-dimensional CAZyme architecture, positioning soda lake and rumen metagenomes as complementary reservoirs for bioprospecting industrially relevant enzymes.IMPORTANCECarbohydrate-active enzymes, or CAZymes, are the molecular machines that microorganisms use to break down plant material and other complex sugars, and they underpin both the global carbon cycle and many industrial processes, from biofuel production to food, feed, and textile manufacturing. In this study, we compared the CAZyme repertoires of two microbial worlds that could hardly be more different: the alkaline, salty soda lakes of the East African Rift Valley, and the anaerobic stomachs of cattle, sheep, and goats. We show that although these communities are taxonomically distinct and their enzyme sequences have diverged dramatically, the three-dimensional shapes of their key carbohydrate-degrading enzymes remain remarkably well preserved. Soda lakes, in particular, hold a large pool of previously uncharacterised enzymes, identifying them as a promising, largely untapped source of robust biocatalysts for sustainable biotechnology and industrial applications.},
}

@article {pmid42153646,
year = {2026},
author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV},
title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0013926},
doi = {10.1128/msphere.00139-26},
pmid = {42153646},
issn = {2379-5042},
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.},
}

@article {pmid42153658,
year = {2026},
author = {Chen, X and Chen, GG and Gong, Z and Zhu, H and Liang, Z and Chan, JYK and Tong, MCF and Chen, Z and Chang, WT},
title = {The middle ear-nasopharyngeal microbiome axis associated with obstructive Eustachian tube dysfunction in chronic otitis media.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0000726},
doi = {10.1128/msystems.00007-26},
pmid = {42153658},
issn = {2379-5077},
abstract = {Obstructive Eustachian tube dysfunction (ETD) commonly complicates chronic otitis media (COM), yet microbial factors at the Eustachian tube (ET) openings remain poorly understood. In this prospective cohort study, we characterized the microbiota at both the middle ear (ME) and nasopharyngeal (NP) ET openings in COM patients undergoing ear surgery and examined associations with obstructive ETD over one year of follow-up. Using 16S rRNA gene sequencing and functional inference, we profiled microbial communities from the ME-side ET opening and the torus tubarius on both surgical-side and contralateral nasopharynx. Among 37 patients (18 with ETD, 19 without), ME and NP microbiota differed significantly in composition. Ears with ETD showed increased ME microbial diversity and enrichment of Neobacillus, Agrobacterium, and Sphingomonas. Paired NP-ME analyses indicated an altered NP-ME microbial relationship in ETD, with Neobacillus showing a nasopharyngeal source signal. Functional prediction revealed increased porphyrin metabolism and decreased pyruvate metabolism in ME microbiota with ETD, suggesting a shift toward biofilm formation and altered redox states. Anaerococcus was increased in the nasopharynx of patients with bilateral COM. These findings identify distinct microbial and metabolic features of COM with obstructive ETD, supporting a role for nasopharyngeal-microbial influence on ME pathology.IMPORTANCEChronic otitis media (COM) is a common and often persistent ear disease, especially when complicated by Eustachian tube dysfunction (ETD). By profiling microbiota at both Eustachian tube openings, this study links upper-airway microbial ecology with middle-ear microbial states in COM and helps clarify where clinically relevant signals may arise along the Eustachian tube pathway. The paired nasopharyngeal-middle ear design revealed that nasopharyngeal microbes may be linked to middle-ear community shifts in COM with obstructive ETD, consistent with a potential upper airway contribution to the middle-ear microbiota, generating testable hypotheses about microbial exchange and persistence. These findings highlight the upper airway microbiome as a potential target for developing new preventive and therapeutic strategies in COM.},
}

@article {pmid42153706,
year = {2026},
author = {Borren, NZ and Paulides, E and Klaassen, MAY and Alm, E and Xavier, RJ and Janneke van der Woude, C and Ananthakrishnan, AN},
title = {Microbiome-Directed Therapy for Fatigue in Quiescent Inflammatory Bowel Disease: A Randomized Placebo-Controlled Trial of Multi-Strain Probiotic Supplementation.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000004056},
pmid = {42153706},
issn = {1572-0241},
abstract = {INTRODUCTION: Fatigue is a challenging symptom for patients with inflammatory bowel diseases (IBD). Emerging evidence links alterations in the gut microbiome with fatigue in IBD, highlighting the potential of microbiome-targeted treatments. Our aim was to evaluate the clinical efficacy and biological effects of a multi-strain probiotic supplementation on fatigue in patients with quiescent IBD.

METHODS: This multi-center, placebo-controlled, randomized controlled trial included patients with quiescent IBD, defined as being in clinical remission and a colonoscopy within 1 year which demonstrated no active disease, and with significant fatigue (FACIT-F score < 43). Patients were randomized to receive either probiotics (Ecologic® BARRIER, containing 9 different bacterial strains) or placebo for 12 weeks. Gut microbiome and serum metabolome were analyzed at baseline and at the end of the study.

RESULTS: Our study enrolled 100 patients (52 Crohn's disease (CD), 44 ulcerative colitis (UC), 4 IBD-unspecified) with quiescent IBD and with a mean age of 41 years; 61% were women. After 12 weeks, 29.4% of the probiotic group and 40.0% of the placebo group met criteria for no fatigue (p=0.34). However, all participants reported an improvement in fatigue (p<0.001) with the most striking change noted at 4 weeks in both groups. Probiotic treatment led to beneficial shifts in gut microbiome and serum metabolome composition, particularly an increase in Bifidobacterium animalis after 12 weeks.

DISCUSSION: While 12 weeks of probiotic administration was not associated with relief of fatigue in patients with quiescent IBD, we observed beneficial alterations in the gut microbiome and serum metabolome. ClincialTrials.gov number, NCT03266484.},
}

@article {pmid42153723,
year = {2026},
author = {O'Sullivan, B and Herbst, KW and Hogan, AH and Maltz-Matyschsyk, M and Radolf, JD and Lawrence, D and Lynes, MA and Salazar, JC and Graf, J and , },
title = {Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0277625},
doi = {10.1128/spectrum.02776-25},
pmid = {42153723},
issn = {2165-0497},
abstract = {UNLABELLED: Most microbiome studies to date rely on sequencing short amplicons of the 16S rRNA gene on Illumina's platforms. Because of the short read length, sequences often can be identified reliably only to the family or genus levels. Long-read sequencing with whole-length 16S rRNA sequencing can improve taxonomic resolution but often only to the species level. StrainID is an alternative approach that amplifies a large segment of the ribosomal operon, including the entire 16S rRNA gene, internal transcribed spacer, and a portion of the 23S rRNA gene. This longer amplicon is designed to allow ribotype-level classification. Although studies have demonstrated the utility of StrainID for several sample types, a direct comparison of StrainID to alternative approaches has not been done for saliva. Here, we compared the performance of StrainID to short-read amplicons with saliva samples as well as a synthetic mock DNA community. Short reads were amplified with primer pairs targeting the V1-V3 region of the 16S rRNA gene and were classified with several different taxonomic databases. We found that StrainID outperformed short reads not only in identifying amplicon sequence variants to the species level but also in demonstrating a key benefit with phylogenetic-based beta-diversity tests. Our results further build on establishing StrainID as a powerful method and specifically for its use with saliva samples.

IMPORTANCE: The interpretation of microbiome composition studies is highly dependent on the methodologies chosen during experimental design, which affects factors such as resolution, throughput, cost, and accuracy. StrainID is an approach that can improve resolution while maintaining high-throughput and similar costs to short-read sequencing. The salivary microbiome represents a diverse community of microbes with links to a variety of health conditions and disease states. Closely related strains of bacteria can have drastically different effects on their host. Establishing StrainID as a valid approach for studying the salivary microbiome opens avenues for research that improve upon alternative methods by increasing sensitivity and accuracy compared to traditional short-read approaches.},
}

@article {pmid42153897,
year = {2026},
author = {Jain, M and Babu, R and Jain, A},
title = {Phosphate binders and the gut microbiota in chronic kidney disease: mechanisms, mixed evidence, and clinical considerations.},
journal = {Journal of nephrology},
volume = {},
number = {},
pages = {},
doi = {10.1093/joneph/aajag023},
pmid = {42153897},
issn = {1724-6059},
abstract = {Chronic kidney disease (CKD) disrupts the gut microbiome through dietary restrictions, uraemia, and polypharmacy, including phosphate binders. This dysbiosis contributes to systemic inflammation, accumulation of uremic toxins, and reduced short-chain fatty acid (SCFA)-producing bacteria. Hyperphosphatemia, a key CKD complication, typically emerges in advanced stages. This review examines the impact of phosphate binders on gut microbiota and explores emerging biological therapies. Phosphate binders are standard treatment for hyperphosphatemia but may influence gut microbiota by altering luminal pH, intestinal transit, and availability of metabolites such as SCFAs and vitamin K. These changes can impair gut barrier integrity and promote inflammation. Evidence on their microbiome effects is mixed: some studies show minimal compositional changes with calcium acetate or sucroferric oxyhydroxide, while others report individual variability and subtle taxon-specific shifts, particularly with iron-based binders. Even when compositional changes are limited, certain binders may modulate uremic toxin levels. Given the limitations of conventional therapies, biological approaches such as probiotics, synbiotics, and phosphate-accumulating organisms (PAOs) are gaining interest. These strategies may reduce intestinal phosphate availability by lowering pH, enhancing calcium-phosphate binding, and promoting microbial phosphate uptake and storage, while supporting gut barrier function. Overall, current evidence remains heterogeneous and limited by small cohorts and preclinical designs. Although microbiota-targeted therapies show mechanistic promise, robust clinical trials are needed before they can be recommended beyond adjunctive use.},
}

@article {pmid42153961,
year = {2026},
author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17087},
doi = {10.1002/advs.202517087},
pmid = {42153961},
issn = {2198-3844},
support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; },
abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.},
}

@article {pmid42154316,
year = {2026},
author = {Ulrich, JF and Redlich, SB and Mohr, A and Vollmers, J and Petersen, J and Wichard, T},
title = {Marine Rhodobacterales as Drivers of Ulva Growth: From Macroalgal-Bacterial Interactions to Bioactive Factor Enrichment.},
journal = {Journal of chemical ecology},
volume = {52},
number = {3},
pages = {},
pmid = {42154316},
issn = {1573-1561},
mesh = {*Ulva/growth & development/microbiology ; *Seaweed/growth & development/microbiology ; },
abstract = {Marine bacteria significantly influence the development and productivity of algal communities. The green seaweed Ulva (Chlorophyta) relies on bacteria that secrete algal growth and morphogenesis-promoting factors (AGMPF). In a reductionist model system of Ulva compressa (cultivar U. mutabilis), the diverse microbiome can be substituted by two key bacteria, Roseovarius sp. MS2 and Maribacter sp. MS6, both of which release AGMPFs, thereby inducing cell division and cell differentiation. Our study examined various algal growth-promoting substances produced by marine Rhodobacterales (Alphaproteobacteria). The exploration survey indicated that 74 of the 97 examined strains demonstrated growth-promoting, cytokine-like action. These findings underscore the extensive impact of marine Rhodobacterales on Ulva growth. Bioactive fractions containing AGMPF activity were enriched from the culture supernatant of Roseovarius sp. strain MS2. Bioactive raw extracts were obtained through bioassay-guided fractionation and semi-preparative high-performance liquid chromatography; cell division-promoting properties were observed, but did not reach the activity level of the harvested supernatant. This study provides new insights that underscore the importance of bacterial-macroalgal interactions for marine ecosystems. Replacing bacteria with AGMPFs, including thallusin, enables the complete thallus formation of axenic Ulva cultures, facilitating various applications in biotechnology and aquaculture.},
}

*Ulva/growth & development/microbiology
*Seaweed/growth & development/microbiology

@article {pmid42154337,
year = {2026},
author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP},
title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42154337},
issn = {1559-1182},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/metabolism/pathology/microbiology ; *alpha-Synuclein/metabolism ; Animals ; Dysbiosis ; *Protein Aggregates ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Parkinson Disease/metabolism/pathology/microbiology
*alpha-Synuclein/metabolism
Animals
Dysbiosis
*Protein Aggregates

@article {pmid42154370,
year = {2026},
author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG},
title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.},
journal = {Advances in therapy},
volume = {},
number = {},
pages = {},
pmid = {42154370},
issn = {1865-8652},
abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.},
}

@article {pmid42154646,
year = {2026},
author = {Alciati, A and Cracò, F and Burgio, A and Pezzano, A and Atzeni, F},
title = {Fibromyalgia and metabolic syndrome: prevalence, potential shared pathophysiological mechanisms and non-pharmacological treatment strategies.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/y4a7s4},
pmid = {42154646},
issn = {0392-856X},
abstract = {Fibromyalgia (FM) is a chronic pain syndrome defined by widespread musculoskeletal pain, fatigue and sleep disturbances, frequently accompanied by metabolic disturbances. Among these, metabolic syndrome (MetS), a cluster of abdominal obesity, hypertension, dyslipidaemia and impaired glucose regulation, stands out because of its strong association with cardiovascular disease and type 2 diabetes. Recent studies suggest that MetS and its individual components, particularly obesity, are highly prevalent in FM populations, raising important clinical and pathophysiological questions.Both FM and MetS are associated with chronic low-grade inflammation, autonomic nervous system dysfunction, and dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis. Moreover, environmental factors, particularly early-life stress, may increase vulnerability by triggering persistent neuroendocrine and immune alterations. These overlapping pathways not only predispose to comorbidity but also contribute to increased symptom burden and therapeutic complexity. Systematic screening for MetS in patients with FM may improve cardiovascular risk stratification and inform more comprehensive treatment strategies. This narrative review summarises current evidence on the comorbidity of FM with MetS and its individual components, highlighting their shared pathophysiology. It also explores the therapeutic potential of non-pharmacological strategies, including structured exercise, dietary interventions, and microbiome-targeted approaches, that address common underlying mechanisms and hold promise for improving long-term outcomes.},
}

@article {pmid42155002,
year = {2026},
author = {Meng, X and Wu, X and Sun, H and Cong, J and Gu, Y},
title = {Maternal-Infant Gut Microbiota Transmission and the Early Origins of Metabolic Liver Diseases: Mechanisms and Interventional Opportunities.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag074},
pmid = {42155002},
issn = {1753-4887},
support = {42307182//National Natural Science Foundation of China/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease is associated with a growing global health burden with increasing prevalence in both adult and pediatric populations. Emerging evidence suggests that the origins of steatotic liver disease may trace back to early life, with the gut microbiota serving as a critical mediator in this developmental programming. This review synthesizes current knowledge on maternal-infant gut microbiota transmission and its role in shaping long-term liver health through the gut-liver axis. We examined key maternal factors, including delivery mode, feeding of breast milk, diet, metabolic status, and antibiotic exposure, that profoundly influence infant microbiota assembly. The critical window of microbiota establishment during the first 1000 days shapes intestinal barrier function, immune development, and metabolic pathways that persist into adulthood. Mechanistically, early dysbiosis contributes to metabolic dysfunction-associated steatotic liver disease pathogenesis through multiple interconnected pathways, including compromised intestinal barrier integrity facilitating endotoxemia, altered short-chain fatty acid production affecting energy metabolism and inflammation, disturbed bile acid signaling disrupting metabolic homeostasis, and epigenetic modifications potentially shaping long-term susceptibility. We critically evaluated emerging microbiota-targeted interventional strategies during pregnancy and infancy, including probiotics, human milk oligosaccharide supplementation, and synbiotic approaches, highlighting their potential for disease prevention. This review uniquely integrates concepts of developmental origins with detailed gut-liver axis mechanisms, emphasizing the maternal-infant microbial continuum as an underexplored but promising target for preventing metabolic liver disease. While significant research challenges remain, particularly in establishing causality and developing personalized interventions, modulation of the early gut microbiome offers an innovative preventive strategy against the rising tide of metabolic dysfunction-associated steatotic liver disease, potentially disrupting the intergenerational cycle of metabolic disease.},
}

@article {pmid42155039,
year = {2026},
author = {Wang, L and Wang, Q and Wolfe, TM and Pinkham, NV and Erickson, R and Yoshinaga, M and Mcdermott, TR and Walk, ST},
title = {Technical and biological factors driving inter-individual body burden of arsenic species in murine models of human arsenic exposure.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfag055},
pmid = {42155039},
issn = {1096-0929},
abstract = {Arsenic is one of the most important environmental toxicants, requiring advanced analytical techniques to resolve individual species. There is little consensus on arsenic speciation methodology for in vivo studies. The objectives of this study were to generate a robust framework for arsenic speciation in murine models of human exposure and evaluate factors influencing the levels of arsenobetaine, inorganic arsenite, dimethylarsinate, monomethylarsonate, and inorganic arsenate resolved by HPLC-ICPMS. Enzyme-assisted digestion by papain vs. pepsin and maceration by bead beating vs. mechanical homogenization were evaluated using chemical standard spiking experiments. Dose-controlled mouse exposures to inorganic arsenite were conducted and species detected in urine and bladder tissue were compared. Species in stool, liver, and bladder were compared between groups of mice eating a standard vs. purified diet; fasted vs. unfasted mice; and conventional vs. germ-free mice. Finally, between-lab differences in HPLC-ICPMS instrumentation/quantification procedures were evaluated. These comparisons led to several important conclusions including: Significant conversion of inorganic arsenate to arsenite by papain, significant inorganic arsenate background in bead-beating lysing matrix, significant arsenobetaine in mice eating standard but not purified chow, significant correlation between species detected in urine and bladder, significant correlation of results between laboratories that differed in absolute quantification, and large inter-individual variability between mice of the same treatment group. Finally, diet type and the presence of a microbiome had the largest effect on arsenic species levels. Our results provide a benchmark for evaluating arsenic species in murine models, including adequate sample sizes for powering studies to avoid erroneous conclusions.},
}

@article {pmid42155496,
year = {2026},
author = {Hull, RC and Liu, Y and Cao, Z and Xuan, KTL and de Lima Headley, DA and Richardson, H and Hennayake, C and Lind, H and McIntosh, E and Pollock, J and Hughes, C and Viligorska, K and Choi, H and Gao, Y and Chotirmall, SH and Shoemark, A and Robertson, K and Burgel, PR and Vendrell, M and Xu, X and Qu, JM and Song, Y and Guan, WJ and Chen, R and Singh, S and Talwar, D and Mohan, BVM and Tripathi, SK and Swarnakar, R and Trivedi, S and Goeminne, PC and Shteinberg, M and De Soyza, A and Altenburg, J and Haworth, CS and Sibila, O and Polverino, E and Loebinger, MR and Ringshausen, FC and Mertsch, P and Lorent, N and Dimakou, K and Mendez, R and Mclaughlin, AM and Borrill, Z and Lord, R and Finch, S and Blasi, F and Burr, L and Crisafulli, M and Keating, R and Middleton, PG and Long, MB and Aliberti, S and Morgan, L and Dhar, R and Chalmers, JD and Xu, JF and , },
title = {Comorbid diabetes disease severity and microbial changes in patients with bronchiectasis: a combined analysis of data from the EMBARC, EMBARC-India, Australian, and BE-China registries.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(26)00057-3},
pmid = {42155496},
issn = {2213-2619},
abstract = {BACKGROUND: Bronchiectasis and diabetes commonly coexist and are associated with immune dysfunction and increased susceptibility to infection. Although diabetes is associated with worse prognosis in cystic fibrosis-related bronchiectasis, data are scarce for its impact on non-cystic fibrosis bronchiectasis. This study aimed to characterise the impact of diabetes on clinical outcomes and microbial and inflammatory profiles in patients with bronchiectasis.

METHODS: This analysis comprised data from the European Bronchiectasis Registry (EMBARC), Respiratory Research Network of India (EMBARC-India), Chinese Bronchiectasis Registry (BE-China), and Australian Bronchiectasis Registry (ABR); 30 263 patients with CT-confirmed bronchiectasis in 33 countries were included in the analysis: 16 963 from EMBARC (Jan 12, 2015, to April 12, 2022), 2361 from EMBARC-India plus additional Asian countries (June 1, 2015, to Sept 1, 2017), 10 324 from BE-China (Jan 10, 2020, to March 31, 2024), and 615 from the ABR (March 7, 2016, to Sept 11, 2018). Clinical data were compared between patients with and without diabetes. Long-term outcome data were available in EMBARC and EMBARC-India. Microbiome and inflammatory profiles were characterised in a sub-cohort of EMBARC patients by sputum 16S rRNA sequencing (n=433) and serum Olink (n=479).

FINDINGS: 2487 (8·2%) of 30 263 patients with bronchiectasis had diabetes. Patients with diabetes had a higher prevalence of comorbidities than those without diabetes, including cardiovascular disorders (53·5% vs 21·8%, p<0·0001), asthma (27·5% vs 21·0%, p<0·0001), and chronic obstructive pulmonary disease (34·3% vs 19·0%, p<0·0001). Patients with diabetes had more severe disease than those without diabetes, with higher Bronchiectasis Severity Index scores (8 [IQR 5-12] vs 7 [4-10], p<0·0001) and UK Medical Research Council (MRC) dyspnoea scores (p<0·0001) and more hospital admissions in the previous year (p<0·0001). After adjustment for confounders, outcomes were significantly worse in patients with diabetes than in those without diabetes, including more frequent exacerbations (incidence rate ratio [IRR] 1·18 [95% CI 1·09-1·28], p<0·0001), hospital admissions (IRR 1·57 [1·40-1·76], p<0·0001), and higher 5-year mortality (hazard ratio 1·80 [1·53-2·12], p<0·0001). The sputum microbiome was significantly altered in patients with diabetes compared to those without diabetes, with increased isolation of Enterobacteriaceae (p<0·0001), Moraxella catarrhalis (p=0·0035), and Haemophilus influenzae (p=0·046). In serum, Gal-4 and GDF-15, established biomarkers of disease severity and cardiovascular risk in diabetes, were significantly increased in patients with diabetes (Gal-4, p<0·0001; GDF-15, p=0·0019).

INTERPRETATION: Patients with diabetes and bronchiectasis are a high-risk population with more severe disease, worse outcomes, increased comorbidities, and increased risk of infections compared with patients without diabetes. These findings support inclusion of diabetes as a risk factor in individualised risk assessments for bronchiectasis.

FUNDING: European Respiratory Society, Armata, AstraZeneca, Boehringer Ingelheim, Chiesi, CSL Behring, GSK, Grifols, Insmed, Janssen, Lifearc, Roche, Verona Pharma, Zambon, National Natural Science Foundation of China, Innovation Program of the Shanghai Municipal Education Commission, Program of the Shanghai Municipal Science and Technology Commission, Program of the Shanghai Shenkang Development Center, EU/European Federation of Pharmaceutical Industries and Associations, Innovative Medicines Initiative, and Inhaled Antibiotics in Bronchiectasis and Cystic Fibrosis Consortium.},
}

@article {pmid42155536,
year = {2026},
author = {Shahvali, N and Adibi, M and Mohebi, A and Mousavianfard, SR and Salehi, M and Zamani, S and Sharifianjazi, F and Chegini, L and Bastami, F},
title = {Mesenchymal stem cell therapy for treatment of medication related osteonecrosis of the jaw (MRONJ): A systematic review.},
journal = {Tissue & cell},
volume = {102},
number = {},
pages = {103489},
doi = {10.1016/j.tice.2026.103489},
pmid = {42155536},
issn = {1532-3072},
abstract = {BACKGROUND: Medication-related osteonecrosis of the jaw (MRONJ) is a significant adverse effect associated with antiresorptive and antiangiogenic therapies. Therapies utilizing mesenchymal stem cells (MSCs) represent a promising regenerative strategy; however, conventional management methods have shown limited effectiveness. This systematic review aimed to evaluate the effectiveness of MSC-based interventions in preventing and treating MRONJ.

METHOD: A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science to identify studies published from 2011 to 2024. Studies examining MSCs therapy in the context of MRONJ were incorporated according to predefined inclusion and exclusion criteria.

RESULTS: Seventeen studies (6 clinical, 11 preclinical) met inclusion criteria. Preclinical models demonstrated that MSCs enhance angiogenesis and bone regeneration, providing mechanistic support for human application. Clinically, 80-90% of patients achieved complete mucosal healing with radiographic evidence of bone regeneration. However, due to species differences in oral microbiome and immunity, animal findings require confirmation in human trials.

CONCLUSION: This review integrates human clinical data with mechanistic insights from preclinical studies. Human evidence shows promising mucosal and bone regeneration, while animal studies elucidate underlying mechanisms-particularly angiogenesis and immunomodulation. Given that animal models cannot replicate the human oral immune environment, these findings should be interpreted as hypothesis-generating. MSC therapy represents a biologically sound but experimental strategy, warranting confirmation through randomized controlled trials.},
}

@article {pmid42155708,
year = {2026},
author = {Biber, P and Muhammad, AR and Hartinger, T and Reisinger, N and Gressley, T and Zebeli, Q and Castillo-Lopez, E},
title = {Elucidating the separate and synergistic impacts of ruminal and hindgut acidosis on fermentation and microbiome of dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27887},
pmid = {42155708},
issn = {1525-3198},
abstract = {The aim of this study was to evaluate the short-term impacts of both subacute ruminal acidosis (SARA) and hindgut acidosis (HGA) on the ruminal and fecal fermentation and microbiome of dairy cows. The study was conducted as a change-over design using 9 rumen-cannulated Holstein cows (724 ± 79 kg body weight and 198 ± 74 d in milk). The SARA was induced by feeding a diet containing 65% concentrate (DM basis), and HGA was induced through daily abomasal infusion of 3 kg of starch (1:1 corn to wheat weight ratio). The evaluated treatments were 1) a control diet containing 40% concentrate (CON), 2) CON+HGA, 3) a diet containing 65% concentrate (SARA), and 4) SARA+HGA. Ruminal pH was measured every 15 min, and the fecal pH was measured 3 times per day (0, 6 and 12 h relative to feeding). Ruminal and fecal samples were collected in the morning before first feeding and were analyzed for microbiome through 16S rRNA gene amplicon sequencing. Additionally, rumen and fecal samples were taken at 0, 6 and 12 h relative to feeding and were analyzed for volatile fatty acids (VFA) and lactate to evaluate postprandial effects of treatments. Results showed that changing from CON to SARA lowered ruminal pH and increased ruminal propionate, without affecting fecal VFA profile or pH. Compared with CON, SARA shifted the ruminal microbiome, decreased α diversity in the rumen and feces, and increased abundance of several taxa such as Succinivibrionaceae UCG-001 (OTU 2994), Lachnospiraceae (OTU 3043), and Acetitomaculum (OTU 80). The HGA decreased fecal pH, increased total fecal VFA at 12 h post-feeding, and increased fecal lactate and butyrate at the expense of acetate and propionate. In addition, HGA shifted the fecal microbiome and increased butyrate producing bacteria such as Lachnospiraceae (OTU 18), Blautia (OTU 508), Acetitomaculum (OTU 622), resulting in positive correlations between fecal butyrate and abundance of these taxa; however, family Ruminococcaceae (OTU 1580), and Christensenellaceae (OTU 550) decreased in feces and correlated negatively with fecal butyrate. Moreover, results showed that SARA in combination with HGA aggravates shifts of the fecal microbiome as revealed by further reductions of microbial α diversity indices and families Ruminococcaceae (OTU 1580) and Christensenellaceae (OTU 550) in cows receiving the SARA diet and abomasal starch infusion. Overall, new findings from this study reveal not only separate effects of SARA and HGA on ruminal and fecal fermentation but also show additive negative impacts particularly on fecal microbial diversity and increase in fecal butyrate and lactate. Such alterations in microbial profile increase the risk of creating niches for pathogens proliferation and fecal shedding.},
}

@article {pmid42155725,
year = {2026},
author = {Intze, E and Schaubeck, M and Arendt, BM and Fleddermann, M and Beyer, K and Clavel, T and Lagkouvardos, I and Hitch, TCA and , },
title = {Mixed feeding and mode of birth modulate the effects of a hydrolyzed synbiotic formula on the gut microbiome in infants at risk of atopic disease.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {103338},
doi = {10.1016/j.clnesp.2026.103338},
pmid = {42155725},
issn = {2405-4577},
abstract = {BACKGROUND AND AIMS: Intestinal colonization by microbial communities is important for infant health. Little knowledge about the effect of infant formula matrix (i.e. form of protein) on the infant microbiome, is available. The main aim of this study was to investigate how mode of birth, cessation of breastfeeding, and the formula matrix i.e. protein matrix of synbiotic infant formulas modulate intestinal colonization in infants.

METHODS: Stool microbiota profiles of 342 healthy term infants participating in a randomized controlled trial were studied. Infants received synbiotic infant formula manufactured from extensively hydrolyzed (eHF) or intact protein (control formula; CF) as exclusive formula feeding or as mixed feeding (MF) with human milk. Stool samples at 4 and 12 months of age were analyzed by 16S rRNA gene amplicon sequencing.

RESULTS: Phylogenetic profiles of the stool microbiota showed age-dependent maturation. Protein hydrolyzation had only minor effects on overall community types. However, compared to CF, eHF feeding was linked to a Bifidobacterium-dominated microbiota at 4 months of age in two subgroups: in infants born by Cesarean section and those who had received MF for less than 3 months.

CONCLUSION: In this comparison of two synbiotic infant formulas, the formula matrix based on hydrolyzed protein was linked to a Bifidobacterium-dominated community, dependent on birth and feeding mode. Because bifidobacteria are positively linked to infant health and allergy-prevention, further studies are needed to confirm these results and to investigate the effects on clinical outcomes.},
}

@article {pmid42155873,
year = {2026},
author = {Sun, Q and Li, X and Wu, J and Zhang, J and Zhu, Y and Dong, Y},
title = {Immune Checkpoint Inhibitor Resistance in Non-Small Cell Lung Cancer: An Updated View Through the Cancer-immunity Cycle.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105382},
doi = {10.1016/j.critrevonc.2026.105382},
pmid = {42155873},
issn = {1879-0461},
abstract = {Despite the transformative impact of immune checkpoint blockade (ICB) in non-small cell lung cancer (NSCLC), durable responses remain limited to a subset of patients. Resistance-either intrinsic or acquired-continues to undermine the full therapeutic potential of immunotherapy. The cancer-immunity cycle provides a useful conceptual scaffold to dissect the multistep requirements for effective antitumor immunity. Recent advances in single-cell technologies, spatial profiling, longitudinal immune monitoring, and real-world clinical datasets have uncovered additional layers of complexity, including non-canonical pathways involving tumor metabolism, stromal architecture, vascular remodeling, epigenetic plasticity, microbiome-immune crosstalk, and host-related determinants of response. In this review, we provide an updated and integrated synthesis of both primary and acquired resistance mechanisms across each phase of the cancer-immunity cycle. We emphasize pathways that have gained mechanistic or clinical relevance in recent NSCLC literature and consolidate them in an updated reference figure (Figure 1). To strengthen translational relevance, we additionally include a dedicated section on host-related determinants of ICI efficacy-including immunosenescence, performance status, comorbidity burden, systemic inflammation, body composition, and concomitant medications-and a stepwise summary of representative primary versus acquired mechanisms with NSCLC clinical anchors (Table 1). Our goal is to frame resistance not as a single lesion, but as a dynamic tumor-host system that must be mapped to inform biomarker development and rational combination strategies.},
}

@article {pmid42155931,
year = {2026},
author = {Gong, J and Mei, X and Jin, Y and Wang, Y and Liu, Y and Song, W and Wang, Z and Yang, M and Ye, C and Liu, Y and Huang, H and Zhu, S and Deng, W},
title = {Synergistic foliar titanium and soil organic fertilizer drive terpenoid-mediated microbiome assembly to restrict Cd/Pb uptake in Panax notoginseng.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142356},
doi = {10.1016/j.jhazmat.2026.142356},
pmid = {42155931},
issn = {1873-3336},
abstract = {Achieving safe utilization of heavy metal-contaminated soils without compromising crop productivity represents a grand challenge for sustainable agriculture. Although foliar titanium (Ti) and soil organic fertilizers (OF) independently alleviate abiotic stress, it remains unclear whether and how aboveground Ti signaling coordinates with OF mediated rhizosphere processes to enhance crop productivity and restrict heavy metal accumulation through plant-metabolite-microbiome networks. Here, using Panax notoginseng as a model, the results showed that co-application of foliar Ti with soil OF significantly outperformed individual applications. This "top-down" strategy synergistically increased root biomass and saponin content (synergistic index > 1), while reducing root Cd and Pb concentrations by 46.60% and 47.23%, respectively. Mechanistically, soil OF established a functional rhizosphere foundation by enhancing nutrient bioavailability and enriching beneficial microbial taxa. Concurrently foliar Ti acted as a systemic trigger to reprogram plant metabolism, upregulating arginine and proline metabolic pathways in leaves and coinciding with enhanced diterpenoid biosynthesis in roots. Specifically, accumulated diterpenoids (forskolin and ingenol) functioned as selective semiochemicals, recruiting a specialized microbiome consortium with enhanced metal-resistant, growth-promoting, and nutrient-solubilizing bacteria (Sphingomonas, Rhodanobacter, Bacillus) and fungi (Penicillium, Aspergillus), while inhibiting the pathogen Ilyonectria. Consequently, this engineered rhizosphere microbiome may have contributed to rhizosphere-level Cd/Pb exclusion or immobilization, thereby decoupling root metal uptake from bulk soil metal pools. This study supports a novel "aboveground trigger-belowground support" framework in which Ti-induced metabolites promote the assembly of functional microbiomes that are further supported by OF. We propose a targeted biofortification strategy leveraging plant-metabolite-microbiome coordination for safe cultivation of crops.},
}

@article {pmid42155948,
year = {2026},
author = {Yang, W and Li, Z and Chen, X and Chen, J and Lu, Z},
title = {Association between a gut microbiota-targeted dietary index and osteoarthritis/rheumatoid arthritis: a cross-sectional study.},
journal = {Clinics (Sao Paulo, Brazil)},
volume = {81},
number = {},
pages = {100995},
doi = {10.1016/j.clinsp.2026.100995},
pmid = {42155948},
issn = {1980-5322},
abstract = {BACKGROUND: Diet plays a key role in regulating the gut microbiota. This study aimed to investigate the association between the Dietary Index of the Gut Microbiome (DI-GM) ‒ a score designed to reflect the potential of a diet to support a healthy gut microbiota ‒ and different types of arthritis, an area where systematic studies remain scarce.

METHODS: Data from the National Health and Nutrition Examination Survey (NHANES) 2007-2018 were analyzed using multivariable logistic regression, Restricted Cubic Spline (RCS) regression, and subgroup analyses to assess associations between DI-GM and Osteoarthritis (OA) and Rheumatoid Arthritis (RA).

RESULTS: A total of 6168 participants were included, among whom 506 had Osteoarthritis (OA) and 303 had Rheumatoid Arthritis (RA). Multivariable analyses showed no significant association between DI-GM and OA (p > 0.05), but significant inverse associations with RA across models (ORs 0.74, 0.64, and 0.74; all p < 0.05). Restricted cubic spline analysis detected no significant nonlinear relationships for either outcome. Subgroup analyses suggested potential associations within certain populations.

CONCLUSION: This cross-sectional study found an inverse association between the diet-based DI-GM score and RA, but no significant association with OA. Given the limitations of the cross-sectional design, the observed association is equally compatible with dietary changes resulting from RA diagnosis and management (reverse causality). As this study did not measure the gut microbiota, the role of the microbiome as a mediator remains speculative. Therefore, these results require confirmation in prospective studies that can account for reverse causation and directly assess the gut microbiome.},
}

@article {pmid42156216,
year = {2026},
author = {Deng, X and Wang, Y and Zhu, H and Guo, Y and Wang, Q and Han, J and Yu, K and Zhou, B},
title = {Metagenomic profiling of resistome and mobilome dynamics in diverse freshwater aquaculture modes.},
journal = {Water research},
volume = {302},
number = {},
pages = {126133},
doi = {10.1016/j.watres.2026.126133},
pmid = {42156216},
issn = {1879-2448},
abstract = {The widespread presence of antibiotic resistance genes (ARGs) in aquaculture environments poses a growing threat to public health. However, comprehensive understanding of ARG distribution and transmission potential across different freshwater aquaculture modes remains limited. This study employed integrated short- and long-read metagenomic sequencing to characterize the resistome, mobilome, and associated microbial communities across three predominant freshwater aquaculture modes (grass carp, crayfish, and crab ponds), using water, sediment, and intestinal samples analyzed at both contig and metagenome-assembled genome (MAG) levels. The results revealed that aquaculture modes and environmental media jointly shaped microbial and ARG compositions. At the contig level, the crayfish system harbored the highest relative abundance of both ARGs and mobile genetic elements (MGEs), with gut samples consistently emerging as the dominant reservoir across all modes. A significant positive correlation between ARG and MGE alpha diversity indicated that the gut microbiome, particularly in crayfish, provides a selective environment that co-enriches resistance genes and their mobile carriers. High-risk core ARGs (Rank I) were at least 19 times more abundant in the crayfish gut than in any other compartment, underscoring the intestinal microbiome as a hotspot for clinically relevant resistance accumulation. At the MAG level, over half of the recovered MAGs met near-complete or high-quality thresholds, and approximately 38% of ARG-carrying MAGs were classified as multidrug-resistant (MDR). MDR MAG abundance was significantly higher in gut than in sediment and water samples, with the crayfish gut as the most enriched compartment. Critically, several crayfish-associated MDR MAGs affiliated with Klebsiella aerogenes carried virulence factor genes (VFGs) and exhibited ARG-MGE-VFG co-localization within prophage sequences, suggesting phage-mediated co-dissemination of resistance and virulence traits. These findings highlight the intestinal microbiome of aquaculture species as a critical hotspot for resistance dissemination and provide a scientific basis for evaluating freshwater aquaculture-associated ARG risks under the One Health framework.},
}

@article {pmid42156361,
year = {2026},
author = {Xiang, N and Liao, T and Xie, M and Wang, Z and Mak, CH and Tang, X and McIlroy, SE and Thibodeau, B and Voolstra, CR and Luo, H},
title = {Decoding coral resistance to eutrophication through the association of hyper‑efficient denitrifiers as key microbial allies.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42156361},
issn = {2041-1723},
support = {GRF14114724//Chinese University of Hong Kong (CUHK)/ ; },
mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Denitrification ; *Eutrophication/physiology ; Coral Reefs ; Nitrates/metabolism ; Hong Kong ; Symbiosis ; Climate Change ; Ecosystem ; Microbiota ; },
abstract = {Coral reefs face a perilous future due to global climate change compounded by the increasing prevalence of local stressors. Prominent among these is nutrient pollution, particularly nitrate eutrophication, which disrupts the coral-algal symbiosis and escalates reef degradation. While microbial denitrification is hypothesized to mitigate nitrate stress, the mechanisms underlying coral resilience remain unknown. Studying Hong Kong's coral "reef oases" that persist under chronic hyper-eutrophication, we discovered that resilience is not mediated by diversity or abundance shifts in denitrifier genera but by the association with specific, hyper-efficient denitrifying populations within the dominant denitrifier genus Ruegeria. By integrating population genomics, subspecies-resolution metabarcoding (resolving both the entire Ruegeria community and the denitrifying sub-community), and direct isotope-based activity assays, we identified and validated putative denitrifying "specialist" populations. These specialists were significantly enriched in corals from high-nitrate waters and exhibited 10-fold higher denitrification rates in low-oxygen incubations, converting nitrate to inert N2 with superior efficiency compared to non-specialists. Our findings reveal that critical ecosystem-scale adaptations to anthropogenic change can occur through a unique association with specialized sub-genus populations, which may be missed in conventional microbiome surveys. As such, our work sheds light into why dominant denitrifying genera are ubiquitous, yet only certain corals thrive in eutrophic conditions. It also provides a framework for future studies delineating ecologically important host-associated microbes.},
}

*Anthozoa/microbiology/physiology
Animals
*Denitrification
*Eutrophication/physiology
Coral Reefs
Nitrates/metabolism
Hong Kong
Symbiosis
Climate Change
Ecosystem
Microbiota

@article {pmid42156377,
year = {2026},
author = {Hu, R and Aronson, HS and Weaver, ME and Price, MN and LaRowe, DE and Liang, Y and Deutschbauer, AM and Coates, JD and Carlson, HK},
title = {Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73281-z},
pmid = {42156377},
issn = {2041-1723},
abstract = {Organic compounds with a negative nominal oxidation state of carbon (NOSC) are thermodynamically recalcitrant in anaerobic ecosystems, but few studies have measured the influence of NOSC on carbon degradation rates, gaseous product yields, or microbiome composition. We amended anaerobic rice paddy sediment microcosms with water-soluble monomeric organic carbon compounds varying in NOSC. Consistent with thermodynamic and stoichiometric predictions, negative NOSC compounds are catabolized more slowly but produce more methane per mole of carbon. Negative NOSC microbiomes have higher alpha diversity, more syntrophs and methanogens, and fewer fermentative bacteria. Strikingly, fermentative bacterial taxa display genomically encoded NOSC catabolic preferences both in the lab and field. Negative NOSC-preferring fermenters have longer predicted doubling times, consistent with the thermodynamic recalcitrance of their preferred substrates. We propose that microbial NOSC catabolic preferences may reflect the thermodynamic niche of microorganisms and we anticipate that extending research on microbial catabolic preferences to a greater variety of organic carbon substrates and diverse microbiomes will improve our understanding of microbial carbon cycling and trait evolution.},
}

@article {pmid42156414,
year = {2026},
author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and , and Guarner, F and Ehrlich, SD},
title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44895-6},
pmid = {42156414},
issn = {2045-2322},
support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; },
abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.},
}