@article {pmid42197533,
year = {2026},
author = {Badhan, A and Li, C and Guan, LL and McAllister, TA},
title = {Rumen-Derived Consortia Shaped by Substrate-Specific Enrichment Show Specialized Lignocellulose Utilization, Diversified Hydrogen Metabolism, and Cryopreservation Stability.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
pmid = {42197533},
issn = {2076-2607},
support = {BCRC FDE.02.24//Beef Cattle Research Council/ ; 2025F3700R//Results Driven Agriculture Research , RDAR/ ; ALLRP 588541 - 23)0//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Efficient utilization of lignocellulosic biomass by the rumen microbiome is critical for improving feed efficiency in ruminants, yet the development of stable, functionally specialized microbial consortia remains limited. This study aimed to assemble substrate-adapted rumen microbial consortia using an ecology-guided enrichment approach. Rumen fluid collected from cannulated Angus × Hereford heifers was sequentially enriched over 10 generations on four substrates with distinct cell wall characteristics: alfalfa, barley straw, carboxymethyl cellulose (CMC), and xylan. Fermentation parameters, including gas production and volatile fatty acids (VFAs), and bacterial community dynamics were analyzed, and selected consortia (alfalfa and xylan) were evaluated for stability following one month of cryopreservation. Across enrichments, total VFA concentrations declined (e.g., xylan: 109.8 mM (G0) to 56.37 mM (G10)), accompanied by reduced gas production and decreased alpha diversity, indicating substrate-driven selection. Distinct functional profiles emerged, including increased propionate in alfalfa consortia, higher acetate in barley straw, lactate-propionate cross-feeding with CMC, and caproate production (6.3 mM at G10) in xylan enrichments associated with Caproiciproducens and Megasphaera. Cryopreserved consortia retained core community structure and fermentation characteristics upon revival. These results demonstrate that substrate-driven enrichment can generate stable, functionally specialized rumen consortia and provide a framework for developing ecologically compatible microbial communities with potential applications in improving rumen fermentation efficiency.},
}

@article {pmid42197547,
year = {2026},
author = {Zhao, M and Zhao, H and Li, P and Peng, S and Lin, F and Wu, Q and Tashi, P and Li, Z},
title = {Multi-Omics Analysis Reveals Age-Related Enhancements in Gut Morphology, Microbiome, and Metabolism of Tibetan Pigs.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
pmid = {42197547},
issn = {2076-2607},
support = {CDKJ-2025QY001.//This research was funded by Changdu City Science and Technology Bureau 2025 District-City Science and Technology Collaborative Innovation Special Project, grant number/ ; },
abstract = {Age-related changes in the gut significantly impact host health, yet the multi-omics dynamics during the maturation of Tibetan pigs remain unclear. This study aimed to investigate the morphological, microbial, metabolic, and transcriptomic transformations in the intestines of aging Tibetan pigs. We analyzed the ileum and colon of 1-year-old and 3-year-old Tibetan pigs using histological evaluation, 16S rRNA sequencing, metabolomics, and transcriptomics. Aging to 3 years significantly improved ileal architecture, notably increasing the villus height to crypt depth ratio. Older pigs exhibited higher colonic microbial diversity, a decreased Firmicutes to Bacteroidota ratio, and enrichment of homeostasis-associated taxa, including Lactobacillus, Prevotellaceae, and Ruminococcaceae. Metabolomics revealed higher abundance of certain metabolites, including docosahexaenoic and arachidonic acids, enriching lipid metabolism and bile secretion pathways. Transcriptomics identified 2363 differentially expressed genes in the ileum, primarily involved in immune regulation and nutrient digestion. Integrated analysis showed strong positive correlations between enriched microbes (Lactobacillus porci) and up-regulated host genes (UGT2B31, CCL28) governing intestinal homeostasis. The transition from 1 to 3 years of age in Tibetan pigs fosters a synergistic host-microbiome environment, enhancing intestinal barrier function, immune capacity, and metabolic efficiency.},
}

@article {pmid42197563,
year = {2026},
author = {Ma, Y},
title = {Microbe-Induced Abiotic Stress Alleviation in Plants: From Hidden Partners to Central Drivers of Resilience.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42197563},
issn = {2223-7747},
abstract = {Our understanding of plant stress biology has shifted with debate toward a more integrative, microbiome-centered perspective [...].},
}

@article {pmid42197619,
year = {2026},
author = {Zhang, J and Zhang, X and Chen, Q},
title = {Biomass Seedling Trays Drive Rhizosphere Microbiome Restructuring and PGPR Enrichment in Tomato.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42197619},
issn = {2223-7747},
support = {2023YFD1901205//National Key Research and Development Program of China, project titled "Technology Model and Application of Soil Ecological Restoration and Green Capacity Enhancement in the Dry-Hot Valley of Southwest China"./ ; },
abstract = {Tomato (Solanum lycopersicum) is a globally important high-value cash crop. However, long-term continuous cropping causes frequent soil-borne diseases and soil microecological imbalance, while overreliance on chemical pesticides leads to pesticide residues and water eutrophication. Plant growth-promoting rhizobacteria (PGPR) are key resources for addressing tomato cultivation challenges, with their functions partly depending on the rhizosphere microenvironment inherently shaped by seedling tray materials. Using rhizosphere soil and substrates of tomato at different growth stages under biomass (BM) and plastic (PM) seedling tray treatments, this study combined culture-independent and culture-dependent techniques to analyze microbial community characteristics and screen high-efficiency PGPR. Results showed that pH and available nitrogen drove microbial community assembly. BM significantly enriched beneficial taxa (e.g., Trichoderma and Bacillus) and enhanced culturable microbial abundance and genetic diversity, while PM enriched potential pathogens (e.g., Fusarium and Pyrenochaeta). The multifunctional strain S25095 from BM, with phosphate-solubilizing, potassium-solubilizing, and indole-3-acetic acid (IAA)-producing abilities, significantly promoted tomato shoot and root growth, outperforming single-functional strains and synthetic consortia. This study reveals the effects of growth stages and seedling tray treatments on tomato rhizosphere microorganisms, providing valuable PGPR resources for tomato cultivation.},
}

@article {pmid42197679,
year = {2026},
author = {Gao, C and Wan, G and Cheng, R and Li, Q and Fan, Q and Cui, J and Wu, L},
title = {Gradient Potassium Application Differentially Regulates Rhizosphere Bacterial and Fungal Communities in Cherry Tomato (Solanum lycopersicum var. cerasiforme).},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42197679},
issn = {2223-7747},
support = {NYHXGG, 2023AA302//Xinjiang Production and Construction Corps/ ; },
abstract = {Potassium (K) is an essential macronutrient for plants and plays a critical role in soil microbial processes. However, its systemic effects on rhizosphere microorganisms in high-value crops like cherry tomato remain poorly understood. This study established a potassium gradient (K0 represents the no-potassium application, K1 represents low-potassium application, K2 represents a moderate-potassium application, K3 represents the conventional-potassium application, and K4 represents excessive-potassium application) to investigate responses in growth and rhizosphere bacterial and fungal communities of cherry tomato. Moderate potassium (K2) significantly enhanced dry matter accumulation in cherry tomato. Bacterial and fungal communities displayed distinct patterns: bacterial structure shifted continuously along the gradient, with specific enrichment of functional genera (nitrogen-fixing Ensifer, biocontrol-related Lysobacter), increased unique OTUs, and gradual co-occurrence network optimization at K2. In contrast, fungal community composition and network structure showed threshold responses to potassium. Low K (K1) suppressed dominant Ascomycota and increased unclassified fungi, while high potassium (K4) enriched parasitic/pathogenic fungi (Alternaria, Curvularia), increased network modularity, and reduced stability. This microbial ecological perspective highlights that optimized potassium application regulates functional microorganisms and differentially shapes rhizosphere communities, providing a theoretical basis for precision potassium management in cherry tomato.},
}

@article {pmid42198214,
year = {2026},
author = {Alkan, Y and Yalçıntaş, YM and Bechelany, M and Karav, S},
title = {Edible Plant-Derived Exosome-like Nanoparticles as Prebiotic Nanocarriers: Gut Microbiota Modulation and Functional Food Potential.},
journal = {Pharmaceutics},
volume = {18},
number = {5},
pages = {},
pmid = {42198214},
issn = {1999-4923},
abstract = {The gut microbiota takes charge in a pivotal role in metabolic equilibrium, immune response, and modulating gut lining stability and has become the main focus of nutrition and functional food research. In this regard, the definition of prebiotics has progressed past the traditional approach limited to indigestible dietary fibers, embracing more targeted, biologically active, and functional delivery systems. In recent years, plant-derived exosomes (PDEs), a subclass of exosomes defined as extracellular vesicles (EVs) in the 30-150 nm size range, have emerged as an innovative class of nanostructures supporting this transformation. Plant-derived exosome-like nanoparticles (PELNs) have been taken into account as natural nanocarriers which are suitable for the gastrointestinal system with the help of their high biocompatibility, low immunogenicity profiles and rich bioactive cargo contents. This review discusses structural features of PELNs, molecular cargo content, and biological roles comprehensively and focuses especially on gut microbiota interactions. MicroRNAs, proteins, lipids, polyphenols, and glycans which PELNs contain are discussed with regard to shaping the microbial composition, regulating microbial metabolic activity, and modulating host-microbe communication. Findings derived from in vitro, in vivo, and limited translational studies indicate that PELNs can modulate specific microbial taxa, increase short-chain fatty acid (SCFA) yield, strengthen mucosal immune homeostasis, and induce source-dependent responses in the gut microbiota. In their traditional definition, prebiotics are taken into account as food components which selectively support proliferation and metabolism of helpful microbes, especially Bifidobacteria and Lactobacilli. Within this framework, PELNs are not only passive carriers of functional components but also evaluated as active systems which can directly affect microbiota composition and metabolic functions. Thus, they are repositioned as "prebiotic nanocarriers." Also this review evaluates the potential of functional food and integration of major edible PELNs into synbiotic formulations by discussing their isolation and characterization methods and stabilities in the gastrointestinal environment. Limitations of clinical applications and lack of research from a prebiotic nanocarrier perspective of PELNs show that this field still contains important research gaps. The novelty of the study lies in its integration of PELN research with nutrition-based approaches to microbiota modulation and innovative functional food strategies under a single multidisciplinary conceptual framework.},
}

@article {pmid42198228,
year = {2026},
author = {Tang, R and Zeng, F and Lyu, C and Tuerheng, J and Guo, Z and He, K and Wu, D},
title = {Advances of Cell Membrane-Coated Nanotechnology and Membrane Vesicles in Intestinal Targeted Drug Delivery Systems.},
journal = {Pharmaceutics},
volume = {18},
number = {5},
pages = {},
pmid = {42198228},
issn = {1999-4923},
support = {Grant No. BRWEP2024W034010103//Beijing Research Ward Excellence Program/ ; Grant No. 3332025015//Fundamental Research Funds for the Central Universities, Peking Union Medical College/ ; Grant No. L232016//Beijing Natural Science Foundation/ ; },
abstract = {Although nanomedicine has enabled significant advances in drug delivery, the clinical translation of conventional synthetic nanocarriers is limited by immune clearance, non-specific biodistribution, and gastrointestinal instability. This poses major challenges for therapy targeting the intestines. Cell membrane-coated nanotechnology (CMCT) and membrane vesicle-based systems have emerged as biomimetic platforms integrating synthetic nanomaterials with naturally derived biological interfaces. These biohybrid systems inherit biological functions originating from cells, including immune evasion, prolonged circulation, lesion homing, and microenvironment-responsive interactions, through the direct transfer of intact membrane components. This review summarizes recent advances in CMCT and membrane vesicle-based strategies for intestinal drug delivery. It covers fabrication methodologies, programmable manufacturing approaches, and functional regulation enabled by diverse membrane sources and hybrid engineering designs. Applications in inflammatory bowel disease, colorectal cancer, and intestinal infections are highlighted, emphasizing key therapeutic mechanisms, such as targeting inflammation, neutralizing toxins, modulating the immune system, and regulating the microbiome. We also discuss the major challenges of translation, such as preserving membrane and coating integrity, ensuring oral stability, achieving batch reproducibility, and ensuring biosafety. Overall, this review establishes a conceptual and engineering framework to guide the transition of membrane-based nanocarriers from passive biomimicry to adaptive, clinically translatable intestinal delivery systems.},
}

@article {pmid42198371,
year = {2026},
author = {Rocha, M and Fierro-Arias, L and Layton, A and Bettoli, V and Dlova, N and Merika, E and Dirschka, T and Rerknimitr, P and Newaj, R},
title = {A Global Delphi Consensus on Acne and the Microbiome: Integrating International Expertise for Innovative Prevention and Therapeutic Strategies.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {5},
pages = {},
pmid = {42198371},
issn = {1424-8247},
abstract = {Acne is a prevalent dermatological condition occurring globally and influenced by a variety of endogenous and exogenous factors. The microbiome and its contribution to skin disease have been increasingly explored, along with the influence of the exposome and host immune responses on this complex microbial system. Nine experts from different countries in Africa, America, Asia, and Europe gathered to harmonise definitions, identify key pathogenic and protective microbial strains, and prioritise the factors that most significantly impact the skin's microbiome in the context of acne. Opportunity areas on the role of the microbiome in the prevention, treatment, recurrence, and sequelae avoidance in acne were identified. The relationships between current treatments and the diversity of the microbiome were described. Current microbiome-targeted strategies were assessed, including practical considerations of innovative future perspectives. The panel discussions emphasise the urgent need for universally adaptable guidelines encompassing alternatives to oral antibiotic therapies, in light of increasing antimicrobial resistance and the significant burden of treatment-related adverse events.},
}

@article {pmid42198430,
year = {2026},
author = {Nagy, C and Miere Groza, F and Ganea, M and Vicaș, LG and Mureșan, ME and Antonescu, A and Vicas, SI and Dobjanschi, L},
title = {The Role of Phytocompounds and the Physiological Response of the Skin in Common Dermatological Conditions: A Narrative Review and Bibliometric Analysis of Trends.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {5},
pages = {},
pmid = {42198430},
issn = {1424-8247},
support = {not applicable//University of Oradea/ ; },
abstract = {Background: The skin, as the largest organ of the human body, plays a crucial role in protection, immunity and homeostasis. Its exposure to environmental and internal factors contributes to the development of various dermatological conditions. Conventional treatments are often associated with adverse effects and increased resistance. This review aims to explore the growing role of phytotherapeutic approaches in dermatology, along with mapping recent research trends in the field. Methods: The paper presents three parts: the first part highlights the mapping of interest in the addressed topic through a systematic selection of the specialized literature using the Web of Science database. A bibliometric analysis was conducted using the Web of Science Core Collection, with data visualized in VOSviewer to identify publication trends, keyword clusters, and collaboration networks across European countries. Subsequently, in the second part of the review, the main topical topics regarding the skin were addressed (the immune and non-immune response system, microbiome composition and physiological responses in different situations). The third part of the paper addresses phytotherapy targeted at the dermatological sphere and controlled release therapeutic systems. Results: The analysis identified a total of 267 publications, with a significant increase in recent years. Key research clusters included phytochemical-based therapies, nanocarrier systems, and inflammatory skin conditions. Keyword co-occurrence analysis revealed emerging trends in nanoformulations and targeted delivery systems. The main research groups focused on polyphenols, antioxidant activity, anti-inflammatory effects and advanced delivery systems, such as nanoparticles and liposomes. In addition, innovative formulations have improved bioavailability and targeted administration. Conclusions: Phytotherapeutic approaches represent a promising alternative to conventional dermatological treatments, offering effective, safer and more sustainable solutions. The integration of natural compounds with modern delivery systems improves therapeutic outcomes and minimizes side effects, supporting their increasing relevance in clinical and pharmaceutical research.},
}

@article {pmid42198436,
year = {2026},
author = {Zou, Y and Hu, RT and Yu, Q and Rao, PL and Cui, HY and Wei, WJ and Cai, X and Li, HK and Shen, YH},
title = {Liuweidihuang Pill Attenuates Early Bleomycin-Induced Pulmonary Fibrosis in Mice and Is Associated with Gut Microbiome.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {5},
pages = {},
pmid = {42198436},
issn = {1424-8247},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; },
abstract = {Background: Pulmonary fibrosis (PF) is a chronic, progressive lung disease with limited treatment options. Liuweidihuang pill (LDP), a classical formula for kidney-yin deficiency, has been reported to have anti-inflammatory and anti-oxidative activities, suggesting potential relevance to PF. Purpose: This study evaluated whether LDP attenuates bleomycin-induced PF in mice and whether gut microbiota remodeling may contribute to its protective effects. Methods: Mice received intratracheal bleomycin followed by LDP gavage. Lung pathology was assessed by hematoxylin-eosin (HE) and Masson staining. Inflammatory cytokines, hydroxyproline (HYP), and α-SMA were measured. LDP and LDP-containing serum were profiled by UPLC-MS. The gut microbiota was analyzed using 16S rDNA sequencing. To further explore whether microbiota-related changes were associated with the protective phenotype, fecal microbiota transplantation (FMT) and probiotic VSL#3 intervention were performed. In addition, LDP-containing serum was tested in a TGF-β1-induced EMT model in A549 cells. Results: LDP reduced lung index, inflammatory infiltration, interstitial fibrosis, α-SMA expression, HYP content, and pro-inflammatory cytokine levels in bleomycin-treated mice. These effects were accompanied by gut microbiota remodeling and transcriptomic changes related to inflammation, metabolism, and fibrosis. VSL#3 partially reproduced the protective phenotype, whereas FMT showed limited efficacy. LDP-containing serum had a limited inhibitory effect on EMT inhibited EMT in vitro, suggesting that systemic host responses may contribute to the in vivo effect. Conclusions: LDP attenuated early bleomycin-induced PF and was associated with reduced inflammation and gut microbiota remodeling. These findings suggest a possible role for microbiota-host interactions in LDP-associated protection; however, causal directionality, key active effectors, and protein-level pathway validation remain unresolved.},
}

@article {pmid42198457,
year = {2026},
author = {Pastras, P and Aggeletopoulou, I and Psalti, V and Triantos, C},
title = {Gut Microbiota in Irritable Bowel Syndrome and Inflammatory Bowel Disease: Differences in Pathophysiology, Biomarkers, and Treatment Implications.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {5},
pages = {},
pmid = {42198457},
issn = {1424-8247},
abstract = {Alterations in the intestinal microbiota have been implicated in both irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). However, their biological significance and therapeutic implications differ substantially between the two conditions. Although dysbiosis is a common feature, the mechanisms by which alterations in the microbiota contribute to disease pathophysiology and clinical expression are distinct. Some pathways are more prominent in IBS (e.g., the gut-brain axis), whereas others are more prominent in IBD (e.g., reduced microbial diversity). Equally important are pathways that appear to play a role exclusively in IBD [e.g., Adherent-invasive Escherichia coli (AIEC) and Paneth cells], as well as others that seem to be specific to IBS (e.g., mast cell activation). In IBD, microbiota changes are primarily linked to immune dysregulation, mucosal barrier impairment, and inflammation-driven pathways, whereas in IBS, they are mainly associated with functional disturbances mediated by neuroimmune signaling and microbial metabolites. Furthermore, several microbiome-associated biomarkers differ between these two diseases, and some are already assessed by international guidelines. Although the microbiota plays a key role in IBS and IBD pathophysiology, microbiome-based treatments remain limited, especially in IBD. There are clinically available treatments in IBS (e.g., rifaximin, low-FODMAP diet), but in IBD, only the probiotic VSL#3 is guideline-approved in ulcerative colitis pouchitis prophylaxis. Nevertheless, the dynamic nature of the microbiota continues to support the investigation of already studied (e.g., probiotics, fecal microbiota transplantation) and potential novel therapeutic approaches at the research level. The aim of this review is to compare the gut-microbiota-related pathophysiological pathways and biomarkers between IBS and IBD, to summarize the microbiome-related medications that have already been studied in both diseases, and to suggest new potential therapeutic options based on the gut microbiota.},
}

@article {pmid42198530,
year = {2026},
author = {Wu, J and Chen, C and Geng, H and Zhao, B and Gao, J},
title = {Source, Monitoring Techniques and Prospects of Bioaerosols: A Review.},
journal = {Toxics},
volume = {14},
number = {5},
pages = {},
pmid = {42198530},
issn = {2305-6304},
support = {42075182//National Natural Science Foundation of China/ ; 202304041101011//the International Scientific and Technological Cooperation Projects of Shanxi (China) for Designated Countries/ ; },
abstract = {Bioaerosols play significant roles in ecological interactions, climate change, and public health. Their diverse origins contribute to a dynamic atmospheric microbiome with considerable spatiotemporal variability, which are generally categorized as natural and anthropogenic sources. Accurate monitoring and source apportionment are critical for assessing environmental impacts and health risks. This review systematically summarizes the characteristics of bioaerosol sources and emphasizes emission risks from intensive human activities. This study also elucidates source apportionment strategies of bioaerosols and analyzes the technological evolution from traditional culture-based methods to advanced molecular and real-time physicochemical systems. In addition, the shift of bioaerosol monitoring technologies towards high-sensitivity, culture-independent, and online monitoring is emphasized in this review. An outlook on future research priorities is provided in the end. We emphasize the pressing need to establish localized characteristic databases, develop integrated real-time monitoring systems coupling rapid screening with deep biological analysis, and optimize the application of machine learning and AI algorithms to enhance the precision of multi-source contribution modeling in complex environments.},
}

@article {pmid42198631,
year = {2026},
author = {Kim, TJ and Schneider, S and Defreitas, A and Walker, LP and Shenker, BJ and Boesze-Battaglia, K},
title = {Cellugyrin (Synaptogyrin-2) Regulates Macrophage Phagocytosis of Aggregatibacter actinomycetemcomitans (Aa).},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
pmid = {42198631},
issn = {2076-0817},
support = {1K08DE032119-01/DE/NIDCR NIH HHS/United States ; 5R01DE023071-09/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Phagocytosis ; *Aggregatibacter actinomycetemcomitans/immunology ; *Macrophages/immunology/microbiology/metabolism ; *Host-Pathogen Interactions/immunology ; },
abstract = {Grade C molar-incisor pattern periodontitis (C-MIP) is a rapidly progressive form of periodontal disease affecting young individuals that is often linked to a highly virulent genotype of Aggregatibacter actinomycetemcomitans (Aa). Although Aa is present in the healthy oral microbiome, its transition into subgingival tissue correlates with the conversion from healthy to diseased status within the periodontal pocket. These changes may be due to immune evasion strategies attributed to Aa exotoxins. We previously demonstrated that a host cell protein, cellugyrin, plays a critical role in exotoxin internalization and subsequent cytotoxicity. Herein, we assess the contribution of cellugyrin to Aa phagocytosis and intracellular trafficking in human macrophages. Confocal imaging demonstrated that Aa co-localizes with cellugyrin. Importantly, cellugyrin-deficient macrophages exhibited a significant reduction in phagocytosed Aa. Furthermore, we analyzed the role of retrograde trafficking in Aa survival. Retro-2-mediated inhibition of this trafficking pathway resulted in increased intracellular Aa, likely due to increased survival. Collectively, our findings suggest that cellugyrin is involved in Aa phagocytosis and that retrograde trafficking may play a role in subsequent host cell clearance of Aa.},
}

Humans
*Phagocytosis
*Aggregatibacter actinomycetemcomitans/immunology
*Macrophages/immunology/microbiology/metabolism
*Host-Pathogen Interactions/immunology

@article {pmid42198714,
year = {2026},
author = {Bako, RS and Kelley, CF},
title = {Unraveling the Rectal Virome: Microbial Crosstalk, Immune Modulation, and Clinical Outcomes in People with and Vulnerable to HIV.},
journal = {Viruses},
volume = {18},
number = {5},
pages = {},
pmid = {42198714},
issn = {1999-4915},
mesh = {Humans ; *HIV Infections/immunology/virology ; *Virome/immunology ; *Rectum/virology/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; Male ; Homosexuality, Male ; },
abstract = {The rectal mucosa houses a large number of viruses with important roles in shaping the local microbial communities and modulating immune responses, which could influence host susceptibility to infection and other diseases. Unique composition of the gut microbiome, including the predominance of clinically significant eukaryotic viruses like herpesviruses, cytomegalovirus, and human papillomavirus, has been described in both people with HIV (PWH) and men who have sex with men (MSM) vulnerable to HIV. Despite these insights, the rectal virome and the clinical implications of virome-bacteriome-immune interactions in the rectal mucosa remain poorly understood. In this review, we synthesize existing data on the composition of the rectal virome, its interactions with the bacteriome and the immune system, and implications on clinical outcomes in people living with or vulnerable to HIV. We also highlight the gaps and research needed to further explore and unravel these relationships.},
}

Humans
*HIV Infections/immunology/virology
*Virome/immunology
*Rectum/virology/microbiology/immunology
*Gastrointestinal Microbiome/immunology
Male
Homosexuality, Male

@article {pmid42198756,
year = {2026},
author = {Guan, F and Zhang, J and Tian, Y and Fu, B and Liu, J and Song, Y and Yan, A and Zhang, B and Chen, L and Zhang, M and Du, P and Wang, L and Yang, X and Guo, S and Yang, C and Zhang, H and Zhang, Q},
title = {Gut Microbiota and Probiotics in Influenza: A Narrative Review of Mechanisms and Emerging Evidence.},
journal = {Viruses},
volume = {18},
number = {5},
pages = {},
pmid = {42198756},
issn = {1999-4915},
support = {2024YFD1800303//Ministry of Science and Technology of China/ ; },
mesh = {Humans ; *Probiotics/therapeutic use ; *Influenza, Human/immunology/virology/microbiology ; Animals ; *Gastrointestinal Microbiome ; Lung/immunology/virology ; Orthomyxoviridae ; },
abstract = {The gut microbiota, often referred to as the "forgotten organ", plays an indispensable role in maintaining host physiological metabolism, immune function, and nutrient absorption. Moreover, the gut microbiome serves as a critical biological barrier against viral infections and is increasingly recognized as a potential target to augment antiviral therapies. Recent studies have revealed that microbial ligands and metabolites derived from the gut microbiota are pivotal in modulating respiratory immune responses, providing compelling evidence of the complex interaction network between microorganisms and the host, particularly the signaling pathways linking the gut to distal organs such as the lungs. This review examines the communication and regulatory mechanisms between the gut microbiota and pulmonary mucosal surfaces during influenza virus infection, emphasizing how gut microbial communities and probiotics influence host immune responses, promote the production of immune-related molecules, and enhance antiviral defenses. The aim is to provide comprehensive insights into the gut-lung axis and its implications for respiratory health.},
}

Humans
*Probiotics/therapeutic use
*Influenza, Human/immunology/virology/microbiology
Animals
*Gastrointestinal Microbiome
Lung/immunology/virology
Orthomyxoviridae

@article {pmid42198807,
year = {2026},
author = {Korth, N and Borrero, I and Rumley, K and Woodley, AL and Choudoir, MJ and Gage, JL},
title = {Investigating GERMs: how genotype, environment, and rhizosphere microbiome interactions underlie heat response in maize and sorghum.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71297},
pmid = {42198807},
issn = {1469-8137},
support = {R35GM151048/NH/NIH HHS/United States ; 2024-38420-41520//National Institute of Food and Agriculture/ ; 2025-67012-44807//National Institute of Food and Agriculture/ ; 7002327//National Institute of Food and Agriculture/ ; 7004439//National Institute of Food and Agriculture/ ; },
abstract = {Plant responses to heat stress emerge from interactions among host genotype, environment, and the rhizosphere microbiome, yet most studies examine these components in isolation. We applied the Genotype × Environment × Rhizosphere Microbiomes (GERMs) framework to test how host-microbe coordination contributes to heat tolerance in cereal crops Zea mays and Sorghum bicolor. We analyzed maize and sorghum grown under optimal and heat-stressed conditions across contrasting soil treatments using integrated plant-microbial metatranscriptomics. Host and microbial gene expression profiles were jointly analyzed alongside microbiome composition and plant phenotypes and compared with amplicon-based profiling. Metatranscriptomics captured microbial community structure comparable to amplicon sequencing while providing enhanced functional and taxonomic resolution. Host genotype and temperature jointly shaped microbial functional profiles. Conserved plant orthologs across maize and sorghum were linked to microbial pathways, specifically microbial d-amino acid metabolism was associated with plant heat tolerance. These findings indicate the rhizosphere microbiome actively participates in plant heat stress responses through coordinated transcriptional interactions with the host. Integrating host and microbial transcriptomes reveals mechanistic insights into plant adaptation and establishes a framework for dissecting plant-microbiome interactions under environmental stress.},
}

@article {pmid42198875,
year = {2026},
author = {Wong, SH and Kwong, TNY and Zhang, R and Lam, TYT and Ho, AMY and Leung, WW and Kang, X and Lau, HCH and Chu, ESH and Wong, MTL and Lau, LHS and Lui, RNS and Tang, RSY and Lau, JYW and Ng, SSM and Yu, J and Sung, JJY},
title = {Comprehensive microbiome profiling reveals mucosal microbiome heterogeneity in patients with left- and right-sided colorectal neoplasia.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0846},
pmid = {42198875},
issn = {2095-3941},
support = {CIRG23jan-0004//Singapore National Medical Research Council Clinician Scientist Individual Research Grant/ ; OFLCG22may-0009//Large Collaborative Grant/ ; OFLCG23may-0031//Large Collaborative Grant/ ; OFLCG24may-0025//Large Collaborative Grant/ ; },
abstract = {OBJECTIVE: Left- and right-sided colorectal cancer (CRC) exhibit distinct molecular and clinicopathologic features. However, little is known about the spatial heterogeneity of microbial signatures. In this study the profiles and ecologic patterns of disease-associated intestinal microbiome were investigated in patients with an adenoma(s) or CRC at different anatomic locations.

METHODS: A total of 690 stool, colonic aspirate, and mucosal biopsy samples were prospectively collected from 32 healthy, 30 adenoma, and 31 CRC patients.

RESULTS: CRC was associated with alterations in fecal and mucosal microbiomes. Furthermore, the overall composition of the mucosal microbiome, stratified by metacommunities, differed between the patients with left- and right-sided neoplastic lesions. Patients with right-sided CRC had an elevated inter-phylum ecologic network, while patients with left-sided CRC had an enriched abundance of Fusobacterium. Interestingly, rectal neoplasia harbored a tumor microbiome that was distinctly different from the tumor microbiome at other anatomic sites.

CONCLUSIONS: The mucosal microbiome of right-sided CRC was distinctly different from the mucosal microbiome of left-sided CRC patients, suggesting distinct microbial ecology and heterogeneous host-microbial ecologic relationships that may contribute to differences in the tumor microenvironment between left- and right-sided CRC.},
}

@article {pmid42198884,
year = {2026},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Rhizosphere microbes are partners in plant stress adaptation.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag254},
pmid = {42198884},
issn = {1460-2431},
}

@article {pmid42198941,
year = {2026},
author = {Briers, Y},
title = {Disruptive innovation in antibiotic development: a vision for lysins.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/14787210.2026.2680018},
pmid = {42198941},
issn = {1744-8336},
abstract = {INTRODUCTION: Antimicrobial resistance is escalating globally, while the development of new antibiotic classes has stagnated. This trend is reminiscent of the late-stage dynamics of S-curve innovation, where incremental advances no longer meet clinical needs. To overcome this impasse, disruptive innovation is required. As protein-based antibacterials, lysins represent a fundamentally different modality from traditional small-molecule antibiotics and offer new opportunities for disruptive innovation in terms of resistance development and microbiome preservation.

AREAS COVERED: Sourced from a vast natural reservoir, lysins exhibit rapid, targeted bactericidal activity with low resistance potential and high specificity. Their narrow-spectrum nature supports a potential for microbiome preservation and the conceptual development of theranostic platforms for precision infectious disease management, combining ultra-fast pathogen detection with targeted therapeutic activity.

EXPERT OPINION: To initiate new innovation cycles, disruptive modalities such as protein-based lysins will be needed, offering a paradigm shift in antimicrobial therapy. Their modular architecture and amenability to protein engineering enable a hit-to-lead development strategy akin to small-molecule pipelines. Their synergistic interactions with standard-of-care antibiotics and booster-like activity could facilitate incremental clinical integration into existing treatment protocols. This positioning supports regulatory acceptance and paves the way for lysins to become transformational components of precision antimicrobial therapy.},
}

@article {pmid42198987,
year = {2026},
author = {Keigler, JI and Leite Nobrega de Moura Bell, JM and Marco, ML},
title = {Myco-foods and the gut microbiome: impacts of mycelial extracts, biomass, and mold-fermented foods.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2677948},
doi = {10.1080/19490976.2026.2677948},
pmid = {42198987},
issn = {1949-0984},
mesh = {Humans ; *Fungi/chemistry/metabolism ; Animals ; *Mycelium/chemistry/metabolism ; *Gastrointestinal Microbiome ; *Fermented Foods/microbiology/analysis ; Bacteria/classification/isolation & purification/metabolism/genetics ; Biomass ; Fermentation ; },
abstract = {Edible filamentous fungi include mushrooms and molds, which are consumed as extracts, mycelial biomass, and fermented foods. These fungal foods are often high in protein and fiber and are generally regarded as nutritious. This narrative review examines current knowledge on how mycelia from molds, including edible strains of Aspergillus, Rhizopus, Neurospora, Fusarium, Mucor, and Paecilomyces, affect the gut microbiome. Allfour human trials on these foods (two extracts, one biomass, and one fermented food) reported a measurable effect on the gut microbiome. These studies, plus the additional eight animal and eight in vitro studies performed, frequently found increases in the proportions of intestinal Akkermansia, Bifidobacterium, and lactobacilli. Bacteroides, Roseburia, and Eubacterium, which are recognized for their roles in fiber metabolism, were also frequently enriched, and numerous studies reported increases in fecal short-chain fatty acids. Notably, effects on the gut microbiome may be fungal species and food format-dependent. Although β-glucans and chitin are likely key determinants of gut microbiome responses to dietary mycelium, future studies should investigate how these and other potentially bioactive components of mycelia and fungal metabolites are metabolized by intestinal microorganisms. Such studies will result in an improved understanding of how myco-foods could support human health.},
}

Humans
*Fungi/chemistry/metabolism
Animals
*Mycelium/chemistry/metabolism
*Gastrointestinal Microbiome
*Fermented Foods/microbiology/analysis
Bacteria/classification/isolation & purification/metabolism/genetics
Biomass
Fermentation

@article {pmid42199000,
year = {2026},
author = {Shamsuzzaman, M and Dahal, RH and Kim, J},
title = {Bifidobacterium intestinale sp. nov., and Blautia caeci sp. nov., from the Human Gut Microbiome with Candidate Probiotic Potential.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2603013},
doi = {10.4014/jmb.2603.03013},
pmid = {42199000},
issn = {1738-8872},
mesh = {Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Feces/microbiology ; DNA, Bacterial/genetics ; *Bifidobacterium/classification/isolation & purification/genetics ; *Probiotics ; *Gastrointestinal Microbiome ; Sequence Analysis, DNA ; Antioxidants ; Genome, Bacterial/genetics ; Bacterial Typing Techniques ; *Eubacteriales/classification/isolation & purification/genetics ; },
abstract = {Two novel Gram-stain-positive, anaerobic, and non-motile bacterial strains, designated M3-R-103[T] and C3-R-101[T], were isolated from human faecal samples and subjected to comprehensive taxonomic characterization together with evaluation of selected functional properties. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain M3-R-103[T] is affiliated with the genus Bifidobacterium, whereas strain C3-R-101[T] belongs to the genus Blautia. Strain M3-R-103[T] exhibited the highest 16S rRNA gene sequence similarity (98.9%) to Bifidobacterium pseudocatenulatum DSM 20438[T], while strain C3-R-101[T] showed 98.6% similarity to Blautia hominis KB1[T]. The draft genome sizes of strains M3-R-103[T] and C3-R-101[T] were 2.08 Mbp and 6.40 Mbp, respectively, with DNA G+C contents of 56.3 mol% and 46.7 mol%. Both strains demonstrated tolerance to simulated gastrointestinal stress conditions, including exposure to acidic pH (2.0) and bile salts (0.3%). In vitro assays revealed measurable antioxidant, α-amylase inhibitory, and anti-inflammatory activities. Specifically, DPPH radical scavenging activity ranged from 38.28 ± 8.35% to 58.83 ± 9.35%, α-amylase inhibition ranged from 47.12 ± 2.76% to 69.19 ± 3.83%, and inhibition of albumin denaturation ranged from 52.99 ± 2.70% to 58.16 ± 8.00%. Based on combined phylogenetic, genomic, and phenotypic evidence, strains M3-R-103[T] and C3-R-101[T] represent two novel species within their respective genera. We therefore propose the names Bifidobacterium intestinale sp. nov. (type strain M3-R-103[T] = KCTC 25443[T] = CGMCC 1.19415[T]) and Blautia caeci sp. nov. (type strain C3-R-101[T] = KCTC 25440[T] = CGMCC 1.17981[T]).},
}

Humans
Phylogeny
RNA, Ribosomal, 16S/genetics
Base Composition
Feces/microbiology
DNA, Bacterial/genetics
*Bifidobacterium/classification/isolation & purification/genetics
*Probiotics
*Gastrointestinal Microbiome
Sequence Analysis, DNA
Antioxidants
Genome, Bacterial/genetics
Bacterial Typing Techniques
*Eubacteriales/classification/isolation & purification/genetics

@article {pmid42199064,
year = {2026},
author = {Goobie, GC},
title = {Molecular mechanisms of environmental risk factors for interstitial lung disease.},
journal = {Current opinion in pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCP.0000000000001286},
pmid = {42199064},
issn = {1531-6971},
abstract = {PURPOSE OF REVIEW: Interstitial lung disease (ILD) comprises a diverse group of conditions characterized by lung inflammation and fibrosis. Cumulative lifetime exposures (i.e. the exposome) contribute to ILD onset and progression by interacting with genetic susceptibility and influencing multiple molecular pathways. This review summarizes current evidence evaluating how environmental exposures interact across the genome, epigenome, transcriptome, proteome, metabolome, and microbiome to drive ILD pathogenesis.

RECENT FINDINGS: Environmental exposures, including air pollution, influence ILD risk through interactions with genetic factors that modify disease susceptibility. Epigenetic mechanisms, particularly DNA methylation, reflect key pathways through which exposures may contribute to ILD onset and progression and serve as sensitive biomarkers of environmental injury. Exposure-associated molecular alterations can be detected across multiple omic layers, including transcriptomic, proteomic, and metabolomic profiles. In parallel, exposures like cigarette smoking, silica, and air pollution influence the respiratory microbiome, with potential downstream effects on immune responses and fibrogenesis. Integrating these findings highlights environmentally-sensitive pathways that may represent novel targets for therapeutic modulation.

SUMMARY: Integration of exposomic and multiomic molecular frameworks offers new opportunities to improve ILD risk stratification, prognostication, and precision therapeutic development, while also strengthening our mechanistic understanding of environmentally-mediated disease.},
}

@article {pmid42199152,
year = {2026},
author = {Zhang, W and Song, Y and Li, C and Luo, Y and Shao, M and Guo, F and Wei, F and Fan, X and Guo, W and Xu, F and Sang, Y and Zhang, D and Zhou, Y and Wang, L and Kang, Z and Yang, Y and Song, C and Liu, Y and Ma, X and Wang, J and Li, C and Ma, S and Zhao, L and Qin, Z and Xing, G and Zhao, Q and Li, J and Song, S and Zhao, D and Huang, T and Wang, Q and Zhao, Y and Qin, G},
title = {Canagliflozin Alleviates Diabetic Glomerular Endothelial Injury via Melibiose in a Microbiota-Dependent Manner.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17222},
doi = {10.1002/advs.202517222},
pmid = {42199152},
issn = {2198-3844},
support = {82170839//National Natural Science Foundation of China/ ; U23A20414//National Natural Science Foundation of China/ ; 82470876//National Natural Science Foundation of China/ ; 82300930//National Natural Science Foundation of China/ ; 251111311500//Key Research and Development Program of Henan Province/ ; 242300421272//Natural Science Foundation of Henan Province/ ; LHGJ20230200//Henan Joint Construction Program/ ; SBGJ202301006//Science and Technology Research Project of Henan Province/ ; },
abstract = {Canagliflozin reduces albuminuria in patients with diabetic kidney disease (DKD) beyond its glucose-lowering effect, but the mechanisms remain unclear. We analyzed 85 patients treated with canagliflozin and 85 controls over 26 weeks to explore whether the gut microbiome and its metabolites contribute to renoprotection. Canagliflozin remodeled the gut microbiota, notably enriching Roseburia intestinalis and increasing plasma melibiose levels. In mice, canagliflozin alleviated glomerular endothelial injury and albuminuria. Similar effects were replicated by fecal microbiota transplantation, Roseburia intestinalis, or melibiose administration. Mechanistically, melibiose bound to and activated glyoxalase 1, reduced methylglyoxal, and suppressed the AGE-RAGE pathway, preserving glomerular endothelial integrity. Furthermore, oral melibiose precursor supplementation reduced albuminuria in patients with early-stage DKD. These findings suggest the involvement of a gut-kidney axis in the renoprotective effects of canagliflozin and indicate that melibiose may serve as a potential therapeutic strategy for DKD.},
}

@article {pmid42199216,
year = {2026},
author = {Suchowiecki, K and Corr, PG and Schurr, A and Asemani, A and Frame, LA},
title = {Evaluating the gut microbiome, dietary patterns, and cognition: a sub-study protocol from the brain health and the gut microbiome study in cognitive decline (bMicrobiome study).},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e8},
pmid = {42199216},
issn = {2632-2897},
abstract = {The aim of this study is to describe the development and implementation of a novel Readiness to Change Nutritional Habits (RCNH) survey for use along with dietary assessment and gut microbiome profiling in a proof-of-concept study in individuals with early Alzheimer's disease dementia (eAD), mild cognitive impairment (MCI), and healthy controls (HC). Overall, this methods paper contributes to emerging research examining how behavioural readiness for change can be integrated with dietary assessment and gut microbiome profiling to better understand the microbiome's influence on the nervous system. This is a sub-study embedded within a multi-prong proof-of-concept, observational study mapping the gut microbiome in 45 participants (15 HC, 15 MCI, 15 eAD) at baseline, 3 months, and 6 months. The parent study collects gut microbiome profiles, dietary patterns, and cognitive assessments. The sub-study develops and administers the 32-item RCNH survey to characterize participants' readiness to adopt nutritional change. This manuscript reports the RCNH survey, its development process, the sub-study protocol including data collection procedures, and planned exploratory analyses. This protocol presents a novel intervention to assess the gut microbiome, individual dietary patterns, and readiness to make lifestyle changes related to diet.},
}

@article {pmid42199361,
year = {2026},
author = {Song, S and Han, M and Moon, K and Lee, H and Ha, S and Seo, J and Lee, S and Jang, S and Lim, SK and Kim, N and Ko, G},
title = {Bifidobacterium stercoris KC84 attenuates IBS-D-like symptoms via modulation of serotonin-related pathways and dendritic cell-mediated IFN-β induction.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100603},
pmid = {42199361},
issn = {2666-5174},
abstract = {Irritable bowel syndrome with diarrhea (IBS-D) is a prevalent disorder that significantly impairs quality of life, yet therapeutic advances remain limited. Serotonin dysregulation, primarily driven by enterochromaffin cells in the intestinal epithelium, is central to IBS-D pathogenesis. We hypothesized that targeted modulation of enterochromaffin cell activity through microbiome-based interventions could provide a novel treatment approach. Here, we screened 128 Bifidobacterium isolates and identified B. stercoris KC84 as a promising candidate. KC84 alleviated IBS-D-like symptoms in both chemically and stress-induced models, accompanied by changes in serotonin-related markers. Transcriptomic analysis revealed activation of type I interferon (IFN)-associated pathways, consistent with ex vivo evidence of KC84-induced IFN-β secretion, predominantly from CD11b[-] dendritic cells. Furthermore, IFN-β treatment attenuated contractile activity in colonic smooth muscle cells. Collectively, these findings suggest that KC84 mitigates IBS-D-like symptoms, potentially through modulation of serotonin-related pathways and activation of a KC84-IFN-β-smooth muscle regulatory axis, supporting KC84 as a mechanism-guided probiotic candidate for IBS-D therapy.},
}

@article {pmid42199372,
year = {2026},
author = {Vijayakumar, K and Paul, BC},
title = {Virulence factors of the microbiome: A functional toolkit for cancer progression (Review).},
journal = {Molecular and clinical oncology},
volume = {25},
number = {1},
pages = {48},
pmid = {42199372},
issn = {2049-9469},
abstract = {The paradigm of cancer biology has shifted to recognize tumor as a complex ecosystem inhabited by a diverse microbiome. Beyond mere association, the molecular mechanisms driven by microbial virulence factors are critical for understanding how these microorganisms contribute to malignancy. The present review describes a virulence factor-centric framework to deconstruct the microbial 'toolkit' and illustrate its role in enabling the Hallmarks of Cancer. The major classes of virulence factors were systematically analyzed, detailing how each contributes to tumor progression. It was described how bacterial adhesins (for example, Fusobacterium adhesin A and Fap2) initiate oncogenic signaling and mediate immune evasion; how secreted toxins drive genomic instability (Colibactin and CDT) and corrupt cellular signaling pathways (CagA and Bacteroides fragilis toxin); how degradative enzymes (gingipains and collagenases) dismantle the extracellular matrix to facilitate physical invasion; how viral oncoproteins (Human Papillomavirus E6/E7 and Epstein Barr virus latent membrane protein 1) hijack core cell cycle machinery; and how microbial structural components (lipopolysaccharides and extracellular vesicles) and metabolites (secondary bile acids) sustain a pro-tumorigenic environment. This analysis reveals a pattern of functional convergence, where diverse microbial agents repeatedly target core host pathways such as NF-κB, Wnt/β-catenin and p53. This mechanistic understanding reframes the microbiome as an active orchestrator of malignancy and reveals a new frontier of therapeutic targets. Strategies aimed at neutralizing specific virulence factors or modulating the tumor ecosystem represent a novel and promising pillar in oncology.},
}

@article {pmid42199404,
year = {2026},
author = {Zhu, M and Li, R and Wu, S and Chen, J and Sun, K},
title = {Multi-omics insights into spondyloarthritis and psoriatic arthritis: integrating genomics, transcriptomics, proteomics, and the microbiome for immunological and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1831823},
pmid = {42199404},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Psoriatic/diagnosis/immunology/genetics/metabolism/microbiology ; Multiomics ; *Proteomics/methods ; *Genomics/methods ; *Microbiota/immunology ; *Spondylarthritis/diagnosis/genetics/immunology/metabolism ; Biomarkers ; Transcriptome ; Gene Expression Profiling ; Translational Research, Biomedical ; Animals ; },
abstract = {Spondyloarthritis (SpA) and psoriatic arthritis (PsA) are interrelated, immune-mediated inflammatory diseases characterized by significant clinical heterogeneity. Early differential diagnosis, accurate disease activity assessment, and the development of personalized treatment strategies remain significant clinical challenges. Single-omics approaches have provided only a limited view of this complexity, highlighting the need for integrative strategies. This review systematically synthesizes findings from multi-omics studies-including genomics, transcriptomics, proteomics, and microbiomics-in SpA and PsA. We focus on their application in three key areas: (i) elucidating shared and distinct immunopathological mechanisms, (ii) facilitating differential diagnosis, and (iii) discovering novel biomarkers. By comparing their molecular landscapes, we explore the shared and distinct immunological foundations of SpA and PsA. Furthermore, we critically evaluate the translational potential of integrated multi-omics strategies for advancing early diagnosis, precision monitoring, predicting treatment responses, and identifying novel therapeutic targets. This integrated, multi-omics framework promises to refine disease taxonomy and guide personalized therapeutic decisions, paving the way for precision medicine in SpA and PsA.},
}

Humans
*Arthritis, Psoriatic/diagnosis/immunology/genetics/metabolism/microbiology
Multiomics
*Proteomics/methods
*Genomics/methods
*Microbiota/immunology
*Spondylarthritis/diagnosis/genetics/immunology/metabolism
Biomarkers
Transcriptome
Gene Expression Profiling
Translational Research, Biomedical
Animals

@article {pmid42199424,
year = {2026},
author = {Zhao, L and Wang, Q and Chen, J and Wang, J},
title = {Multi-omics analyses reveal significant differences in the gut microbiota and metabolites in children with Kawasaki disease in Northwest China.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1767902},
pmid = {42199424},
issn = {1664-3224},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/metabolism ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenomics/methods ; China/epidemiology ; *Metabolome ; Metabolomics/methods ; Infant ; Feces/microbiology ; Bacteria/classification/genetics ; Child ; },
abstract = {BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis characterized by mucocutaneous lymph node syndrome and aberrant immune activation. Previous studies have indicated substantial disruptions in the gut microbiota during the acute phase of KD. However, the detailed characteristics of the gut microbiota and metabolome in children with KD, as well as their clinical relevance, remain poorly understood.

METHODS: 31 children with KD (KDs) and age/sex-matched healthy controls (HCs) were enrolled to collect their fecal and blood samples. Shotgun metagenomic sequencing and untargeted metabolomic analyses were conducted on these samples.

RESULTS: Significant reductions in alpha diversity and microbial richness were observed in the gut microbiota of KDs at both species and genus levels. Pathogenic species including Enterococcus avium, Streptococcus peroris and Clostridioides difficile were significantly abundant in the KDs group, while beneficial species containing Faecalibacterium prausnitzii, Anaerostipes hadrus, Akkermansia muciniphila, Eubacterium hallii, Agathobaculum butyriciproducens, Ruminococcus bicirculans, and Roseburia intestinalis were markedly decreased. A total of 49 metabolic pathways were differentially enriched between the two groups, with 22 pathways including nucleotide, carbohydrate, energy, and amino acid metabolism being abundant in KDs, while the other 27 pathways were enriched in HCs. For metabolites, both fecal and blood metabolomes exhibited significant alterations. Notably, fecal metabolites including indole, L-tryptophan, L-lactic acid, 5-HETE, indol-3-acetamid, tetraethylammonium and dopaquinone were elevated in KDs, whereas butyrate, methylxanthine, phosphocholine, methylhistidine, ADP-ribose, vitamin A acid, and chenodeoxycholic acid were reduced. In plasma, cholesterol, phosphocholine, porphobilinogen, pantothenate, cortisol, bile acids and related compounds were enriched in KDs, while amino acids, indole and tryptamine derivatives, nucleotides, nucleic acids, and sugar metabolites were more abundant in HCs.

CONCLUSIONS: This study represents the first systematic multi-omics investigation of KD in a pediatric population from Northwest China. It establishes a foundational resource characterizing the gut microbiome and metabolome in KD, offering novel biological insights, suggesting potential therapeutic targets, and supporting further mechanistic and clinical research.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/microbiology/metabolism
Female
Multiomics
Male
*Gastrointestinal Microbiome
Child, Preschool
Metagenomics/methods
China/epidemiology
*Metabolome
Metabolomics/methods
Infant
Feces/microbiology
Bacteria/classification/genetics
Child

@article {pmid42199468,
year = {2026},
author = {Groß, VE and Cheng, KO and Cristóvão, B and Gürel, E and Himmel, M and Fernández-Fernández, C and Schuchardt, JV and Dietschmann, A and Montaño, DE and Gresnigt, MS},
title = {An In Vitro A-431 Epithelial Cell Infection Model for Studying Fungal Pathogenicity and Immune Responses Associated With Vulvovaginal Candidiasis.},
journal = {Bio-protocol},
volume = {16},
number = {10},
pages = {e5693},
pmid = {42199468},
issn = {2331-8325},
abstract = {Vulvovaginal candidiasis (VVC), also known as vaginal thrush, is an infection of the vulvovaginal mucosa caused by fungi of the Candida genus. Particularly for patients suffering from recurrent infection, the disease has a significant impact on their quality of life. The still unknown aspects of disease pathogenesis, as well as factors driving the development of infections and recurrence, represent a challenge for both clinical practitioners and patients. Mouse models and patient studies have suggested important roles of the microbiome, deployment of fungal pathogenicity mechanisms in the vagina, and dysregulated immune responses for VVC pathology. Dissecting their individual contributions can reveal specific processes associated with infection and may inspire novel therapeutic strategies. Epithelial in vitro infection models have been playing a key role in dissecting a crucial interaction during VVC, the invasion and infection of the vaginal mucosa. They have been instrumental in characterizing candidalysin as a fungal toxin that damages epithelial cells and elicits initial inflammatory responses to catalyze downstream inflammation. Moreover, they have also revealed potential protective immune pathways. Such a standardized epithelial cell infection model offers high versatility and compatibility with different downstream assays to link epithelial responses with other processes during VVC. This protocol describes a general A-431 vulvovaginal epithelial cell-Candida infection model in detail and provides several adaptations, such as live-cell imaging and mRNA silencing, as well as possible follow-up readouts, like the quantification of cytokine release, cytotoxicity, and neutrophil recruitment to study diverse processes relevant to VVC research. Key features • This protocol describes the use of the A-431 epidermoid carcinoma cell line as an in vitro infection model of vulvovaginal candidiasis. • The protocol can be adapted to answer research questions relevant to vulvovaginal candidiasis (epithelial damage, release of inflammatory cytokines, recruitment and activation of neutrophils). • Live-cell imaging can be used to study dynamic infection processes. • mRNA silencing can be applied to interrogate the function of genes of interest in the host-pathogen interaction. This protocol is used in.},
}

@article {pmid42199542,
year = {2026},
author = {Cycoń, M},
title = {Bioaugmentation as microbiome engineering: a framework for evaluating functional performance, persistence, and safety.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1835468},
pmid = {42199542},
issn = {1664-302X},
abstract = {Bioaugmentation is increasingly applied to enhance the degradation of contaminants in environmental and engineered systems, yet its effectiveness is often evaluated using endpoints that do not establish whether the introduced microbial function was expressed, sustained, or responsible for the observed outcome. This review considers bioaugmentation as an approach to microbiome engineering rather than a discrete inoculation step. It outlines an evaluation framework based on three complementary criteria: functional performance, functional persistence, and safety. Emphasis is placed on the microbiological determinants of successful implementation, including pathway completion, expression of terminal transformation steps, functional redundancy, ecological compatibility, and the maintenance of introduced activity under variable environmental conditions. The analysis also examines how inoculum design, delivery, selective pressure, retention, and biomonitoring influence the establishment of degradative functions within complex microbial communities. A central theme is the need to distinguish genuine inoculum-driven effects from outcomes generated by biostimulation, modified mass transfer, or changes in contaminant bioavailability. Available evidence indicates that robust interpretation requires an integrated assessment of substrate-to-product relationships, functional and activity markers, community-level responses, and, where appropriate, indicators of biological effect. Microbiological safety considerations are also reviewed, including selective pressures and resistance-related consequences in systems exposed to biologically active contaminants. Bioaugmentation should therefore be evaluated as a controlled microbiotechnological intervention in which function, persistence, mechanistic attribution, and safety are assessed collectively.},
}

@article {pmid42199545,
year = {2026},
author = {Wang, Z and Guo, X and Shi, Y and Ma, N and Ma, Y and Pei, Y and Li, Y and Xu, H and Ma, F and Li, Y and Li, J and Gao, Y},
title = {Impacts of off-flavor on microbial community structure, nutritional traits and metabolite profiles in whole-plant corn silage.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1827817},
pmid = {42199545},
issn = {1664-302X},
abstract = {Off-flavor in corn silage compromises feed quality and animal performance, yet the microbial-metabolic changes driving its formation remain poorly understood. In this study, microbiome profiling, metabolomics, and sensory evaluation were integrated to elucidate the changing factors driving off-flavor formation. Silage samples from 10 dairy farms were classified by sensory score into control (CON, 15-20) and abnormal silage groups (ASG, <15). The bacterial community structure was analyzed, metabolites were identified and quantified using gas chromatography-mass spectrometry (GC-MS), and the associations between microorganisms and metabolites were explored via Spearman correlation analysis. Compared with the CON, the ASG exhibited significantly lower concentrations of dry matter (p = 0.01), starch (p = 0.04), lactic acid (p = 0.03), and acetic acid (p = 0.04), while those of neutral detergent fiber (p = 0.02), acid detergent fiber (p = 0.03), propionic acid (p = 0.01), and butyric acid (p = 0.02) were significantly higher. The pH value of the ASG was increased to 4.99 compared to that of the CON (3.74), with a significant difference observed between them. Meanwhile, the abundances of phylum Firmicutes (p-Firmicutes) and genus Lactobacillus (g-Lactobacillus) in the ASG were both significantly lower than CON. After further screening from the 32 differentially abundant metabolites (excluding 16 redundant metabolites and 2 that remained unannotated due to database limitations), a total of 14 core differential metabolites associated with off-flavor in silage were identified. Among these, compounds contributing acetic and waxy aromas were enriched in the ASG. Spearman correlation analysis showed Corynebacterium and JC017 were positively correlated with fatty and waxy compounds (methyl linoleate, oleic acid), while Massilia and Paenibacillus_D were negatively correlated with phenylacetic acid. These findings demonstrate that off-flavor in corn silage arises from Lactobacillus decline, aerobic spoilage bacteria overgrowth, and subsequent accumulation of phenylacetic acid coupled with gallic acid depletion. This microbiome-metabolomics interaction provides a mechanistic framework for developing targeted strategies to control silage off-flavors.},
}

@article {pmid42199549,
year = {2026},
author = {Wang, Y and Zhao, H and Sun, Y and Mi, M and Hu, X and Ye, D and Wang, X and Dou, L and Wang, J and Yang, Z},
title = {Prevalence of Lawsonia intracellularis and characteristics of gut microbiomes of the infected pigs in Shaanxi province, China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1834533},
pmid = {42199549},
issn = {1664-302X},
abstract = {OBJECTIVES: Lawsonia intracellularis is an obligately intracellular enteric bacterium that infects intestinal epithelial cells and causes porcine proliferative enteropathy (PPE). This study aimed to investigate the epidemiological prevalence of L. intracellularis in large-scale pig farms in Shaanxi Province, China, and analyze the differences in fecal microbial communities of growing pigs with natural L. intracellularis infection.

METHODS: A total of 672 fecal samples and 300 serum samples were collected from five intensive pig farms in Shaanxi during 2022-2023. Quantitative PCR (qPCR) was used to detect L. intracellularis in feces and quantify its fecal load, while enzyme-linked immunosorbent assay (ELISA) was employed to detect the seroprevalence of anti-L. intracellularis antibodies in serum. 16S rRNA gene sequencing was performed on fecal samples from L. intracellularis-positive and -negative growing pigs.

RESULTS: The results showed an overall fecal positive rate of 15.3% (95% CI: 12.7-18.3%) and a serum seroprevalence of 14.7% (95% CI: 11.0-19.3%) for L. intracellularis in the surveyed farms, with growing pigs exhibiting the significantly highest positive rate and fecal pathogen load (p < 0.05). Tongchuan exhibited a significantly lower fecal positive rate than the other surveyed regions (p < 0.05). Fecal microbial diversity analysis revealed that L. intracellularis-positive fecal samples exhibited significantly higher bacterial species richness. LEfSe analysis indicated a significant enrichment of Lactobacillus in L. intracellularis-positive feces relative to negative samples. Network analysis demonstrated a positive correlation between Desulfovibrionaceae and Lachnospiraceae, and random forest analysis identified Erysipelotrichaceae_UCG.003 as the critical microbial biomarker for L. intracellularis infection.

CONCLUSION: This study elucidates the epidemiological characteristics of L. intracellularis in Shaanxi and its interaction with the porcine gut microbiome, thereby providing a theoretical basis for the precise prevention and control of PPE, as well as for further investigations into the interactions between the gut microbiota and L. intracellularis.},
}

@article {pmid42199803,
year = {2026},
author = {Liu, Y and Yang, M and Liao, Y and Hu, Z},
title = {Global research trends, reporting and handling of missing data in observational studies of type 2 diabetes mellitus with mild cognitive impairment from 2020 to 2025: a systematic review.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1649881},
pmid = {42199803},
issn = {1664-2392},
mesh = {*Diabetes Mellitus, Type 2/complications/epidemiology ; *Cognitive Dysfunction/epidemiology/complications ; Humans ; *Observational Studies as Topic ; Bibliometrics ; },
abstract = {BACKGROUND: Missing data is common in observational studies, and even more so in type 2 diabetes mellitus with mild cognitive impairment(T2DM-MCI), which limits the completion of assessments. We evaluated the extent, current reporting, and handling of missing data, as well as the prevailing research trends in observational studies related to T2DM-MCI.

METHODS: A systematic search of PubMed, Embase, and Cochrane Library was conducted from January 2020 to April 2025 to identify observational studies related to T2DM-MCI. Bibliometrics was performed using VOSviewer and CiteSpace to evaluate publishing trends, authors, journals, and keywords. The reporting and handling of missing data were assessed according to the guidelines recommended by STROBE and Sterne et al., with a focus on the recording, causes, mechanisms, processing methods, and sensitivity analysis of missing data. Data analysis was conducted using SPSS 26, and visualization was performed using Origin Pro 2024.

RESULTS: Among the 4,471 screened records, 88 studies (78 in English and 10 in Chinese) were included in this analysis. Among the 78 English articles, the annual publication volume exhibited fluctuations, peaking in 2024. Chinese institutions and authors led in research output. Diabetes, Metabolic Syndrome, and Obesity had the highest publication volume (7, 8.97%). Keyword identified five clusters: 1) resting-state functional magnetic resonance imaging, 2) metabolic disorders, 3) clinical assessment tools, 4) molecular mechanisms, and 5) emerging fields such as the gut microbiome.

MISSING DATA: Only 22.7% (n = 20) of the studies quantified the missing data, with an average of 9.1%. Among studies with missing data (n = 23), 52.2% (n = 12) provided reasons for missing data, primarily citing poor quality of data collection (41.7%) and loss to follow-up (41.7%). Complete case analysis was the predominant method for addressing missing data (93.3%). No study articulated the hypothesized mechanisms underlying the missing data, and only 4.4% (n = 1) performed a sensitivity analysis.

CONCLUSION: In the domain of T2DM-MCI, research outcomes post-COVID-19 pandemic indicate a rebound, with China maintaining a leading position in scientific research output. However, the reporting of missing data remains ambiguous, and the methods employed to handle such data are insufficient, which may potentially introduce bias.

https://doi.org/10.17605/OSF.IO/EZDXM.},
}

*Diabetes Mellitus, Type 2/complications/epidemiology
*Cognitive Dysfunction/epidemiology/complications
Humans
*Observational Studies as Topic
Bibliometrics

@article {pmid42199861,
year = {2026},
author = {Xu, T and Roy, SP and Hadia, R and Annu, and Bhowmik, S and Panchal, A},
title = {The gut-brain axis in pharmacology: microbiome-driven modulation of CNS drugs and neuropsychiatric outcomes.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1826681},
pmid = {42199861},
issn = {1663-9812},
abstract = {BACKGROUND: The gut-brain axis has emerged as a critical regulator of Central Nervous System (CNS) pharmacology, significantly influencing drug response and neuropsychiatric outcomes through complex interactions between the gut microbiota and host systems.

OBJECTIVE: This review aims to examine the role of gut microbiota in modulating the pharmacokinetics and pharmacodynamics of CNS drugs, and to explore their implications in neuropsychiatric disorders.

KEY FINDINGS: Accumulating evidence indicates that microbial enzymes and metabolites can alter drug absorption, metabolism, and bioavailability, particularly for antidepressants such as Selective Serotonin Reuptake Inhibitors (SSRIs) and Tricyclic Antidepressants (TCAs). In turn, psychotropic medications can modify gut microbial composition, leading to dysbiosis and variability in therapeutic outcomes. Microbiota-derived metabolites, immune signaling pathways, and host genetic factors (e.g., cytochrome P450 polymorphisms) collectively contribute to interindividual differences in drug efficacy and safety.

CONCLUSION: Integration of microbiome profiling into pharmacological research holds significant potential for advancing precision medicine in neuropsychiatry. However, challenges such as methodological heterogeneity, limited longitudinal clinical data, and lack of standardized biomarkers must be addressed to enable clinical translation.},
}

@article {pmid42200243,
year = {2026},
author = {Li, J and Lian, Z and Wang, Y and Meng, H and Fu, F and Qu, Y},
title = {[Association of acute kidney injury with gut microbiota: a study integrating Mendelian randomization and real-world clinical cohort].},
journal = {Zhonghua wei zhong bing ji jiu yi xue},
volume = {38},
number = {4},
pages = {337-345},
doi = {10.3760/cma.j.cn121430-20250903-00472},
pmid = {42200243},
issn = {2095-4352},
mesh = {Humans ; *Acute Kidney Injury/microbiology ; Mendelian Randomization Analysis ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Cohort Studies ; Female ; Male ; },
abstract = {OBJECTIVE: To investigate the association between acute kidney injury (AKI) and the gut microbiota by integrating 16S sequencing analysis with mendelian randomization (MR).

METHODS: 1) MR analysis: The genome-wide association study (GWAS) dataset for AKI from the FinnGen consortium and the GWAS dataset for gut microbiota composition from the Dutch Microbiome Project were selected to screen single nucleotide polymorphism (SNP) associated with AKI as instrumental variable (IV) for genetic variation, using AKI as the exposure factor. Potential causal associations between AKI and gut microbiota were analyzed using a two-sample, one-way MR analysis with the primary analysis method of inverse variance weighted (IVW). Heterogeneity analysis was performed using the Cochran Q test. Potential pleiotropy was assessed using the MR-Egger intercept test. Sensitivity analysis was performed using the leave-one-out test. 2) Clinical cohort study: Consecutive patients admitted to the intensive care unit (ICU) of Qingdao Municipal Hospital between December 2024 and March 2025 were prospectively enrolled. Patients were classified into the AKI group or the non-AKI group based on the occurrence of AKI during their ICU stay, according to the diagnostic criteria from Kidney Disease: Improving Global Outcomes (KDIGO) clinical practice guidelines (2012). Baseline clinical data were collected within 48 hours of ICU admission, including gender, age, height, weight, body mass index (BMI), major comorbidities, vital signs, serum creatinine (SCr), blood routine, C-reactive protein (CRP), interleukin-6 (IL-6), etc. Anal swabs were collected from patients within 48 hours of ICU admission for 16S rDNA high-throughput sequencing. Significant difference analysis and linear discriminant analysis effect size (LEfSe) were performed to characterize the gut microbiota profile in AKI patients and to further validate the findings from the MR analysis.

RESULTS: 1) MR analysis results: Using the GWAS summary statistics for gut microbiota and AKI, the MR analysis revealed that the genetic liability to AKI was associated with decreased abundance in six gut microbial taxa and increased abundance in one taxon. IVW analysis showed that at the genus level, genetic susceptibility to AKI was associated with lower abundance of Collinsella (β=-0.144, P=0.029), Lachnospiraceaenoname (β=-0.131, P=0.040), Roseburia (β=-0.126, P=0.047), and Parasutterella (β=-0.198, P=0.023). At the species level, AKI genetic susceptibility was linked to reduced abundance of Parasutterellaexcrementihominis (β=-0.197, P=0.024) and Roseburia unclassified (β=-0.280, P=0.012), while being associated with increased abundance of Bacteroidesintestinalis (β=0.358, P=0.013). Cochran Q test showed no heterogeneity, MR-Egger intercept test revealed no pleiotropy, and leave-one-out analysis verified the robustness of the results. 2) Clinical cohort study results: A total of 129 patients were initially enrolled. After excluding 25 patients with incomplete clinical data and 10 whose samples failed to generate sufficient 16S rDNA gene amplification for sequencing, 94 patients were included in the final analysis comprising 72 cases in the AKI group and 22 cases in the non-AKI group. Apart from higher SCr levels in the AKI group than those in the non-AKI group, no statistically significant differences were observed in other baseline clinical characteristics between the two groups. 16S rDNA high-throughput sequencing yielded 6 868 647 high-quality reads, which were clustered into 13 025 amplicon sequence variant (ASV). Significant difference analysis at the species level showed that, compared with the non-AKI group, patients in the AKI group had a relative enrichment of Streptococcus anginosus and Novosphingobium sp. B0.09-8. Conversely, the relative abundances of uncultured Prevotellasp., Alistipesshahii, uncultured Coprococcussp., Collinsellatanakaei, Streptococcus equinus, Alistipesindistinctus, Klebsiellasp. GRB36, and uncultured Oscillospirasp. were significantly lower in the AKI group. LEfSe analysis identified Veillonella unclassified, Ligilactobacillus unclassified, Collinsellatanakaei, Atopobium unclassified, and Streptococcus anginosus as potential biomarkers for the AKI group, whereas Alistipesshahii, uncultured Prevotella sp., and Agathobacter unclassified were more characteristic of the patients in the non-AKI group.

CONCLUSIONS: The MR analysis suggests that the occurrence of AKI exerts an influence on the gut microbiota profile, characterized by a reduction in the abundance of the genus Collinsella. Findings from the real-world study further indicate significant differences in gut microbiota composition between patients with and without AKI. Overall, the gut microbiota of AKI patients is characterized by an enrichment of pro-inflammatory bacteria and a depletion of commensal symbionts. The genus Collinsellamay may serve as a potential biomarker for AKI.},
}

Humans
*Acute Kidney Injury/microbiology
Mendelian Randomization Analysis
Polymorphism, Single Nucleotide
Genome-Wide Association Study
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S
Cohort Studies
Female
Male

@article {pmid42200271,
year = {2026},
author = {Vázquez-Reyes, S and Esposito, E and Rosell, A and Lizasoain, I and Lo, EH and Moro, MA and Hayakawa, K},
title = {Immune System of the Ischemic Brain: Old Paradigms Revisited.},
journal = {Stroke},
volume = {},
number = {},
pages = {},
doi = {10.1161/STROKEAHA.125.051471},
pmid = {42200271},
issn = {1524-4628},
support = {R01 NS137979/NS/NINDS NIH HHS/United States ; },
abstract = {The central nervous system was once viewed as immunologically privileged, but it is now recognized that brain-immune interactions are dynamic and critical. After central nervous system injury or disease, microglia and perivascular macrophages survey the damaged tissue, while diverse immune cells infiltrate through various barriers, driving neurovascular dysfunction and neuroinflammation. Depending on timing and phenotype, systemic immune responses can also promote brain repair and recovery. Recent studies show that brain-peripheral organ communication profoundly affects both injury progression and healing. These insights redefine the neurovascular-immune interface and the concept of the brain's immune system. This review examines immune cell infiltration and highlights emerging brain-peripheral circuits that regulate neuroinflammation and recovery after stroke.},
}

@article {pmid42200417,
year = {2026},
author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X},
title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70046},
pmid = {42200417},
issn = {1365-2583},
support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; },
abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.},
}

@article {pmid42200499,
year = {2026},
author = {Plocek, MR and Dunham, NT and Amato, KR},
title = {Comparative Analysis of Fecal Microbiome Composition in Zoo-Housed Colobines: The Influence of Dietary Macronutrients, Browse Provisioning, and Phylogeny.},
journal = {American journal of primatology},
volume = {88},
number = {5},
pages = {e70169},
doi = {10.1002/ajp.70169},
pmid = {42200499},
issn = {1098-2345},
support = {(CS2020-028)//Cleveland Metroparks/ ; },
mesh = {Animals ; *Feces/microbiology ; *Animals, Zoo/microbiology ; *Diet/veterinary ; Phylogeny ; Nutrients/analysis ; *Colobinae/microbiology/physiology ; RNA, Ribosomal, 16S/analysis ; *Gastrointestinal Microbiome ; Animal Feed/analysis ; Male ; Female ; Feeding Behavior ; },
abstract = {This study investigated the interplay between dietary macronutrient composition, browse provisioning frequency, and host phylogeny in shaping the gut microbiome of zoo-housed colobine monkeys. We focused on four species (Colobus guereza, Colobus angolensis, Trachypithecus cristatus, and Trachypithecus francoisi) housed across 20 AZA-accredited institutions and integrated detailed dietary records with fecal microbiome profiling. Diets were categorized using Partition Around Medoids clustering based on macronutrient content, while browse offerings were classified by provisioning frequency (low, moderate, and high). Microbial diversity and community composition were evaluated using high-throughput 16S rRNA sequencing. The results revealed that browse provisioning frequency was the strongest predictor of microbiome alpha diversity, with moderate and high browse categories supporting significantly greater microbial richness and evolutionary breadth than low browse frequency. While diet cluster and phylogeny did not significantly affect alpha diversity metrics, all three factors significantly influenced the overall microbiome composition, as indicated by the unweighted and weighted UniFrac analyses. Notably, diet clusters with the highest relative crude fat (16.33%) or protein (23.27%) content, as well as sugar-rich diets promoted distinctive shifts in microbial community structure and function, fostering bacteria linked to dietary macronutrient processing, and in low-fiber contexts, reduce the abundance of key fiber-degrading taxa. These findings emphasize the necessity of frequent browse provision and an appropriate fiber balance to maintain gut microbial diversity and ecosystem stability in zoo-housed colobines. These results provide evidence-based recommendations for husbandry practices to promote nutritional and microbiome health in managed primate populations.},
}

Animals
*Feces/microbiology
*Animals, Zoo/microbiology
*Diet/veterinary
Phylogeny
Nutrients/analysis
*Colobinae/microbiology/physiology
RNA, Ribosomal, 16S/analysis
*Gastrointestinal Microbiome
Animal Feed/analysis
Male
Female
Feeding Behavior

@article {pmid42200521,
year = {2026},
author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI},
title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001739},
pmid = {42200521},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; },
abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.},
}

*Metagenomics/methods
Humans
*Metagenome
*Bacteria/classification/genetics
Genome, Bacterial
Sequence Analysis, DNA/methods
Computational Biology/methods
Microbiota/genetics

@article {pmid42200614,
year = {2026},
author = {Hourigan, D and Draper, L and Leahy, SC and Attwood, GT and Kelly, WJ and Stanton, C and Hill, C and Ross, RP},
title = {The Hungate1000 prokaryotic culture collection encodes a wide variety of bacteriocins.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019526},
doi = {10.1128/msystems.00195-26},
pmid = {42200614},
issn = {2379-5077},
abstract = {Bacteriocins are antimicrobial peptides/proteins that are widely distributed among bacteria and are gathering traction as natural alternatives to antibiotics, modulators of the microbiota, and interbacterial signaling peptides. The Hungate1000 is a culture collection of isolated prokaryotic microorganisms and their genomes from ruminant animals that aims to expand the knowledge base of rumen ecology. In this study, 410 rumen-isolated prokaryotes within the collection were mined to expand upon the bacteriocin-producing potential of the rumen. A total of 408 novel bacteriocin gene clusters were identified across 308 genomes. Bacteriocins in novel species within the Hungate1000 were identified, such as Pseudobutyrivibrio sp. UC1225, which has two novel natural nisin variants, Clostridium sp. DSM 8431 with a novel peptide 81% identity to amylocyclicin and Lachnobacterium C7 encoding a novel circular bacteriocin with 55% identity to the circular bacteriocin NKR-5-3B. A novel class II lanthipeptide gene cluster was also identified containing eight distinct core peptides encoded within the genome of a novel Butyrivibrio species. Bacteriocin biosynthetic potential was noted within species unknown to produce bacteriocins, such as Lachnobacterium bovis DSM 14045, Lachnospira multipara D15d, Eubacterium callanderi NLAE-zl-G225, Eisenbergiella tayi NLAE-zl-G231, and Muricomes contorta NLAE-zl-C134. The frequency of putative bacteriocin production within ruminal strains was 30%, doubling the frequency previously suggested in the mammalian gastrointestinal tract. This number increases to ~70% when encompassing groups of peptides with limited knowledge of antibacterial activity, such as ranthipeptides and auto-inducing peptides. We also show that the bacteriocin core peptides mined from the Hungate1000 culture collection are found in the microbiomes of other ruminant animals and the human gut microbiome. These findings highlight the Hungate1000 as a rich biosynthetic reservoir of cultured strains that can be experimentally explored for functional antimicrobial activity. The presence of diverse bacteriocin-producing lineages in rumen-associated microbes provides a foundation for future strategies aimed at targeted microbiome modulation, including approaches to improve rumen function and potentially mitigate enteric methane emissions using bacterial strains or their natural products.IMPORTANCEBacteriocins are gathering traction as a possible alternative to antibiotics in some instances. Therefore, it is crucial to discover novel bacteriocins to expand the bacteriocin knowledge base if these peptides are to be translated to the clinic for use in humans or developed as veterinary interventions to modulate rumen function. Here, we use in silico methods to identify the biosynthetic potential of the Hungate1000 culture collection of rumen bacterial strains. We discover 408 novel bacteriocin gene clusters across 308 genomes and identify that the frequency of bacteriocin gene clusters is over 30%, which is double the incidence rate from previous studies of the mammalian gastrointestinal tract. This number increases to approximately 70% when including bacteriocin classes such as ranthipeptides and cyclic-lactone-autoinducer peptides. Together, these findings position the rumen microbiome as a rich and underexplored reservoir of antimicrobial diversity, with potential for the development of targeted microbiome-modulating therapeutics, livestock interventions aimed at improving rumen function, and strategies aligned with One Health goals, including antimicrobial stewardship and methane mitigation.},
}

@article {pmid42200648,
year = {2026},
author = {Gomez, A and Tisa, LS},
title = {A longitudinal roadside study of the New Hampshire alder root nodule microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0044626},
doi = {10.1128/aem.00446-26},
pmid = {42200648},
issn = {1098-5336},
abstract = {UNLABELLED: Actinorhizal plants are pioneer plants that colonize harsh environments and have been used for land reclamation. Their ability to thrive under these harsh conditions is due to their symbiotic association with the nitrogen-fixing bacterium Frankia and forming a root nodule structure. Although the plant root nodule primarily contains the symbiont Frankia, other members of the nodule community have been identified. This study represents an investigation of the effects of different environments on the nodule microbiome of Alnus rugosa, a shrub actinorhizal tree found at different locations within New Hampshire over a 3-year period. We utilized 16S rRNA and ITS amplicon sequencing to map the seasonal bacterial and fungal communities in the A. rugosa root nodule microbiome compared to rhizosphere and bulk soil communities. The relative abundance of Frankiaceae in root nodules fluctuated seasonally and by site. Sites with lower relative abundance of Frankiaceae in nodules had higher relative abundances of fungal nodule occupants. The roadside bacterial communities were distinct from those at the rural site, with Chitinophagaceae and Nitrosomonadaceae being characteristic members of the roadside rhizospheres and bulk soils, respectively. Soil zinc significantly affected all microbial communities. Our results indicate that the A. rugosa root nodule and soil microbiomes are responsive to different environmental variables like roadways and other microorganisms, and these responses need to be further elucidated for the optimization of future in situ actinorhizal projects.

IMPORTANCE: Actinorhizal plants like alders are important ecologically and economically as pioneering plants. The symbiotic association with Frankia greatly accelerates the growth of the host plant and indirectly does the same for neighboring plants. Actinorhizal trees provide an excellent mechanism to restore disrupted environmental sites and have been used to reclaim land that has been used for strip-mines, gravel pits, and soil stabilization of other landscapes disturbed by the effects of erosion and water runoff. Actinorhizal plants are found on coastal lands around the estuaries, and some are proven to be salt tolerant. Elucidating the dynamics of microbial community structure of the alder root nodules will help our understanding of the ability of these pioneering plants to reclaim degraded lands and to survive in diverse harsh environments. The role that other members of actinorhizal plant root nodule plays may be important to that survival ability. This field study reports on the influence of soil variables, habitats, and seasons on the dynamics of the actinorhizal microbiome.},
}

@article {pmid42200649,
year = {2026},
author = {Peng, Y and Wu, J and Zhang, X and Wang, X and Wang, B and Zhang, C and Wang, C and Zhang, H and Liu, F and Lian, K and Li, Y and Liu, Q and Wang, H},
title = {A horizontal connectivity mode in coastal oceans: transport overrides stratification to govern microbiome network stability.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0044826},
doi = {10.1128/aem.00448-26},
pmid = {42200649},
issn = {1098-5336},
abstract = {UNLABELLED: Coastal ecosystems are critical biogeochemical reactors and biodiversity reservoirs, yet the mechanisms governing the community connectivity and stability of their foundational microbiomes remain poorly understood, particularly in anthropogenically influenced coastal oceans. Here, we systematically analyzed prokaryotic and microeukaryotic communities along both vertical and horizontal gradients in the Bohai-Yellow Sea, a model anthropogenically influenced and multi-stressed coastal ocean. We found that horizontal gradients, primarily driven by distance to coastline and latitudinal transitions, surpassed vertical gradients as the principal force governing microbial community assembly, connectivity, and stability. These horizontal factors overwhelmingly shaped microbial diversity, niche breadth, and biogeographic patterns, with prokaryotes displaying broader environmental adaptability and stronger cross-regional dispersal potential than microeukaryotes. Consequently, prokaryotes maintained higher spatial connectivity than microeukaryotes across both dimensions. This prokaryotic connectivity advantage was most pronounced within intermediate water masses. In contrast, vertical connectivity weakened with intensified water column stratification from the well-mixed Bohai Sea to the hydrographically complex South Yellow Sea. Horizontal gradients directly steered microbial co-occurrence network properties, driving a depth-dependent decline in network complexity and stability. This regional disparity was further underscored by distinct stability trade-offs: the semi-enclosed Bohai Sea fostered robust, modular networks, whereas the Yellow Sea systems formed highly connected but less modular, and thus more vulnerable, network architectures. Our findings reveal a dominant horizontal connectivity mode in coastal microbiomes, establishing a mechanistic link between large-scale environmental gradients and microbial network stability. This is a crucial advance for predicting ecological responses to anthropogenic and climate perturbations in vulnerable coastal zones.

IMPORTANCE: Coastal microbial communities drive global biogeochemical cycles, yet the principles governing their large-scale connectivity and microbial network stability remain elusive, particularly in anthropogenic disturbances regions. Focusing on the Bohai-Yellow Sea system, we establish that horizontal transport processes, modulated by land-sea exchange and latitudinal gradients, override vertical stratification as the dominant force structuring microbial assembly and interaction networks. We demonstrate that prokaryotes possess a stronger horizontal dispersal advantage than microeukaryotes, sustaining higher connectivity through intermediate water layers. This horizontal connectivity governs microbial network stability. Networks shift from robust, prokaryote-driven modular architectures in shallow coastal waters to fragile, microeukaryote-dominated patterns in deeper, stratified regions. These findings define a "horizontal connectivity mode" as a central organizing principle for coastal microbiomes, moving beyond descriptive biogeography to provide a mechanistic framework for predicting community resilience to anthropogenic and climate forcing.},
}

@article {pmid42200658,
year = {2026},
author = {Blanchard, JL},
title = {Learning R with generative AI in a metagenomic data science course.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0034325},
doi = {10.1128/jmbe.00343-25},
pmid = {42200658},
issn = {1935-7877},
abstract = {Generative artificial intelligence (AI) tools are increasingly used by students in introductory coding courses; however, evidence-based guidance for integrating these tools into biology education remains limited. We examined student experiences with generative AI in a beginner R programming course focused on metagenomic data analysis. An anonymous survey (n = 43) captured quantitative ratings and qualitative reflections on how AI influenced learning, productivity, and problem-solving practices. Most respondents entered the course with little to no prior coding experience (79%) and reported frequent AI use throughout the semester, indicating that AI quickly became embedded in students' workflows. Students rated AI as highly helpful for suggesting R code, explaining syntax and logic, and brainstorming analyses, with over 70% endorsing each use case. However, AI errors were common: over 90% of students encountered incorrect output at least sometimes, including domain-specific misinterpretations and overcomplicated or syntactically incorrect code. Notably, students identified a need for clearer instructional support in core AI-mediated practices. The most frequent recommendation for course redesign was to introduce foundational R concepts prior to AI use, highlighting a threshold-competency principle for effective AI integration. Together, these findings suggest that generative AI can support novice coders but does not substitute for foundational instruction. Effective AI integration requires deliberate pedagogical scaffolding and reflection rather than code generation alone. These principles are likely to remain critical as AI tools become more capable and more widely adopted in undergraduate biology education.},
}

@article {pmid42200660,
year = {2026},
author = {Guo, C and Yang, A and Zhang, X and Bai, W and Zhang, W-H},
title = {Leaf- and root-associated bacterial communities differ in their resistance and resilience to N disturbance in a temperate steppe.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0033226},
doi = {10.1128/aem.00332-26},
pmid = {42200660},
issn = {1098-5336},
abstract = {Enhanced deposition of nitrogen (N) has great impacts on grassland ecosystems. A decline in N deposition has occurred in many regions across the globe. Changes in N deposition alter the structure and functions of grassland ecosystems and bacterial community of soil and rhizosphere. However, the responses of plant microbiomes to N deposition and cessation of N input in terms of resistance and resilience have not been systematically evaluated. We examined the effects of N addition and cessation of N addition on leaf- and root-associated bacterial communities through a consecutive N addition and cessation of N addition experiment in a temperate grassland. We found that leaf-associated bacterial community exhibited lower resistance to N enrichment than root-associated bacterial community, which was mainly steered by leaf soluble sugars and leaf morphology via regulating functional taxa. In contrast, the root-associated bacterial community showed stronger resilience to cessation of N addition than leaf-associated bacterial community, which may be explained by the high N accumulation in roots and root morphology via regulating functional taxa. The greater resistance and resilience in the root-associated bacterial community may be attributed to the presence of host-related factors. Additionally, N enrichment-induced suppression of beneficial symbiotic microbes associated with the N cycle in the leaf-associated bacterial community was not readily recovered after cessation of N input. Conversely, microbes involved in carbon cycle and ecological restoration in the root-associated bacterial community showed a quick recovery after cessation of N enrichment. Our results offer valuable insights into the mechanisms by which changes in N input influence the plant microbial community.IMPORTANCEAs an integral component of ecosystems, the plant microbiome plays an important role in the response of grassland ecosystems to enhanced N deposition. Changes in N deposition influence bacterial communities of soil and rhizosphere of grassland ecosystems. However, whether and how the N deposition and cessation of N input impact microbiomes of plant species of temperate grasslands remain unexplored. Based on a long-term N-addition experiment in a temperate steppe, we discover that leaf- and root-associated bacterial communities respond differently to N addition and subsequent cessation of N addition. The leaf-associated bacterial community exhibits lower resistance to N enrichment than the root-associated bacterial community due to the unique environment of the phyllosphere, whereas the root-associated bacterial community shows stronger resilience to cessation of N addition than the leaf-associated bacterial community due mainly to the higher root N accumulation and morphology. These findings offer valuable insights into the impact and mechanism of N interference on the plant microbial community.},
}

@article {pmid41826827,
year = {2026},
author = {Duduk, B and Galic, I and Stanojević, N and Stankovic, N and Rekanović, E},
title = {Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41826827},
issn = {1471-2180},
support = {451-03-136/2025-03/200214//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-136/2025-03/200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; },
abstract = {BACKGROUND: Phloem-sap-feeding planthopper Reptalus artemisiae is an emerging vector of rubbery taproot disease (RTD) and syndrome basses richesses (SBR) in sugar beet, diseases associated with 'Candidatus Phytoplasma solani' and 'Candidatus Arsenophonus phytopathogenicus', respectively. Despite studies on related cixiids, the microbiome of R. artemisiae remains uncharacterized. Using a PCR-free metagenomic long-read shotgun sequencing approach, this study investigates the bacterial diversity associated with R. artemisiae, and provides genomic insight into two plant pathogens 'Ca. P. solani' and 'Ca. A. phytopathogenicus'.

RESULTS: Taxonomic assignment revealed six prokaryotic taxa in R. artemisiae: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts – three primary endosymbionts ('Candidatus Vidania', 'Candidatus Purcelliella', and 'Candidatus Karelsulcia') and a secondary endosymbiont (Wolbachia). Community profiles showed a consistent presence of all four endosymbionts across five evaluated R. artemisiae individuals. Phylogenetic analyses of 16S rRNA gene sequences of primary endosymbionts confirmed strong congruence with the cytochrome oxidase subunit I phylogeny of the insect host, indicative of long coevolution and vertical transmission. In contrast, plant pathogen presence in R. artemisiae varied, with 'Ca. P. solani' and 'Ca. A. phytopathogenicus' each detected in three individuals. Genome assembly yielded a complete 774 kb circular chromosome for 'Ca. P. solani' with streamlined metabolism featuring limited biosynthetic pathways, but a full arsenal of genes related to host–pathogen interactions and pathogenicity typical for this biotrophs. The draft genome of 'Ca. A. phytopathogenicus' comprising 18 scaffolds totalling 3.11 Mb and two plasmids shows a self-sufficient metabolism with several missing metabolic modules and presence of genomic islands, virulence factors, and a dynamic mobilome indicating a bacterium in transition that is reorganizing its genetic material, possibly in response to host interactions.

CONCLUSION: These findings represent the first in-depth characterization of R. artemisiae microbiome, highlighting a stable endosymbiont consortium and variable pathogen presence that emphasize ecological complexity in vector-pathogen-endosymbiont interactions. The assembled genomes enhance the understanding of microbial ecology, pathogen adaptation and transmission, offering resources for comparative genomics and potential applications in disease management strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04915-x.},
}

@article {pmid41975251,
year = {2026},
author = {Zhang, Y and Lai, W and Wang, M and Lai, S and Liu, Q and Luo, Q and Chen, Z and Zhao, D and Wang, Z and Yang, F},
title = {Gut microbial metabolic disorder in depression: insights from computational modeling and mediation analysis.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41975251},
issn = {1471-2180},
support = {62102065,62272321//National Natural Science Foundation of China/ ; 2022J05055//Joint Funds for the Innovation of Science and Technology, Fujian province/ ; XRCZX2022003//Fujian Medical University Research Foundation of Talented Scholars/ ; 24ywa61//Science and Technology Plan Project of Taizhou/ ; },
abstract = {UNLABELLED: Depression is increasingly recognized as a disorder not only of the brain but also of systemic metabolic dysfunction, particularly involving the gut microbiota. Integrating multi-cohort gut microbiome data with constraint-based metabolic modeling, this study investigates how microbial metabolic fluxes mediate depressive symptoms. Significant alterations in microbial pathways, notably those related to amino acid metabolism and neurotransmitter precursors, were identified. Causal mediation analysis showed that gut microbial composition influenced depressive symptoms, significantly mediated by specific metabolites including butyrate, Cu[2+], and tryptophan-derived compounds. This study, employing systems biology and mediation analysis, suggests that microbial metabolic activity mediates the gut-brain axis’s role in depression development and severity. These results enhance our understanding of microbiota-related mechanisms in mental health and highlight potential metabolic targets for depression treatment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04991-z.},
}

@article {pmid42183319,
year = {2026},
author = {Barzi, SM and Naderi, P and Haririzadeh Jouriani, F and Torkamaneh, M and Siadat, SD and Shamkani, F and Javadian, S and Ebrahimi-Rad, M and Saghiri, R and Nojoumi, SA},
title = {Impact pattern of heavy metals on gut microbiota in the polluted city of Tehran.},
journal = {Iranian journal of microbiology},
volume = {18},
number = {2},
pages = {204-216},
pmid = {42183319},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: This article focuses on the effects of six heavy metals on gut microbiota, which plays a key role in human health. Gut microbiota plays a key role in metabolism, immunity, and maintaining homeostasis. Heavy metals can affect microbiota composition and function, with health consequences. Consuming large amounts of heavy metals may have harmful impacts, including alteration in microbial composition and bacterial population changes.

MATERIALS AND METHODS: Six heavy metals-cadmium, chromium (toxic metals), copper, zinc, iron, and selenium (beneficial trace elements)-were detected in peripheral blood, serum, or urine, while feces were used for 16S rRNA sequencing. Serum samples from 100 volunteers from Tehran (polluted area) and Firoozkooh (clean city) were collected. Subjects were analyzed for the presence of Escherichia coli, Bacteroides fragilis, Bifidobacterium longum, Lactobacillus acidophilus, Clostridium clostridioforme, Faecalibacterium prausnitzii and Akkermansia muciniphila to evaluate correlations between metals and microbial composition using biochemical, microbial, and molecular methods.

RESULTS: Escherichia coli and Bifidobacterium longum levels in polluted areas were not significantly different from those in unpolluted areas. Bacteroides fragilis in polluted areas was significantly higher compared to non-polluted locations. Clostridium, Akkermansia, Faecalibacterium, and Lactobacillus acidophilus were significantly lower in polluted areas, amounting to less than half the levels in clean areas. Heavy metal concentrations showed no gender differences in either location.

CONCLUSION: Some heavy metals change intestinal microbiota composition and metabolic profiles, potentially resulting in metabolic diseases and environmental risks.},
}

@article {pmid42183324,
year = {2026},
author = {Karimi Behnagh, A and Bourbour, M and Moghaddam Shiri, S and Asadi, O and Honardoost, M},
title = {Microbiome and thyroid diseases: future precision studies of the gut-thyroid axis to facilitate the adjuvant treatment.},
journal = {Iranian journal of microbiology},
volume = {18},
number = {2},
pages = {172-185},
pmid = {42183324},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: The gut microbiome is a key determinant of overall health, impacting numerous bodily functions, such as those of the endocrine glands. The effect of the microbiota on thyroid function has become a matter of interest, more so since the revelation of the possible link between intestinal disease and autoimmune thyroid disorders (AITDs). This review aims to provide an in-depth insight into the possible link between gut microbiota and thyroid diseases and metabolism of thyroid hormones.

MATERIALS AND METHODS: A set of online sources including, PubMed, Scopus, Google Scholar and CENTRAL were comprehensively searched to find the studies relevant to the topic of the review. Only reports in English were included in this review.

RESULTS: It has been proposed that damage to the intestinal barrier is a key element in the passage of antigens from the lumen into the bloodstream and their subsequent contact with the immune system. In addition to AITDs, dysbiosis has been shown to be linked with thyroid cancers, in which higher counts of certain bacteria associated with inflammation and carcinogenesis have been identified.

CONCLUSION: The majority of the available literature is focused on the differences in the microbial strain composition in individuals with thyroid disorders compared to that of healthy controls. Nonetheless, the current body of evidence has implied on possible role gut microbiome in the development of thyroid diseases.},
}

@article {pmid42183327,
year = {2026},
author = {Abd El Rahmen, RA and Alghamdi, KS},
title = {Gut microbiome signatures associated with iron-deficiency anemia in young adults.},
journal = {Iranian journal of microbiology},
volume = {18},
number = {2},
pages = {186-196},
pmid = {42183327},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Iron is vital for both the body of the host and the metabolism of microbes. Pathogenic Enterobacteria need iron to grow and cause disease, but many good gut bacteria, like lactobacilli, do not require as much iron. Changes in the amount of iron available in the gut may therefore affect the makeup of the gut microbiome. Iron-deficiency anemia (IDA) represents the most prevalent nutritional disorder globally, concerning about 1.24 billion, mostly women and young people in low- and middle-income countries. This cross-sectional study looked at the link between iron-deficiency anemia and the makeup of the gut microbiome in young adults aged 18 to 30.

MATERIALS AND METHODS: We looked at hematological and iron status parameters as well as gut microbiota profiling using 16S rRNA gene sequencing. Differences in microbial diversity, taxonomic composition, and the relative abundance of bacteria that make short-chain fatty acids between people with IDA and healthy controls were investigated.

RESULTS: The results show that iron-deficiency anemia is linked to different gut microbiome signatures. This suggests that there may be connections between iron levels and the structure of microbial communities.

CONCLUSION: These results show how important it is to study the gut microbiome to understand iron-deficiency anemia. They also show how important it is to do long-term, interventional studies to figure out how these associations work and what they mean for health.},
}

@article {pmid42183373,
year = {2026},
author = {Petty, CJ and Isaman, M and Perez, LP and Millard, S and Ortiz, M and Freeman, LR},
title = {Sex differences in hedonic feeding and characterizing the effects of antibiotic-induced microbiome disruption.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9557496/v1},
pmid = {42183373},
issn = {2693-5015},
abstract = {Background Obesity continues to be a public health issue in our country. Additionally, there continues to be a higher incidence of severe obesity for women compared to men. Among the proposed causes of obesity is increased hedonic feeding: food intake driven by pleasure and palatability rather than physiological hunger. While hedonic feeding is not the sole culprit for the obesity epidemic, it is a major contributing factor. Emerging evidence shows that the gut microbiome impacts feeding behavior and studies have shown that individuals with obesity exhibit an altered gut microbiome. Methods Here, we used a novel behavioral economics (BE) approach to evaluate hedonic feeding in male and female Sprague-Dawley rats for a high-fat palatable (HFP) reward pellet, before and after antibiotic administration. Specifically, we measured demand elasticity (α), the rate at which demand falls when the price or effort required increases, and demand at null cost (Q 0), a prediction of consumption at null effort extrapolated from the animals' consumption at low price. Results We determined a higher demand at null cost (Q 0) for the HFP reward pellet for females compared to males, as we have observed previously. Next, we administered an antibiotic cocktail in the drinking water to disrupt the gut microbiome and investigate a role of the gut microbiome in hedonic feeding. Female rats administered antibiotics continued to have a higher demand at null cost compared to male control rats, but no statistically significant differences were determined between male and female rats administered antibiotics. We characterized the fecal microbiome genus-level composition and short chain fatty acid (SCFA) levels before and after antibiotic administration. We also characterized serum SCFA and bile acid levels at the end of the study. Conclusions We did not determine a significant effect of antibiotics on hedonic feeding, despite disruption to the fecal microbiome. Additionally, we did not observe striking baseline sex differences in fecal microbiome diversity and composition. This brings to question whether the gut microbiome contributes to sex differences in hedonic feeding. More research will be necessary for network factors such as microbiome - bile acid effects on feeding that exhibit sex differences.},
}

@article {pmid42184156,
year = {2026},
author = {Sumner, JT and Hartmann, EM},
title = {Uncovering Mechanistic Determinants of Host Phenotypes Using Microbial Systems Biology.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icag052},
pmid = {42184156},
issn = {1557-7023},
abstract = {Host phenotypes are caused by a multitude of interacting factors, including but not limited to the microbiome. The advent of high throughput sequencing technology revolutionized our ability to characterize host-associated microbial communities. Early microbiome profiling studies often focused on strategies such as 16S rRNA gene amplicon sequencing to assess the relative abundance of host-associated microbiota. Waves of technological improvement and an ever-increasing knowledge base led to accessible multiomic profiling (i.e. integration of multiple different 'omics assays). Rather than just associating phenotypes with patterns of microbial taxa, we can leverage multiple omics to advance mechanistic explanations for how microbiota cause or are affected by host phenotypes. However, it is still challenging to determine which assays (or combinations of assays) to use and how best to integrate their results. We review bioinformatic strategies for integrating diverse microbiome sequencing data and experimental approaches for validating correlative findings. We also present perspectives on how systems biology connects observational and experimental microbiology. We analyze the strengths of different 'omics methods and how complementary combinations economically improves biological discovery. Augmenting relative abundance data with absolute quantitation (i.e. exact measurement of microbial biomass) can dramatically change the resulting insights. Functional profiling (i.e. measurement of microbial gene content or expression using high-throughput sequencing) ultimately enables linking microbial profiles with phenotypic trait expression. Finally, while many sequencing studies are observational and thus limited to correlative findings, it is critical to integrate experimental validation to mechanistically explain relationships between the microbiome and host phenotypes. Host-associated microbial ecosystems are complex. Confounded microbial and host factors make it challenging to determine the mechanisms underlying host-microbiome dynamics. Innovative experimental systems, including non-model organisms, synthetic consortia, and tissue-culture models, enable high-throughput manipulation of microbiomes to test hypotheses generated from correlative results and advance translational research.},
}

@article {pmid42184295,
year = {2026},
author = {Wong, SH},
title = {The human microbiome at translational crossroads: an ecological and causal perspective.},
journal = {Singapore medical journal},
volume = {67},
number = {5},
pages = {279-287},
pmid = {42184295},
issn = {2737-5935},
mesh = {Humans ; *Translational Research, Biomedical ; Probiotics/therapeutic use ; *Microbiota ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Ecology ; },
abstract = {The human microbiome has emerged as a central focus of biomedical research, driven by interest in its translational potential for chronic diseases. Although compelling associations link microbial alterations to gastrointestinal, metabolic, neuropsychiatric and systemic conditions, successful clinical translation remains limited. This perspective contends that the principal barrier is not biological relevance but the application of reductionist thinking to an inherently complex ecological system, compounded by an incomplete understanding of causality. This review examines the gradient of causal confidence across gut-organ axes, from established roles in digestive disorders to less established distal associations, as well as highlights the epistemological challenges underlying microbiome research. A critical appraisal of current strategies, including probiotics, live biotherapeutics and faecal microbiota transplantation, suggests that progress requires ecological reasoning, causal rigour and systems-level integration. Moving from association to intervention demands approaches that account for host-microbiome complexity rather than oversimplified microbial targeting.},
}

Humans
*Translational Research, Biomedical
Probiotics/therapeutic use
*Microbiota
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
Ecology

@article {pmid42184480,
year = {2026},
author = {Sihra, N and Malde, S},
title = {Pathophysiological mechanisms underlying the overactive bladder.},
journal = {Autonomic neuroscience : basic & clinical},
volume = {266},
number = {},
pages = {103440},
doi = {10.1016/j.autneu.2026.103440},
pmid = {42184480},
issn = {1872-7484},
abstract = {Overactive bladder is a heterogenous condition, with several phenotypes, and a complex pathophysiology. The principal pathophysiological mechanisms for the development of OAB are based on the urotheliogenic, myogenic, neurogenic and urethrogenic theories. The most well-described contributors to these pathophysiological mechanisms are metabolic syndrome, sex hormone deficiency, altered urinary microbiota, functional gastrointestinal disorders, affective disorders, autonomic nervous system dysfunction, and bladder outflow obstruction. This review describes the normal physiology of the lower urinary tract, and summaries the pathophysiological mechanisms behind overactive bladder.},
}

@article {pmid42184529,
year = {2026},
author = {Wang, R and Chen, H},
title = {Metagenomic insights into vertical migration of soil antibiotic and metal(loid) resistance genes under long-term organic fertilizer application and irrigation.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142479},
doi = {10.1016/j.jhazmat.2026.142479},
pmid = {42184529},
issn = {1873-3336},
abstract = {Agricultural irrigation is associated with antibiotic resistance gene (ARG) transmission and resistome succession through the integration of exogenous and indigenous soil communities. However, the long-term field-scale impacts of organic irrigation on vertical resistome migration and its ecological consequences remain underexplored. This study employed metagenomic analyses and field surveys to bridge these knowledge gaps. The results showed that ARGs and metal(loid) resistance genes (MRGs) were most abundant and diverse at 0-20 cm depth, with distinct characteristics in deeper layers depending on manure type. Cattle manure-irrigated soils exhibited a greater potential for vertical ARG diffusion than chicken manure-irrigated soils, despite lower surface-level enrichment. ARG distribution was more strongly associated with groundwater and soil background factors than with organic fertilizer inputs. Mobile genetic elements (MGEs) and heavy metal concentrations were key factors associated with resistome succession. Compared to the control, contigs associated with both ARGs and MRGs increased 5.8-fold and 3.1-fold in chicken and cattle manure-irrigated soils, respectively, suggesting a potentially important role for prophages. While control contigs were distributed in deeper layers, irrigated soils showed pronounced surface enrichment. Irrigation was linked to increased network density and complexity, with chicken manure-irrigated soils exhibiting higher levels of antibiotic-resistant bacteria (ARB). Notably, opportunistic pathogens carrying ARGs, including Ralstonia pickettii and Stenotrophomonas maltophilia, were enriched in irrigated profiles. Microbiome, MGEs, and abiotic factors were collectively associated with resistome succession, with deterministic processes contributing substantially to community assembly. This study provides new insights into the vertical distribution and inferred succession of the resistome in organically irrigated soils.},
}

@article {pmid42184614,
year = {2026},
author = {Pradhan, S and Nischay, and Shivay, YS and Sharma, S},
title = {Transplantation of rhizosphere microbiome from tomato enhances salinity stress tolerance in chilli and bell pepper.},
journal = {Plant physiology and biochemistry : PPB},
volume = {235},
number = {},
pages = {111323},
doi = {10.1016/j.plaphy.2026.111323},
pmid = {42184614},
issn = {1873-2690},
abstract = {Salinity stress adversely affects plant growth and development, leading to reduced quality and yield. Traditional approaches, including chemical amendments and bioinoculants, often show limited effectiveness under natural conditions. To overcome these limitations, this study employed a top-down rhizosphere engineering approach through rhizosphere microbiome transplantation (RMT) to mitigate salinity stress. First, a salt stress-acclimatized microbiome was generated by repeated plant growth cycles (PGCs) through RMT by ramping up salinity levels along the PGCs in a salt-susceptible tomato cultivar. Then, the generated salt stress-acclimatized rhizosphere microbiome was transplanted to mitigate salinity stress in chilli and bell pepper. RMT effectively increased various plant growth parameters in both plant model systems under salinity stress (150 mM in chilli and 170 mM in bell pepper). In rhizosphere microbiome treated plants, there was a reduction in stress markers, viz., malondialdehyde and proline levels. Further, the K[+]/Na[+] ratio increased by 1.94- to 3.47- fold in plants with RMT + salt stress. In addition, the expression level of salt stress-responsive gene, SlHKT1;1, increased in RMT plants under salt stress in both chilli and bell pepper compared to only salt treated plants. Our study showed that salt stress-acclimatized RMT from tomato is an effective and sustainable strategy to enhance salinity tolerance in other plants of the Solanaceae family, under natural conditions.},
}

@article {pmid42184623,
year = {2026},
author = {Su, Y and Mai, X and Wang, Z and Feng, C and Huang, Z and Li, Z},
title = {Multi-omics-based characterization and differentiation of fecal microbiota and metabolite profiles in high- and low-yielding laying hens.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107003},
doi = {10.1016/j.psj.2026.107003},
pmid = {42184623},
issn = {1525-3171},
abstract = {Egg-laying rate is a crucial economic trait that significantly contributes to the poultry industry. Compelling evidence has clearly demonstrated that gut microbiota is closely associated with production performance in chickens. Given that suboptimal egg production performance has become one of the bottlenecks constraining the development of the indigenous layer industry in China, the present study aimed to systematically compare the fecal microbiome and metabolome data from high-yielding (HR) and low-yielding (LR) Tianfu powder-shell laying hens, and further evaluate the potential interactions between microbes and metabolites. Our results revealed that fecal microbiota diversity and composition in HR chickens were significantly different from those in LR chickens. Moreover, Lactobacillus, Bacillus, and Bacteroides were highly enriched in HR chickens and exhibited a significantly positive correlation with laying rate. In contrast, Romboutsia and Aerococcus were more abundant in LR chickens, and Aerococcus was significantly negatively correlated with laying rate. The KEGG pathway enrichment analysis suggested that the fecal microbiota of HR chickens was mainly enriched in phosphotransferase system, glycerophospholipid metabolism, and amino sugar metabolism. Through untargeted metabolomics analysis, we observed that the abundances of L-glutamic acid, L-threonine, L-valine, curcumin, fumaric acid, and L-glutamine were obviously higher in HR chickens and were significantly positively correlated with laying rate. Furthermore, the correlation analysis revealed that the abundances of Akkermansia, Bacteroides, Christensenellaceae_R-7 group, and Parabacteroides were positively correlated with most of the identified key metabolites. These findings offer a promising strategy to manipulate the gut microbiota and metabolites, ultimately improving egg production in the poultry industry.},
}

@article {pmid42184640,
year = {2026},
author = {Fang, L and Zhang, H and Sun, C and Hu, X and Wright, D and Zhou, H},
title = {The current and future perspective of ChickenGTEx project and its applications in precision breeding.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107132},
doi = {10.1016/j.psj.2026.107132},
pmid = {42184640},
issn = {1525-3171},
abstract = {The Chicken Genotype-Tissue Expression (ChickenGTEx) project was established to systematically characterize the regulatory landscape of the chicken genome and to accelerate the translation of functional genomics into precision breeding. By integrating whole-genome sequencing with multi-tissue transcriptomic profiling, ChickenGTEx provides a comprehensive atlas of gene expression regulation across diverse tissues and physiological systems. Current findings demonstrate that complex production traits are governed by coordinated regulatory networks rather than isolated loci, with substantial contributions from tissue-specific gene expression, structural variation, and genotype-by-sex interactions. Sex-dependent regulatory effects further refine the genetic architecture of metabolic, immune, and reproductive traits, highlighting the importance of incorporating sex as a biological variable in genomic analyses. Application of integrative omics frameworks within elite layer populations has revealed multilayer regulatory mechanisms underlying extended laying performance, feed efficiency, metabolic health, and eggshell quality. By partitioning phenotypic variance into genetic, regulatory, and host-microbiome components, these approaches move beyond association-based mapping toward causal inference and biological interpretation. Importantly, validated regulatory loci identified through ChickenGTEx and related analyses provide actionable markers for genomic selection and rational targets for precision genome modification. Looking forward, continued expansion of regulatory atlases, incorporation of single-cell and longitudinal data in diverse environmental conditions, and integration of functional annotation into breeding pipelines will further enhance prediction accuracy and sustainable genetic improvement. The ChickenGTEx project thus represents a foundational platform bridging functional genomics and practical poultry breeding.},
}

@article {pmid42184718,
year = {2026},
author = {El-Sehrawy, AAMA and Soleimani Samarkhazan, H},
title = {The silent pharmacist: Harnessing the gut microbiome to improve therapy in hematologic malignancies.},
journal = {Translational oncology},
volume = {70},
number = {},
pages = {102833},
doi = {10.1016/j.tranon.2026.102833},
pmid = {42184718},
issn = {1936-5233},
abstract = {The gut microbiome, a complex ecosystem of microorganisms, is now recognized as a key determinant of drug efficacy and toxicity, giving rise to the field of pharmacomicrobiomics. This review decodes the profound influence of the gut microbiome on treatment outcomes for hematologic malignancies. We explore the tripartite mechanistic pathways through which gut microbes act: the direct enzymatic biotransformation of chemotherapeutic agents, the indirect immunomodulation of systemic and anti-tumor responses, and the preservation of mucosal barrier integrity to prevent devastating complications like graft-versus-host disease (GVHD). The manuscript details how the microbiome interacts with specific drug classes, from conventional chemotherapies like cyclophosphamide to cutting-edge immunotherapies like immune checkpoint inhibitors and CAR-T cells, shaping their clinical success. Furthermore, we discuss the translational potential of targeting this "silent pharmacist" through fecal microbiota transplantation, next-generation probiotics, and dietary interventions. Finally, we highlight the main translational opportunities, current limitations, and future clinical priorities for integrating microbiome science into hematology, paving the way for more personalized and improved cancer care.},
}

@article {pmid42184757,
year = {2026},
author = {Azadi, S and Fadaei-Kenarsary, M and Sahebi, K and Baneshi, M and Tajbakhsh, A and Niknahad, H and Negahdaripour, M},
title = {Metformin as a promising therapeutic option for reducing substance withdrawal syndromes: A narrative review.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {200},
number = {},
pages = {119553},
doi = {10.1016/j.biopha.2026.119553},
pmid = {42184757},
issn = {1950-6007},
abstract = {Substance withdrawal syndromes pose significant challenges in addiction treatment, often leading to poor treatment adherence and high relapse rates. This review evaluates metformin's potential as a therapeutic option for substance withdrawal syndromes, focusing on its mechanisms (AMPK activation, neurotransmitter modulation, gut microbiome effects) and clinical implications. Proposed mechanisms of action, including the involvement of signaling pathways, neurotransmitter regulation, and gut microbiome modulation, are also discussed. The study also highlights key areas requiring further investigation, such as the need for well-designed clinical trials, exploration of metformin dosage and treatment duration, and a deeper understanding of the specific molecular pathways underlying metformin's impact on withdrawal syndromes. Preclinical and clinical evidence suggest that metformin alleviates withdrawal symptoms and reduces relapse risk, but further research is needed to optimize dosing and validate efficacy. Overall, this review supports metformin's potential as a promising therapeutic option for managing substance withdrawal syndromes, offering improved treatment outcomes and reduced relapse rates and vulnerabilities.},
}

@article {pmid42184815,
year = {2026},
author = {Bełkot, Z and Adamski, MG and Strzałkowska, ZJ and Domańska, ED and Kłosińska, D and Kunstman, G and Skoczek, D and Pławińska-Czarnak, J},
title = {Full-Length 16S and 18S rRNA Long-Read Sequencing Reveals Gut Microbiome Diversity in the European Brown Hare (Lepus europaeus).},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70358},
doi = {10.1111/1758-2229.70358},
pmid = {42184815},
issn = {1758-2229},
mesh = {Animals ; *Hares/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 18S/genetics ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; },
abstract = {The European brown hare (Lepus europaeus) is a declining wildlife species of ecological and epidemiological importance, yet its intestinal microbiome remains poorly characterized. Here, Oxford Nanopore long-read sequencing was used to analyse full-length 16S and 18S rRNA genes from pooled large-intestine contents of 30 healthy hares divided into three groups. Comparative taxonomic assignment at 95% and 80% sequence identity thresholds revealed striking differences in diversity estimates, with the lower threshold uncovering up to ten-fold more taxa. Across all samples, 40 phyla, 360 families, 1027 genera, and 3373 species were identified, including 30 taxa not previously reported in lagomorphs. These included Monoglobus pectinilyticus, Ruminococcus champanellensis, Odoribacter splanchnicus, Butyricimonas virosa, and Akkermansia muciniphila, associated with pectin degradation, cellulose hydrolysis, butyrate production, mucin degradation, bile acid transformation, and nitrogen recycling. Several taxa relevant to both animal and human health were also detected, supporting hares as sentinels of environmental microbiota within a One Health framework. These findings show that analytical parameter selection strongly shapes microbiome interpretation and provide the most comprehensive gut microbiome profile of the European brown hare to date. The study expands lagomorph microbial ecology and highlights long-read sequencing as a valuable tool for wildlife microbiome surveillance in undercharacterized host species globally.},
}

Animals
*Hares/microbiology
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 18S/genetics
Phylogeny
Sequence Analysis, DNA
Biodiversity

@article {pmid42184816,
year = {2026},
author = {Miao, J and Zhang, C and Jiang, Q and Yao, Z and Cao, K and Chen, J and Wang, H and Liu, N},
title = {Complete Genome of an Alkali-Resistant Rhizobium anhuiense Symbiont of Pea Reveals Species-Specific Plasmid Fusion and Genomic Plasticity.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70366},
doi = {10.1111/1758-2229.70366},
pmid = {42184816},
issn = {1758-2229},
support = {//Team development funding from Xianghu Laboratory, the Xiaoshan District Government and the Zhejiang Provincial Government/ ; //2025 Special Cooperation Program between Xianghu Laboratory and Chinese Academy of Agricultural Science/ ; },
mesh = {*Plasmids/genetics ; *Genome, Bacterial ; *Pisum sativum/microbiology/growth & development ; Symbiosis ; Phylogeny ; *Rhizobium/genetics/isolation & purification/classification/physiology/drug effects ; *Alkalies/pharmacology ; Root Nodules, Plant/microbiology ; Gene Transfer, Horizontal ; },
abstract = {The rhizosphere microbiome is crucial for plant growth and stress resilience in sustainable horticulture. Here, we report the complete genome assembly and functional characterisation of Rhizobium anhuiense Xianghu001, a nitrogen-fixing symbiont isolated from pea (Pisum sativum) root nodules. A hybrid assembly strategy combining PacBio reads and Illumina reads yielded a 7.36 Mb high-quality assembly comprising one chromosome, one megaplasmid and four accessory plasmids, encoding 6899 protein-coding genes, of which 66.64% are located on the chromosome. Phylogenomics and synteny confirmed its placement within R. anhuiense. We detected a lineage-specific plasmid fusion forming the megaplasmid, while three accessory plasmids appear to be strain-specific and potentially acquired via horizontal gene transfer. Insertion sequence profiling suggests genome rearrangement shaping plasmid structure. To explore intraspecies diversity, we sequenced six additional local R. anhuiense isolates from pea. Despite their close geographic origin, genomic comparison revealed extensive divergence. Phenotypic assays demonstrated that Xianghu001 significantly promotes pea growth under nitrogen-deficient conditions, increasing chlorophyll content and nitrogen accumulation. It synthesises high levels of IAA (~184 mg/L), tolerates mild salinity (≤ 0.15% NaCl) and grows optimally at alkaline pH (8.0-10.0). Our findings provide a comprehensive genomic and functional framework for R. anhuiense Xianghu001 and underscore its potential as a biofertiliser.},
}

*Plasmids/genetics
*Genome, Bacterial
*Pisum sativum/microbiology/growth & development
Symbiosis
Phylogeny
*Rhizobium/genetics/isolation & purification/classification/physiology/drug effects
*Alkalies/pharmacology
Root Nodules, Plant/microbiology
Gene Transfer, Horizontal

@article {pmid42184901,
year = {2026},
author = {Green, JB and Haykal, D},
title = {AI and longevity medicine: unlocking predictive and preventive strategies for healthy aging.},
journal = {Presse medicale (Paris, France : 1983)},
volume = {},
number = {},
pages = {104359},
doi = {10.1016/j.lpm.2026.104359},
pmid = {42184901},
issn = {2213-0276},
abstract = {Longevity medicine is transforming healthcare by shifting the focus from disease treatment toward the preservation of function, resilience, and healthspan. In parallel, artificial intelligence (AI) has emerged as a powerful catalyst accelerating this transition through the integration and interpretation of multidimensional biological and behavioral data. AI-driven systems can now analyze genomics, epigenomics, proteomics, microbiome signatures, digital biomarkers, lifestyle metrics, and environmental exposures to identify early deviations from healthy aging trajectories before clinical disease manifests. These predictive capabilities enable personalized preventive strategies tailored to an individual's biological aging profile rather than chronological age alone. AI-supported longevity medicine therefore facilitates precision prevention through adaptive interventions involving nutrition, metabolic optimization, sleep regulation, stress management, continuous biosensing, and targeted therapeutics. Moreover, AI contributes to the evolution of healthcare systems from reactive episodic care toward adaptive and continuously monitored models emphasizing long-term physiological resilience. However, the integration of AI into longevity medicine also raises important scientific, ethical, and societal challenges, including data fragmentation, unequal access to preventive technologies, risks of overmedicalization, and concerns regarding privacy and governance. Bridging siloed biomarker ecosystems through interoperable data infrastructures, federated learning, and digital twin technologies will be essential for clinically meaningful predictive models. Ultimately, AI has the potential to redefine modern preventive medicine by enabling proactive, personalized, and age-resilient healthcare. The future success of AI-enhanced longevity medicine will depend on ensuring that technological innovation remains accurate, ethically grounded, clinically relevant, and equitably accessible across populations.},
}

@article {pmid42184963,
year = {2026},
author = {Riben Grundström, C and Lund, B and Bostanci, N and Silbereisen, A and Pennhag, A and Koistinen, IS and Zha, Y and Damdimopoulos, A and Belibasakis, GN and Hultin, M},
title = {Systemic Antibiotics in the Surgical Treatment of Peri-Implantitis: Impact on the Salivary Microbiome.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70143},
pmid = {42184963},
issn = {1600-051X},
support = {//Region Uppsala/ ; //Swedish Dental Association/ ; //Public Health Agency of Sweden/ ; //Steering Group for Collaborative Odontological Research at Karolinska Institutet and Stockholm City County/ ; //Centre for Innovative Medicine (CIMED)/ ; //Folktandvårdens Region Uppsala/ ; },
abstract = {AIM: To exploratorily compare the shifts in the salivary microbiome composition after administration of two combined systemic antibiotic regimens used in the surgical treatment of peri-implantitis.

MATERIALS AND METHODS: A subset of 27 patients treated surgically for peri-implantitis with an adjunctive 7-day course of systemic antibiotics were included (group A, amoxicillin and metronidazole; group B, phenoxymethylpenicillin and metronidazole). Unstimulated saliva was collected before surgery followed by 8 days, 14 days, 6 months and 12 months post surgery. Microbiome profiling was performed using standardised and automated pipelines for DNA extraction and whole genome shotgun sequencing (WGS).

RESULTS: WGS identified 498 species across 194 genera and 16 phyla, with Firmicutes and Actinobacteria being the most abundant. A distinct decrease in alpha diversity was observed on Day 8 relative to baseline across both antibiotic regimens, with signs of richness recovery by Day 14. Alpha and beta diversity analyses showed no statistically significant differences between interventions over the 12-month observation period.

CONCLUSION: Both adjunctive antibiotic regimens applied in the surgical treatment of peri-implantitis caused comparable ecological disturbances in the salivary microbiome, with no microbiological or clinical evidence supporting the superiority of one regimen over the other.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT02185209.},
}

@article {pmid42185030,
year = {2026},
author = {Gould, AAM and Walsh, NP and Tipton, MJ and Zurawlew, MJ and Robson, SC and Shute, JK and Watts, JEM and Tyson, HC and Robinson, MR and Roberts, AJ and Rawcliffe, AJ and Hemingway, R and Corbett, J},
title = {Gastrointestinal microbiota and barrier integrity in individuals who develop exertional heat illness and pair-matched controls: A prospective observational cohort study.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP093100},
pmid = {42185030},
issn = {1469-445X},
support = {//Ministry of Defence/ ; },
abstract = {It has been hypothesised that the composition of the gastrointestinal (GI) microbiota contributes to exertional heat illness (EHI) aetiology, but relevant empirical data in humans are lacking. Utilising a unique prospective study design, stool samples and resting blood samples were obtained from 550 individuals prior to (within 3 days) undertaking a 6.4-mile/10.3 km loaded march (median (IQR) duration = 66 (1) min), during which 79 individuals developed an EHI (mild, n = 55; severe, n = 24). These individuals were pair-matched for body mass index and cardiorespiratory fitness to individuals who did not develop an EHI during the same exercise (non-EHI). Our primary outcome measure was the composition of the gut microbiota, determined using 16S ribosomal RNA (rRNA) amplicon sequencing of stool samples. Secondary outcomes included the concentration of baseline blood biomarkers of GI barrier integrity (intestinal fatty acid binding protein, claudin 3, zonulin, lipopolysaccharide binding protein, and soluble cluster of differentiation 14). No significant differences in the composition of the GI microbiota (α-diversity, β-diversity, relative abundance, differential abundance) were observed between EHI cases and matched non-EHI controls (P > 0.05). Similarly, no significant between-group differences in biomarkers of GI barrier integrity were observed. These findings persisted when conducting additional sub-group analysis of severe EHI cases only, and additional sensitivity analysis excluding individuals who reported non-steroidal anti-inflammatory drug use and/or GI disorders. In conclusion, when potential confounding factors are controlled for, the composition of the GI microbiota and baseline GI barrier integrity do not appear to predispose to increased EHI risk during strenuous exercise.},
}

@article {pmid42185048,
year = {2026},
author = {Gibson, OR},
title = {The gut microbiome and thermoregulatory response: Relevance of the microbiota in heat-related illness?.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP093905},
pmid = {42185048},
issn = {1469-445X},
}

@article {pmid42185250,
year = {2026},
author = {Dar, HY and Fang, J and Patil, S and Roy, NK and Agarwal, S and Weitzmann, MN and Jones, RM and Bilezikian, JP and Pacifici, R},
title = {Bacterial specificity of the gut microbiome predicts bone density in primary hyperparathyroidism.},
journal = {Bone research},
volume = {14},
number = {1},
pages = {},
pmid = {42185250},
issn = {2095-4700},
support = {DK124821//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DK124821//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone Density/physiology ; Animals ; *Hyperparathyroidism, Primary/microbiology/physiopathology ; Female ; Male ; Middle Aged ; Mice ; Th17 Cells/immunology ; Aged ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Primary hyperparathyroidism causes mild-to-severe bone loss, but the reason for this heterogeneity is unclear. We investigated the role of the microbiome in 50 primary hyperparathyroidism patients. Microbiome transfers from primary hyperparathyroidism patients with and without osteoporosis to germ-free mice replicated the human bone phenotype and regulated TNF[+] T cells and Th17 cells in mice. Accordingly, circulating TNF[+] T cells and Th17 cells and TNF/IL17 production predicted bone density in primary hyperparathyroidism patients. Bifidobacterium longum, TNF[+] T cells, and Th17 cells were mediators of bone loss in primary hyperparathyroidism patients, while Bifidobacterium longum supplementation caused PTH to expand TNF[+] T cells and Th17 cells and induce bone loss in mice. Our findings link Bifidobacterium longum-induced TNF[+] T cells and Th17 cells to bone loss in patients with primary hyperparathyroidism. Bifidobacterium longum abundance may determine the skeletal phenotypes of patients with primary hyperparathyroidism and allow prediction of their risk of bone loss. Microbiome modifications by antibiotics or precision probiotics might offer novel preventive approaches for the skeletal complications of primary hyperparathyroidism.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bone Density/physiology
Animals
*Hyperparathyroidism, Primary/microbiology/physiopathology
Female
Male
Middle Aged
Mice
Th17 Cells/immunology
Aged
Tumor Necrosis Factor-alpha/metabolism

@article {pmid42185302,
year = {2026},
author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R},
title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01021-8},
pmid = {42185302},
issn = {2055-5008},
support = {2020/06077-9//São Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//São Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; },
abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.},
}

@article {pmid42185318,
year = {2026},
author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR},
title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73524-z},
pmid = {42185318},
issn = {2041-1723},
support = {U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R35GM137828//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.},
}

@article {pmid42185319,
year = {2026},
author = {Lima, RD and Bauer, OR and Pauer, H and Hajiarbabi, K and Moreira, DA and Parente, TE and Ferreira, RBR},
title = {Cutibacterium acnes inhibits Staphylococcus lugdunensis biofilm formation through inhibition of autolysis and purine biosynthesis.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01014-7},
pmid = {42185319},
issn = {2055-5008},
abstract = {Cutibacterium acnes is a key member of the human skin microbiome that contributes to host homeostasis. Staphylococcus lugdunensis, while also a resident of the skin microbiota, is an opportunistic pathogen capable of causing severe infections, associated with its ability to form biofilms. We previously showed that C. acnes secretes molecules that inhibit S. lugdunensis biofilm formation without affecting planktonic growth. Here, we demonstrate that C. acnes-derived molecules also significantly reduced S. lugdunensis adherence to and invasion of human epithelial cells, as well as adhesion to keratinocytes. Transcriptomic analysis revealed repression of genes involved in S. lugdunensis purine biosynthesis and induction of the autolysis negative regulators, lrgA and lrgB. Functional assays confirmed that exposure to C. acnes molecules inhibits autolysis and extracellular DNA (eDNA) release and decreases intracellular guanine levels in S. lugdunensis. Crucially, the addition of exogenous guanine suppressed the effect of C. acnes molecules on both biofilm formation and lrgA gene expression. Collectively, our data indicate that C. acnes molecules inhibit S. lugdunensis biofilm formation by depleting the intracellular guanine pool, leading to repression of autolysis, and reduced eDNA release, a key component of biofilm structural integrity. These findings underscore the importance of interspecies microbiome interactions in pathogen exclusion.},
}

@article {pmid42185548,
year = {2026},
author = {Guo, X and Wang, Y and Wang, L and Lei, Y and Sa, RN and Li, L and Xia, S and Lin, X and Liu, C and Shao, Y},
title = {An integrated multi-omics approach for deciphering podophyllotoxin-induced nephrotoxicity via the microbiome-gut-kidney (MGK) axis based on the toxicological evidence (TEC) concept.},
journal = {Journal of molecular histology},
volume = {57},
number = {3},
pages = {},
pmid = {42185548},
issn = {1567-2387},
support = {Grant 24A360023//he Key Scientific Research Projects of Henan Higher Education Institutions/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Podophyllotoxin/toxicity ; *Kidney/drug effects/pathology/metabolism ; Male ; *Metabolomics/methods ; Mice, Inbred ICR ; *Kidney Diseases/chemically induced/pathology/metabolism ; Dysbiosis ; Multiomics ; },
abstract = {Podophyllotoxin (PPT), a potent antitumor natural lignan, is clinically limited by nephrotoxicity, with the microbiome-gut-kidney (MGK) axis's role unclear. Guided by the Toxicological Evidence Chain (TEC) framework, this study used multi-omics approaches in ICR mice (control, low/high-dose PPT) to explore mechanisms. The physiological indices of mice, health status, renal pathological changes, injury and proinflammatory biomarkers, gut microbiota, metabolism, and transcriptional changes were determined to collect toxicity evidence. Besides, an integrated multi-omics approach, including 16S rRNA gene sequencing, metabolomics coupled with LC-MS/MS, and transcriptomics, was employed to systematically elucidate the potential nephrotoxicity mechanism of PPT. Results showed that PPT significantly induced health deterioration, including reduced activity and body weight, hemorrhage, hunched posture, and severe diarrhea. The dose-dependent nephrotoxicity caused, including decreased kidney organ index, pathological structural changes, and elevated renal injury indices, particularly BUN, Cr, KIM-1, IL-18, and mAlb. Furthermore, gut microbiota dysbiosis (enriched Escherichia-Shigella, depleted Lactobacillus), disrupted tryptophan/ascorbate metabolism, and downregulated key metabolic genes were also observed after PPT intervention. Integrated analysis confirmed gut microbiota dysbiosis mediates PPT-induced nephrotoxicity via the MGK axis. Our research evidence chain implies that PPT promotes intestinal flora dysbiosis, thereby redirecting tryptophan metabolism toward the kynurenine pathway and suppression of the ascorbate and aldarate metabolism pathway abolishes its renoprotective effects simultaneously, triggering amplified inflammatory cascades and ultimately leading to renal dysfunction and nephrotoxicity. This study identifies a novel mechanism, actionable mitigation targets, and supports TEC's application in toxicological assessment.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Podophyllotoxin/toxicity
*Kidney/drug effects/pathology/metabolism
Male
*Metabolomics/methods
Mice, Inbred ICR
*Kidney Diseases/chemically induced/pathology/metabolism
Dysbiosis
Multiomics

@article {pmid42185684,
year = {2026},
author = {Miyake, T and Kojima, M and Tani, S and Muramoto, K and Maehira, H and Kaida, S and Shimizu, T and Tani, M},
title = {Gut microbiota profiles in reactive and metastatic lymphadenopathy in colorectal cancer: a tumor location-stratified analysis.},
journal = {International journal of colorectal disease},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00384-026-05154-2},
pmid = {42185684},
issn = {1432-1262},
abstract = {PURPOSE: Preoperative lymphadenopathy in colorectal cancer may represent nodal metastasis or reactive change. We aimed to compare gut microbiota profiles between reactive and metastatic lymphadenopathy and to explore microbial features associated with nonmetastatic lymph node enlargement.

METHODS: We conducted a retrospective observational study of colorectal cancer patients with radiological lymphadenopathy who underwent resection at Shiga University of Medical Science Hospital between 2018 and 2021. For the primary analysis, we included patients with radiological lymphadenopathy on preoperative CT. An additional analysis restricted to right-sided colon cancer compared no lymphadenopathy without pathological lymph node metastasis (NN), lymphadenopathy without pathological lymph node metastasis (PN), and lymphadenopathy with pathological lymph node metastasis (PP).

RESULTS: Pathological nodal metastasis was identified in 34 patients, whereas 29 had reactive lymphadenopathy. Fecal samples showed higher alpha diversity than tumor tissues. In left-sided colorectal cancer, no notable bacterial taxa exceeded the predefined LDA threshold. In right-sided colon cancer, Proteobacteria were enriched in metastatic cases, whereas Firmicutes were more abundant in reactive lymphadenopathy. Predicted pathway analysis suggested distinct metabolic profiles between the two groups. In the additional right-sided analysis, alpha and beta diversity did not significantly differ among NN, PN, and PP, although taxon-level differences were observed between NN and PN.

CONCLUSION: Gut microbiota profiles differed between reactive and metastatic lymphadenopathy in colorectal cancer, with more distinct findings in right-sided tumors. These findings suggest an association between microbial patterns and reactive lymphadenopathy.},
}

@article {pmid42185899,
year = {2026},
author = {Wang, Z and Wang, Z and Ji, X and Zhao, L and Zheng, K and Yu, W and Zhang, H and Chang, H and Liu, F},
title = {CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08301-z},
pmid = {42185899},
issn = {1479-5876},
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an integrative genetic and multi-omics framework, we investigated complement receptor 1 (CR1) as a candidate regulator of this immunosuppressive niche.

METHODS: We combined Mendelian randomization (MR) and metabolite mediation analyses with bulk, single-cell, and spatial transcriptomics to define the role of CR1 in HCC. Public datasets included the TCGA-HCC cohort, a single-cell RNA-sequencing dataset comprising 53,474 high-quality cells from 21 samples, and two spatially profiled HCC sections. Clinical validation was performed in 30 paired HCC and adjacent liver tissues. Functional assays were conducted in THP-1-derived macrophages using CR1 gain- and loss-of-function approaches, phagocytosis assays, and macrophage-CD8[+] T-cell co-culture experiments.

RESULTS: MR analyses implicated CR1 in HCC susceptibility at both the protein and transcript levels. pQTL analysis linked genetically predicted circulating CR1 levels to HCC risk (IVW OR = 1.403, p = 0.017), and mediation analysis identified specific metabolites as candidate intermediates. Integrative multi-omics analyses showed that CR1 was preferentially enriched in TAMs, spatially co-localized with the M2 marker CD206, and associated with reduced CD8[+] T-cell infiltration, enhanced T-cell exhaustion signatures, advanced clinicopathological features, and poorer survival. In 30 paired clinical samples, CR1-high tumors exhibited increased M2-like macrophage accumulation and reduced CD8[+] T-cell infiltration. Functionally, CR1 overexpression drove macrophages toward an M2-like phenotype, enhanced phagocytic activity, increased PD-L1 expression, and suppressed CD8[+] T-cell proliferation as well as IFN-gamma and granzyme B production, whereas CR1 knockdown produced the opposite phenotype.

CONCLUSIONS: Our study provides the first integrated genetic, spatial, and functional evidence that CR1[+] TAMs constitute a clinically relevant immunoregulatory axis in HCC. These findings extend current understanding of complement-associated immunosuppression beyond canonical complement cascade activity and support CR1 as a candidate biomarker and therapeutic target for macrophage reprogramming, with potential translational relevance for combination strategies involving immune checkpoint blockade.},
}

@article {pmid42186042,
year = {2026},
author = {Salgueiro, AM and Ferreira-Marques, M and Ribeiro, RFN and Lopes, SM and Pereira, D and Costa, DG and Santana, MM and de Almeida, LP and Cavadas, C},
title = {Ketogenic diet as a therapeutic strategy for neurodegenerative diseases: from mechanisms to translational challenges.},
journal = {Translational neurodegeneration},
volume = {15},
number = {1},
pages = {},
pmid = {42186042},
issn = {2047-9158},
support = {UIDB/04539/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04539/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0058/2020(JPND/ 0001/2022//Fundação para a Ciência e a Tecnologia/ ; DOI: 10.54499/JPND/0001/2022; JPND/0002/2022//Fundação para a Ciência e a Tecnologia/ ; DOI: 10.54499/JPND/0002/2022//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/120023/2016; 2020.04850.BD//Fundação para a Ciência e a Tecnologia/ ; 2022.11293.BD//Fundação para a Ciência e a Tecnologia/ ; GeneT project-The Gene Therapy CoE at the Center of Portugal (Project ID: 101059981//HORIZON EUROPE Widening participation and spreading excellence/ ; DOI: 10.3030/101059981); GCure - From Gene to Cure//HORIZON EUROPE Widening participation and spreading excellence/ ; ID: 101186929//HORIZON EUROPE Widening participation and spreading excellence/ ; DOI:10.3030/101186929; GeneH - Excellence Hub for Advancing Innovation in Gene Therapy//HORIZON EUROPE Widening participation and spreading excellence/ ; ID: 101186939//HORIZON EUROPE Widening participation and spreading excellence/ ; DOI: 10.3030/101186939//HORIZON EUROPE Widening participation and spreading excellence/ ; },
mesh = {Humans ; *Diet, Ketogenic/methods ; *Neurodegenerative Diseases/diet therapy/metabolism ; Animals ; *Translational Research, Biomedical/methods ; Gastrointestinal Microbiome/physiology ; Oxidative Stress/physiology ; },
abstract = {The ketogenic diet (KD) is increasingly recognized as a promising therapeutic strategy for neurodegenerative disorders because of its multifaceted impacts on key pathophysiological mechanisms. This review explores the molecular pathways through which KD may protect against neurodegeneration, including the use of ketone bodies as alternative energy substrates, reduction of oxidative stress and inflammation, modulation of autophagy and protein aggregation, and impact on the gut microbiome. The potential benefits of KD are explored across neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and multiple sclerosis, based on both preclinical and clinical evidence that supports its feasibility. However, challenges in long-term safety, patient adherence, and clinical practicality limit its widespread adoption. This review underscores the potential of KD for treating neurodegeneration on the basis of current scientific evidence while highlighting the need for further research to optimize its application and address existing gaps.},
}

Humans
*Diet, Ketogenic/methods
*Neurodegenerative Diseases/diet therapy/metabolism
Animals
*Translational Research, Biomedical/methods
Gastrointestinal Microbiome/physiology
Oxidative Stress/physiology

@article {pmid42186076,
year = {2026},
author = {Liping, Y and Xingzhi, Y and Jie, T and Xiaohua, D},
title = {Yajieshaba extract improves alcohol‑induced liver injury by regulating hepatic lipid metabolism and gut microbiota.},
journal = {BMC complementary medicine and therapies},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12906-026-05421-3},
pmid = {42186076},
issn = {2662-7671},
support = {202101AZ070001-321//he Joint Special Project of Traditional Chinese Medicine of Basic Research Program of Science and Technology Department of Yunnan Province/ ; 202101AZ070001-321//he Joint Special Project of Traditional Chinese Medicine of Basic Research Program of Science and Technology Department of Yunnan Province/ ; 202101AZ070001-321//he Joint Special Project of Traditional Chinese Medicine of Basic Research Program of Science and Technology Department of Yunnan Province/ ; 202101AZ070001-321//he Joint Special Project of Traditional Chinese Medicine of Basic Research Program of Science and Technology Department of Yunnan Province/ ; },
abstract = {BACKGROUND: Yajieshaba, a commonly used Dai medicine formula, is renowned for its hepatoprotective properties. This study aimed to investigate the therapeutic effects and underlying mechanisms of Yajieshaba on alcoholic liver disease (ALD) in mice, focusing the gut-liver axis.

METHODS: Male C57BL/6 mice were pair-fed the Lieber-DeCarli control or ethanol-containing diet for 8 weeks, with or without Yajieshaba co-administration. Serum biomarkers were assessed using biochemical kits. Liver pathology was evaluated by hematoxylin and eosin (H&E) and Oil Red O staining. Intestinal barrier integrity was assessed by H&E staining and immunofluorescence of tight junction proteins (occludin, ZO-1). Hepatic lipid composition was analyzed by liquid chromatography-mass spectrometry (LC-MS), and gut microbiota diversity was profiled by 16 S rRNA sequencing.

RESULTS: Yajieshaba significantly attenuated ethanol-induced liver injury, steatosis, and intestinal barrier disruption. Multi-omics integration revealed that Yajieshaba mitigated ALD progression by restoring gut microbial homeostasis and regulating hepatic lipid metabolism.

CONCLUSION: This study elucidates the therapeutic mechanism of Yajieshaba from the perspective of the gut microbiome-lipid metabolism axis, providing a novel perspective and experimental basis for further ALD management.},
}

@article {pmid42186163,
year = {2026},
author = {Eterovick, PC and Glos, J and Burkart, F and Overmann, J and Ruthsatz, K},
title = {Interplay of Diet, Heat Stress, and the Microbiome Shapes Health and Escape Behaviour in Amphibian Larvae.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70331},
doi = {10.1111/1462-2920.70331},
pmid = {42186163},
issn = {1462-2920},
support = {546565602//Deutsche Forschungsgemeinschaft/ ; 459850971//Deutsche Forschungsgemeinschaft/ ; 101151070-AMPHISTRESS//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; },
mesh = {Animals ; Larva/microbiology/physiology/growth & development ; *Diet ; *Rana temporaria/microbiology/physiology/growth & development ; *Gastrointestinal Microbiome ; *Heat-Shock Response ; Hot Temperature ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota ; },
abstract = {Diet influences animal health and their microbiomes, potentially affecting how they cope with environmental stressors such as rising temperatures and altered food quality associated with climate change. Using a multifactorial experiment, larvae of the frog Rana temporaria were reared on three diets differing in protein, fat, and animal-derived components (low-, intermediate-, and high-quality), at two temperatures (18°C and 24.5°C), and either exposed or not to a simulated heatwave (28°C for 48 h). We examined how these treatments and associated shifts in gut bacterial indicators and predicted microbial metabolic pathways related to nutrient assimilation, host health (body condition and developmental rate), and escape behaviour. Larvae maintained body condition and developed faster at 24.5°C, with higher diet quality further accelerating development. An intermediate-quality diet reduced responsiveness to an aversive stimulus at 24.5°C, although this effect disappeared following heatwave exposure. Heatwave conditions were associated with increased abundance of Klebsiella and a predicted increase in the myo-inositol degradation pathway, which may influence membrane dynamics and signalling and may increase attention levels. Despite microbial shifts, host performance remained similar across most treatments, suggesting substantial microbiome plasticity and the presence of functionally redundant enterotypes that help buffer environmental stress.},
}

Animals
Larva/microbiology/physiology/growth & development
*Diet
*Rana temporaria/microbiology/physiology/growth & development
*Gastrointestinal Microbiome
*Heat-Shock Response
Hot Temperature
Bacteria/classification/genetics/isolation & purification/metabolism
*Microbiota

@article {pmid42186183,
year = {2026},
author = {Wang, H and Jin, Z and Di, S and Alizadeh, H},
title = {Exercise-Induced Exerkines: Multi-Nodal Suppression of the NLRP3 Inflammasome and Translational Potential.},
journal = {Medicinal research reviews},
volume = {},
number = {},
pages = {},
doi = {10.1002/med.70063},
pmid = {42186183},
issn = {1098-1128},
abstract = {Chronic low-grade inflammation driven by persistent NLRP3 inflammasome activation is a unifying pathophysiological feature of most non-communicable diseases (NCDs). Whereas single-target pharmacological inhibitors exhibit limited breadth and durability, regular moderate-intensity exercise confers robust multi-system protection through a diverse network of exerkines. This narrative review synthesizes evidence that exercise-released myokines (irisin, Metrnl, context-reprogrammed IL-6), hepatokines/adipokines (FGF21, adropin, adiponectin), metabolites (lactate, β-hydroxybutyrate), microbiota-derived factors (SCFAs, betulinic acid), and extracellular vesicle (EV)-delivered non-coding RNAs converge on every regulatory node of the canonical NLRP3 inflammasome to achieve multi-nodal suppression that is currently unmatched by any single pharmacological approach based on available evidence. Acute high-intensity exercise transiently activates NLRP3 via canonical danger signals, whereas chronic moderate-intensity training (150-300 min·wk[-1], 60%-75% HRmax) induces profound basal suppression through NF-κB attenuation, mitochondrial protection, direct interference with NEK7-NLRP3 interaction and ASC oligomerization, post-transcriptional silencing, and enhanced autophagic clearance. These mechanisms are supported by preclinical structural data and human biomarker studies across cardiovascular, metabolic, neurodegenerative, and musculoskeletal disorders. We propose a precision exercise medicine framework integrating exerkine/genetic/microbiome profiling to minimize non-responders, together with emerging mimetics, RNA therapeutics, and synergistic pharmacology, to deliver scalable systems-level modification of NLRP3-driven metaflammation.},
}

@article {pmid42186196,
year = {2026},
author = {Smith, RE and Holtappels, D},
title = {The role of phages in plant-associated microbial communities.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250035},
pmid = {42186196},
issn = {1744-1358},
support = {NE2335//USDA | National Institute of Food and Agriculture (NIFA)/ ; },
abstract = {Microbial communities deliver essential functions in ecosystems. In plant environments, the plant microbiome facilitates nutrient uptake, supports plants during abiotic stress, and counteracts disease. As implementation of synthetic microbial communities becomes more of a realistic strategy for mitigating the effects of biotic and abiotic stressors on plant productivity, it is increasingly important to understand how interactions between microbes, which are essential for ecosystem function (hub microbes), are maintained. Recent research highlights the ecological role of bacteriophages, the viruses of bacteria, in host-associated microbial communities. Current evidence demonstrates the influence of the phageome on microbiomes, ranging from effects on an individual (transduction, lysogenic conversion, and evolutionary pressure) to entire populations and communities, such as Kill-the-Winner dynamics. These dynamics appear to affect the overall function of microbial communities and support plant growth. In this review, we lay out recent insights on the role of bacteriophages in plant-associated microbiomes through an eco-evolutionary lens and future directions of research to broaden our understanding of the ecological implications of bacteriophages.},
}

@article {pmid42186200,
year = {2026},
author = {Diaz-Amigo, C and Bartolomé Del Pino, LE and Lejeune, J and Pinto Ferreira, J and Bessy, C},
title = {Antimicrobial resistance and the human gut microbiome-a food safety perspective.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-29},
doi = {10.1080/10408398.2026.2629533},
pmid = {42186200},
issn = {1549-7852},
abstract = {The gastrointestinal environment is where the resident gut microbiome encounters foodborne microorganisms, antimicrobial resistance genes (ARGs), and bioactive substances from food, all of which may influence the acquisition and dissemination of antimicrobial resistance (AMR). Although resistant bacteria and ARGs are frequently detected in food and food production environments, their contribution to the gut resistome remains unclear. Most ingested microbes are transient and constrained by ecological barriers; however, the conditions that enable horizontal gene transfer in vivo are not well characterized. Multiple factors (e.g., microbial composition and density, the presence of mobile genetic elements, antimicrobial residues, and host physiology) can modulate ARG persistence and mobility, but their relative impact within the gut ecosystem and its associated resistome needs to be better understood. Resistance acquisition also depends on fitness costs and adaptive responses within complex microbial communities. Methodological variability and limited in vivo data further limit comparability and interpretation. This review summarizes current knowledge of AMR dynamics in the gut following dietary exposure and highlights significant knowledge gaps that limit our understanding of factors influencing ARG transfer and persistence in the gastrointestinal environment. Reducing these uncertainties is crucial for strengthening AMR risk assessment and designing more effective mitigation strategies.},
}

@article {pmid42186240,
year = {2026},
author = {Jiang, K and Saha, S and Peterson, CB},
title = {Bayesian Sparse Regression for Microbiome-Metabolite Data Integration.},
journal = {Statistics in medicine},
volume = {45},
number = {13-14},
pages = {e70607},
doi = {10.1002/sim.70607},
pmid = {42186240},
issn = {1097-0258},
support = {R01 HL158796/NH/NIH HHS/United States ; CCSG P30CA016672/CA/NCI NIH HHS/United States ; //Andrew Sabin Family Fellowship/ ; },
mesh = {Bayes Theorem ; Humans ; Colorectal Neoplasms/microbiology/metabolism ; Computer Simulation ; *Gastrointestinal Microbiome ; *Microbiota ; Models, Statistical ; Regression Analysis ; *Metabolome ; },
abstract = {Numerous studies have shown that microbial metabolites, which represent the products of bacteria in the human gut, play a key role in shaping cancer risk and response to treatment. However, metabolite data typically contain a large proportion of missing values, which may result from either low abundance or technical challenges in data processing. Moreover, given the compositionality of microbiome data, where the observed abundances can only be interpreted on a relative scale, standard variable selection methods are not applicable. In this project, we propose a novel Bayesian regression method to address these challenges in the integration of metabolite and microbiome data. Key features of our proposed model include modeling the two different mechanisms of missingness for the metabolite data and adopting a Bayesian prior designed to address the compositional characteristics of microbiome data. We demonstrate on simulated data that our proposed model can accurately impute the unobserved true metabolite values and correctly select the relevant microbiome predictors. We further illustrate our method using real data from a study focused on understanding the interplay between the microbiome and metabolome in colorectal cancer.},
}

Bayes Theorem
Humans
Colorectal Neoplasms/microbiology/metabolism
Computer Simulation
*Gastrointestinal Microbiome
*Microbiota
Models, Statistical
Regression Analysis
*Metabolome

@article {pmid42186272,
year = {2026},
author = {Kris-Etherton, PM and Rogers, CJ and Oh, ES and West, SG and Sandhu, AK and Burton-Freeman, B and Huang, Y and Proctor, DN and Petersen, KS},
title = {Cardiometabolic and Microbiome Effects of Spices and Herbs.},
journal = {Nutrition reviews},
volume = {84},
number = {Supplement_1},
pages = {70-75},
pmid = {42186272},
issn = {1753-4887},
support = {//McCormick Science Institute/ ; /TR/NCATS NIH HHS/United States ; UL1 TR002014/NH/NIH HHS/United States ; },
mesh = {Humans ; *Spices ; *Cardiovascular Diseases/prevention & control ; *Gastrointestinal Microbiome/drug effects ; Cardiometabolic Risk Factors ; *Plants, Medicinal/chemistry ; },
abstract = {This article appears as part of the supplement "The Role of Spices and Herbs on Supporting Healthy Diets and Improving Nutritional Status," sponsored by the McCormick Science Institute. Studies conducted at Penn State University to evaluate the effects of spices and herbs (S&H) on risk factors for cardiovascular disease (CVD) are summarized herein. We also report effects of S&H on phytochemical metabolites and the microbiome. Results demonstrate beneficial effects of S&H on postprandial endothelial function, insulin and triglycerides, pancreatic lipase, inflammatory markers, and measures of oxidative defense. In a controlled-feeding trial that evaluated 3 doses of S&H (0.5, 3.3, and 6.6 g/d per 2100 kcal) in the context of an average American diet, the high-S&H diet improved 24-hour blood pressure after 4 weeks, the moderate-S&H diet decreased proinflammatory cytokines, and the high-S&H diet reduced monocyte adherence. Our research also identified polyphenol metabolites that may have important functional properties for CVD risk reduction. Finally, we report benefits of S&H on gut bacterial composition, which suggests possible benefits on CVD risk.},
}

Humans
*Spices
*Cardiovascular Diseases/prevention & control
*Gastrointestinal Microbiome/drug effects
Cardiometabolic Risk Factors
*Plants, Medicinal/chemistry

@article {pmid42186275,
year = {2026},
author = {Diacova, T and Heber, D and Li, Z},
title = {Spices Beyond Antioxidants: From the Gut to the Brain.},
journal = {Nutrition reviews},
volume = {84},
number = {Supplement_1},
pages = {52-69},
pmid = {42186275},
issn = {1753-4887},
mesh = {Humans ; *Spices ; *Antioxidants/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Brain/drug effects ; Gastrointestinal Tract/microbiology ; },
abstract = {OBJECTIVES: The objective of this review was to summarize evidence of the effects of select spices/herbs on human health with a focus on the work conducted at the University of California-Los Angeles (UCLA) Center for Human Nutrition.

BACKGROUND: Herbs/spices have been used in various countries around the world for centuries. The purposes for using herbs/spices include improvement in food organoleptic properties and use as food preservatives and medicine. As interest in ethnic cuisines is gaining popularity, more Americans are interested in adding spices/herbs to their daily diets for health benefits. Health benefits conferred by herbs/spices include protection against oxidative stress, neurodegeneration, cardiovascular disease among others and may be at least partially due to their high (poly)phenolic content. (Poly)phenols are not accessible by the human digestive enzymes and are metabolized by the gut microbiome, earning them the status of "prebiotics." This is confirmed by a vast body of evidence pointing to the herbs'/spices' ability to affect gut microbiota composition/functionality.

METHODS: In vitro experiments and human trials conducted at the UCLA Center for Human Nutrition were collated and results summarized. Reference lists of these publications were scanned and relevant literature extracted. Multiple additional searches relating to the select herbs/spices and their effects on human health were conducted in PubMed.

RESULTS: A total of 8 human trials and 12 in vitro experiments were conducted at the UCLA Center for Human Nutrition between 2010 and 2024. These experiments included interventions with individual herbs/spices, including cinnamon, chili pepper, and turmeric, as well as spice mixes. Additional relevant original research and reviews/meta-analyses were identified and included to supplement the discussions.

CONCLUSION: While further research of herbs/spices is undeniably warranted, several considerations should be kept in mind. These include the relatively small amounts of herbs/spices consumed by the general population on a daily basis, cooking methods, as well as effects of digestive/metabolic processes on the bioavailability of herb/spice (poly)phenols. While much is already known, there are still substantial gaps in knowledge that need to be addressed.},
}

Humans
*Spices
*Antioxidants/pharmacology
*Gastrointestinal Microbiome/drug effects
*Brain/drug effects
Gastrointestinal Tract/microbiology

@article {pmid42186278,
year = {2026},
author = {Crowe-White, KM and Senkus, KE and DiNatale, JC},
title = {Spices for Targeting the Gut Microbiome to Improve Cardiometabolic Health.},
journal = {Nutrition reviews},
volume = {84},
number = {Supplement_1},
pages = {49-51},
pmid = {42186278},
issn = {1753-4887},
support = {//McCormick Science Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Spices ; Prebiotics ; Polyphenols/pharmacology ; Cinnamomum zeylanicum/chemistry ; *Cardiovascular Diseases/prevention & control ; Zingiber officinale/chemistry ; Fatty Acids, Volatile/metabolism ; },
abstract = {The intricate balance between the gut microbial ecosystem and cardiometabolic health underscores the importance of cultivating a healthy gut microbiome. A noteworthy strategy for harnessing the potential of this ecosystem is the consumption of prebiotics-non-digestible compounds promoting the growth of beneficial bacteria. While dietary polyphenols are emerging as significant modulators of microbial proliferation and systemic therapeutic effects, the prebiotic functionality of spice polyphenols remains understudied. It is, however, hypothesized that metabolism of spice polyphenols by intrinsic microflora in the colon may elicit downstream cardiometabolic effects resulting from the stimulated release of gut-derived metabolites, specifically short-chain fatty acids. This brief article highlights research on the functionality of spices, namely cinnamon and ginger, to influence microbial proliferation, the production of gut-derived metabolites and hormones, and prospective health outcomes.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Spices
Prebiotics
Polyphenols/pharmacology
Cinnamomum zeylanicum/chemistry
*Cardiovascular Diseases/prevention & control
Zingiber officinale/chemistry
Fatty Acids, Volatile/metabolism

@article {pmid42186489,
year = {2026},
author = {Dong, X and Guo, L and Chen, H},
title = {Phosphorus availability enriches Massilia in the root microbiome to enhance resistance against Sclerotinia sclerotiorum in rapeseed.},
journal = {Molecular breeding : new strategies in plant improvement},
volume = {46},
number = {6},
pages = {53},
pmid = {42186489},
issn = {1572-9788},
abstract = {UNLABELLED: Phosphorus is an essential macronutrient for plant growth and development, especially in P-sensitive crops such as rapeseed (Brassica napus). However, the role of phosphorus (P) availability in plant disease resistance mediated by the root-associated microbiome remains poorly understood. Here, we investigated how P homeostasis regulates rapeseed resistance to Sclerotinia sclerotiorum through modulation of the root-associated microbiome. P deficiency significantly inhibited plant growth and increased susceptibility to S. sclerotiorum in multiple rapeseed ecotypes, including spring, semi‑winter, and winter types. Microbiome profiling revealed that Massilia was a key P-responsive biomarker genus significantly enriched under P-sufficient conditions. Both foliar application and root inoculation with Massilia effectively suppressed S. sclerotiorum infection in rapeseed. Mechanistically, Massilia colonization strongly activated the expression of pathogenesis‑related (PR) genes, antioxidant genes, and jasmonic acid (JA) signaling genes. Overall, this study establishes a P-mediated tripartite interaction linking root microbiota assembly and plant immunity. These results highlight that optimizing P supply to enrich beneficial microbes such as Massilia can enhance rapeseed resistance to S. sclerotiorum, providing a sustainable strategy for disease management.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-026-01669-2.},
}

@article {pmid42186656,
year = {2026},
author = {Kimura, M and Taketani, T},
title = {Hemoglobin Response to a Low-Iron Dose in Infantile Anemia.},
journal = {Cureus},
volume = {18},
number = {4},
pages = {e107641},
pmid = {42186656},
issn = {2168-8184},
abstract = {INTRODUCTION: Iron-deficiency anemia (IDA) is common during infancy, especially among infants exclusively breastfed after six months of age. The recommended therapeutic iron dose is 3-6 mg/kg/day; however, excessive iron load can be harmful due to alteration of the gut microbiome and oxidative stress to the developing organs. Lower doses of iron have shown efficacy in treating IDA in adults. This retrospective study evaluated the hemoglobin (Hb) response to a lower iron dose in infantile anemia.

METHODS: During health checkups for 9- to 10-month-old infants, anemia screening was conducted for those who were exclusively breastfed. Clinical parameters, including birth date, gestational age, birth weight, and body weight at the start of iron supplementation, were recorded. Venous blood samples were collected for a complete blood count (CBC). Infants with either Hb levels below 11.0 g/dL or mean corpuscular volume below 70 fL received a therapeutic iron trial. From March 2016 to November 2018, a fixed dose of elemental iron (soluble ferric pyrophosphate) 15 mg/day was administered (reference group), and from November 2018 to December 2023, a dose of 1 mg/kg/day was given (low-dose group). CBC measurements were repeated after four weeks, and Hb responses were compared between the two regimens.

RESULTS: A total of 26 children in the reference group and 27 in the low-dose group were finally analyzed. The fixed 15 mg/day dose in the reference group corresponded to 1.8 (1.6-1.9) (median (interquartile range) mg/kg/day). Baseline clinical variables showed no statistically significant differences between the two groups. The median Hb increase was 1.6 g/dL and 1.5 g/dL, with 69% (18/26) and 70% (19/27) of children achieving an Hb level ≥ 1 g/dL, in the reference and low-dose groups, respectively. All 15 children (15/27, 56%) in the low-dose group, who met the new WHO anemia definition at the age of 6-23 months of Hb < 10.5 g/dL, had an Hb response ≥ 1.0 g/dL, with a median Hb response of 2.2 g/dL.

CONCLUSION: An iron dose of 1 mg/kg/day was as effective as 15 mg/day (median: 1.8 mg/kg/day) in the Hb response. In all children with Hb < 10.5 g/dL, the iron dose of 1 mg/kg/day showed substantial Hb responses. These findings suggest that therapeutic iron doses lower than conventional recommendations may be effective for managing IDA and mitigating the harmful effects.},
}

@article {pmid42186662,
year = {2026},
author = {Mueller, MK and Rousseau, SR and Hark, GM and Shaffer, LR and Rizvanović, BF and Nuelle, JAV},
title = {The Role of the Gut Microbiota in Functional Recovery after Peripheral Nerve Injury: A Narrative Review.},
journal = {Orthopedic reviews},
volume = {18},
number = {},
pages = {162156},
pmid = {42186662},
issn = {2035-8164},
abstract = {INTRODUCTION: While researchers have previously pointed to the peripheral nervous system as a method of transportation for the gut microbiota metabolites to distant organs, researchers have more recently studied the impact of gut microbiota on the peripheral nerves. The purpose of this review was to synthesize the literature on how modulation of the gut microbiota impacts functional recovery following peripheral nerve injury.

METHODS: Electronic searches were conducted in Ovid/Medline and PubMed to identify articles that discuss gut microbiome interventions following peripheral nerve injury in sciatic nerve chronic constriction injury or crush injury animal models and the effects on peripheral nerve regeneration and functional recovery.

RESULTS: Twelve articles met inclusion criteria; all were prospective studies in animal models. Four interventions were identified by the twelve studies, including probiotics, antibiotics, intermittent fasting, and naturopathic compounds. Probiotic treatment and dietary interventions targeted at modulating the gut microbiota improved histological, sensory, and motor outcomes following peripheral nerve injury. While antibiotic treatment negatively impacted recovery after peripheral nerve injury, co-treatment with probiotics or reconstitution of the gut microbiota through fecal microbiota transplantation was able to rescue these negative effects.

CONCLUSION: Alterations in the gut microbiota, whether induced by antibiotics, probiotics, intermittent fasting, or dietary interventions, impact functional recovery, neuropathic pain, and inflammatory processes. However, future research should focus on identifying the specific microbial taxa responsible for neuroregenerative effects and developing standardized protocols for probiotic treatment to optimize improvement in peripheral nerve recovery after injury.},
}

@article {pmid42186771,
year = {2026},
author = {Zhang, Y and Li, X and Zhang, X and Wang, Y and Chen, Z and Lin, X and Zheng, X and Hao, H and Zhang, X},
title = {Ketogenic Diet Modulates Depressive-Like Behavior via Gut Bacterial Metabolism of Tyrosine.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {10},
pages = {e71966},
doi = {10.1096/fj.202504666RRR},
pmid = {42186771},
issn = {1530-6860},
support = {2024YFA1308200//MOST | National Key Research and Development Program of China (NKPs)/ ; 2021YFA1301300//MOST | National Key Research and Development Program of China (NKPs)/ ; 82321005//MOST | National Natural Science Foundation of China (NSFC)/ ; BK20240095//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; },
mesh = {Animals ; *Diet, Ketogenic/methods ; *Gastrointestinal Microbiome/physiology ; Mice ; *Depression/metabolism/diet therapy/microbiology ; Male ; Mice, Inbred C57BL ; *Tyrosine/metabolism ; Behavior, Animal ; Brain/metabolism ; },
abstract = {Emerging evidence suggests the therapeutic potential of ketogenic diet (KD) for mood disorders such as depression, yet the underlying mechanisms are poorly understood. Here we report a gut microbe-to-brain signaling pathway through which KD protects against depressive-like behavior in mice. We show that KD feeding triggers a prompt and dynamic remodeling of the gut microbiome, the depletion of which abrogates the protective effect of KD against depressive-like behavior in stressed mice. Colonization with Roseburia intestinalis (R. intestinalis), which is enriched by 1-week KD, sustains the protective effect of KD against depressive-like behavior in mice. The protective effect of KD is linked to the reduction of a host-microbe co-metabolite p-Cresol sulfate (p-CS), the supplementation of which negates the protective effect of KD against depressive-like behavior. Mechanistically, p-CS enters the brain and activates lateral habenula (LHb) to counteract the protective effect of KD. Our findings uncover a gut microbiota-brain axis mechanism for KD consumption to protect against depressive-like behavior.},
}

Animals
*Diet, Ketogenic/methods
*Gastrointestinal Microbiome/physiology
Mice
*Depression/metabolism/diet therapy/microbiology
Male
Mice, Inbred C57BL
*Tyrosine/metabolism
Behavior, Animal
Brain/metabolism

@article {pmid42187072,
year = {2026},
author = {John, JM and Manjarres, Z and Zulkifly, NI and Plumb, AN and Pratt, ML and Sadler, KE},
title = {Male-specific analgesic effects of minocycline in sickle cell disease are mediated by microglia and the microbiome.},
journal = {Pain},
volume = {},
number = {},
pages = {},
doi = {10.1097/j.pain.0000000000004008},
pmid = {42187072},
issn = {1872-6623},
abstract = {Over 50% of individuals with sickle cell disease (SCD) experience chronic pain that is phenotypically distinct from their acute, vaso-occlusive crisis pain. Chronic SCD pain is commonly managed with opioid-based drugs that are associated with unwanted side effects, incomplete pain relief, and-in this population-accessibility issues. Thus, new treatments for chronic SCD pain are desperately needed. Here, we examined the analgesic efficacy of acute minocycline treatment in transgenic SCD mice. Sickle cell disease mice exhibit gut dysbiosis and chronic inflammation. Therefore, we hypothesized that minocycline would provide robust analgesia in this model given the drug's antibiotic and anti-inflammatory properties, respectively. Six days of minocycline treatment reversed chronic mechanical hypersensitivity only in male SCD mice. We identified 2 potential mechanisms underlying these sex-specific effects. First, we observed increased microgliosis only in the dorsal horn of male SCD mice. Minocycline treatment had opposite effects on microglial number in male and female SCD spinal cords. Second, minocycline treatment altered the gut microbiota in a sex-specific fashion; fecal microbiota transplant (FMT) from minocycline-treated female SCD mice induced widespread pain in recipients, whereas FMT from minocycline-treated male SCD mice did not. In summary, these experiments highlight novel sex-specific mechanisms of minocycline analgesia and support future exploration of minocycline use for SCD pain management, but only in male patients.},
}

@article {pmid42187337,
year = {2026},
author = {Cheng, X and Shi, H},
title = {Melatonin-Mediated Alleviation of Plant Response to Heavy Metals: From Integrative Mechanisms to Potential Applications.},
journal = {Journal of pineal research},
volume = {78},
number = {4},
pages = {e70150},
doi = {10.1111/jpi.70150},
pmid = {42187337},
issn = {1600-079X},
mesh = {*Melatonin/pharmacology/metabolism ; *Metals, Heavy/toxicity/metabolism ; *Plants/metabolism/drug effects ; Biodegradation, Environmental ; Plant Growth Regulators/metabolism ; },
abstract = {Global heavy metal (HM) stresses pose serious threats to environmental plants and animals. Melatonin has shown potent effects on improving plant stress resistance and phytoremediation upon HM stress, however, the systematic discussion of these extensive mechanisms and the gaps to practical applications remain elusive. This review aims to systemically provide the mechanistic understanding and environmental implication of melatonin integrative effects on alleviating HM toxicity. On the one hand, melatonin modulates HM homeostasis, induces HM detoxification, keeps photosynthesis and nutrient balance, and activates antioxidant defense systems to improve plant defense resistance to HM. On the other hand, melatonin triggers multiple transcriptional gene networks and extensive phytohormone crosstalks in plant defense responses. Notably, melatonin and melatonin-producing microbes exhibit potential applications in keeping plant growth and improving phytoremediation under HM conditions, indicating their effects on plant-microbiome-soil synergistic feedbacks. Finally, the current challenges and future perspectives of melatonin integrative mechanisms and applications are elucidated, highlighting that basic scientific questions and combined technologies should be further integrated to promote its practical applications. In summary, this review clarifies the multifaceted mechanisms of melatonin-integrated plant responses and potential remediation applications for environmental HMs, providing relative broad-spectrum and long-term strategies.},
}

*Melatonin/pharmacology/metabolism
*Metals, Heavy/toxicity/metabolism
*Plants/metabolism/drug effects
Biodegradation, Environmental
Plant Growth Regulators/metabolism

@article {pmid42187510,
year = {2026},
author = {Burjanivova, T and Buday, T and Mokra, D and Hanzlikova, Z and Babusikova, E and Podlesniy, P and Holubekova, V and Budis, J and Szemes, T and Plevkova, J},
title = {Challenges and Solutions in Low-Biomass Respiratory Microbiome Profiling: A Workflow for Bronchoalveolar Lavage Fluid Sequencing in Guinea Pigs.},
journal = {Physiological research},
volume = {75},
number = {2},
pages = {337-348},
pmid = {42187510},
issn = {1802-9973},
mesh = {Animals ; Guinea Pigs ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Workflow ; *DNA, Bacterial/genetics ; Male ; },
abstract = {Accurate profiling of the respiratory microbiome in low-biomass samples remains technically challenging due to host DNA contamination and limited microbial yield. This study aimed to optimize a methodological workflow for 16S rRNA sequencing of bronchoalveolar lavage fluid (BALF) obtained from guinea pig models with differing microbial statuses-specific pathogen-free (SPF) and conventionally bred (CON) animals. Using a comparative approach, we evaluated six commercial DNA extraction kits and tested different input DNA concentrations (1 ng vs. 0.5 ng) to enhance microbial detection while minimizing host DNA interference. Among the tested kits, only the ZymoBIOMICS DNA Microprep Kit yielded sufficient microbial DNA for downstream analysis. Real-time PCR and droplet digital PCR confirmed the microbial origin of the extracted DNA. Sequencing libraries were prepared from the V1-V3 regions of 16S rRNA genes and sequenced using the Illumina iSeq 100 platform. Taxonomic assignment and diversity metrics were analyzed using the MicrobAT pipeline. Our findings revealed significant differences in microbial composition between SPF and CON animals, notably in Mycoplasma abundance, which dominated the microbiota in CON but was nearly absent in SPF animals. Alpha and beta diversity metrics showed consistent stratification by animal group and input DNA concentration. However, a high proportion of unclassified reads-particularly in SPF samples-correlated strongly with sequences mapping to the Cavia porcellus genome, indicating substantial host DNA contamination. This study demonstrates the feasibility of microbiome profiling from low-biomass BALF samples in guinea pigs while highlighting the limitations of current sequencing and bioinformatic tools in distinguishing microbial from host-derived DNA. Our optimized workflow supports future respiratory microbiome studies in animal models and provides a foundation for improving host DNA depletion and reference databases tailored to non-human species.},
}

Animals
Guinea Pigs
*Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
Workflow
*DNA, Bacterial/genetics
Male

@article {pmid42187628,
year = {2026},
author = {Scocca, V and Sarnelli, G and Pesce, M and Navarro-Cuéllar, C and Dell'Aversana Orabona, G},
title = {Oral Manifestations in Patients with Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis.},
journal = {Dentistry journal},
volume = {14},
number = {5},
pages = {},
pmid = {42187628},
issn = {2304-6767},
abstract = {Background/Objectives: Oral manifestations are recognized extra-intestinal features of inflammatory bowel disease (IBD); however, their prevalence and clinical relevance remain controversial. This study aims to quantify the prevalence of individual oral outcomes in IBD patients and to evaluate their association with the disease compared with healthy controls. Methods: A systematic review was conducted in accordance with PRISMA guidelines. Eligible studies were identified through searches of PubMed/MEDLINE, Cochrane Library, Scopus, Ovid MEDLINE, and EMBASE. Studies reporting oral signs and symptoms in IBD patients were included. A single-arm meta-analysis was performed for oral ulcerations, dry mouth, halitosis, tongue alterations, oral aphthae, stomatitis, and taste changes. Risk of bias was assessed using the Newcastle-Ottawa Scale. Results: Twenty-one studies including 7791 participants (5914 IBD patients and 1877 controls) were analyzed. The pooled prevalence of oral ulcerations was 20% (95%CI11-33), dry mouth 32% (95%CI14-59), halitosis 22% (95%CI7-51), and tongue alterations 11% (95%CI4-24). Comparative analyses showed no statistically significant differences between IBD patients and controls for these outcomes. Conclusions: Although oral manifestations are frequently reported in IBD patients, their prevalence does not significantly differ from that of the general population. Standardized, multicenter studies are required to clarify disease-specific associations.},
}

@article {pmid42187670,
year = {2026},
author = {Bordbar-Khiabani, A},
title = {Simulated Body Fluids for Dental Implant Corrosion: A Practical Guide.},
journal = {Dentistry journal},
volume = {14},
number = {5},
pages = {},
pmid = {42187670},
issn = {2304-6767},
abstract = {Background/Objectives: Electrolytes used in in vitro corrosion testing critically determine the behavior inferred for metallic dental implants, yet formulations and their justifications are inconsistently reported across the literature. This review compiles and compares electrolytes employed to simulate the oral cavity and the bone-implant interface, linking their chemical composition to the corrosion mechanisms they target. Methods: This structured narrative review synthesized peer-reviewed literature on simulated electrolytes used for in vitro corrosion testing of metallic dental implants and implant-related alloys. Literature was identified using database searches and targeted reference screening, with emphasis on artificial saliva formulations, physiological simulated fluids, challenge chemistries, protein-containing media, hydrodynamic conditions, and microbiological models. Relevant formulations were standardized to grams per liter and grouped according to application domain and targeted corrosion mechanisms. Results: The analysis maps electrolyte selection to corresponding corrosion modes, including uniform dissolution, pitting, crevice, galvanic, and microbiologically influenced corrosion. Consolidated composition tables highlight how pH, halide concentration, calcium-phosphate balance, proteins, gas control, and flow conditions modify passive-film stability and metal-ion release. Dental-specific gaps are identified, notably the lack of a standardized fluoride-pH matrix and limited guidance for microbiome-integrated assays. Conclusions: Aligning electrolyte formulations with the research question enhances reproducibility and mechanistic interpretation. However, current in vitro corrosion data should be interpreted cautiously because quantitative links between simulated-fluid testing and clinical outcomes such as peri-implantitis, peri-implant bone loss, and implant failure remain insufficiently established. The adoption of shared reporting standards, dynamic programmable chemistries, and interoperable datasets may improve the translational value of future corrosion studies.},
}

@article {pmid42187679,
year = {2026},
author = {Guzmán-Flores, JM and Meza-Rodríguez, S and Vázquez-Jiménez, SI and Medrano-González, IDC and Gallegos-García, BL and Hernández-Villalobos, AL and Yañez-Acosta, MF and Alonso-Sanchez, CC},
title = {In Silico Identification of Dual-Action Compounds Targeting TLR2 and Streptococcus mutans Proteins for the Prevention of Early Childhood Caries.},
journal = {Dentistry journal},
volume = {14},
number = {5},
pages = {},
pmid = {42187679},
issn = {2304-6767},
abstract = {Background/Objectives: Early childhood caries (ECC) remains a major public health concern, with Streptococcus mutans as a primary etiological agent. Current treatments rely on broad-spectrum antimicrobials, which can disrupt the oral microbiome and promote resistance. This study applied a structure-based in silico pipeline to identify molecule modulators of Toll-like receptor 2 (TLR2), a key host receptor implicated in ECC, and to explore their binding potential against major S. mutans proteins. Methods: ECC-related genes were collected from public databases and analyzed by functional enrichment and protein-protein interaction (PPI) network analysis. Hub genes were ranked using centrality algorithms. Virtual screening on TLR2 (DrugCLIP) was followed by molecular docking of selected compounds against the TLR1/TLR2 heterodimer and 50 S. mutans proteins, complemented by in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling. Results: Fifty-four ECC-related genes and nine hub genes were identified, with TLR2 and cathelicidin antimicrobial peptide (CAMP) as central nodes. Virtual screening yielded five lead compounds fulfilling drug-likeness and toxicity criteria. Docking to TLR1/TLR2 showed favorable binding energies, with Z7684613096 showing the most consistent binding. V026-2549 displayed the highest number of strong interactions with S. mutans targets, including dTDP-glucose 4,6-dehydratase (rmlB), NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (gapN), glucosyltransferase C (gtfC), and 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (metE). Conclusions: Five candidate compounds with promising dual activity against TLR1/TLR2 and S. mutans proteins were prioritized for experimental validation, including TLR2 functional assays and in vitro anti-biofilm studies.},
}

@article {pmid42187718,
year = {2026},
author = {Wen, F and Chen, X and Chen, Q and Li, L and Zhao, Y and You, Y and Niu, S and Xia, Z},
title = {Nutrient Supply Gradients Modulate Cultivation-Driven Restructuring of Microbial Communities in Desert Soils.},
journal = {Biology},
volume = {15},
number = {10},
pages = {},
pmid = {42187718},
issn = {2079-7737},
abstract = {Understanding how cultivation conditions influence the recovery of microbial diversity is critical for interpreting cultivation-derived communities in relation to in situ microbial ecology, particularly in nutrient-limited environments such as desert soils. In this study, we investigated how an oligotrophic nutrient gradient shapes cultivation outcomes and enrichment-derived bacterial community structure in soils from the Taklimakan Desert. Three enrichment treatments representing decreasing nutrient availability-standard low-nutrient medium (R2A), diluted medium (DR2A), and sterile water-were used to compare enrichment-derived communities with the original soil microbiome. Amplicon sequencing revealed that cultivation substantially altered community composition and reduced both taxonomic richness and diversity relative to the original soil. Across enrichment treatments, bacterial communities were dominated by a limited number of taxa, whereas the original soil contained a broader range of low-abundance lineages. Within the enrichment system, variation in nutrient supply influenced the relative abundance of specific taxa, with differential responses observed at the genus level. In contrast, beta diversity analysis showed only limited separation among enrichment treatments, and co-occurrence network analysis indicated generally simple and weakly connected community structures across all conditions. Overall, our results demonstrate that cultivation represents the primary selective force shaping enrichment-derived bacterial communities, while nutrient supply intensity acts as a secondary modulator of taxon-specific enrichment. These findings highlight the importance of incorporating nutrient gradients into cultivation strategies to improve ecological interpretation and facilitate the recovery of oligotrophy-associated microorganisms from desert soils.},
}

@article {pmid42187725,
year = {2026},
author = {Ma, R and Lu, H and Zhang, S and Ji, H and Xin, F and Wang, G},
title = {Gut Microbiota Mediates Host Responses to Microplastic Exposure in Artemia salina.},
journal = {Biology},
volume = {15},
number = {10},
pages = {},
pmid = {42187725},
issn = {2079-7737},
support = {3160190//National Natural Science Foundation of China/ ; ZR2022MC167//the Natural Science Foundation of Shandong Province/ ; },
abstract = {BACKGROUND: Microplastics, derived from plastic degradation and industrial sources, are widely detected in aquatic environments and food systems, posing increasing environmental and ecological risks.

AIMS: This study aimed to investigate how microplastics affect host physiology and gut microbiota, as well as determine whether microbiota changes actively modulate host responses.

METHODS: Using A. salina as a model organism, we combined physiological assays, oxidative stress analysis, gut microbiome profiling, and bacterial functional validation under chronic polystyrene microplastics exposure.

RESULTS: Polystyrene microplastics accumulated in the gut and significantly impaired growth and survival, accompanied by reduced digestive enzyme activity and immune function, as well as increased oxidative stress, indicating disruption of physiological homeostasis. Microplastic exposure also induced microbial dysbiosis, characterized by decreased diversity and compositional shifts. Functional assays demonstrated that a bacterium enriched under exposure, Pseudomonas knackmussii, partially restored host growth and physiological functions while reducing oxidative stress.

CONCLUSIONS: These findings demonstrate that gut microbiota are not only altered by microplastic exposure but also actively modulate host responses to environmental stress, providing new insight into microbiota-mediated resilience under pollutant stress.},
}

@article {pmid42187733,
year = {2026},
author = {Sui, J and Wang, N and Wang, H and Li, Y and Wang, J and Duan, M and Liao, M and Jiang, Y and Zhou, X},
title = {Soil-Nutrient Depletion and Microbial Community Restructuring in Continuous Celery Cropping: Opposing Responses of Bacteria and Fungi.},
journal = {Biology},
volume = {15},
number = {10},
pages = {},
pmid = {42187733},
issn = {2079-7737},
support = {32001929//National Natural Science Foundation of China/ ; K25LD351//Development of Compound Microbial Inoculant for Soil Microecological Regulation Based on Wheat-maize Rotation/ ; K26LD069//Creation and Demonstration of Microbial Remediation Agent for Rhizosphere Regulation in Wheat on Saline-Alkaline Soil/ ; 202510447005//National College Student Innovation Training Program/ ; },
abstract = {Continuous cropping obstacles represent a major constraint in agricultural production, yet the underlying microbial mechanisms remain incompletely understood. This study systematically compared soil physicochemical properties, microbial diversity, community composition, and nutrient-microbe relationships between continuous cropping (CC) and non-continuous cropping (CK) celery rhizospheres using high-throughput sequencing, soil physicochemical analysis, and Mantel tests. The results revealed that CC soils exhibited severe depletion of available potassium (AK, 69.9% decreased) and alkali-hydrolyzable nitrogen (AN, 65.9% decreased), accompanied by a modest but statistically significant accumulation of total phosphorus (TP, 8.0% increased). Strikingly, bacterial and fungal communities displayed diametrically opposed diversity responses: CC significantly reduced bacterial α-diversity (Shannon: 5.66 vs. 6.67, p < 0.01) and richness (ACE: 2018 vs. 2623, p < 0.01), whereas fungal diversity and richness more than doubled under CC (ACE: 619 vs. 296, p < 0.01; Shannon: 4.13 vs. 3.34, p < 0.01). β-diversity analyses (NMDS and ANOSIM) confirmed fundamental community restructuring in CC soils for both microbial domains. At the taxonomic level, CC soils showed significant depletion of beneficial plant growth-promoting rhizobacteria (PGPR), including Bacillus (↓89.3%), Mesobacillus (↓72.8%), and Pseudomonas (↓30.8%), coupled with dramatic enrichment of the phytopathogenic genus Fusarium (10.9-fold increase, 8.81% vs. 0.81%, p < 0.001). LEfSe analysis identified Fusarium, Arrhenia, and Mortierella as specific biomarkers of CC soils, whereas Bacillus, Mesobacillus, Cladosporium, and Alternaria were biomarkers of CK soils. Mantel tests further revealed that CC significantly altered nutrient-microbe coupling relationships, with bacterial communities significantly correlated with TP, AN, and OC, and fungal communities with TP, TK, AP, and AN. Collectively, these findings demonstrate that continuous celery cropping shifts the rhizosphere microbiome from a bacterial-dominated profile associated with beneficial taxa (e.g., Bacillus, Pseudomonas) toward a fungal-enriched profile dominated by the pathogen Fusarium, suggesting a potential transition from a putatively disease-suppressive to a disease-conducive microbial state.},
}

@article {pmid42187739,
year = {2026},
author = {Ernstberger, H and Palmieri, G and Sun, JS},
title = {How Drosophila suzukii Acquires and Interacts with Its Microbiome Across Ecological Contexts.},
journal = {Biology},
volume = {15},
number = {10},
pages = {},
pmid = {42187739},
issn = {2079-7737},
support = {Presidential Postdoctoral Research Fellowship//Rutgers, The State University of New Jersey/ ; Goyette Family Endowment//Rutgers, The State University of New Jersey/ ; },
abstract = {Spotted wing drosophila (Drosophila suzukii; SWD) has become a globally invasive pest by ovipositing in ripening, intact fruit rather than decaying material, a niche distinct from most other drosophilids. An expanding body of work implicates microbes and microbially derived chemistry as key drivers of this ecology, shaping fly biology across life stages. However, much of this evidence is derived from microbiome surveys and observational comparisons, further constrained by uncontrolled diet history, laboratory rearing, and insufficient ecological context. We examine how the SWD microbiome differs in which taxa are present (composition), how flies pick up those taxa from fruit and maternal sources (acquisition), how long those taxa are retained across life stages (persistence), and how each of these varies with diet, geography, season, and host crops. We then address how microbial cues and fermentation state function as context-dependent drivers of adult attraction, avoidance, and oviposition, and how microbe-mediated interspecific interactions reshape substrate suitability and competition among drosophilids. Throughout, we critically evaluate experimental designs and identify gaps that impede causal inference. These include limited strain-level resolution, incomplete fungal characterization, and weak linkages between microbial community structure and host phenotypes. Key unresolved questions include how SWD maintains performance across diverse hosts, how microbes modulate sensory processing during seasonal shifts, and which microbial metabolites drive attraction, avoidance, and competition. Resolving these questions is a direct prerequisite for field-stable integrated pest management (IPM), including microbially informed behavioral lures, oviposition deterrents derived from pathogen- and competitor-associated volatiles, and competitor-mediated suppression strategies. The experimental priorities identified here translate directly into a roadmap for the next generation of mechanistically grounded, ecologically realistic SWD management tools.},
}

@article {pmid42187885,
year = {2026},
author = {Albusta, N and Isa, S and Alrahma, H},
title = {Lean Metabolic-Dysfunction-Associated Steatotic Liver Disease (MASLD): Pathophysiology, Diagnostic Challenges, Clinical Outcomes, and Management.},
journal = {Diseases (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
pmid = {42187885},
issn = {2079-9721},
abstract = {BACKGROUND/OBJECTIVES: Lean metabolic dysfunction-associated steatotic liver disease (lean MASLD) is an increasingly recognized phenotype occurring in individuals with normal body mass index (BMI), despite clinically important hepatic and cardiometabolic risk. This narrative review summarizes current evidence on its epidemiology, pathophysiology, diagnostic challenges, clinical outcomes, and management.

METHODS: A narrative literature review was conducted using PubMed, Embase, and Cochrane Library from database inception to March 2026. Relevant studies on lean MASLD/lean NAFLD, including cohort studies, meta-analyses, clinical trials, consensus statements, and practice guidelines, were prioritized.

RESULTS: Lean MASLD reflects interactions between visceral adiposity, insulin resistance, genetic susceptibility, sarcopenia, dietary and lifestyle factors, vitamin D deficiency, and gut microbiome alterations. Diagnosis is challenging because BMI and aminotransferase levels may underestimate metabolic vulnerability, MASH, or clinically significant fibrosis. Available data suggest increased liver-related events, liver-related mortality, and all-cause mortality compared with individuals without steatotic liver disease, although comparisons with non-lean MASLD remain heterogeneous. Resmetirom and semaglutide have expanded treatment options for noncirrhotic MASH with moderate to advanced fibrosis, but lean patients are underrepresented in pivotal trials.

CONCLUSIONS: Lean MASLD is an underrecognized but clinically important phenotype. Earlier recognition, fibrosis risk stratification, sarcopenia assessment, cardiometabolic optimization, and lean-specific therapeutic research are needed to improve outcomes.},
}

@article {pmid42187995,
year = {2026},
author = {Schauer, IE and Kuhn, K and Bradford, AP and Fought, AJ and Frank, DN and Kotter, CV and Robertson, CE and Duffy, K and Santoro, N},
title = {Effects of a Reprometabolic Syndrome-Inducing Eucaloric High-Fat Diet on Insulin Sensitivity, Body Composition, the Lipidome, and the Microbiome.},
journal = {Metabolites},
volume = {16},
number = {5},
pages = {},
pmid = {42187995},
issn = {2218-1989},
support = {R01HD087314//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; },
abstract = {Background: We previously demonstrated recapitulation of the relative hypogonadotropic hypogonadism of obesity, the Reprometabolic Syndrome (RMS), in women of normal BMI with a one-month high-fat, eucaloric diet (HFD). Objective: Assess effects of HFD on sleep, body composition and lifestyle and metabolic secondary outcomes and correlate insulin sensitivity changes with the RMS. Methods: A total of 18 normally cycling women aged 18-38 with BMI 18-24 kg/m[2] were enrolled for a four-month study including a eucaloric HFD (48% calories from fat) for one menstrual cycle. Activity, sleep, body composition, and the lipidome were measured in all participants. Fecal microbiome was analyzed in the last nine participants, and insulin sensitivity by two-stage hyperinsulinemic euglycemic clamp was measured before and after HFD in 15 participants. Results: Relative to the pre-diet period, BMI, activity and sleep measures did not change, except for waking after sleep onset (WASO), which appeared to decrease during and post HFD. DXA revealed statistically significant decreases in total percent fat, total fat mass, visceral fat volume, and trunk fat volume. Whole-body insulin sensitivity decreased with the HFD while adipocyte insulin sensitivity was unaffected. Insulin sensitivity changes did not correlate with change in gonadotropins or response to gonadotropin releasing hormone (GnRH). Multiple significant changes in plasma lipids were observed, including increased ceramides and glucosylceramides. Microbiome analysis revealed increased microbial diversity. Conclusions: A one-month eucaloric HFD that induced RMS in normal-weight, reproductive-aged women also induced whole-body insulin resistance (IR) and multiple lipidomics changes potentially associated with IR. These changes in IR occurred despite overall stable activity, BMI and sleep, but did not correlate with the HPO axis defects. The unexpected decrease in body fat and increase in microbial diversity may be related to specific dietary elements of the HFD.},
}

@article {pmid42188006,
year = {2026},
author = {Zhang, Y and Feng, T and Dong, Z and Ke, T and Storebakken, T and Cai, W and Shi, B and Huang, L},
title = {Lysolecithin Improves Lipid Metabolism and Gut Microbiota: An Integrated Transcriptome and Microbiome Analysis in Largemouth Bass (Micropterus salmoides) Fed Stearin-Based High-Lipid Diets.},
journal = {Metabolites},
volume = {16},
number = {5},
pages = {},
pmid = {42188006},
issn = {2218-1989},
support = {2025SNJF091//Zhejiang 'San-Nong Jiu-Fang' Agri-Tech Cooperation Initiative/ ; },
abstract = {Background: Supplementing aquafeeds with emulsifiers can enhance lipid utilization, yet the physiological effects of lysolecithin, derived from enzymatic lecithin conversion, remain under-explored. Objectives: This study examined the effects of lysolecithin supplementation on hepatopancreatic transcriptome and gut microbiota in largemouth bass (Micropterus salmoides) fed stearin-based high-lipid diets. Methods: Two diets were formulated: a control containing 130 g kg[-1] stearin fish oil (SO), and in the experimental diet (SL), 3.1 g kg[-1] rapeseed oil was replaced with 3.1 g kg[-1] lysolecithin oil. Each diet was fed to three replicate groups for 56 days. Hepatopancreas and distal intestine were sampled for transcriptome profiling, and gut microbiota were characterized at 28 and 56 days. Results: Lysolecithin supplementation resulted in 424 differentially expressed genes compared with the control (322 up- and 102 downregulated). KEGG enrichment indicated major effects on lipid metabolic processes, notably activation of the PI3K-AKT signaling pathway, enhanced adipocyte lipolysis, and modulation of adipocytokine signaling, suggesting improved insulin sensitivity and lipid mobilization. Histological analysis showed mild distal intestinal inflammation in the SO group. Gut microbiota composition shifted over time; lysolecithin increased the relative abundance of Cetobacterium and reduced potential opportunistic taxa compared with the control. Conclusions: Overall, dietary inclusion of lysolecithin improved lipid utilization in largemouth bass, likely by enhancing lipid metabolism and promoting beneficial gut microbial profiles. These findings support lysolecithin as a promising feed additive for optimizing high-lipid aquafeeds.},
}

@article {pmid42188162,
year = {2026},
author = {Tao, M and Zhang, J and Fan, Y},
title = {Metagenomic Analysis of Gut Microbiome Across Developmental Stage of Asian Corn Borer (Ostrinia furnacalis).},
journal = {Insects},
volume = {17},
number = {5},
pages = {},
pmid = {42188162},
issn = {2075-4450},
support = {Grant No. 32402469//National Natural Science Foundation of China/ ; },
abstract = {Ostrinia furnacalis is one of the most important agricultural pests in Asia. Previous studies utilizing 16S rRNA sequencing have established a foundational understanding of the taxonomic composition of its gut microbiota; however, the dynamic functional transitions across the host's entire life cycle remain poorly understood. In this study, we used metagenomic sequencing to systematically characterize the gut microbiome across six groups representing different life stages and sexes of O. furnacalis: first-instar, third-instar, and fifth-instar larvae, pupae, and adults (both males and females). Microbial richness and evenness vary significantly across six groups representing different life stages and sexes. Species richness is highest in the first-instar larvae (L1D2), while evenness is relatively high in both first- and third-instar larvae (L1D2 and L3D2). Additionally, no sex-based differences were observed in either indicator during the adult stage. Enterococcus mundtii is the primary species driving community succession and rapidly achieves dominance after the third-instar stage. Co-occurrence network analysis revealed that the first-instar larval network exhibits the highest complexity, with positive correlations accounting for 96.6% of all edges. Conversely, the fifth-instar larvae exhibits the greatest proportion of negative correlation edges at 29.13%, while the pupal stage network is the most dispersive, indicating microbial reorganization during metamorphosis. Functional annotation reveals that carbohydrate and amino acid metabolism pathways are significantly enriched during the larval stage. In contrast, the pupal stage is characterized by enrichment in environmental information processing and a notable increase in polysaccharide lyases (PLs). This shift indicates that the microbiota transitioned from degrading plant polysaccharides to foraging host-derived glycans. The number of resistance genes in the first-instar larvae is significantly higher than that in all other groups representing different life stages and sexes. Collectively, this study systematically reveals the dynamic succession patterns of the gut microbiome throughout the life cycle of O. furnacalis and provides a theoretical foundation for the development of microbiome-based pest management strategies.},
}