@article {pmid41703607,
year = {2026},
author = {Li, L and Sun, W and Tan, T and Xu, J and Chen, Y and Chen, Y and Gao, G and Ai, X and Zhou, J and Li, Y and Zhang, D and Lei, S},
title = {Limonin attenuates hyperlipidemia by regulating the gut microbiota-bile acid-farnesoid X receptor axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {},
pages = {},
pmid = {41703607},
issn = {1479-5876},
support = {2024ZD0532700//National Major Science and Technology Projects of China/ ; 2023AFB302//Natural Science Foundation of Hubei Province/ ; Q20234308//Youth Project of Scientific Research Project of Hubei Provincial Department of Education/ ; 2018YFZD025//Key science and technology project of Jingmen under Grant/ ; 2023YFZD043//Key science and technology project of Jingmen under Grant/ ; 2024ZDYF006//Key science and technology project of Jingmen under Grant/ ; WJ2023M173//Health and Family Planning Commission of Hubei Province/ ; 2022BCE060//Hubei Province key R & D project under Grant/ ; },
abstract = {BACKGROUND: Hyperlipidemia is an established risk factor for cardiovascular disease. Limonin, a natural tetracyclic triterpenoid compound found in the traditional Chinese herb Tangerine peel and citrus fruits, has been shown to ameliorate hyperlipidemia, although the underlying mechanisms of action are unknown. The present study employed a comprehensive approach integrating to assess the efficacy of Limonin in the treatment of hyperlipidemia and to explore its molecular mechanisms.

METHODS: Hyperlipidemia model was induced by high-fat diet (HFD). The effects of Limonin on hyperlipidemia were evaluated through serum, liver lipid, and Hematoxylin & eosin (H&E). Then, the mechanism of Limonin alleviates hyperlipidemia was explored by network pharmacology. Targeted metabolism was used to measure bile acids (BAs)’ changes in serum and fecal, and 16 S rDNA sequencing of gut microbiota. Finally, the expression of genes and proteins about FXR/FGF15, ASBT, and FGF15/FGFR4 signaling pathways in the distal ileum or liver was detected by qPCR, immunohistochemistry, and Western blotting.

RESULTS: The results confirmed the significant anti-hyperlipidemia effect of Limonin. Network pharmacology analysis revealed that Limonine alleviates hyperlipidemia is possibly closely pertaining to BAs metabolism. In a mouse model of hyperlipidemia, Limonin altered the colonic BAs profile, especially in terms of elevated levels of conjugated BAs. Limonin reshaped the structure of the gut microbiome by decreasing bile salt hydrolase (BSH)-producing genera, including Lactobacillus, Bacteroides, Clostridium, Streptococcus, and Adlercreutzia. Decreased BSH activity increased levels of conjugated BAs, which inhibited activation of ileum FXR, facilitated BAs synthesis and fecal BAs excretion. The decreased FXR activity resulted in lower expression of FGF15 and ASBT in the distal ileum, lower expression of FGF15 and its receptor in the liver, and increased expression of CYP7A1 in the liver.

CONCLUSION: Limonin remodels the gut microbiota to reduce BSH activity and to activate BAs synthesis pathways, thereby ameliorating dyslipidemia. These results provide a theoretical basis for clinical investigations into the use of Limonin in anti-hyperlipidemia therapies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07826-7.},
}

@article {pmid41709254,
year = {2026},
author = {Parlak, HM and Ozkul, C and Akman, AC and Guncu, GN and Ergunay, K and Akyon, Y},
title = {Submucosal microbiota profile in peri-implant health, peri-implant mucositis, and different severity levels of peri-implantitis.},
journal = {BMC oral health},
volume = {26},
number = {},
pages = {},
pmid = {41709254},
issn = {1472-6831},
abstract = {BACKGROUND: The unique and complex peri-implant microbiota harbors many species, mostly bacteria, and dysbiotic shift in microbiota induces peri-implant diseases. The aim of the study was to investigate the compositions and differences in submucosal microbial profiles in subject with different peri-implant heath statues, from peri-implant healthy (PH) to advanced peri-implantitis (PI).

METHODS: Submucosal plaque samples were obtained from 78 individuals with PH, peri-implant mucositis (PM), early, moderate, and advanced PI (PH:16, PM:16, PI-early: 14, PI-moderate: 16, and PI-advanced:16) and analyzed using sequencing of 16S rRNA gene. Differences of submucosal microbiome profiles between groups were evaluated with taxonomic abundances and microbial diversity using the alpha-diversity metrics (observed features, Shannon index, and Chao1 index), beta-diversity metrics (Bray–Curtis dissimilarity, unweighted, and weighted UniFrac distance), and linear discriminant analysis effect size analysis.

RESULTS: According to alpha-diversity and beta-diversity analysis, the submucosal microbiota diversity showed no difference in the PI, PM, and PH sites. Prevotella, Fusobacterium, Bacteroides, Treponema, Porphyromonas, Fretibacterium, and Veillonella genera showed high abundance in the PI groups. At the genus-level, compositional differences between two distinct clinical groups were found. Pseudoramibacter was significantly enriched in PM and PI groups compared to PH. Fretibacterium was the most discriminative taxa between PI-early and PH.

CONCLUSIONS: Despite similar overall microbial diversity, distinct compositional shifts in the submucosal microbiota were observed across peri-implant health and disease. Specific genera, particularly Fretibacterium and Pseudoramibacter, were associated with disease conditions and may serve as potential candidates for future biomarker research. These findings suggest that microbial composition, in addition to diversity, could be relevant to understanding peri-implant disease processes and may inform the development of diagnostic and preventive strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-07942-2.},
}

@article {pmid41714986,
year = {2026},
author = {Lu, S and Zhou, N and Song, X and Song, X and Qiao, X},
title = {Comparison of severe and general Mycoplasma pneumoniae pneumonia in children: a targeted next-generation sequencing based study.},
journal = {BMC infectious diseases},
volume = {26},
number = {},
pages = {},
pmid = {41714986},
issn = {1471-2334},
abstract = {BACKGROUND: The incidence and severity of Mycoplasma pneumoniae pneumonia (MPP) in children have increased after the pandemic of COVID-19, raising public concern. However, factors that affect the severity of MPP have not been well described. This study aimed to investigate the influence of Mycoplasma pneumoniae characters, respiratory co-existing pathogens, and host response on the severity of MPP.

METHODS: Clinical characteristics of 288 children hospitalized for MPP between November 2023 and July 2024 were analyzed retrospectively. Patients were divided into severe MPP (SMPP) and general MPP (GMPP) groups according to disease severity. Targeted next-generation sequencing (tNGS) was employed to analyze the respiratory pathogens of patients.

RESULTS: Of 288 cases, there were 113 SMPP and 175 GMPP. Compared with GMPP group, children with SMPP had significantly higher levels of neutrophil percentage, Neutrophil to Lymphocyte Ratio (NLR), C-Reactive Protein (CRP), Alanine aminotransferase (ALT), Lactic dehydrogenase (LDH) and D-D dimer (all P < 0.05), which reflected a higher host immune response in SMPP group. Meanwhile, tNGS based pathogen analysis showed that Mycoplasma pneumoniae characters (A2063G mutation or not, pathogen concentration) were not associated with the severity of MPP (P > 0.05). Furthermore, co-existing pathogens analysis showed that the SMPP group had a lower number of co-detected pathogens, children with human respiratory syncytial virus (RSV) co-existing were more frequent in the SMPP group (all P < 0.05). Multivariate analysis showed that lower number of co-detected pathogens (decreased microbial diversity), RSV co-existing, elevated CRP, and LDH were independent risk factors for SMPP.

CONCLUSION: Collectively, our data showed that respiratory microbiome and host response may play important roles in the pathology of MPP, decreased microbial diversity, RSV co-existing, CRP, and LDH level can predict the severity of MPP.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12914-6.},
}

@article {pmid41872963,
year = {2026},
author = {Kim, B and Kim, HN and Cheong, HS and Jeong, S and Kim, J and Park, DI and Joo, EJ},
title = {Fecal microbiota from hepatitis B-infected individuals alters triglyceride metabolism and microbial pathways in mice.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00825-5},
pmid = {41872963},
issn = {1757-4749},
support = {RS-2023-KH135855//Korea Health Industry Development Institute/Republic of Korea ; NRF-2021R1A2C4002454//National Research Foundation of Korea/ ; },
}

@article {pmid41873297,
year = {2026},
author = {Katsanos, A and Benekos, K and Karavasili, M and Gorgoli, K and Kostoulas, C and Gartzonika, K and Christodoulou, DK and Katsanos, K and Georgiou, I},
title = {Intestinal Microbiome of Newly Diagnosed Patients With Neovascular Age-Related Macular Degeneration: A 16S rRNA Gene Sequencing Study.},
journal = {Cureus},
volume = {18},
number = {2},
pages = {e103984},
pmid = {41873297},
issn = {2168-8184},
abstract = {BACKGROUND: This study aims to explore differences in the intestinal microbiome between patients with newly diagnosed neovascular age-related macular degeneration (AMD) and controls using 16S rRNA gene sequencing.

METHODOLOGY: In this cross-sectional study, stool samples from newly diagnosed White patients with neovascular AMD and controls were used for the assessment of the intestinal microbiome. The DNeasy PowerSoil Pro Kit (QIAGEN, Hilden, Germany) was used to extract microbial DNA before sequencing the V3-V4 hypervariable region of the 16S rRNA gene on the Illumina MiSeq system (Illumina, San Diego, CA). Bioinformatic analysis was performed on the Nephele platform using the DADA2 pipeline in R (ClinicalTrials.gov identifier: NCT05757674).

RESULTS: Thirty-three patients (age: 75 ± 7 years, 17 women) and 34 age- and sex-matched controls (age: 73 ± 7 years, 18 women) were analyzed. No differences in height, weight, body mass index, smoking, or systemic comorbidities were noted between the groups. The most prevalent phyla in both groups were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. The most prevalent genus was Bacteroides in both groups. Neither alpha nor beta diversity was different among the groups. The differential abundance analysis using Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2) showed that some Amplicon Sequence Variants (ASVs) from the Coprococcus genus were more abundant in controls than in patients with AMD, whereas several ASVs from Bacteroides were more abundant in the AMD group.

CONCLUSIONS: In our sample, the intestinal microbiome of newly diagnosed patients with neovascular age-related AMD showed some small but noteworthy differences compared to matched healthy controls. Some Bacteroides ASVs were enriched in AMD patients, while certain Coprococcus ASVs were more abundant in controls.},
}

@article {pmid41873486,
year = {2026},
author = {Pulaski, M and Weber, HC},
title = {Microbiome-derived signaling molecules and the brain-gut axis: emerging mechanisms and clinical implications.},
journal = {Current opinion in endocrinology, diabetes, and obesity},
volume = {},
number = {},
pages = {},
pmid = {41873486},
issn = {1752-2978},
abstract = {PURPOSE OF REVIEW: Recent advances in metabolomics, multi-omics integration, and neurogastroenterology have fundamentally reshaped understanding of the human gut microbiome. Rather than microbial composition alone, emerging evidence highlights microbial secretory and signaling activity as a central regulator of brain-gut communication. Understanding how microbiome-derived molecules interact with epithelial, immune, endocrine, and neural pathways is essential for advancing mechanistic insight and precision interventions in disorders of gut-brain interaction (DGBI).

RECENT FINDINGS: Recent studies demonstrate that the gut microbiome functions as a metabolic and endocrine signaling system, producing compounds such as short-chain fatty acids, bile acids, tryptophan-derived metabolites, polyamines, and lipid mediators that act on enteroendocrine cells, immune circuits, mechanosensory pathways, and vagal afferents. These signals are integrated centrally through brainstem and cortical networks, shaping gastrointestinal motility, visceral sensitivity, stress responsiveness, and affective processing. Functional dysbiosis and altered microbial signaling - rather than consistent taxonomic changes - appear to be primary modulators of brain-gut axis dysregulation.

SUMMARY: Emerging data calls for a reframing of gut-brain disorders as conditions of disrupted microbial signaling. Clinically, they support mechanism-based stratification and targeted dietary, microbiome-directed, and neuromodulatory therapies. The findings identify a need for functional biomarkers and targeted molecular approaches to advance precision medicine in DGBIs.},
}

@article {pmid41873937,
year = {2026},
author = {Wang, X and Liu, X and Zhou, G and Miao, Y and Zhao, X and Cao, Y and Wang, Z and Deng, D},
title = {A Watermelon-Like Micro/Nano Hierarchical Delivery Platform for Ulcerative Colitis by Regulating Redox Homeostasis and Remodeling Gut Microbiota.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e05873},
doi = {10.1002/adhm.202505873},
pmid = {41873937},
issn = {2192-2659},
support = {2022YFF1100303//National Key R&D Program of China/ ; 82172085//National Natural Science Foundation of China/ ; CPU2022QZ14//Double FirstRate Construction Plan of China Pharmaceutical University/ ; BK20190028//Distinguished Young Scholars/ ; },
abstract = {Ulcerative colitis (UC) is a refractory inflammatory bowel disease marked by mucosal barrier damage, immune dysregulation, and microbial imbalance. Current treatments are limited by systemic toxicity and inadequate targeting. Drawing inspiration from the "watermelon seed and watermelon" concept, this study employs microfluidic technology to encapsulate chondroitin sulfate (CSU) based nanoparticles (NPs) loaded with the antioxidant quercetin (Qu@CSCP) within hyaluronic acid/calcium alginate (HACM) hydrogel microspheres. This process yields a "watermelon-like" micro/nano hierarchical hydrogel microsphere system (QC@HACM) specifically designed for targeted combination therapy of UC. The HACM shell protects Qu@CSCP from the harsh gastrointestinal (GI) environment and enables targeted accumulation in inflamed colon tissue. Owing to its colon-adhesive properties, QC@HACM enhances the expression of tight junction proteins and reshapes the gut microbiota, enriching beneficial probiotics. Upon localized release, Qu@CSCP NPs activate the Nrf2/HO-1 antioxidant pathway, induce M2 macrophage polarization, and modulate the Bax/Bcl-2 ratio to suppress epithelial apoptosis. This dual mechanism effectively relieves oxidative stress and promotes mucosal healing. The therapeutic efficacy of these microspheres was further validated in a murine model of UC, as evidenced by reduced levels of pro-inflammatory cytokines accompanied by restoration of gut microbiota homeostasis. Consequently, this oral delivery platform represents a promising stepwise therapeutic strategy for comprehensive UC management.},
}

@article {pmid41873970,
year = {2026},
author = {Valenzuela-Diaz, S and Dikareva, E and Hickman, B and Kiljunen, S and Kolho, K-L and de Vos, W and Salonen, A and Korpela, K},
title = {Impact of phage enrichment on the observed infant gut phageome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0215325},
doi = {10.1128/spectrum.02153-25},
pmid = {41873970},
issn = {2165-0497},
abstract = {The human gut microbiota, particularly during infancy, plays a pivotal role in shaping long-term health outcomes. While research on the bacterial microbiota has advanced rapidly, the infant gut virome-dominated by bacteriophages-remains underexplored due to technical challenges in viral DNA detection and recovery. To address this, we optimized a polyethylene glycol (PEG)-based protocol for phage DNA enrichment tailored to the constraints of infant fecal samples, focusing on maximizing viral yield from minimal input material. We validated the optimized protocol on fecal samples from 41 infants at 1, 6, and 12 months of age and assessed the impact of phage enrichment on the observed gut phageome. The results demonstrate that the optimized protocol improves viral DNA recovery and significantly alters the observed virome composition, especially in older infants. Without appropriate enrichment, key features of the gut virome may be underrepresented or missed entirely. These findings underscore the importance of protocol optimization in virome studies and provide a scalable, cost-effective method for robust infant gut virome profiling.IMPORTANCEUnderstanding the viral component of the infant gut microbiome is essential for uncovering its role in early-life health, yet technical limitations have hindered its study. This work presents a systematically optimized and validated protocol for enriching viral DNA from infant stool samples, designed specifically for low-input material typical of early life. By adapting polyethylene glycol-based precipitation methods, we achieved consistent and scalable recovery of viral DNA across infants of different ages. Application of this protocol revealed key age- and delivery mode-specific differences in phage diversity and replication strategies that were undetectable using standard approaches. Our findings demonstrate that careful protocol optimization is critical for accurate virome profiling in infants and offer a practical solution to overcome longstanding methodological challenges in the field.},
}

@article {pmid41874128,
year = {2026},
author = {Yıldırım, S and Zhu, W and Cope, E and Lindemann, S and Suez, J and Shade, A},
title = {Sex-specific microbiome-host interactions: from infection to chronic disease-call for papers.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0015626},
doi = {10.1128/msystems.00156-26},
pmid = {41874128},
issn = {2379-5077},
}

@article {pmid41874175,
year = {2026},
author = {Ibarguren-Quiles, C and Blasco, L and López-Causape, C and Bleriot, I and Fernández-García, L and Arman, L and Barrio-Pujante, A and Ortiz-Cartagena, C and Aracil, B and Menéndez-Rodriguez, O and Mariñas-Pardo, L and Cantón, R and Oliver, A and Tomás, M},
title = {Identification and functional insights into new phage tail-like bacteriocins targeting Pseudomonas aeruginosa as new antimicrobials.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0289425},
doi = {10.1128/spectrum.02894-25},
pmid = {41874175},
issn = {2165-0497},
abstract = {The current health crisis caused by multidrug-resistant (MDR) pathogens is one of the health problems of most concern globally. Infections caused by these pathogens, such as Pseudomonas aeruginosa, lead to high rates of complications, particularly in compromised patients such as cystic fibrosis (CF) patients. The need to counteract and minimize the forecast future impact has led to the rescue of phage therapy. The use of bacteriophages has important advantages, including highly specific targeting, self-amplification at the infection site, minimal disruption of the microbiome, safety, and biocompatibility. However, the capacity of bacteria to escape these entities results in a form of resistance that compromises the effectiveness of the therapy. This involves the search for potential alternatives, such as the phage tail-like bacteriocins (PTLBs), also named as tailocins. These high-molecular-weight particles resemble the tail structure of bacteriophages and are characterized by the absence of genetic material, avoiding the development of resistance, one of the major handicaps associated with phage therapy. In this study, we detected 34 different PTLBs in 75 P. aeruginosa genomes, with different serotypes and sequence types, 11 of which were characterized as novel F-type PTLB subtypes (F13-F24). Furthermore, we report that four selected PTLBs (R1, F15, F19, and R3-F24) can deal with bacterial infection, with the R1 and the F15 PTLBs being the most efficient in clearing infection in vitro, yielding a survival rate of more than 75% in the Galleria mellonella larvae in vivo model. This reaffirms the potential of PTLBs to control P. aeruginosa infections, which can cause chronic infections in some patients, such as people with CF, due to its strong impact as a MDR bacterium.IMPORTANCEThe 75 Pseudomonas aeruginosa genomes from people with cystic fibrosis in the study collection included at least one phage tail-like bacteriocins (PTLB) cluster. From the 34 different PTLBs detected in the study collection, 7 were R-type, 10 were complex (R- and F-type encoded), and 14 were F-type PTLBs. Eleven new F-type PTLBs were described in the P. aeruginosa collection under study. An association between the O-antigen present on the surface of the P. aeruginosa isolate and the encoded PTLB subtype was detected. The R1 and F15 PTLB subtypes display high antimicrobial activity both in vitro and in vivo (Galleria mellonella).},
}

@article {pmid41874177,
year = {2026},
author = {Poursalavati, A and Laforest-Lapointe, I and Fall, ML},
title = {SS-VIME: a single-source virome-microbiome extraction protocol toward comprehensive soil community analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0332325},
doi = {10.1128/spectrum.03323-25},
pmid = {41874177},
issn = {2165-0497},
abstract = {Integrated analysis of soil microbiomes and their associated viromes is critical for understanding ecosystem function, yet is hampered by the profound spatial heterogeneity of soil, which introduces significant bias when using separate extraction workflows and/or subsampling strategies to capture fungal, bacterial, and viral communities. Here, we present single-source extraction for unified soil virome-microbiome profiling (SS-VIME), a protocol that overcomes this limitation. Based on extended cellulose column chromatography, this method sequentially elutes distinct DNA and double-stranded RNA (dsRNA) fractions from a single soil lysate. We validated the protocol using sterilized soil co-spiked with a ZymoBIOMICS microbial community standard and a synthetic viral dsRNA fragment. Sequencing confirmed that the DNA fraction accurately recovered the theoretical bacterial (16S rRNA gene) and fungal (ITS) community profiles, while the dsRNA fraction demonstrated highly specific recovery of the target viral signature. The protocol was then successfully applied to characterize the complex native communities in environmental soil samples. The SS-VIME protocol provides a streamlined approach for isolating high-quality nucleic acids suitable for downstream applications. By using dsRNA as a proxy for viral activity and eliminating subsample bias, this method provides a robust, accessible, and unified platform to investigate virus-host dynamics in situ, paving the way for a more holistic understanding of the soil microbiome.IMPORTANCEThe study of soil microbes and their viruses, which are central to ecosystem health, is fundamentally limited by technical barriers. Separate extraction workflows for each group introduce sampling bias, obscuring the true ecological relationships within soil's spatially complex micro-environments. Our single-source virome-microbiome extraction (SS-VIME) protocol directly overcomes this by efficiently recovering both microbial DNA and viral double-stranded RNA (dsRNA) from one sample. This unified approach is not only cost-effective but, by using dsRNA as a signature of viral activity, captures a more accurate and representative profile of the soil active virome. SS-VIME provides the foundation for robustly investigating how viruses modulate soil health, carbon cycling, and agricultural productivity, moving the field from correlational studies toward a direct, integrated view of the soil ecosystem.},
}

@article {pmid41874180,
year = {2026},
author = {Garzon, A and Miramontes, C and Weimer, BC and Profeta, R and Hoyos-Jaramillo, A and Fritz, HM and Pereira, RV},
title = {Characterizing the nasopharyngeal microbiome and resistome of dairy cattle with and without bovine respiratory disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0264825},
doi = {10.1128/spectrum.02648-25},
pmid = {41874180},
issn = {2165-0497},
abstract = {Bovine respiratory disease (BRD) remains a significant economic challenge in dairy cattle despite extensive vaccination programs that have been developed and implemented during the last few decades. This study investigated the nasopharyngeal microbiome and resistome of dairy cattle across various life stages to understand the roles of microbial communities associated with BRD. A case-control study was conducted on three commercial dairy farms in Northern California, collecting nasopharyngeal swabs from 69 animals, including preweaned calves, weaned heifers, and lactating cows with and without BRD. Shotgun metagenomic sequencing was used to characterize both microbiome and resistome profiles observed at the time of BRD diagnosis. Results revealed that BRD is associated with distinct microbial community patterns, rather than the increased abundance of a specific pathogen. Age was a critical factor influencing microbial diversity, with adult cows showing the highest diversity and weaned heifers with BRD showing the lowest. A total of 1,164 bacterial species were identified, with BRD cases harboring 14 unique species compared to control animals. BRD cases were characterized by the co-occurrence of multiple respiratory pathogens, including Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mesomycoplasma species, which showed positive correlation with BRD cases but negative correlations in BRD controls, while BRD control animals showed significantly higher abundance of commensal Staphylococcus species. Resistome analysis identified 65 antimicrobial resistance genes, with BRD cases harboring more unique resistance genes than BRD controls. These findings challenge traditional single-pathogen models and demonstrate that BRD is likely the result of complex microbial community interactions and changes in community abundance, providing new potential targets to explore when considering prevention strategies toward promoting microbial communities that prevent or reduce the risk of BRD.IMPORTANCEBovine respiratory disease (BRD) represents one of the most economically challenging conditions in cattle production, with an estimated direct cost that exceeds $165 million annually in the United States alone. Despite decades of vaccination efforts targeting known pathogens, BRD prevalence remains unchanged, indicating an incomplete understanding of disease pathogenesis. This study provides critical insights by shifting focus from individual pathogens to entire microbial communities, revealing that BRD involves complex bacterial interactions, as well as the role of the understudied nasal commensal microbiome in healthy animals. The identification of distinct "pathobiomes" associated with disease and protective commensal communities in healthy animals fundamentally changes approaches to BRD prevention and treatment. The discovery that age significantly influences microbiome stability highlights critical intervention periods. Furthermore, the association between BRD and increased antimicrobial resistance genes raises concerns about current treatment and overall management practices, selecting for drug-resistant communities. This research provides a foundation for developing microbiome-based diagnostic tools and interventions supporting healthy microbial ecosystem development.},
}

@article {pmid41874246,
year = {2026},
author = {Koh, H},
title = {Phylogeny-informed random forests for human microbiome studies.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0345125},
doi = {10.1128/spectrum.03451-25},
pmid = {41874246},
issn = {2165-0497},
abstract = {UNLABELLED: Random Forest is a widely used tree-based ensemble learning algorithm that efficiently captures complex nonlinear relationships and higher-order feature interactions with no distributional assumptions to be satisfied. It is also well-suited to human microbiome studies, where the data are highly skewed, overdispersed, discrete, and irregular. Here, I pay particular attention to the phylogenetic tree information that reflects evolutionary ancestry and functional relatedness among microbial features. Proper incorporation of phylogenetic tree information into microbiome data analysis has provided new insights and improved analytical performance. In this paper, I introduce an extension of the Random Forest algorithm that incorporates phylogenetic tree information, named Phylogeny-Informed Random Forests (PIRF), to improve predictive accuracy in human microbiome studies. The core mechanism of PIRF lies in its localized approach; rather than treating all features as competing globally to be selected or weighted, PIRF identifies informative features within each phylogenetic cluster (i.e., a localized group of microbial features that are evolutionarily and functionally related), thereby enriching functional representations while reducing tree-to-tree correlation. I demonstrate the high predictive accuracy of PIRF, compared with other off-the-shelf tools, across seven benchmark tasks: four classification problems (gingival inflammation, immunotherapy response, type 1 diabetes, and obesity) and three regression problems (cytokine level, age based on oral microbiome, and age based on gut microbiome).

IMPORTANCE: PIRF is an extension of the Random Forest algorithm that incorporates phylogenetic tree information to improve predictive accuracy in human microbiome studies. PIRF can serve as a useful tool for microbiome-based disease diagnostics and personalized medicine. The software and tutorials are freely available as an R package, named PIRF, at https://github.com/hk1785/PIRF.},
}

@article {pmid41874370,
year = {2026},
author = {Liu, C and Dan, L and Wang, X and Chen, L and Yuan, X},
title = {Gut microbiota impact on lung diseases: a mini review of clinical evidence.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0043025},
doi = {10.1128/iai.00430-25},
pmid = {41874370},
issn = {1098-5522},
abstract = {The gut-lung axis represents a bidirectional communication network through which the gut microbiota (GM) influences respiratory health. This mini-review synthesizes clinical evidence on the role of the GM in lung diseases. We focused exclusively on human clinical trials, randomized controlled trials, meta-analyses, and systematic reviews, sourced from major databases after duplicate removal. The evidence indicates that GM dysbiosis is a significant risk factor for the susceptibility and severity of various respiratory conditions, including asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), and infections, such as COVID-19 and pneumonia. Specific microbial signatures and metabolic profiles, particularly involving short-chain fatty acids (SCFAs), are associated with disease states and outcomes. Interventions like probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) show promise in modulating the GM and improving clinical parameters, though their efficacy can be inconsistent and influenced by confounding factors. In conclusion, the GM is a promising therapeutic target for lung diseases. However, future research must prioritize large-scale, longitudinal clinical trials and deeper mechanistic investigations to establish causality and develop effective, personalized microbiome-based therapies.},
}

@article {pmid41874395,
year = {2025},
author = {Park, G and Chakrabarty, P and Efron, PA and Nagpal, R},
title = {Dysbiosis and the gut-brain axis impairment in the pathophysiology of Alzheimer's disease and related dementias: is 'pathobiome' an etiological element?.},
journal = {Essays in biochemistry},
volume = {69},
number = {6},
pages = {},
doi = {10.1042/EBC20253055},
pmid = {41874395},
issn = {1744-1358},
mesh = {Humans ; *Dysbiosis/microbiology/complications/physiopathology ; *Alzheimer Disease/physiopathology/microbiology/etiology/metabolism/pathology ; *Gastrointestinal Microbiome ; *Brain/metabolism/physiopathology ; Animals ; *Dementia/physiopathology/microbiology/etiology ; },
abstract = {The gut microbiome plays a pivotal role in host metabolic, cardiovascular, and immune health. Increasing evidence also links it to aging-associated neurocognitive decline and neurodegenerative disorders, including Alzheimer's disease (AD) and related dementias. While the precise mechanisms of the gut-microbiome-brain axis remain incompletely understood, recent findings challenge the traditional view of AD as a disease confined to the central nervous system. Aging-associated gut dysbiosis, marked by loss of beneficial microbes, expansion of opportunistic pathogens, and reduced microbial diversity, can compromise intestinal barrier integrity, leading to 'leaky gut' and increased translocation of microbial components or pathogens into the circulation. These elements may cross a weakened blood-brain barrier, triggering neuroinflammation, amyloid-beta accumulation, tau hyperphosphorylation, and neuronal injury. Such pathobiome-driven inflammatory cascades may initiate or accelerate AD pathology, shifting the etiological perspective beyond the amyloid and tau hypotheses toward systemic and peripheral contributors. Our work and others' have identified distinct dysbiotic microbiome signatures in AD, supporting the possibility that AD pathogenesis may begin in the gut. Restoring microbial homeostasis through targeted interventions could attenuate neuroinflammatory and neurodegenerative processes, offering a novel preventive and therapeutic avenue. This emerging paradigm underscores the need for comprehensive, mechanistic, and longitudinal studies to define how aging-driven microbiome alterations influence the gut-brain axis and contribute to AD progression.},
}

Humans
*Dysbiosis/microbiology/complications/physiopathology
*Alzheimer Disease/physiopathology/microbiology/etiology/metabolism/pathology
*Gastrointestinal Microbiome
*Brain/metabolism/physiopathology
Animals
*Dementia/physiopathology/microbiology/etiology

@article {pmid41874416,
year = {2026},
author = {Koseli, E and Tyc, KM and Buzzi, B and Akbarali, HI and Damaj, MI},
title = {The Role of the Gut Microbiome in Nicotine Withdrawal and Dependence.},
journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco},
volume = {},
number = {},
pages = {},
doi = {10.1093/ntr/ntag057},
pmid = {41874416},
issn = {1469-994X},
abstract = {INTRODUCTION: Smoking is considered a global pandemic with more than 1.3 billion people being active smokers. Increasing evidence suggests that nicotine exposure can lead to changes in the gut microbiome, increases in permeability, and impaired mucosal immune responses in the gastrointestinal tract. However, the literature on behavioral aspects of nicotine-microbiome interaction, such as dependence and withdrawal, is limited. In this study, we used homologous fecal material transplants (FMT) to modify the gut microbiome and its impact on the intensity of nicotine withdrawal in mice.

METHODS: We used osmotic minipumps as an application of chronic nicotine for 15 days and orally gavaged FMT 2x a day to the mice. We assessed the nicotine withdrawal by measuring the number of somatic signs and anxiety-like behaviors at 24 h and 1 week after the mini pump removal. Fecal samples were also collected points to identify the gut microbiome changes.

RESULTS: Fecal transplants reduced the number of somatic signs and anxiety-like behaviors in nicotine-treated mice up to a week after the removal of minipumps. The shotgun metagenomic results of the fecal samples from 24 h after minipumps removal time point show altered gut microbiome with a significant shift in the species composition between the nicotine treated and its homologous FMT treatment.

CONCLUSIONS: Our results indicate that under our experimental conditions fecal transplant can reduce the severity of nicotine withdrawal. This suggests that interactions along the gut-brain axis are important for the development of nicotine dependence and might help lower the risk of cancer and other serious health problems in humans.},
}

@article {pmid41874734,
year = {2026},
author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM},
title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41874734},
issn = {1573-0972},
abstract = {UNLABELLED: This study explores the root-associated microbiome of Calotropis procera, a drought-adapted, invasive plant thriving in Brazil. We analyzed microbial communities from the root endosphere, rhizosphere, and adjacent soil in two contrasting ecosystems: Caatinga (semi-arid) and Restinga (coastal). Using 16S rDNA sequencing and shotgun metagenomics, we tested three hypotheses: (I) environmental specificity of the rhizospheric bacterial microbiome, (II) continuity of bacterial composition between bulk soil and rhizosphere, and (III) host-driven filtering of the endophytic microbiome. Despite differing soil conditions – more sodium in Restinga and higher organic carbon in Caatinga – microbial profiles in root compartments remained consistent. The root endosphere was enriched with stress-tolerant bacteria and novel archaea, while fungal genera included Fusarium and Puccinia. Results partially supported environmental specificity and showed moderate soil-rhizosphere continuity, with evidence of plant-mediated selection. Host filtering was evident for bacteria and fungi but not archaea. These data indicate a C. procera-mediated regulation of its root microbiome composition, whereby the plant may either selectively recruit specific taxa from prevalent soil microbial communities (e.g., through root exudates) or vertically transmit a conserved subset of its microbiome via seeds. Our study enhances understanding of the C. procera microbiome and its microbial interactions, identifying potential candidates for future biotechnological applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04902-4.},
}

@article {pmid41874766,
year = {2026},
author = {Tamang, A and Chaudhary, S and Pandey, SS and Hallan, V},
title = {Plant viruses and the microbiome: a complex network shaping plant health and disease resistance.},
journal = {Archives of virology},
volume = {171},
number = {4},
pages = {},
pmid = {41874766},
issn = {1432-8798},
support = {CSIR - Indian Institute of Chemical Biology//CSIR - Indian Institute of Chemical Biology/ ; },
mesh = {*Microbiota ; *Plant Diseases/virology/microbiology/immunology ; *Plant Viruses/physiology ; *Plants/virology/microbiology/immunology ; *Disease Resistance ; Host-Pathogen Interactions ; },
abstract = {Plant viruses and microbiomes are pivotal to plant health, growth, and their ability to withstand environmental challenges. However, the extent to which viruses engage in direct or indirect crosstalk with plant-associated microbial communities remains largely unexplored. Traditionally, plant viruses are considered as harmful agents that disrupt normal plant functions, but new research indicates they may also engage in complex interactions with the plant's microbiome. On the other hand, the plant microbiome, comprising a diverse assembly of bacteria, fungi, and other microbes, can influence the plant's responses to viral infections, potentially altering the course of the disease. Thus, we emphasize the intricate interplay between plant viruses and microbiomes, particularly how viruses might "communicate" with microbial communities to alter the host environment or bypass immune defenses. The mechanisms driving these interactions, such as virus-induced shifts in plant metabolism, signaling pathways, and immune responses that indirectly affect microbiome composition are also discussed. The beneficial effect of plant-associated microbial communities against viral infections and the strategy of microbiome-based approaches for managing viral diseases are also focused. By moving beyond the traditional view of pathogen-host interactions, this review will highlight the importance of considering the three-way relationship among plants, viruses, and microbiomes to advance our understanding of plant health and foster innovative solutions for sustainable agriculture.},
}

*Microbiota
*Plant Diseases/virology/microbiology/immunology
*Plant Viruses/physiology
*Plants/virology/microbiology/immunology
*Disease Resistance
Host-Pathogen Interactions

@article {pmid41874795,
year = {2026},
author = {Kwinten, KJJ and Johnson, JE and van Altena, AM and Hoogerbrugge, N and Davidson, EJ and de Hullu, JA},
title = {Prevention strategies for hereditary gynaecological cancer in Lynch syndrome.},
journal = {Familial cancer},
volume = {25},
number = {2},
pages = {},
pmid = {41874795},
issn = {1573-7292},
support = {NIHR304303//NIHR Research Professorship/ ; NIHR203308//NIHR Manchester Biomedical Research Centre/ ; },
abstract = {Lynch syndrome is a hereditary cancer predisposition condition associated with an elevated lifetime risk of colorectal, endometrial, ovarian, and several other malignancies. This review provides an updated overview of evidence-based prevention strategies for gynaecological cancers in patients with Lynch syndrome. Risk-reducing hysterectomy with bilateral salpingo-oophorectomy is the most effective intervention for lowering cancer incidence and mortality, but is associated with surgical morbidity and requires careful consideration of reproductive plans and the adverse consequences of premature menopause. Gynaecological surveillance using transvaginal ultrasound and endometrial biopsy is widely implemented as an alternative; however, available evidence is heterogeneous and indicates no benefit in reducing mortality. Novel approaches—such as biomarker-based detection using DNA methylation analysis of cervicovaginal samples, liquid biopsy techniques, and microbiome profiling—offer promising, non-invasive alternatives but require prospective validation in Lynch-specific populations. Chemoprevention with hormonal agents and aspirin may reduce cancer risk, while vaccine-based prevention strategies are under active investigation. Adoption of a healthy lifestyle is recommended for overall health, although its impact on gynaecological cancer risk in Lynch syndrome remains uncertain. Future research should prioritise prospective trials to establish optimal cancer prevention protocols, validate novel biomarkers and preventive cancer vaccine strategies, and evaluate the long-term effectiveness, acceptability, and cost-effectiveness of combined preventive approaches to improve outcomes in this high hereditary-risk population.},
}

@article {pmid41874898,
year = {2026},
author = {Son, JS and Lee, SY and Sang, MK and Spinelli, F and Ryu, CM},
title = {Protective holobiome promotes strawberry tolerance of biotic stresses.},
journal = {Stress biology},
volume = {6},
number = {1},
pages = {},
pmid = {41874898},
issn = {2731-0450},
support = {. RS-2022-RD010288//RDA/ ; CN00000022//Italian Academy for Advanced Studies in America, Columbia University/ ; KRIBB202434//Korea Research Institute of Bioscience and Biotechnology/ ; },
abstract = {The commercial cultivation of strawberry (Fragaria × ananassa) is increasingly challenged by biotic stresses such as plant pathogens and insect pests, while climate change exacerbates abiotic stresses. Reliance on chemical fumigants and broad-spectrum pesticides presents risks to human health, environmental quality, and microbial diversity. The strawberry holobiome, defined as the integrated community of plant-associated microorganisms that inhabit the rhizosphere, phyllosphere, endosphere, and fruit surface, is emerging as a key determinant of plant health and productivity. Recent metagenomic and metabolomic studies have identified cultivar-specific microbial consortia that suppress plant disease, enhance stress tolerance via induced systemic resistance, and modulate fruit quality. The engineering of synthetic microbial communities (SynComs) offers a targeted approach to microbiome augmentation, but the lack of high-resolution functional data hinders the development of effective SynComs, especially in hydroponic and substrate culture systems. This review synthesizes recent advances in holobiome profiling, evaluates microbial biocontrol strategies against major pathogens, and outlines future directions, including AI (artificial intelligence)-driven community design, integrated multi-omics analysis, and microbiome-assisted breeding. Addressing these gaps will enable precision management of the strawberry microbiome to sustain yield, quality, and resilience under dynamic environmental conditions.},
}

@article {pmid41875058,
year = {2026},
author = {Martínez Ruiz, M and Tabor-Simecka, L and Graham, JL and Randolph, C and Fox, R and Lan, R and Pack, L and LeRoith, T and Stanhope, KL and Yeruva, L and Havel, PJ and Piccolo, BD},
title = {Improvement of glucose homeostasis during leptin treatment does not alter the intestinal microbiome in male diabetic UC Davis Type-2 Diabetes Mellitus rats.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00412.2025},
pmid = {41875058},
issn = {1522-1547},
support = {6026-10700-001-00D//USDA | Agricultural Research Service (ARS)/ ; UM1TR004909//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; 1K12TR004924//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; U24DK135074//HHS | NIH | NIDDK | Division of Diabetes, Endocrinology, and Metabolic Diseases (DEM)/ ; R01AG085572//HHS | NIH | National Institute on Aging (NIA)/ ; },
abstract = {Gut dysbiosis contributes to type 2 diabetes (T2DM) progression according preclinical evidence. Alterations in gut microbiome, energy metabolism, and barrier function were observed in individuals with obesity and insulin resistance. However, it remains unclear whether therapeutic interventions can reverse these alterations. This study aimed to evaluate whether improvements of glucose homeostasis resulting from leptin administration can lead to changes in colonic epithelial metabolism and barrier function in male UC Davis Type 2 Diabetic Mellitus (UCD-T2DM) rats. Male UCD-T2DM rats (age: 173 ± 41 days) with 6 weeks post-onset of diabetes were randomized to receive daily subcutaneous injections of either PBS (control; n=12) or recombinant leptin (0.5 mg/kg; n=12) for four weeks. Metabolic and intestinal outcomes were assessed, including glucose tolerance, insulin sensitivity, GLP-1 levels, gut permeability, microbiota composition, short chain fatty acids (SCFA) content, epithelial hypoxia, intestinal morphology, and gene/protein expression. Leptin treatment significantly reduced food intake and improved glucose homeostasis and insulin sensitivity without affecting body weight. No changes were observed in microbiome composition, gut permeability, or epithelial hypoxic gradients. Ileal villus height was decreased, while colonic crypt depth was not different between leptin-treated rats and control rats. Butyric, isocaproic, and valeric acids levels were increased in colonic content, colonic expression of Pparg and Ldha was downregulated, while PHD2 and Occludin protein levels were upregulated in leptin-treated compared with control. Despite improvements of glucose homeostasis, chronic leptin treatment did not modify gut microbiota or barrier function markers, and colonic metabolic gene expression showed no clear adaptive shift.},
}

@article {pmid41875216,
year = {2026},
author = {Castillo-Moral, Á and Toda-Ferran, C and Bulló, M and Teichenné, J and Escoté, X},
title = {Nutraceuticals and the Microbiota-Gut-Brain Axis: A Pathway for Preventing Cognitive Decline.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag017},
pmid = {41875216},
issn = {1753-4887},
support = {//Vicente Lopez Program (Eurecat)/ ; //Autonomous Government of Catalonia/ ; 2021 SGR 00213//Departament de Recerca i Universitats de la Generalitat de Catalunya to the Nutrition and Metabolic Health Research Group/ ; 2021 SGR 01556//Precision Nutrition, Wellness and Prevention of Metabolic Diseases/ ; },
abstract = {With the global rise in aging populations, cognitive impairment and neurodegenerative diseases, such as Alzheimer's disease (AD), present a growing public health issue. Current pharmacological treatments primarily target symptoms rather than underlying causes, necessitating the exploration of alternative preventive strategies. Nutraceuticals have emerged as promising candidates for neuroprotection due to their ability to modulate oxidative stress, neuroinflammation, and mitochondrial function. This narrative review aimed to evaluate the neuroprotective potential of nutraceuticals and their interactions with the microbiota-gut-brain axis in preventing age-related cognitive decline. A comprehensive search of the scientific literature using the PubMed, Scopus, and Web of Science databases was undertaken, focusing on publications during the period 2010-2025. Nutraceuticals, including vitamins, omega-3 fatty acids, coenzyme Q10, polyphenols, and isothiocyanates, exhibit neuroprotective properties through antioxidant, anti-inflammatory, and mitochondrial-support mechanisms. The gut microbiota plays a crucial role in regulating the bioavailability and efficacy of these compounds. Microbiome-based interventions, such as prebiotics, probiotics, and fecal microbiota transplantation demonstrate potential in modulating neuroinflammatory responses and supporting cognitive function. Nutraceutical and microbiome-targeted interventions represent promising, low-risk strategies for preventing cognitive decline. Their ability to modulate neuroinflammation and oxidative stress underscores their potential for future clinical applications. Further large-scale studies are needed to validate their efficacy and explore personalized approaches adapted to individual microbiome profiles.},
}

@article {pmid41875499,
year = {2026},
author = {Li, F and Liang, X and Li, J and Cui, M and Ho, TE and Li, J and Yuan, Z and Meng, W and Man Lo, EC and Fan, M and Zhang, Z and Jin, L and Chen, X and Lu, H and Jiang, Y},
title = {Oral microbiome perturbations link periodontal health to cognitive ageing in a large community cohort.},
journal = {EBioMedicine},
volume = {126},
number = {},
pages = {106231},
doi = {10.1016/j.ebiom.2026.106231},
pmid = {41875499},
issn = {2352-3964},
abstract = {BACKGROUND: Emerging evidence implicates the oral-brain axis in neurodegeneration, yet large community-based studies remain limited. This study aimed to examine associations between periodontal health, oral microbiome, and cognitive performance, and to explore potential biological pathways underlying these relationships.

METHODS: We conducted a cross-sectional analysis of 1157 participants from the community-based Taizhou Imaging Study, all of whom underwent comprehensive periodontal examinations, salivary microbiome profiling, and cognitive assessments. Periodontal health and microbiome features were treated as exposures, and cognitive performance as the outcome. Associations between periodontal indices and cognitive scores were assessed using beta regression models adjusted for relevant confounders. Cognition-related microbial features were identified using Multivariate Associations with Linear Models (MaAsLin3), followed by mediation analyses to explore potential pathways linking periodontal health to cognitive function.

FINDINGS: Five clinical periodontal indices were found to be inversely associated with cognitive performance. Ten microbial genera (e.g., Haemophilus), 21 functional pathways (e.g., FoxO signalling), and two co-abundance modules, including a Treponema module, were significantly related to cognitive function. Mediation analysis suggested that 11 features, including nitrate-reducing taxa and a Treponema-driven inflammatory module, may partially mediate the relationship between periodontal health and cognition.

INTERPRETATION: These community-based findings reveal microbiome-mediated links along the oral-brain axis and highlight periodontal health and oral microbial homoeostasis as potential targets for early prevention of cognitive decline.

FUNDING: This work was supported by the National Key R&D Program of China (2023YFC3606300), National Natural Science Foundation of China (82373658), Clinical Research General Project of the Shanghai Municipal Health Committee (202240355), Clinical Research General Project of Shanghai Municipal Health Commission (202440188), Noncommunicable Chronic Diseases-National Science and Technology Major Project (2023ZD0510000), Brain Science and Brain-like Intelligence Technology-National Science and Technology Major Project (2022ZD0211600).},
}

@article {pmid41875611,
year = {2026},
author = {Yang, Z and Zhang, F and Yang, S and Anayyat, U and Mo, Y and Ying, Y and Wang, X},
title = {Orally deliverable Perilla frutescens-derived nanovesicles as natural bioactive nanocarriers for colon-targeted colitis therapy via microenvironment reprogramming.},
journal = {Biomaterials advances},
volume = {184},
number = {},
pages = {214832},
doi = {10.1016/j.bioadv.2026.214832},
pmid = {41875611},
issn = {2772-9508},
abstract = {Effective oral therapy for inflammatory bowel disease (IBD) requires overcoming gastrointestinal barriers to modulate the dysregulated mucosal niche. Here, we present edible nanovesicles derived from Perilla frutescens (PLENs) as an intrinsically stable, bioactive nanotherapeutic. Multi-omics profiling defined a robust lipid-bilayer architecture encapsulating a synergistic cargo of proteins, miRNAs, and antioxidant metabolites. This structural integrity enabled PLENs to survive gastrointestinal transit and exhibit preferential fluorescence localization with prolonged retention in the inflamed colonic region, as indicated by in vivo imaging. Upon localization, PLENs executed a "dual-hit" therapeutic strategy: they reprogrammed the immune microenvironment, accompanied by reduced activation of the TLR4/MyD88-NF-κB axis and a phenotypic shift from pro-inflammatory M1 to reparative M2 macrophages. Concurrently, PLENs fundamentally restructured the gut ecosystem, accompanied by enrichment of taxa linked to saccharolytic fermentation and recovery of cecal short-chain fatty acids. Notably, fecal microbiota transplantation (FMT) further supported that this microbial remodeling contributed to the protective phenotype, highlighting the microbiome as an important component of efficacy.},
}

@article {pmid41875802,
year = {2026},
author = {Balakrishnan, D and Magudeeswari, P and Surapaneni, M and Kumar, AP and Anantha, MS and Saiprasad, SV and Neelamraju, S and Sundaram, RM},
title = {Genotyping by sequencing of wild interspecific mapping population detected novel genetic locus harbouring OsPT11 for rice yield under nutrient stress conditions.},
journal = {Plant physiology and biochemistry : PPB},
volume = {233},
number = {},
pages = {111231},
doi = {10.1016/j.plaphy.2026.111231},
pmid = {41875802},
issn = {1873-2690},
abstract = {Nutrient deficiency is a major constraint to crop production, severely impairing crop establishment and yield. The development of high-yielding cultivars with enhanced tolerance to limited nutrient availability is therefore essential for sustainable crop production. Wild introgression lines, which have evolved to grow and reproduce under adverse environmental conditions, represent valuable genetic resources and potential donors of traits and genes that confer adaptation to nutrient-limited environments. In this study, wild introgression lines derived from Oryza rufipogon were evaluated across six environments, comprising four environments under the recommended dose of phosphorus (RDP) and two environments under low-phosphorus (low P) conditions. Genotyping-by-sequencing (GBS) enabled the identification of 113 quantitative trait loci (QTLs) associated with key agronomic traits. Of these, 41 major QTLs were detected under RDP, while 21 major QTLs were identified under low P stress, explaining up to 28.06% and 30.23% of the phenotypic variance, respectively. Notably, two major QTLs governing grain yield were consistently detected under low-phosphorus conditions, with favourable alleles enhancing yield derived from O. rufipogon. QTLs for days to 50% flowering, number of tillers per plant, and number of productive tillers per plant were consistently identified across both environments. Furthermore, a QTL hotspot region was detected on chromosome 1, harbouring eight QTLs associated with biomass, total tiller number, productive tiller number, total dry matter, and thousand-grain weight. Candidate gene analysis within this hotspot region identified the Pi transporter gene OsPT11, which is involved in phosphorus acquisition and translocation and plays a key role in activating mycorrhizal symbiosis. These findings suggest that this QTL region represents a promising target for improving grain yield under low-nutrient conditions and may enhance root-microbiome interactions, facilitating more efficient nutrient uptake under stress.},
}

@article {pmid41876480,
year = {2026},
author = {Evenepoel, M and Daniels, N and Moerkerke, M and Prinsen, J and Steyaert, J and Boets, B and Joossens, M and Alaerts, K},
title = {The role of the oxytocinergic system in oral microbiome composition in children with autism: evidence from a randomized controlled trial of intranasal oxytocin.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-03964-0},
pmid = {41876480},
issn = {2158-3188},
abstract = {Atypical oxytocinergic functioning and altered microbiome compositions have both been implicated in autism, with growing evidence of interactions between these systems. However, how exogenous oxytocin influences the oral microbiome remains largely unexplored. This exploratory study examined for the first time how oral microbiome alterations link to oxytocinergic signalling in school-aged autistic (n = 80) and non-autistic children (n = 40). Additionally, we investigated the effect of four-weeks of intranasal oxytocin administration in autistic children on oral microbiome compositions immediately post-treatment (T1) and at four-weeks follow-up (T2). At baseline, lower endogenous salivary oxytocin levels were linked to greater microbial evenness and diversity, with twelve genera showing significant associations with oxytocin levels. In autistic children, four weeks of oxytocin administration was associated with significant increases in the abundances of Centipeda immediately post-treatment (T0-T1), alongside decreases in Moraxella (T0-T1), and subsequent reductions in Rothia observed at the four-week follow-up (T1-T2). Particularly, the genus Moraxella emerged as relevant, as lower baseline abundance was associated with higher endogenous oxytocin levels, and a stronger oxytocin-induced downregulation of its abundance correlated with greater increases in endogenous oxytocin levels, accompanied by hypomethylation of the oxytocin receptor gene. All results persisted after adjusting for nutrition and dental care. This exploratory study provides initial evidence for a role of the oxytocinergic system in shaping the oral microbiome in autistic children. These results may facilitate the integration of oral microbiome profiling into autism diagnostic criteria and stimulate future studies on the use of oxytocin as a therapeutic option targeting oral microbiome alterations.},
}

@article {pmid41876505,
year = {2026},
author = {Wang, Z and Cao, B and Li, L and Cui, H and Wei, B and Cui, J and Wang, X},
title = {Acid-tolerant injectable bioadhesive for sutureless repair of large gastric perforation.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71031-9},
pmid = {41876505},
issn = {2041-1723},
support = {52573186, 52373162, 82572862//National Natural Science Foundation of China (National Science Foundation of China)/ ; F252056, L256034, L244037, 7262018//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; 2024048519//Beijing Nova Program/ ; },
abstract = {Bioadhesives represent promising alternatives to sutures towards gastric perforation management, however, significant challenges persist concerning instant wet adhesion and durable stability in gastric perforation sealing, particularly in direct contacting with acidic gastric fluids on large perforation injuries. Here we report an injectable acid-tolerant hydrogel composed of FDA-approved components for sutureless repair of large gastric defects. The hydrogel displays rapid in situ gelation, instant wet adhesion, and high burst pressure for efficient sealing despite excessive mechanical challenges, tissue irregularities and gastric juices. The enhanced hydrogen bonding interactions among amide-linked skeleton enable robust acid-tolerant interfaces to accommodate durable adhesion under the fluidically, chemically and mechanically dynamic in-vivo environments. A larger-scale porcine gastric perforation is applied to validate the sealing efficacy via a combined laparoscopic-endoscopic technique. The negligible postoperative adhesion, suppressed inflammation and interference-free transcriptome and microbiome verify the therapeutic outcomes. The proposed bioadhesives hold great promise for clinical treatment of digestive diseases.},
}

@article {pmid41876637,
year = {2026},
author = {Wang, R and Ma, R and Cai, Y and Zhang, L and Lu, W and Zheng, W and Kong, J and Miao, Q and Li, X and Guan, L and Gao, Y and Chen, K and Kwan, ATH and McIntyre, RS and Xu, G and Yu, CK and Lam, BY and So, KF and Lin, K},
title = {Exploratory characterization of gut microbiota and cognitive profiles in adolescents with subthreshold depression: a shotgun metagenomics sequencing study.},
journal = {Npj mental health research},
volume = {5},
number = {1},
pages = {},
pmid = {41876637},
issn = {2731-4251},
support = {No. 2021A1515011361//Natural Science Foundation of Guangdong Province/ ; No. 202102020735//Science and Technology Program of Guangzhou/ ; No. 2024SRP208//Guangzhou Medical University Research Capacity Enhancement Program/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 82171531//National Natural Science Foundation of China/ ; No. PX-66221557//Guangzhou Medical University student innovation ability enhancement Program/ ; STG STG1/M-501/23-N//the Hong Kong RGC theme-based Strategic Target Grant Scheme/ ; },
abstract = {Subthreshold depression (SD) in adolescents is a prevalent condition associated with significant functional impairment and an increased risk of developing major depressive disorder. Currently, the lack of reliable objective markers complicates its accurate identification. Investigating the gut microbiome may offer novel insights into its underlying mechanisms. This study aimed to investigate the association between gut microbiome and cognitive function in adolescents with subthreshold Depression (SD). Thirty-eight adolescents with SD and 139 clinically-well (CW) adolescents were recruited. Gut microbiome and cognitive function were assessed by metagenomic sequencing and the MATRICS Consensus Cognitive Battery (MCCB), respectively. Compared with the CW adolescents, the SD group showed higher relative abundance of Spirochaetes, Synergistetes, Spirochaetia, Synergistia, Spirochaetales, Rhizobiales, Synergistales, Thermoanaerobacterales, Rhodospirillales, Synergistaceae, and Oxalobacteraceae at four levels. The Spatial Span scores were higher in the SD group compared to the CW group. Moreover, EggNOG analyses showed a significant negative correlation of the intracellular trafficking secretion, and vesicular transport with the Spatial Span scores. The KEGG pathway of the neurodegenerative diseases and translation was depleted in the microbiome of adolescents with SD. The higher abundance of Spirochaetes, Spirochaetia, and Spirochaetales was the best predictor of SD in adolescents. Our findings suggest that gut microbiome abnormalities, depressive symptoms, and cognitive influences co-occur in adolescents with SD, which may play a crucial role in the pathogenesis of SD and cognitive function in adolescent. Gut microbiome may serve as a potential biomarker for the identification and treatment of adolescents with SD.},
}

@article {pmid41876749,
year = {2026},
author = {Jamshidi, N and Nigam, SK},
title = {Aryl hydrocarbon receptor in the kidney regulates metabolic cross-talk with the liver and gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44083-6},
pmid = {41876749},
issn = {2045-2322},
support = {R01-5R01DK109392/DK/NIDDK NIH HHS/United States ; },
}

@article {pmid41876773,
year = {2026},
author = {Xu, Y and Lyu, X and Yang, Y and Akar-Ghibril, N and Telatin, M and Tang, R and Chang, C and Sun, J},
title = {Unmasking the Impact of Air Pollution on Allergic Rhinitis.},
journal = {Clinical reviews in allergy & immunology},
volume = {69},
number = {1},
pages = {},
pmid = {41876773},
issn = {1559-0267},
support = {7191008//Beijing Natural Science Foundation-Key Project/ ; },
}

@article {pmid41876795,
year = {2026},
author = {Singh, S and Goel, I and Rana, A and Gul, A and Quadri, JA and Mridha, AR and Malhotra, L and Kashyap, N and Radha, B and Nayek, A and Ajmeriya, S and Prasad, J and Dhar, R and Karmakar, S},
title = {IGFBP3 repression driven by inflammation links air pollution to placental and developmental defects.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {41876795},
issn = {1757-4684},
support = {68.10.2023(SK).NCD-II//MOHFW | DHR | Indian Council of Medical Research (ICMR)/ ; R.11012/03/2020-HR//MOHFW | Department of Health Research, India (DHR)/ ; },
abstract = {Air particulate matter (PM2.5 and PM10), can cross the placental barrier, triggering oxidative stress and inflammation that compromise fetal development. These insults lead to placental dysfunction and complications including preterm birth, low birth weight, and preeclampsia. In cell line and placental explant models, urban particulate matter (UPM) increased pro-inflammatory cytokines and oxidative stress pathways, impairing trophoblast invasion, angiogenesis, and nutrient transport, while also altering epigenetic modifications and endoplasmic reticulum function. Rodent studies revealed reduced litter size, placental abnormalities, and fetal growth arrest along with postnatal neurodevelopmental alterations. Human cohorts from high-exposure regions showed elevated low birth weight rates. Proteomic and transcriptomic analyses of rat placenta revealed an inflammatory signature and altered metabolic networks, while gut microbiome dysbiosis suggested links to metabolic disturbances. Importantly, transcriptomic analysis identified IGFBP3 as a major downregulated gene following UPM exposure. IGFBP3, a key regulator of IGF bioavailability, was suppressed by IL1β, establishing inflammation-driven repression as the mechanism. These findings underscore UPM's multidimensional impact on maternal-fetal health and highlight preventive strategies as urgent priorities.},
}

@article {pmid41877100,
year = {2026},
author = {Ji, X and Geng, Y and Guo, C and Zhang, S and Li, H and Li, C and Du, Y and Guo, X and Miao, B and Hu, Y and Lv, J and Zhou, Z and Gong, J and Sun, Y},
title = {Analysis of pharyngeal microbiome characteristics in HIV-infected individuals: correlation between the degree of immunosuppression and microbial dysbiosis.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13075-2},
pmid = {41877100},
issn = {1471-2334},
support = {2022YFC2504800//National Key Research and Development Program of China/ ; 102393240020020000003//Enhancement of Communicable Disease Surveillance and Control Technical Capabilities/ ; },
}

@article {pmid41877243,
year = {2026},
author = {Lin, YN and Peng, WH and Huang, YC and Lai, CY and Hsu, JR and Wang, JY and Kao, YC and Wu, LL},
title = {Nfil3 integrates circadian rhythm and microbial metabolite signaling to maintain gut-liver immune-metabolic homeostasis under high-fat diet stress.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08000-9},
pmid = {41877243},
issn = {1479-5876},
support = {110-2320-B-002-080-MY3//National Science and Technology Council/ ; 111-2314-B-A49-072//National Science and Technology Council/ ; 112-2314-B-A49-028-MY3//National Science and Technology Council/ ; 113-2321-B-A49-014//National Science and Technology Council/ ; 113-2740-B-A49-003//National Science and Technology Council/ ; 114-2321-B-A49-004//National Science and Technology Council/ ; 114-2740-B-A49-003-//National Science and Technology Council/ ; CI-115-33//Yen Tjing Ling Medical Foundation/ ; PTH110001//TYGH-NYCU Joint Research Program/ ; 11210//Ministry of Health and Welfare/ ; 11310//Ministry of Health and Welfare/ ; },
abstract = {BACKGROUND: Disruption of circadian regulation and gut microbial homeostasis is a hallmark of metabolic dysfunction associated with steatotic liver disease (MASLD). Nuclear factor interleukin 3 (Nfil3) integrates circadian and immune signaling; however, how Nfil3 interfaces with microbiota-associated metabolic cues in MASLD remains incompletely understood. We investigated the role of Nfil3 in linking microbial functional states to hepatic metabolic and immune responses under high-fat diet (HFD) stress and assessed the modulatory impact of probiotic VSL#3 intervention.

METHODS: We integrated exploratory human peripheral blood mononuclear cell (PBMC) transcriptomic profiling with genetic Nfil3 deletion and probiotic VSL#3 supplementation in HFD-fed mice. Experimental assessments included liver histopathology, metabolic phenotyping, immune flow cytometry, gut epithelial barrier analysis, 16S rRNA microbiome profiling with predictive functional inference, and RT-PCR.

RESULTS: Exploratory PBMC transcriptomic analysis of obese individuals suggested that NFIL3 may function as a candidate transcriptional node associated with circadian-related genes and short-chain fatty acid (SCFA) sensing receptors in inflammatory signaling pathways. In mice, HFD feeding was associated with increased Nfil3 expression, hepatic steatosis, metabolic dysfunction, immune cell expansion, and impaired intestinal epithelial barrier integrity. Probiotic VSL#3 supplementation mitigated several HFD-associated phenotypes, including weight gain, glucose intolerance, dyslipidemia, transaminase elevation, hepatic lipid accumulation, and gut epithelial permeability, while partially normalizing intrahepatic immune cell composition. Nfil3-deficient mice displayed attenuated responses to several HFD-induced metabolic and inflammatory alterations, with partial phenotypic overlap with probiotic-treated wild-type (WT) mice. Microbiome analyses showed that VSL#3 enriched SCFA- and mucin-associated taxa while suppressing endotoxin-associated bacteria (Desulfovibrionaceae, Romboutsia). Predictive functional profiling suggested restoration of microbial pathways related to amino acid, redox, and energy metabolism, alongside reduced representation of lipopolysaccharide and toxin biosynthesis pathways.

CONCLUSIONS: These findings support a role for Nfil3 as a regulatory node linking microbial functional potential with immune and metabolic responses in MASLD. Although preclinical in nature, this work provides a mechanistic framework that may inform future translational investigations into how microbiota-associated metabolic reprogramming influences host immune-metabolic homeostasis. Further circadian-resolved and metabolite-level studies, together with human interventional validation, will be required to determine the clinical relevance of the microbiota-Nfil3 axis.},
}

@article {pmid41877267,
year = {2026},
author = {Peirson, LE and McKenney, EA and Patterson, JR and Beasley, JC and Périquet-Pearce, S and Cloete, C and Melton, MH and PetersonWood, B and Portas, R and Aschenborn, O and Lafferty, DJR},
title = {African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00553-w},
pmid = {41877267},
issn = {2524-4671},
support = {Financial Assistance Award no. DE-EM0005228//U.S. Department of Energy/ ; Peter White Scholar Award//Northern Michigan University/ ; },
abstract = {Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.},
}

@article {pmid41877434,
year = {2026},
author = {Xu, F and Tong, L and Ding, F and Wang, K and Li, P and Xu, M and Bai, C and Chen, Z and Li, J and Xie, Y and Wang, H and Zhang, Q and Liu, J and Zhu, Y and Pang, J and Xu, W},
title = {Plasma membrane H[+]-ATPase OsA1 enhances soil organic phosphorus mineralization via Bacillus cereus recruitment in rice.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71115},
pmid = {41877434},
issn = {1469-8137},
support = {42307419//National Natural Science Foundation of China/ ; 32472825//National Natural Science Foundation of China/ ; U25A20695//National Natural Science Foundation of China/ ; 2024J09028//The Natural Science Foundation of Fujian Province/ ; 2023J01468//The Natural Science Foundation of Fujian Province/ ; SKLAWR-2024-03//Open Research Fund of State Key Laboratory of Efficient Utilization of Agricultural Water Resources/ ; JAT220063//Research Fund of the Education Department of Fujian Province/ ; },
abstract = {Organic phosphorus (P), which accounts for c. 50% of total soil P, is not directly available for plant uptake and must be first mineralized. Plasma membrane (PM) H[+]-ATPase facilitates the mobilization of insoluble inorganic P by energizing the release of organic anions from roots. However, its role in modulating the rhizosphere microbiome to facilitate soil organic P mineralization remains unclear. To address the gap, we investigated the role of PM H[+]-ATPase in recruiting microbiota for soil organic P mineralization through high-throughput sequencing and metabolite analysis. Under low P (LP) conditions in nonsterilized soil, wild-type (WT) rice seedlings exhibited 59%, 73%, and 66% greater shoot P concentration than three PM H[+]-ATPase gene OsA1 mutants, that is, osa1-1, osa1-2, and osa1-3, respectively. Such growth advantage reduced to 33%, 47%, and 39% in sterilized soil, suggesting a microbial contribution. Under LP conditions, organic P mineralization efficiency in the WT rhizosphere was four times greater than under normal P (NP) conditions, whereas no significant difference was observed in the osa1-1 mutant. The abundance of Bacillus was significantly higher in the WT rhizosphere than in osa1-1 under LP. Compared with the osa1-1 rice, WT exhibits significantly higher malate concentration, which could stimulate the growth of Bacillus cereus. Inoculation with B. cereus significantly increased P uptake in both WT and OsA1 mutants compared with the uninoculated control under LP. Together, these findings suggest that OsA1 promoted soil organic P mineralization by recruiting Bacillus through malate exudation. This highlights a cooperative interaction between PM H[+]-ATPase and the rhizosphere microbiome, with important implications for enhancing soil organic P mineralization and P-use efficiency in rice production.},
}

@article {pmid41877507,
year = {2026},
author = {Lee, JG and Lim, J and Cho, NJ and Park, S and Gil, HW and Seo, H and Song, HY and Park, SH and Oh, KH and Kim, YL and Bieber, BA and Pisoni, RL and Lee, EY and , },
title = {Xerosis elevates the risk of catheter-related infections in peritoneal dialysis patients.},
journal = {Kidney research and clinical practice},
volume = {},
number = {},
pages = {},
doi = {10.23876/j.krcp.24.275},
pmid = {41877507},
issn = {2211-9132},
abstract = {BACKGROUND: Catheter-related infections, such as exit-site infection and tunnel infection, are major complications in peritoneal dialysis (PD) patients, affecting their prognosis. This study investigates the association between skin conditions and catheter-related infections.

METHODS: Data from two distinct sources were analyzed: (1) 626 PD patients in the Korean arm of the Peritoneal Dialysis Outcomes and Practice Patterns Study (PDOPPS) and (2) skin microbiome data from 76 dialysis patients at Soonchunhyang University Cheonan Hospital. The relationship between catheter-related infection and self-reported xerosis and pruritus severity was assessed by Cox regression. Risk factors for xerosis and pruritus were evaluated by logistic regression. Furthermore, we discovered the relationship between the severity of pruritus and the relative abundance of Staphylococcus aureus on the skin.

RESULTS: The risk of catheter-related infections in PD patients increased with xerosis (hazard ratio [HR], 2.71; 95% confidence interval [CI], 1.19-6.18) and pruritus (HR, 2.57; 95% CI, 1.27-5.22), particularly increasing the risk of S. aureus-associated catheter-related infections (xerosis: HR, 5.66; 95% CI, 1.97-16.30; pruritus: HR, 5.93; 95% CI, 2.18-16.15). The relative abundance of S. aureus was notably higher in patients with severe pruritus. Moreover, patients were more likely to exhibit severe xerosis if they owned pets, had higher serum creatinine levels, and elevated calcium-phosphorus product levels.

CONCLUSION: Xerosis and pruritus significantly increase the risk of catheter-related infections, especially those caused by S. aureus. Instead of relying solely on prophylactic antibiotics for infection prevention, this study highlights the need for new preventive strategies in PD patients, focusing specifically on effective skin management.},
}

@article {pmid41877508,
year = {2026},
author = {Liu, X and Li, Z and Liu, H and Xiao, M and Zhang, X and Deng, Y and Tian, B and Sun, Y and Xiao, X},
title = {Diet-microbiota-kidney axis reprogramming: mechanistic insights into microbial metabolite-driven precision nutrition for chronic kidney disease.},
journal = {Kidney research and clinical practice},
volume = {},
number = {},
pages = {},
doi = {10.23876/j.krcp.25.312},
pmid = {41877508},
issn = {2211-9132},
abstract = {Medical nutrition therapy serves as the cornerstone in the management of chronic kidney disease (CKD). While conventional approaches emphasize macronutrient restriction and meal timing adjustments, research highlights the critical mediating role of gut microbiota in translating dietary patterns into physiological effects through metabolite production. Meanwhile, CKD progression is closely associated with dynamic interactions between gut microbiota and their metabolic derivatives. This review introduces the "diet-microbiota- metabolite-kidney axis" framework to elucidate how nutritional components modulate CKD progression via microbial compositional changes and subsequent metabolite alterations. Based on synthesized evidence, this review identifies promising directions for precision nutrition strategies targeting microbial metabolites, including artificial intelligence-assisted dietary planning, engineered bacterial therapies, and metabolite analog development. However, significant interindividual variability in host genetics and baseline microbiota composition necessitates overcoming heterogeneity challenges in nutritional interventions. Consequently, the precise modulation of individualized diet-microbiota-metabolite interactions represents a critical research direction to be prioritized in CKD management.},
}

@article {pmid41877524,
year = {2026},
author = {Wight, M and Brooks, CN and Scott Chialvo, CH and West, CA and de Souza, AMA and Bleich, RM},
title = {The impact of weight cycling on gut microbiome richness and diversity in female rats.},
journal = {Physiological reports},
volume = {14},
number = {6},
pages = {e70828},
doi = {10.14814/phy2.70828},
pmid = {41877524},
issn = {2051-817X},
support = {N/A//Appalachian State University (ASU)/ ; 19CDA34660328//American Heart Association (AHA)/ ; 940246//American Heart Association (AHA)/ ; W81XWH2110201//U.S. Department of Defense (DOD)/ ; KL2TR001432//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; P30-CA051008-29S2//HHS | NIH | National Cancer Institute (NCI)/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; Rats, Inbred F344 ; Rats ; Feces/microbiology ; *Body Weight ; *Caloric Restriction ; Biodiversity ; },
abstract = {Female Fischer 344 rats were divided into control (access to food ad libitum) and weight cycling (60% diet restriction followed by ad libitum refeeding) groups. The weight cycles consisted of two weeks dietary restriction and three weeks refeeding for three cycles. Fecal microbiome samples were collected following the initial dietary restriction, the initial refeeding, and the final refeeding periods (and corresponding times in control rats). We observed significant differences in alpha diversity between fecal microbiomes following the initial dietary restriction and the final refeeding period. We additionally observed a significant recovery of alpha diversity following the first refeeding period that we did not observe following the third refeeding in the weight cycling group. Differences in relative abundances of taxa included a higher relative abundance of Bacillota (synonym Firmicutes) in the weight cycling group. Species richness of the weight cycling fecal microbiomes significantly decreased across the study period. Inguinal fat tissue was significantly lower in the weight cycling than ad libitum group, yet heart weight and postprandial HOMA-IR were significantly higher. Together, these results suggest that repeated weight cycling from repeated periods of dietary restriction has adverse effects on host condition and microbial diversity, potentially leading to long-term negative health outcomes.},
}

Animals
Female
*Gastrointestinal Microbiome/physiology
Rats, Inbred F344
Rats
Feces/microbiology
*Body Weight
*Caloric Restriction
Biodiversity

@article {pmid41877779,
year = {2026},
author = {Sun, S and Long, F and Su, B and Chen, J and Luo, Y and Zhong, Y and Zhang, G},
title = {The gut microbiome in colorectal anastomotic leakage: from mechanisms to precision.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1781458},
pmid = {41877779},
issn = {2296-858X},
abstract = {Anastomotic leakage after curative colorectal cancer resection remains a frequent and severe complication that increases short-term mortality, worsens long-term oncologic outcomes, and places substantial burdens on individuals and health systems despite advances in surgical technique and perioperative care. Emerging evidence redefines anastomotic failure as not only a technical event but also a biologically driven process in which the gut microbiome regulates inflammation, epithelial repair, and barrier integrity at the healing interface. This review summarizes current data on the dual role of the intestinal microbiome in promoting physiological anastomotic healing and driving pathological leakage when perioperative stressors cause dysbiosis. Mechanistic sections describe how a diverse, metabolically active community supports collagen stability through short-chain fatty acid production, immune regulation, and maintenance of mucus and tight junction architecture. In contrast, the enrichment of microbial groups such as Enterococcus faecalis, Fusobacterium nucleatum, and Alistipes onderdonkii together with fungal and viral shifts, has been associated with extracellular matrix degradation and excessive inflammation. Furthermore, the review examines microbiome-related biomarkers for risk assessment, including DNA-based microbial signatures, metabolite profiles, and host immune markers. It also discusses how integrated multi-omics models combined with machine learning may outperform traditional clinical scores for preoperative and early postoperative prediction. Finally, the article critically evaluates perioperative microbiome-directed strategies ranging from dietary prehabilitation and microbial supplementation to selective decontamination and fecal microbiota transplantation, highlighting promising signals, variability of effect, safety considerations, and key methodological limitations that currently prevent routine implementation. In summary, this review addresses three interconnected domains-mechanisms of microbiome-driven anastomotic failure, microbiome-derived biomarkers for risk stratification, and perioperative intervention strategies-underscoring that AL is best understood as a host-microbiome interaction rather than a purely technical failure. This framing offers surgeons and perioperative teams a biologically rational basis for prevention, yet clinical translation will require causal validation, standardized intervention algorithms, and interpretable computational tools embedded into real-world perioperative practice.},
}

@article {pmid41877865,
year = {2026},
author = {Wu, G and Wang, M and Si, Y and Wang, X and Li, H and Wang, L and Wang, R and Zhang, L},
title = {Exploring the causal link between microbiota and tic disorders: a gene sequencing and Mendelian randomization approach.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20812},
pmid = {41877865},
issn = {2167-8359},
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Tic Disorders/microbiology/genetics ; Genome-Wide Association Study ; Child ; Male ; Female ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Tic disorders (TD), including Tourette syndrome (TS), are common childhood-onset neurodevelopmental conditions with unclear etiology. Emerging observational data suggest that gut-microbiota (GM) dysbiosis accompanies TD, but causality is unresolved. We aimed to determine whether specific bacterial genera are causally implicated in TD susceptibility.

METHODS: Two-sample Mendelian randomization (MR) was performed by integrating the largest available GM genome-wide association study (GWAS) (18,340 Europeans, 211 taxa) with the PGC-TS-2019 GWAS (4,819 cases/9,488 controls). Inverse-variance-weighted estimates were complemented with sensitivity analyses and reverse-MR. Findings were validated in an independent pediatric case-control cohort (10 TD vs seven healthy children) profiled by 16S rRNA V3-V4 sequencing; between-group differences were tested with the Mann-Whitney U test.

RESULTS: Genetically predicted abundance of Anaerotruncus, Butyrivibrio and Ruminococcaceae UCG-002 conferred protection against TS (OR 0.69-0.86, p = 0.014-0.016), whereas Dialister and Ruminiclostridium 6 increased risk (OR 1.28-1.32, p = 0.030-0.041); Sutterella showed no causal effect (p = 0.103). No heterogeneity, directional pleiotropy or reverse causation was detected. Sequencing analyses mirrored MR directions: TD cases exhibited significantly lower relative abundance of the protective genera and higher levels of risk taxa compared with controls (p < 0.05).

CONCLUSIONS: By integrating unbiased genetic instrumentation with targeted microbiome profiling, this study offers exploratory evidence suggesting that specific gut bacteria may be associated with TD pathogenesis. Ruminococcaceae UCG-002, Anaerotruncus, and Butyrivibrio emerge as potentially protective taxa, while Dialister and Ruminiclostridium 6 may represent candidate risk markers. These preliminary, mechanistically grounded insights should be considered exploratory and may inform future, larger-scale microbiome-directed precision interventions in TD.},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
*Tic Disorders/microbiology/genetics
Genome-Wide Association Study
Child
Male
Female
Case-Control Studies
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology

@article {pmid41877915,
year = {2026},
author = {Nicolas, CS and Lloret, F and Carton, T and Beuvin, L and Rème, CA},
title = {Beneficial effects of a prebiotic-postbiotic supplement on digestive health and fecal microbiota in dogs and cats.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1797178},
pmid = {41877915},
issn = {2297-1769},
abstract = {Gastrointestinal (GI) disorders are a frequent concern for pet owners and veterinarians. Dietary management of mild GI disorders is often essential in order to correct imbalances in the gut flora. In this context, "biotics," including probiotics, prebiotics, and postbiotics, have received increasing attention for their potential to favorably modulate the gut microbiota and support digestive function. In this study, we investigated the effect of a nutritional supplement containing a specific blend of prebiotics (baobab fruit pulp and acacia gum) and postbiotics (inactivated L. helveticus and selected yeast fractions) on digestive signs exhibited by healthy dogs and cats with mild GI imbalances, such as soft stools, increased quantity of stools or flatulence. The supplement was tested over a 28-day period. Digestive signs were evaluated on 57 dogs and 57 cats and the microbiota analysis was conducted on samples from 35 dogs and 27 cats. Questionnaires completed by the pet owners at regular intervals were used to evaluate digestive signs, while changes in the intestinal microbiota were assessed by fecal sample analysis performed before and after supplementation. The supplement was accepted either alone or mixed with food by 94% of dogs and 91% of cats. In both cats and dogs, the supplementation significantly improved digestive health as of day 7 (p < 0.001). Animals starting the study with impaired stool consistency or high quantity of stools showed significant improvement by day 7. The stool odor also improved from the first week. The proportion of dogs and cats with flatulence was reduced by 45 and 63%, respectively, by day 28 (p < 0.001), and the proportion of pets vomiting was reduced by 51 and 54%, respectively (p < 0.001). The impact on gut microbiota involved mainly changes on multiple subdominant taxa (such as Megamonas and Peptacetobacter in dogs, Anaerotignum and Succinivibrio in cats), without altering the overall microbial community architecture (as shown by diversity indices). Altogether, these results show that the supplement tested (Floragest™ soft chews, Virbac) can help support the digestive health of dogs and cats with mild gastrointestinal disorders.},
}

@article {pmid41878129,
year = {2026},
author = {Wang, P and Ye, Y and Mei, K and Chen, B and Kankala, RK and Tong, F},
title = {Nanoscale Approaches to Oro-Dental Tissue Engineering: A Review of Strategies, Composites, and Translational Challenges.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {575296},
pmid = {41878129},
issn = {1178-2013},
mesh = {Humans ; *Tissue Engineering/methods ; Dental Pulp/cytology ; Stem Cells/cytology/drug effects ; Anti-Bacterial Agents/pharmacology/administration & dosage ; Animals ; Drug Delivery Systems ; Nanostructures/chemistry ; Mouth ; Nanotechnology/methods ; Dental Implants ; },
abstract = {Oral health is vital to human well-being. As a result, various conditions in the oral cavity, including exposure to dentin and edentulous states, lead to diverse oral issues and tissue loss. Although conventional treatments are available, they often have limitations in drug delivery and tissue regeneration. For example, delivered drugs may fail to disrupt bacterial biofilms, thereby increasing resistance within the oral microbiome and weakening immune responses. Additionally, the limited regenerative capacity of dental pulp cells can lead to serious dental emergencies. To address these challenges, innovative nanoarchitectures have been developed to improve their antimicrobial effects and enhance the regenerative potential of oral tissues for oro-dental tissue engineering. This review discusses different nanotechnological strategies for delivery and subsequent tissue engineering in the oral cavity. We first explore concepts to boost regenerative capacity, emphasizing the roles of various nanomaterials that act as antibacterial agents, activate the differentiation of human dental pulp stem cells, and support their integration with soft oral tissues. Beyond nano-therapeutic strategies involving dental implants, we also discuss nanotoxicity issues and remaining challenges in oral health. Finally, we offer perspectives on translating these developments into clinical practice.},
}

Humans
*Tissue Engineering/methods
Dental Pulp/cytology
Stem Cells/cytology/drug effects
Anti-Bacterial Agents/pharmacology/administration & dosage
Animals
Drug Delivery Systems
Nanostructures/chemistry
Mouth
Nanotechnology/methods
Dental Implants

@article {pmid41878283,
year = {2026},
author = {Urquhart, DS and Linnane, B and Saunders, CJ and Abkir, M and Georgiopoulos, AM and Dobra, R and Carroll, S and Still, M and Cox, DW and Fitzpatrick, E and Beegan, A and Thursfield, R and Balfe, J and Tarr, A and Lester, K and Cunningham, A and Perrem, L and Davies, JC and McNally, P and , },
title = {ENHANCE: a community partnership charting the evolution of early-life cystic fibrosis disease manifestations in a new era of management.},
journal = {ERJ open research},
volume = {12},
number = {2},
pages = {},
pmid = {41878283},
issn = {2312-0541},
abstract = {ENHANCE is a multicentre, longitudinal study examining the natural history of early cystic fibrosis (CF) disease manifestations in children. We hypothesise that the prevalence, presentation and natural history of disease manifestations of CF in young children will change significantly in the next decade with advances in the understanding and treatment of CF, including the use of therapies aimed at improving CFTR function. The study has been co-developed with the CF community, in order to try to answer questions of key importance to people with CF and their caregivers. The study will longitudinally monitor lung health using nitrogen multiple breath washout testing and spirometry, lung structure using spirometry-controlled computed tomography scanning, gastrointestinal health using gut microbiome, gut inflammation and abdominal symptom scores, pancreatic function using faecal elastase, liver function using liver blood tests and liver ultrasound, and sweat chloride. Mental health will be longitudinally assessed using questionnaires for mood (PROMIS, GAD-7), quality of life (CFQ-R) and psychosocial functioning (Pediatric Symptom Checklist). There are three cohorts in the study: infants with CF diagnosed by newborn screening (n=250), children aged 0-6 years and currently attending CF centres (n=200) and healthy newborn infant controls (100). The study will be conducted over 5 years in the first phase with a plan to extend through further phases in the future. We envisage that the study will provide important evidence to enable healthcare staff and families to guide the care of children with CF in the future.},
}

@article {pmid41878551,
year = {2026},
author = {Blicharz, L and Bukowska-Ośko, I and Perlejewski, K and Navarro-López, V and Czuwara, J and Waśkiel-Burnat, A and Samochocki, Z and Olszewska, M and Rudnicka, L and Radkowski, M},
title = {Gut Microbiota Influence Host Metabolism and Immune Responses in Atopic Dermatitis: A Next-Generation Sequencing-Based Functional Profiling Study.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {571034},
pmid = {41878551},
issn = {1178-7015},
abstract = {PURPOSE: Gut dysbiosis has been linked to immune imbalance in allergic diseases, but the underlying mechanisms remain unclear. We aimed to verify whether gut microbiota composition is associated with cellular, metabolic, and immune pathways in atopic dermatitis.

PATIENTS AND METHODS: Fifty adults with atopic dermatitis and 25 sex- and age-matched healthy controls were enrolled. Gut microbiome composition was assessed using V3-V4 16S rRNA sequencing. Functional pathways were inferred from microbiome data using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States).

RESULTS: Despite only subtle differences in microbiota composition between patients with atopic dermatitis and controls, PICRUSt analysis identified significant differences in 149 functional pathways. Key pathways enriched in atopic dermatitis involved signal transduction mediated by protein kinases, as well as carbohydrate and lipid metabolism. Downregulated pathways included those related to energy metabolism, amino acid and nucleotide metabolism, antigen processing, and innate immune responses. In patients with atopic dermatitis, microbial diversity increased with EASI scores and IgE levels, correlating with additional predicted functional shifts.

CONCLUSION: Our results suggest that even subtle structural differences in gut microbiota may exert significant functional effects in atopic dermatitis. Altered pathways could contribute to immune imbalance and impaired epidermal barrier function. These findings underscore the importance of incorporating functional analyses into future gut microbiota studies of atopic dermatitis to help identify therapeutic targets, including candidate probiotic strains for supplementation.},
}

@article {pmid41878631,
year = {2026},
author = {MacDonald, KV and Pai, N and Burow, C and deBruyn, JC and Huynh, HQ and Otley, A and Rozario, S and Marshall, DA},
title = {Balancing safety and effectiveness: parent preferences for fecal microbiota transplant and established therapies in pediatric inflammatory bowel disease-results of a multicenter Canadian study.},
journal = {Crohn's & colitis 360},
volume = {8},
number = {1},
pages = {otag016},
pmid = {41878631},
issn = {2631-827X},
abstract = {BACKGROUND AND AIMS: Treatment decision-making in pediatric inflammatory bowel disease (IBD) is complex, with many existing and emerging options. However, little is known about parent preferences for these therapies. This multi-center Canadian study provides the first quantitative data on parent preferences for pediatric IBD treatments and explores characteristics associated with differing preferences.

METHODS: We conducted a cross-sectional survey including a discrete choice experiment (DCE) with Canadian parents (n = 159) of children diagnosed with UC/IBD-U, recruited from four pediatric IBD clinics. The DCE assessed preferences across four treatment attributes: chance of clinical remission, severity and chance of known side effects, severity of rare unknown side effects, and mode of treatment delivery. Latent class modeling was used to explore preference heterogeneity.

RESULTS: Parents prioritized safety, particularly the risk of rare unknown side effects, followed by likelihood of remission. Latent class analysis identified two distinct groups: one most concerned about rare unknown side effects, and another prioritizing treatment effectiveness. Thirty-eight percent of parents were open to fecal microbiota transplant (FMT), an emerging therapy that uses donor stool to help restore gut microbiome health. Younger parents and those with children experiencing more severe disease and on multiple medications were more likely to accept FMT. Across the cohort, many parents were willing to trade off less desirable delivery modes or increased risk in exchange for better treatment outcomes.

CONCLUSIONS: Parents value both safety and effectiveness in IBD treatment decisions. Recognizing these preferences may support shared decision-making, particularly when discussing novel therapies like FMT.},
}

@article {pmid41878738,
year = {2026},
author = {Xiao, M and Chen, C and Yao, R and Wang, X and Liu, G},
title = {Synergistic nano-bioorganic amendments enhance soil properties and microbial structure in coastal saline soils.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1720097},
pmid = {41878738},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil salinization threatens global food security and sustainable land use. Ameliorating coastal saline soils with exogenous amendments is crucial. Bio-organic fertilizer (OF) and nano-carbon (NC) are promising green amendments, but their comparative and combined effects on soil properties and microbial communities are not fully understood.

METHODS: A field experiment was conducted in coastal saline soil (Ninghe District, Tianjin, China). Four treatments were established: control (CK, no amendment), OF application, NC application, and combined application of OF and NC (FC). Soil physicochemical properties and microbial community structure (via 16S and ITS rRNA gene sequencing) were analyzed.

RESULTS: The FC treatment most effectively improved soil properties, significantly reducing bulk density, pH, salinity, and sodium adsorption ratio (SAR), while increasing porosity, water content, and nutrient (N, P) availability. Soil bacterial diversity (Ace, Chao1, Shannon indices) increased significantly in all amendment treatments compared to CK, with the highest values in NC and FC treatments. Amendment application altered microbial community composition, enriching specific bacterial taxa (e.g., Firmicutes, Desulfobacterota in FC) and fungal taxa. Redundancy analysis identified soil salinity and pH as key drivers of bacterial community structure, whereas fungal communities showed a distinct, less correlated response pattern.

DISCUSSION: The synergistic application of nano-carbon and bio-organic fertilizer (FC) created a more favorable soil habitat, rapidly ameliorating physicochemical conditions which directionally shaped the bacterial community. Bacterial and fungal communities responded differently to amendments, suggesting divergent assembly mechanisms. The FC strategy demonstrates high potential for the initial restoration of saline-alkali soils by enhancing soil health primarily through rapid physicochemical improvement and modulation of the soil microbiome, particularly bacteria. Future work should focus on functional validation of predicted metabolic shifts and assessment of agronomic outcomes.},
}

@article {pmid41878750,
year = {2026},
author = {Du, Z and Li, L and Liu, J and Wang, H and Li, J and Xu, Y and Cui, L and Yin, J},
title = {Wheat-Dependent Exercise-Induced Anaphylaxis Patients on a Wheat-Free Diet Exhibit a Gut Microbiota Composition More Similar to Healthy Individuals.},
journal = {Journal of asthma and allergy},
volume = {19},
number = {},
pages = {464532},
pmid = {41878750},
issn = {1178-6965},
abstract = {PURPOSE: There are limited studies on the intestinal microbiome in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA), and changes in the gut microbiome in WDEIA patients after wheat-free diet have not been studied.

METHODS: This is a cross-sectional analysis. Fecal samples and clinical data were collected from 26 non-wheat-free patients with WDEIA, 11 wheat-free patients with WDEIA, and 24 healthy controls (HCs). The gut microbiota was evaluated through metagenomic sequencing.

RESULTS: The sequencing revealed differences in the gut microbiome between patients with WDEIA on a non-wheat-free diet and HCs; more specifically, the non-wheat-free group exhibited a downregulation of two families (Rikenellaceae and Odoribacteraceae), three genera (Alistipes, Odoribacter, and Catenibacterium), and four species (Bacteroides_stercoris, Alistipes_putredinis, Bacteroides_intestinalis, and Bacteroides_cellulosilyticus). A wheat-free diet is associated with intestinal flora more similar to the structure of healthy individuals. The species Bacteroides_stercoris was negatively correlated with T-IgE, and the genus Catenibacterium was negatively correlated with T-IgE, as well as wheat, gluten, or gliadin-specific IgE. The genus Catenibacterium was positively correlated with the healthy control-enriched "Apoptosis (ko04210)" pathway and negatively correlated with the non-wheat-free WDEIA group-enriched "Thyroid hormone signaling pathway (ko04919)" pathway.

CONCLUSION: Patients with WDEIA exhibit a specific gut microbiota signature and function, which demonstrated the potential association between the gut microbiome and WDEIA development. WDEIA patients on a wheat-free diet exhibit a gut microbiome composition more similar to healthy individuals.},
}

@article {pmid41878919,
year = {2026},
author = {Jiang, C and Peng, B},
title = {Gut microbiota-supportive dietary patterns and rheumatoid arthritis: the mediating role of the systemic immune-inflammation index.},
journal = {Nutricion hospitalaria},
volume = {},
number = {},
pages = {},
doi = {10.20960/nh.06113},
pmid = {41878919},
issn = {1699-5198},
abstract = {BACKGROUND: the gut microbiota has emerged as a potential contributor to autoimmune diseases, including rheumatoid arthritis (RA), through its role in modulating systemic inflammation. However, few studies have evaluated whether adherence to microbiota-supportive dietary patterns is associated with RA in population-based settings.

METHODS: this study analyzed data from 21.352 adults in the 2010-2020 cycles of the National Health and Nutrition Examination Survey (NHANES). The Dietary Index for Gut Microbiota (DI-GM), ranging from 0 to 14, was used to quantify the extent to which habitual diets support gut microbial health. Logistic regression and restricted cubic spline models were used to examine the association between DI-GM and RA. Mediation analysis was conducted to evaluate whether the systemic immune-inflammation index (SII) mediated this association.

RESULTS: higher DI-GM scores were significantly associated with lower odds of RA. Each 1-point increase in DI-GM was linked to a 5 % reduction in RA odds [OR = 0.95 (0.92-0.99)]. Compared with individuals in the lowest DI-GM category (0-3), those with scores ≥ 6 had significantly reduced odds of RA [OR = 0.81 (0.66-0.99)]. Mediation analysis showed that SII partially mediated the DI-GM-RA association, accounting for approximately 21.3 % of the total effect.

CONCLUSION: higher adherence to a gut microbiota-supportive dietary pattern was associated with lower odds of RA, partly through reduced systemic inflammation. These findings support the potential value of microbiome-informed dietary strategies in RA prevention.},
}

@article {pmid41879259,
year = {2026},
author = {Wang, H and Cao, Y and Zhang, X and Wu, H and Zhou, T and Yang, Y and Ji, K and Wu, J and Xiong, B},
title = {Alterations in the Gut Microbiota of Cirrhosis Patients with Sarcopenia and PH after TIPS.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000001021},
pmid = {41879259},
issn = {2155-384X},
abstract = {BACKGROUND AIMS: TIPS can effectively reduce PH and may associated with improvement in muscle status; however, its impact on the gut microbiota and muscle condition remains unclear. Therefore, this prospective study aimed to evaluate gut microbiota alterations in patients with sarcopenia and PH following TIPS treatment.

METHODS: Gut microbiota analysis was prospectively conducted in 20 cirrhosis patients with sarcopenia and PH receiving TIPS and their first-degree healthy family between December 2019 and July 2021 in our center. Fecal samples were collected before and 3 months after TIPS and analyzed by 16S rRNA sequencing. Microbial diversity and composition were assessed using standard bioinformatic pipelines. Sarcopenia was defined by L3 skeletal muscle index according to EASL criteria.

RESULTS: Compared with healthy controls, cirrhosis patients with sarcopenia and PH exhibited significantly reduced α-diversity (Chao1, Shannon, Simpson; all p < 0.001) and distinct β-diversity clustering, confirming gut dysbiosis. Although TIPS did not significantly alter overall α-diversity, a significant increase in the order Burkholderiales and a reduction in Pseudomonadales and Staphylococcales were detected after TIPS. Analysis of the family taxonomic rank revealed that TIPS was followed by an increase in a greater abundance of Ruminococcaceae and Sutterellaceae and decreased levels of Tannerellaceae, Marinifilaceae and Pseudomonadaceae. At the genus level, after TIPS placement, increased levels of Lachnospiraceae_ND3007_group, Intestinibacter, Fusicatenibacter, and Faecalibacterium and lower abundances of Pseudomonas, Prevotella, Peptostreptococcus, Parabacteroides, Muribaculaceae, and Butyricimonas were detected.Sarcopenia reversal was observed in 25% of patients, characterized by enrichment of SCFA-producing genera such as Faecalibacterium and Streptococcus, whereas patients without improvement showed high abundance of Fusicatenibacter and low levels of beneficial taxa.

CONCLUSION: TIPS induces significant taxonomic shifts without changing overall diversity in cirrhosis patients with sarcopenia and PH, suggesting partial microbial restoration. Enrichment of SCFA-producing bacteria may correlates with improved sarcopenia, whereas pro-inflammatory taxa may indicate poor recovery and higher risk of complications. These findings highlight the gut-muscle-liver axis and support microbiome-based biomarkers and interventions to optimize outcomes after TIPS.},
}

@article {pmid41879296,
year = {2026},
author = {Penney, R and Buchanan, LB and Rojas-Vargas, J and Lin, J and Khan, Y and Davidson, J and Wilson, CA and Tai, V and Russo, TA and Hope, TJ and Wilcox, H and Monari, B and Ravel, J and Al, KF and Dave, S and Wang, PZT and Burton, JP and Prodger, JL},
title = {Pathological phimosis is associated with foreskin immune cell infiltration but not microbiota composition.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0072525},
doi = {10.1128/msphere.00725-25},
pmid = {41879296},
issn = {2379-5042},
abstract = {UNLABELLED: The penile microbiota has been implicated in genital inflammation and increased risk of HIV, HPV, HSV-2, and female-partner bacterial vaginosis in adult males, yet its development during childhood and potential role in pediatric foreskin pathologies remain unknown. We characterized the coronal sulcus microbiota of 75 pediatric males (median age 8.5 years; 43% with pathological phimosis) before and after circumcision and compared these profiles to 56 uncircumcised adult men. Pediatric penile microbiota were highly diverse, dominated by strict and facultative anaerobes, and loosely structured compared to adults, who exhibited two distinct, ecologically organized communities. Circumcision markedly reduced anaerobic taxa and increased Corynebacterium and Staphylococcus. Pathological phimosis (the inability to retract the foreskin due to scarring) was associated with increased densities of CD3+ T cells, CD4+ cells, and CD11c+ dendritic cells, suggesting an adaptive immune mechanism; however, pathological phimosis was not associated with microbiota composition. Nonetheless, Mobiluncus was negatively correlated with CD11c+ dendritic cells, while Campylobacter and Peptoniphilus were negatively correlated with CD56+ NK cells, suggesting microbe-immune interactions. Our data suggest pathologic phimosis is driven by adaptive immune responses but not by specific bacteria; the pathology may be driven by differences in host responses to bacteria or by other stimuli, such as fungal antigens. Our data also demonstrate that the transition to adulthood is accompanied by reorganization of penile communities into structured types previously linked to infection risk, highlighting puberty as a potential window for interventions that promote protective adult microbiota and improve lifelong sexual and reproductive health.

IMPORTANCE: The human penis hosts complex bacterial communities that can influence inflammation, infection risk, and sexual health, but little is known about how these communities form early in life or whether they contribute to childhood foreskin inflammatory disorders. We combined 16S rRNA sequencing with quantitative microscopy to investigate the penile microbiota in boys and its relationship to pathological phimosis, a common condition marked by foreskin scarring. We found that phimosis is associated with infiltration of T cells and dendritic cells, indicating an adaptive immune process, but with no associations with specific bacteria. We also show that penile microbiota reorganize during puberty into structured community types previously linked to HIV and sexually transmitted infection risk. These findings suggest that childhood pathologic phimosis is mediated by adaptive immune responses rather than driven by specific bacterial communities and identify puberty as a critical period for shaping adult penile microbiota, with implications for lifelong genital health.},
}

@article {pmid41879306,
year = {2026},
author = {Xia, JY and Sawhney, M and Hussain, HK and Machicado, JD},
title = {Endoscopic management of biliary stricture in primary sclerosing cholangitis.},
journal = {Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society},
volume = {},
number = {},
pages = {},
doi = {10.1097/LVT.0000000000000866},
pmid = {41879306},
issn = {1527-6473},
abstract = {Primary sclerosing cholangitis (PSC) is a progressive fibroinflammatory disease characterized by multifocal biliary strictures, recurrent cholangitis, and a markedly increased lifetime risk of cholangiocarcinoma (CCA). Endoscopic retrograde cholangiopancreatography (ERCP) remains central to the diagnosis of CCA and management of PSC-related complications. This review synthesizes current evidence guiding the use of ERCP in patients with PSC, highlighting the importance of careful patient selection to mitigate adverse events. We review traditional ERCP techniques for the evaluation of dominant strictures such as brush cytology, fluorescence in situ hybridization (FISH), and biopsies, which exhibit limited sensitivity for detecting CCA in PSC. We also review the role of advanced endoscopic approaches including cholangioscopy, endoscopic ultrasound, and confocal endomicroscopy, alongside novel molecular diagnostics (next generation sequencing, DNA methylation markers), metabolomics, bile microbiome, and radiomics, which shown promise for risk stratification and CCA detection in PSC. Therapeutically, we review evidence supporting the use of balloon dilation as first line therapy for the management of PSC strictures and discuss settings where plastic stents might be beneficial. Furthermore, we review the endoscopic management of other PSC complications such as cholangitis, stones, acute cholecystitis, and post-transplant strictures. Finally, we provide best practice recommendations to minimize risk of complications, including use of peri-procedural antibiotic prophylaxis, technique modifications, and individualized sphincterotomy decisions. As innovative diagnostic and therapeutic strategies for PSC continue to evolve, rigorous multicenter, prospective studies are needed to assess efficacy, safety, and cost-effectiveness of these strategies prior to widespread adoption.},
}

@article {pmid41879310,
year = {2026},
author = {Qin, M and Wen, Y and Li, S and Li, S and Li, X and Lin, Y and Hu, L and Xia, H and Pang, Y and Li, L},
title = {The respiratory microbiome in pulmonary tuberculosis: a meta-analysis reveals niche-specific microbial and functional signatures.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0156325},
doi = {10.1128/msystems.01563-25},
pmid = {41879310},
issn = {2379-5077},
abstract = {UNLABELLED: Tuberculosis (TB) remains a major global health challenge. The close relationship between the microbiome and the host is becoming increasingly notable. While studies on the respiratory microbiome in pulmonary tuberculosis (PTB) exist, a comprehensive understanding of microbial characteristics across the entire respiratory tract is still lacking. To address this, we conducted a meta-analysis by integrating data from common and representative respiratory samples. We integrated 16S rRNA data from 11 public datasets encompassing upper respiratory tract specimens (URTs), sputum, and bronchoalveolar lavage fluid (BALF). Ecological patterns were investigated through co-occurrence networks and neutral community modeling, while taxonomic and functional analyses were conducted with QIIME2 and PICRUSt2. The respiratory microbiota in PTB exhibited dynamic variations while sharing common genera, such as Streptococcus, Prevotella, Veillonella, and Neisseria. Alpha diversity was consistently higher in PTB than in healthy controls, with BALF exhibiting the greatest microbial diversity. Several differentially abundant genera were identified among the three sample types, Serratia being almost exclusively detected in BALF. Notably, the microbial interaction network in sputum was more complex and demonstrated the best fit to the neutral community model. Functional predictions highlighted enriched pathways such as peptidoglycan maturation and ABC transporters, and Bacillus was linked to multiple metabolic pathways. Several KO functions were predicted to be more active in URTs and sputum than in BALF. Our multi-scale analysis delineates a niche-specific biogeography of the respiratory microbiome in PTB. By elucidating community assembly and microbe interplay, we position the respiratory microbiota as an active contributor to TB. This work paves the way for novel microbiota-based diagnostics and ecologically informed therapies.

IMPORTANCE: Pulmonary tuberculosis (PTB) remains a leading cause of global mortality, yet the ecological principles shaping its respiratory microbiome are poorly understood. By integrating 16S rRNA datasets from upper and lower airway specimens, this study provides the first comprehensive meta-analysis of respiratory microbial diversity and function in PTB. We reveal distinct community structures and functional potentials among upper airways, sputum, and bronchoalveolar lavage fluid, driven by niche-specific ecological processes rather than stochastic assembly. These findings establish a baseline framework for interpreting microbial biogeography across the respiratory tract and highlight potential microbial biomarkers for site-specific monitoring and therapeutic targeting in PTB.},
}

@article {pmid41879323,
year = {2026},
author = {Mortensen, GA and Schmidt, H and Radivojac, P and Ye, Y and Haas, DM},
title = {Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0315525},
doi = {10.1128/spectrum.03155-25},
pmid = {41879323},
issn = {2165-0497},
abstract = {The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and gestational diabetes mellitus (GDM) remains poorly understood. This study explores how the gut microbiome differs between pregnant women with these conditions and healthy controls, using metagenomic sequencing to analyze microbial composition and function. Our findings reveal that women with GH and GDM exhibit greater microbiome variability and distinct shifts in bacterial communities compared to healthy pregnancies. Key beneficial bacteria, such as Bacteroides fragilis and Roseburia intestinalis, were reduced in cases, suggesting potential disruptions in gut-related metabolic and immune functions. In addition to multiple differentially abundant species of Sphingobacterium in cases versus controls, functional analysis indicated changes in carbohydrate and lipid metabolism, reinforcing the microbiome's connection to metabolic health. Furthermore, machine learning models demonstrated promising results in predicting disease status based on microbiome data, underscoring the potential for gut bacteria as potential predictive biomarkers for pregnancy-related conditions. These insights highlight the gut microbiome's role in pregnancy health and suggest it may be a promising target for future interventions aimed at reducing complications and improving maternal-fetal outcomes.IMPORTANCEGut microbial dysbiosis has been implicated in pregnancy complications, yet most studies rely on 16S rRNA sequencing, which limits resolution and functional insight. Here, using shotgun metagenomic sequencing and machine learning, we identified robust microbial taxonomic and functional signatures that distinguish gestational hypertension and gestational diabetes from healthy pregnancies. A combined feature set enabled accurate classification of disease status, with overlapping features between statistical and predictive frameworks underscoring biological relevance. Altogether, our study defines high-resolution microbiome signatures with translational potential as predictive biomarkers for maternal health, while also providing an open, reproducible analysis pipeline to support future investigations.},
}

@article {pmid41879429,
year = {2026},
author = {Valenzuela, CF and Lopez, KM and Iturralde-Carrillo, A and Mancero-Montalvo, R},
title = {Gut feelings about alcohol risk.},
journal = {The American journal of drug and alcohol abuse},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/00952990.2026.2639481},
pmid = {41879429},
issn = {1097-9891},
}

@article {pmid41879544,
year = {2026},
author = {Mochalov, I and Kryvtsova, M and Tsuperiak, S and Mykhailychenko, B and Guzo, N and Kizim, A},
title = {Species composition and antibiotic susceptibility of microorganisms present in the maxillary sinus and other biotopes during the sinus lift procedure.},
journal = {Folia medica},
volume = {68},
number = {1},
pages = {},
doi = {10.3897/folmed.68.e161534},
pmid = {41879544},
issn = {1314-2143},
mesh = {Humans ; *Maxillary Sinus/microbiology/surgery ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Sinus Floor Augmentation/methods ; Microbial Sensitivity Tests ; Male ; Female ; },
abstract = {Lateral sinus lift is a common procedure in the field of dentistry, employed for the purpose of preparing the maxilla for subsequent dental implantation. This procedure is associated with a significant risk of intra- and postoperative complications, largely attributable to the presence of pathogenic microorganisms within the oral cavity and maxillary sinus.},
}

Humans
*Maxillary Sinus/microbiology/surgery
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Sinus Floor Augmentation/methods
Microbial Sensitivity Tests
Male
Female

@article {pmid41699596,
year = {2026},
author = {Hu, S and Chen, T and Liu, X and Wu, Z and Wang, X},
title = {Effects of aerobic exercise on inflammation and gut microbiota in obese mice: a metagenomic and metabolomic analysis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41699596},
issn = {1479-5876},
support = {2025AFB925//Natural Science Foundation of Hubei Province/ ; XZ202501ZR0140//Key project of Natural Science Foundation of Tibet Autonomous Region/ ; SNSBJKJJHXM2024023//Shannan Science and Technology Plan Project/ ; Yz2024179//National Resource Center for the First-Year Experience and Students in Transition, University of South Carolina/ ; JY2024066//the University-level teaching and research project of Yangtze University/ ; (25Y117)//Philosophical and Social Science Research Project of the Education Department of Hubei Province/ ; 2025csz005//Key Project of Social Sciences Fund of Yangtze University/ ; },
abstract = {BACKGROUND: Aerobic exercise can ameliorate insulin resistance (IR). However, the mechanism by which aerobic exercise regulates the gut microbiome to ameliorate IR and obesity remains unexplored.

METHODS: Obese models were established by feeding C57BL/6 male mice a high-fat diet. A total of 26 mice were randomly divided into control group (group A, N = 8) and high-fat diet group (HFD group, N = 18). Successfully modeled mice were further assigned to model group (group B, N = 8) and exercise group (group C, N = 8). Group C underwent a 6-week treadmill exercise program (12 m/min, 60 min per day, 5 days per week). After intervention, colon tissue morphology was observed through hematoxylin-eosin staining, serum lipids and inflammatory indicators levels were detected by ELISA. The changes in the intestinal microbiota of the mice were also examined using metagenomic sequencing and UPLC-MS non-targeted metabolomics.

RESULTS: Compared with the group A, the body weight, TC, TG, LDL-C, blood glucose, insulin, and IR in the group B significantly increased (P < 0.01), while the levels of pro-inflammatory cytokines TXNIP, TNF-α, NLRP3, IL-1β, and IL-18 significantly increased (P < 0.05 or P < 0.01). Compared with the group B, aerobic exercise reduced the body weight, TC, blood glucose, insulin, IR, TXNIP, TNF-α and other indicators in obese mice (P < 0.05 or P < 0.01). Moreover, aerobic exercise can regulate the imbalance of the intestinal flora in obese mice and ameliorate the disorder of metabolites. The metabolic pathways including arachidonic acid metabolism and histidine metabolism showed the most significant differences after the intervention of aerobic exercise.

CONCLUSIONS: In conclusion, aerobic exercise can ameliorate glucose and lipid metabolism, IR, inflammatory response, and regulate the intestinal microecology and metabolic disorders in obese mice. The mechanism may be closely related to enhancing the diversity of intestinal flora, regulating the metabolism of arachidonic acid and histidine.},
}

@article {pmid41807420,
year = {2026},
author = {de Oliveira Ignacio, MA and Marconi, C and Bidinotto, LT and Balsanelli, E and Belleti, R and da Silva, MG and Duarte, MTC},
title = {Characteristics associated with Lactobacillus-depleted vaginal microbiota in women with different sexual behavior.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41807420},
issn = {2045-2322},
support = {2018/14770-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2015/04224-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {UNLABELLED: The aim of this study was to compare the vaginal microbiome of women with different sexual behaviors and to examine characteristics associated with Lactobacillus-deprived community state type IV. In this prospective study performed in a community-based population in a city of approximately 150,000 inhabitants in Southeast region of Brazil, vaginal swabs were obtained of 109 participants, including women who only had sex with women (n = 54) and women who only had sex with man (n = 55). Sociodemographic data, sexual and intimated hygiene practices of the participants were also assessed. Vaginal microbiota was assessed by sequencing the hypervariable regions V3 and V4 of 16 S ribosomal nucleic acid gene (Illumina 250 PE). Alpha diversity (Shannon index) was compared between the two groups by the Mann-Whitney test. Logistic regression analyses were performed to estimate odds ratios (OR) and 95% confidence intervals (CI) for the association between covariates with the Lactobacillus-deprived community state type IV. Results showed that overall distribution of vaginal CSTs did not differ between the two study groups (P = 0.19). However, alpha diversity was increased in women that only have sex with women (P = 0.0018). Lactobacillus-deprived community state type IV was associated with lower income (OR: 4.15, 95% CI: 1.04–16.46) and use of sex toys (OR: 3.97, 95% CI: 1.09–14.45). In conclusion, nearly one-third of women that only have sex with women had a sub-optimal vaginal microbiome and show evidence of sex transmissibility of CST-IV associated organisms.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34977-2.},
}

@article {pmid41868365,
year = {2026},
author = {Li, J and Li, Q and Wang, M and Xu, S and Zhang, D},
title = {Crop rotation-driven changes in secondary metabolites of potato rhizosphere soil exert stronger regulation on soil microbial community.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768797},
pmid = {41868365},
issn = {1664-302X},
abstract = {INTRODUCTION: Crop rotation promotes ecological effects and production by regulating belowground processes, particularly the shaping of the rhizosphere soil microbiome. Rhizosphere metabolites are a key driver of belowground processes and play a crucial role in shaping soil microbial community composition. However, the rhizosphere metabolites of different potato rotations have rarely been reported, and the regulation of key metabolites on the rhizosphere soil microbiome remains unclear.

METHODS: This study measured agronomic traits of potatoes, collected potato rhizosphere soils from three crop rotations, including potato monoculture (P-P), maize (Zea mays)-potato rotation (M-P), cowpea (Vigna unguiculata)-potato rotation (V-P), to determine rhizosphere soil metabolites and analyze defense metabolites, and assess the soil bacterial and fungal diversity and community composition.

RESULTS: Compared to monoculture, the potato rotations had positive effects on growth and yield. Potato rotations had more primary metabolites, such as amino acids and carbohydrates and conjugates, but significantly reduced secondary metabolites with defensive functions in rhizosphere soils including phenols and other benzene derivatives, flavonoids, alkaloids and other N-containing compounds, and terpenoids. Potato rotation systems supported higher diversity of bacteria and fungi and enriched beneficial bacteria such as biocontrol, nitrogen fixation, C degradation, denitrification, and pollutant degradation bacteria, while suppressing pathogenic fungi in the rhizosphere soils. Rhizosphere soil metabolites strongly correlated with the microbial community composition. The secondary metabolites, which are predominantly alkaloids, terpenoids, and flavonoids, exerted a dominant regulatory effect on the composition of soil microbial community.

DISCUSSION: These results demonstrate the important regulation of rhizosphere metabolites on soil microbial community composition, deepening our understanding of the benefits of crop rotation via the belowground effect.},
}

@article {pmid41868371,
year = {2026},
author = {Bel Mokhtar, N and Stathopoulou, P and Asimakis, E and Augustinos, A and Salgueiro, J and Alleck, M and Sookar, P and Dembilio, Ó and Segura, DF and Tsiamis, G},
title = {Evolutionary dynamics of type VI secretion systems in fruit fly-associated Enterobacter.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755534},
pmid = {41868371},
issn = {1664-302X},
abstract = {Species in the genus Enterobacter are widely distributed and occupy diverse ecological niches. Although many species within this genus have been extensively isolated and characterized, their symbiotic associations with Tephritidae fruit flies remain understudied, particularly through comparative genomic analyses. To address this gap, we conducted a whole-genome comparative analysis of thirteen Enterobacter strains isolated from the most economically significant fruit fly species: Anastrepha fraterculus, Bactrocera dorsalis, Bactrocera zonata, Ceratitis capitata, and Zeugodacus cucurbitae. The results revealed that different fruit flies harbor distinct Enterobacter species, with Enterobacter hormaechei being the most prevalent across hosts. Notably, distinct E. hormaechei subspecies were associated with specific hosts, suggesting a potential host-driven adaptation and coevolution. Pangenome analysis highlighted a dynamic genetic structure among these strains, with significant differences in the core, shell, and species-specific gene composition. The high proportion of metabolism-related genes in the core genome suggests a conserved role in essential biological functions, whereas the enrichment of mobile genetic elements (prophages and transposons) and cell motility genes within the shell and species-specific genomes highlights the genomic plasticity and potential host-specific adaptations. Three distinct subtypes of T6SS (type VI secretion systems) gene clusters, T6SS_C1, T6SS_C2, and T6SS_C3, were detected across Enterobacter strains. T6SS_C1 and T6SS_C2 were identified in most Enterobacter strains, whereas T6SS_C3 cluster was restricted to a single isolate. Although these clusters contained thirteen core T6SS genes, they were characterized by different gene synteny and effector/immunity gene content, suggesting that different Enterobacter strains may utilize distinct mechanisms for interbacterial interactions, host manipulation, and environmental adaptation. Overall, our findings reveal the genetic basis of the symbiosis between Enterobacter species and fruit flies, shedding light on their evolutionary dynamics, diversity of T6SS, and functional traits. These results open new avenues for developing microbiome-based strategies for pest management, including the targeted manipulation of microbial communities to enhance sterile insect technique (SIT) outcomes.},
}

@article {pmid41868375,
year = {2026},
author = {Gao, Y and Wang, Z and Cheng, J and Fu, Y and Wang, Y and Sun, Y and Geng, G and Sun, Y},
title = {Effects of Sphingomonads on sugar beet growth and rhizosphere microbiota under continuous cropping.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1793515},
pmid = {41868375},
issn = {1664-302X},
abstract = {INTRODUCTION: Sugar beet is a crucial sugar crop, and its yield and quality are vulnerable to the adverse effects of continuous cropping. Plant growth-promoting rhizobacteria function as biological control agents and exhibit high potential for crop growth promotion.

METHODS: In this study, soil subjected to continuous sugar beet cropping was selected as the experimental substrate to evaluate the effects of Sphingobium abikonense strain W2, Sphingomonas panni strain W9, Sphingomonas sp. strain W13, and their mixed bacterial suspension on sugar beet seedling growth and soil properties using pot experiments. High-throughput sequencing was used to characterize changes in the rhizosphere soil microbial community structure.

RESULTS: The results indicated that Sphingomonads inoculation significantly improved the agronomic performance of sugar beet seedlings, as evidenced by increased plant height, stem diameter, aboveground and root fresh weight, and enhanced nitrogen and phosphorus uptake. In addition, inoculation increased soil pH, available potassium content, and sucrase activity. Microbial community analysis revealed that all inoculation treatments markedly altered the diversity and composition of the rhizosphere microbiome. Compared with the continuous cropping control, the inoculated soils exhibited a significantly higher abundance of Pseudomonadota, exceeding that observed under crop rotation. Moreover, beneficial genera (e.g., Pseudomonas, Cupriavidus, Massilia, and Novosphingobium) were enriched. Functional prediction demonstrated a significant enhancement of key metabolic processes, including ureolysis and xylanolysis.

CONCLUSION: Overall, Sphingomonad inoculation effectively regulated the structure and function of the rhizosphere microbial community, improved soil enzyme activity and nutrient availability, and promoted sugar beet seedling growth. This study provides a theoretical foundation and potential biocontrol strategy for mitigating continuous cropping obstacles in sugar beet cultivation.},
}

@article {pmid41868536,
year = {2026},
author = {Liu, Y and Wang, S and Liu, Y and Yu, D and Wang, Q and Tian, Y and Ma, L},
title = {Impact of Dupilumab on the Skin Microbiome in Children Aged 6-12 years with Moderate-to-Severe Atopic Dermatitis.},
journal = {Journal of asthma and allergy},
volume = {19},
number = {},
pages = {570878},
pmid = {41868536},
issn = {1178-6965},
abstract = {PURPOSE: We aimed to investigate alterations in the skin microbiome following treatment and discontinuation of dupilumab in children with atopic dermatitis (AD).

METHODS: In all, 24 pediatric AD patients and 10 pediatric health volunteers (HVs) were included. AD patients were treated with dupilumab for 16 weeks and following by a 12-week discontinuation. Cutaneous samples were collected from HVs, and AD patients at baseline and during dupilumab application period (Week 2, Week 4, Week 8, Week 12, and Week 16) and discontinuation period (Week 22 and Week 28) to conduct sequencing targeting the 16s rRNA V3-V4 regions. Clinical severity was assessed using the Eczema Area and Severity Index (EASI), Individual Signs Score (ISS), Children's Dermatology Life Quality Index scores (CDLQI), Patient Oriented Eczema Measure (POEM), and peak pruritus Numerical Rating Scale (NRS itch).

RESULTS: Dupilumab treatment significantly improved AD characteristics, with reductions in EASI, ISS, CDLQI, POEM, and NRS itch scores (all P < 0.01). Concurrently, 16s rRNA sequencing indicated decline in Staphylococcus aureus abundance and increase in microbial diversity. These changes began to reverse upon treatment discontinuation, coinciding with a trend toward worsening EASI scores. Moreover, a dupilumab-responsive reduction in other bacterial genera such as Aggregatibacter, and Megasphaera were observed; and these alterations could be reversed after treatment cessation.

CONCLUSION: We provided a dynamical pattern of skin bacterial community during and after dupilumab therapy in pediatric AD patients. Our findings suggest that the therapeutic action of dupilumab may extend to modulating a wider range of bacteria than previously recognized. The roles of our identified candidate microbial taxa require further investigation in larger and functional studies.},
}

@article {pmid41868611,
year = {2026},
author = {Jimenez-Arenas, P and Ferrer, M and Ruiz-Rivera, M and Júlvez, J and Bustamante, M and Gascon, M},
title = {The relationship between the gut microbiota and neuropsychological development and behaviour during childhood and adolescence: a systematic review of epidemiological studies.},
journal = {Brain, behavior, & immunity - health},
volume = {53},
number = {},
pages = {101212},
pmid = {41868611},
issn = {2666-3546},
abstract = {Mounting evidence suggests that early-life microbial colonization might shape cognitive development and behaviour. This systematic review summarizes current research on the relationship between the gut microbiota and neuropsychological development and behaviour in children and adolescents (0-18 years). Following PRISMA guidelines, we conducted a comprehensive search across MEDLINE, Scopus, and Web of Science, identifying 78 eligible studies covering both clinical neurodevelopmental disorders and general-population neuropsychological outcomes. We observed a high heterogeneity across studies regarding study design, statistical analyses and the consideration of confounding factors (e.g., diet, medication use), gut microbiota determinations and the assessment of neurobehavioural outcomes. Only 42% of studies used longitudinal designs, and confounding factors were frequently unaddressed. Microbiome alterations in autism spectrum disorder (n = 23 studies) included community structure shifts, elevated Clostridium and Sutterella, and reduced Blautia, Lactobacillus, and Bifidobacterium. Functional and metabolomic analyses suggest immunomodulatory and neuroactive processes as main contributors, including elevated levels of the short-chain fatty acids propionate and valerate. For attention-deficit/hyperactivity disorder (n = 7) findings were less consistent. Associations were modest in the general paediatric population, with Veillonella and Bifidobacterium appearing across multiple studies being more abundant in children with enhanced neuropsychological development. Overall, the evidence highlights potential microbial signatures associated with neurodevelopment, yet methodological limitations constrain causal inference. Most of the studies were of poor to fair quality, often due to technical shortcomings in microbiome assessment and statistical limitations. Future research should prioritize standardized exposure/outcome assessment protocols and multi-omics integration, while underlining the potential of methodological rigour in translating findings into clinically actionable knowledge.},
}

@article {pmid41868718,
year = {2026},
author = {Jia, S and Liu, P and Zhang, H and Zeng, H and Chen, G and Zhao, L},
title = {Why the COPD Microbiome Matters: How Airway Microbes Shape Disease Severity and Treatment Response.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {21},
number = {},
pages = {531521},
pmid = {41868718},
issn = {1178-2005},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy/diagnosis/physiopathology/immunology/drug therapy ; *Microbiota ; *Lung/microbiology/drug effects/physiopathology/immunology ; Dysbiosis ; *Bacteria/drug effects/immunology/pathogenicity/growth & development/classification ; Severity of Illness Index ; Treatment Outcome ; Host-Pathogen Interactions ; Disease Progression ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease caused by multiple factors, with diverse clinical manifestations leading to varying treatment outcomes. Dysbiosis of the respiratory microbiome is one of the key contributors to this variability.

OBJECTIVE AND METHODS: Due to differences in microbial detection technologies and sample collection methods, studies on the characteristics of respiratory prokaryotic microbiota and how these microbes influence host functions in COPD patients have yielded variable results. In this review, we conducted a comprehensive search of relevant literature from PubMed, ScienceDirect, and Elsevier, summarizing studies on the characteristics and functional analyses of prokaryotic microbiota under various technical approaches. The goal was to identify common patterns of microbiota changes in COPD across different disease states, as well as individual microbial influences on host functions.

RESULTS: Compared with healthy adults, in stable-phase COPD patients, the relative abundance of Prevotella species in the Bacteroidetes phylum is significantly reduced. During acute exacerbations, the predominant microbiota is composed of Moraxella, Haemophilus, and Streptococcus species from the Proteobacteria and Firmicutes phyla. Clinical indicators in COPD patients are correlated with the abundance of Streptococcus (Firmicutes) and Prevotella (Bacteroidetes) species. Furthermore, the different phyla of respiratory prokaryotic microbiota are associated with innate immunity, metabolism, and inflammation factors related to COPD.

CONCLUSION: This review summarizes evidence on dynamic changes in the airway prokaryotic microbiome during COPD progression. It highlights the dual role of these microbial changes as biomarkers of disease progression and modifiable targets for personalized care. Observed patterns-such as reduced Prevotella abundance in stable disease and the dominance of Moraxella, Haemophilus, and Streptococcus during acute exacerbations-provide a basis for stratifying patients and designing individualized treatment plans. Microbiome analysis may aid in early identification of high-risk patients for preventive strategies, guide pathogen-specific antimicrobial or immunomodulatory therapy, and allow treatment response to be monitored through microbial shifts. By linking distinct microbial profiles to host immune and inflammatory pathways, this approach supports the development of tailored interventions to restore microbial balance. These strategies could improve clinical outcomes and advance precision medicine in COPD management.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/therapy/diagnosis/physiopathology/immunology/drug therapy
*Microbiota
*Lung/microbiology/drug effects/physiopathology/immunology
Dysbiosis
*Bacteria/drug effects/immunology/pathogenicity/growth & development/classification
Severity of Illness Index
Treatment Outcome
Host-Pathogen Interactions
Disease Progression
*Respiratory System/microbiology

@article {pmid41868793,
year = {2026},
author = {Yan, N and Zhang, Y and Wang, S and Hu, S and Ruan, L and Wang, Y and Feng, W and Xiong, W and Zhang, W and Wei, Y and Yao, C},
title = {CAMK1D as a potential therapeutic target for gut microbiota-driven promotion of lung adenocarcinoma development.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20985},
pmid = {41868793},
issn = {2167-8359},
mesh = {Humans ; *Adenocarcinoma of Lung/genetics/microbiology ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/microbiology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; *Calcium-Calmodulin-Dependent Protein Kinase Type 1/genetics/metabolism ; Mendelian Randomization Analysis ; },
abstract = {BACKGROUND: The gut microbiome is closely associated with malignant tumors; however the specific mechanisms by which it contributes to the development of lung adenocarcinoma remain unclear. In this study, we performed a two-sample bidirectional Mendelian randomization (MR) analysis to assess the causal relationship between the gut microbiome and lung adenocarcinoma. By identifying single nucleotide polymorphism markers linked to gut microbiome species, we aimed to discover potential biomarkers for lung adenocarcinoma. These findings may offer new insights into the role of the gut microbiome in the prevention and treatment of lung adenocarcinoma.

METHODS: We used genome-wide association study (GWAS) summary statistics to assess the association between the gut microbiome and lung adenocarcinoma through two-sample MR analysis. Sensitivity analyses were performed to confirm the robustness of the findings. Reverse MR analysis and GWAS data integration were employed to identify potential genetic and therapeutic targets. Bioinformatics analysis and quantitative Real-Time PCR (qRT-PCR) were utilized to validate gene expression and explore the underlying mechanisms of key genes.

RESULTS: Our analysis identified two bacterial taxa, Prevotella9 and Parabacteroides, as being causally associated with lung adenocarcinoma, both showing positive causal relationships. Sensitivity analyses confirmed the robustness of these associations. The reverse MR analysis revealed no evidence of reverse causality. GWAS data identified 15 genes (DNAH1, PDE10A, DOCK2, INSYN2B, DNAI3, SUOX, LINC01505, SULT4A1, NT5ELP, LINC02895, calcium/calmodulin dependent protein kinase 1D (CAMK1D), ENSG00000253557, BCAS3, C18orf63, MYO18B) that passed the summary-data-based MR test. The transcriptomic data revealed that five genes (CAMK1D, BCAS3, DNAH1, PDE10A, and C18orf63) were differentially expressed between lung adenocarcinoma patients and healthy individuals. Through qRT-PCR validation, the CAMK1D gene was markedly upregulated in lung adenocarcinoma cell lines, whereas BCAS3, DNAH1, PDE10A, and C18orf63 genes exhibit ed substantially reduced expression.

CONCLUSION: Our study identified specific gut microbial taxa as risk factors for lung adenocarcinoma and proposes CAMK1D as a microbiota-related candidate biomarker and potential therapeutic target that may inform personalized treatment and drug development strategies in the future.},
}

Humans
*Adenocarcinoma of Lung/genetics/microbiology
*Gastrointestinal Microbiome/genetics
*Lung Neoplasms/genetics/microbiology
Genome-Wide Association Study
Polymorphism, Single Nucleotide
*Calcium-Calmodulin-Dependent Protein Kinase Type 1/genetics/metabolism
Mendelian Randomization Analysis

@article {pmid41868872,
year = {2026},
author = {Kyrochristou, I and Kyrochristou, G and Fousekis, F and Katsanos, K and Schizas, D and Vlachos, K and Lianos, GD},
title = {Determinants of the healthy gut microbiome: core features, modifying factors and normal functions.},
journal = {Annals of gastroenterology},
volume = {39},
number = {2},
pages = {191-201},
pmid = {41868872},
issn = {1108-7471},
abstract = {The human gut microbiome represents a complex and dynamic ecosystem that is central to maintaining health and preventing disease. Defining a "normal" gut microbiome remains challenging, given the significant variability arising from host physiology, lifestyle, genetics, geography and environmental exposures. This review synthesizes current evidence regarding the composition and functions of the gut microbiota in healthy individuals from diverse populations. At the taxonomic level, healthy gut microbial communities are typically dominated by the phyla Firmicutes and Bacteroidetes, with additional contributions from Actinobacteria and Proteobacteria. However, substantial inter-individual and regional differences are observed, such as a higher prevalence of Prevotella in populations consuming fiber-rich Eastern diets, and greater Bacteroides abundance in Western cohorts. Anatomical location and health status also influence alpha-diversity, underscoring the need to interpret diversity metrics within context. Furthermore, the gut microbiome performs essential functional roles across multiple organ systems, including fermentation of dietary fibers into short-chain fatty acids, regulation of immune responses, modulation of the gut-brain axis, maintenance of intestinal barrier integrity, and support of cardiovascular and hepatic functions. These findings support the conceptualization of the microbiome as a multifunctional organ system that integrates host and environmental signals. In summary, a healthy gut microbiome is best understood as a dynamic equilibrium, characterized by functional resilience and adaptability, rather than a fixed microbial profile. Interpreting this variability is crucial for developing targeted interventions to prevent disease.},
}

@article {pmid41869364,
year = {2026},
author = {Wang, B and Zhang, Y and Lin, L and Wang, S and Yang, S},
title = {Psoriasis: microbiome dysbiosis and pathogenic mechanisms.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1714515},
pmid = {41869364},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Psoriasis/microbiology/immunology/etiology/therapy ; *Gastrointestinal Microbiome/immunology ; Animals ; *Microbiota/immunology ; Skin/immunology/microbiology ; },
abstract = {Psoriasis is a chronic immune-mediated inflammatory disease whose pathogenesis is a triad of genetic predisposition, immune dysregulation, and environmental triggers. This review provides a novel, in-depth synthesis arguing that microbial dysbiosis is not merely an associative phenomenon but a central regulatory node within this triad, actively shaping immune responses and clinical phenotypes. We move beyond cataloging microbial shifts to construct a detailed mechanistic framework of the gut-skin axis. Gut dysbiosis; characterized by reduced diversity, a diminished Bacteroidetes/Firmicutes ratio, and depleted SCFA producers, compromises intestinal barrier integrity, reduces systemic immunoregulatory tone via diminished SCFA signaling, and promotes Th17 polarization. This systemic inflammation is directly communicated to the skin. Concurrently, cutaneous dysbiosis, featuring Staphylococcus aureus dominance and fungal alterations, disrupts the local barrier, provides chronic antigenic stimulation, and amplifies IL-17-driven inflammation, creating a self-sustaining loop. Crucially, we analyze how specific infections (HCV, H. pylori, Streptococcus) act as environmental triggers by sharing or activating these very pathways. The bidirectional relationship with therapy is dissected: while biologics induce drug-specific microbiome shifts that often correlate with clinical normalization, they also carry infection risks that must be strategically managed. Emerging microbiome-targeted interventions like specific probiotics show promise but are hampered by methodological inconsistencies. This review uniquely highlights the causality gap and proposes that future breakthroughs require a shift from correlation to mechanism. We conclude that the microbiome is a dynamic interface between genes and environment in psoriasis; its successful integration into diagnostic and therapeutic paradigms demands standardized multi-omics approaches, functional validation, and personalized medicine strategies that target this critical axis.},
}

Humans
*Dysbiosis/immunology/microbiology
*Psoriasis/microbiology/immunology/etiology/therapy
*Gastrointestinal Microbiome/immunology
Animals
*Microbiota/immunology
Skin/immunology/microbiology

@article {pmid41869707,
year = {2026},
author = {Wang, Z and Fu, Y},
title = {Bacteria weigh up costs and benefits of mobile weapons.},
journal = {eLife},
volume = {15},
number = {},
pages = {},
pmid = {41869707},
issn = {2050-084X},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteria/genetics/metabolism ; },
abstract = {Gaining the ability to kill rival microbes is not always an advantage for bacteria in complex gut microbiomes.},
}

*Gastrointestinal Microbiome
Humans
*Bacteria/genetics/metabolism

@article {pmid41869810,
year = {2026},
author = {Zhang, C and Sun, Z and Lin, Y and Long, W and Zhang, R and Huang, H and Liang, W},
title = {Pulmonary mucoid Pseudomonas aeruginosa infection and association with higher species richness and stronger inflammatory immune response.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0229525},
doi = {10.1128/spectrum.02295-25},
pmid = {41869810},
issn = {2165-0497},
abstract = {The mucoid phenotype of Pseudomonas aeruginosa (PA) is regarded as a comprehensive adaptive stress response to difficult environmental circumstances. However, there is little knowledge about the relationship between the prevalence of mucoid PA and species richness and immune inflammatory response. A case-control study was conducted in hospitalized patients with pulmonary infections caused by mucoid and non-mucoid PA. Sputum samples were subjected to 16S rDNA sequencing to characterize microbial diversity and taxonomic composition, while serum levels of TNF-α, IL-6, IL-8, IL-10, and IL-17 were measured using enzyme-linked immunosorbent assays. Subsequent statistical analysis using R 4.0 revealed significant correlations between differentially abundant microbial taxa and cytokine profiles. Compared to the non-mucoid PA group, the mucoid PA group demonstrated significantly higher α-diversity indices in terms of species richness, as indicated by the Chao1 (P = 0.0015) and Observed-species metrics (P = 0.0014). Furthermore, distinct β-diversity patterns were observed between the two groups (P < 0.05). LefSe analysis revealed significant enrichment of Veillonella spp., Haemophilus spp., Porphyromonas spp., Prevotella spp., Actinomyces spp., Lactobacillus spp., and Rothia spp. in the mucoid PA group, while Stenotrophomonas spp., Acinetobacter spp., Parvimonas spp., and Serratia spp. dominated in the non-mucoid PA group. The mucoid PA infections showed marked elevation of IL-8 (P = 0.0137), TNF-α (P = 0.0048), IL-10 (P = 0.0042), IL-17 (P = 0.0220), and IL-6 (P = 0.0001). Spearman correlation revealed Veillonella spp./Rothia spp./Porphyromonas spp./Prevotella spp. positively correlated with IL-10/TNF-α/IL-17/IL-6, whereas Haemophilus spp. showed a negative relationship with IL-17. Stenotrophomonas spp. exhibited strong negative correlations with IL-10/IL-6, and Serratia spp. was inversely associated with TNF-α in non-mucoid PA infections. Clinically distinct microbial ecosystems in mucoid PA correlate with exacerbated inflammation. This phenotype-driven dichotomy provides actionable biomarkers for stratified antimicrobial/immunomodulatory therapies in chronic lung disease.IMPORTANCEThis study holds significant clinical and scientific importance, as it elucidates the critical differences between mucoid and non-mucoid Pseudomonas aeruginosa (PA) infections in pulmonary patients. By demonstrating that mucoid PA infections are associated with distinct microbial ecosystems (higher species richness and different taxonomic compositions) and more severe inflammatory responses (elevated TNF-α, IL-6, IL-8, IL-10, and IL-17), the research provides crucial insights into phenotype-specific pathogenesis. The identified correlations between specific bacterial species (e.g., Veillonella/Rothia with pro-inflammatory cytokines) offer potential biomarkers for clinical stratification. These findings are particularly valuable for developing targeted therapeutic strategies, as they suggest mucoid PA infections may require different antimicrobial/immunomodulatory approaches compared to non-mucoid variants. The study bridges an important knowledge gap in understanding how bacterial phenotypic adaptation influences host-microbiome interactions and disease outcomes in chronic lung infections.},
}

@article {pmid41869813,
year = {2026},
author = {Mancabelli, L and Palomba, E and Magni, F and Chatenoud, L and Olgiati, I and Buracchi, C and Bugarin, C and Gaipa, G and Abbruzzese, C and Filippini, M and Forastieri, A and Fumagalli, R and Geraldini, F and Picetti, E and Terranova, L and Vaschetto, R and Zoerle, T and Ventura, M and Citerio, G and Gori, A and Bandera, A and Alagna, L and Turroni, F},
title = {Microbial signatures and host immune responses associated with the development of ventilator-associated pneumonia among patients with neurological injuries.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0319325},
doi = {10.1128/spectrum.03193-25},
pmid = {41869813},
issn = {2165-0497},
abstract = {Ventilator-associated pneumonia (VAP) remains a leading complication in mechanically ventilated patients, yet the contribution of the respiratory microbiota remains poorly understood. The PULMIVAP study is a multicenter, longitudinal cohort investigation of respiratory microbiota composition and host immune responses in critically ill adults intubated for non-pulmonary conditions. A total of 146 intubated adult patients were enrolled across eight Italian ICUs, forming matched groups of 73 with VAP and 73 without. Oropharyngeal swabs and endotracheal aspirates were collected at intubation and either at VAP diagnosis or at a matched point in controls for a total of 584 biological samples. Metataxonomic analyses revealed substantial temporal shifts in microbial communities across both upper and lower respiratory compartments, with a trend toward reduced microbial richness in patients who developed VAP. Several genera, such as Corynebacterium, were more abundant in no-VAP patients, whereas Escherichia-Shigella and Peptoniphilus were enriched in VAP samples. Cytokine-microbiota correlation analysis suggested a pro-inflammatory signature in VAP patients, with Citrobacter positively associated with IFN-γ and TNF-α, while several commensal genera were inversely correlated with inflammatory mediators. Additionally, taxa associated with VAP correlated with lower PaO2/FiO2 ratios, implicating them in disease severity. Consistently, several bacteria, such as Corynebacterium, appeared to be linked to better respiratory outcomes, suggesting protective or risk-associated microbial profiles. Overall, these findings highlight the complex interplay between microbial communities and mucosal immunity in the pathogenesis of VAP. The identification of condition-associated microbial and immunological signatures may inform future strategies for risk stratification and targeted prevention.IMPORTANCEVentilator-associated pneumonia (VAP) remains a major complication of mechanical ventilation, yet most microbiome studies have focused on late-stage infection or single airway compartments, limiting insight into early microbial dynamics associated with VAP risk. By longitudinally characterizing upper and lower airway microbiota before and during VAP development, this study provides new insights into microbial and immune patterns associated with susceptibility and disease severity in humans. These findings contribute to the current understanding of VAP pathogenesis by suggesting a role for early airway dysbiosis and local immune responses alongside clinical factors. Remarkably, the identification of taxa associated with risk or protection supports the potential for microbiota-informed monitoring and future risk stratification strategies during mechanical ventilation.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT04849039.},
}

@article {pmid41869814,
year = {2026},
author = {Yang, K and Yang, Z and Li, H and Liu, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T},
title = {Effects of heavy metal exposure on oral microbial communities in women with different menopausal status.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0312325},
doi = {10.1128/spectrum.03123-25},
pmid = {41869814},
issn = {2165-0497},
abstract = {This study investigates the effects of long-term heavy metal exposure on the oral mucosal microbiota in women. By measuring both external environmental heavy metal exposure and internal heavy metal exposure indicators in the human body, it aims to elucidate the complex interactions between external environmental exposure and internal exposure, as well as their potential association with menopausal status. We analyzed oral microbial composition, function, and co-occurrence networks in 47 women from polluted and control areas. Heavy metal exposure significantly altered oral microbial diversity and functional pathways, with molybdenum (Mo) exhibiting a uniquely strong influence. Key metabolic pathways related to cardiovascular disease and carbohydrate metabolism were enriched in specific groups. Network analysis revealed a loss of keystone species and structural simplification in postmenopausal women from the polluted area. These findings suggest that heavy metal exposure alters oral microbial communities, and these alterations correlate with shifts in host metabolic pathways that are known to be associated with menopausal hormonal changes, potentially impacting women's health during this transition.IMPORTANCEThis study reveals, for the first time, how chronic heavy metal exposure and menopause interact to disrupt the female oral microbiome. We identify Mo as a key metal, correlating strongly with specific bacteria and linked to downregulated cardiovascular and metabolic pathways. Critically, postmenopausal women in polluted areas exhibit a severe loss of keystone species and a collapsed microbial network structure. These findings position the dysregulated oral microbiome as a potential mechanistic link between environmental metal exposure and the heightened systemic risks-such as metabolic disorders and chronic inflammation-observed in postmenopausal women, highlighting new targets for preventive health strategies.},
}

@article {pmid41869817,
year = {2026},
author = {Chong, Q and Cheng, M and Cao, Q and He, J and Xiao, M and Li, Y and Wang, Z and Wang, J and Zhang, K and Gou, H},
title = {Systematic evaluation of phage cocktail-ciprofloxacin combination therapy against multidrug-resistant Salmonella Typhimurium induced gut dysbiosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0264025},
doi = {10.1128/spectrum.02640-25},
pmid = {41869817},
issn = {2165-0497},
abstract = {Phage therapy, despite its promise as a novel therapeutic alternative for multidrug-resistant (MDR) bacterial infections, is hampered by clinical limitations such as narrow host range and therapeutic inconsistency. This research has engineered a phage-antibiotic synergistic therapy enabling precision eradication of drug-resistant Salmonella Typhimurium (S. Typhimurium). From slaughterhouse wastewater and fecal samples, three Felixounavirus phages (TSP_TW2, TSP_SW1, and TSP_SJ5) were isolated. Compared to the clinical phage repository, these phages demonstrated more superior broad-spectrum activity, successfully lysing over 85% of the tested wild-type isolates. The in vitro study, validated by laser confocal fluorescence imaging demonstrates that compared to solitary phage, phage cocktail delays the emergence of resistance to 24 h while also achieving effective biofilm eradication. In the murine intestinal infection model, the experimental group treated with phage cocktail in combination with ciprofloxacin (CIP) demonstrated significant therapeutic effects, reaching 90% survival rate, restoring the CD4[+]/CD8[+] T cell balance, and decreasing the levels of pro-inflammatory factors, which were significantly superior to those of phage or CIP alone. In addition, the susceptibility of S. Typhimurium to β-lactams, quinolones, and observed four- to eightfold reduction in tetracycline minimal inhibitory concentration (MIC) demonstrated effective restoration of antibacterial activity after therapeutic intervention. 16S rRNA high-throughput sequencing showed that the index of intestinal flora diversity of mice in the treatment group was not significantly difference to healthy control group, while specifically promoting the growth of beneficial microbial populations such as Lactobacillus spp. The innovative phage-antibiotic combination therapy established in this study demonstrated dual therapeutic advantages: effective clearance of antimicrobial-resistant strains and maintenance of enteric microbiome homeostasis, thereby offering a clinically promising strategy for controlling infections caused by antimicrobial-resistant S. Typhimurium.IMPORTANCEFoodborne Salmonella infections threaten global public health, as conventional antibiotics accelerate resistance and disrupt microbial balance. We pioneer a synergistic phage-ciprofloxacin cocktail strategy that overcomes multidrug-resistant Salmonella infection through three key advances: First, it delays resistance evolution while eradicating biofilm matrices; second, the therapy synergistically enhances antibiotic sensitivity to restore efficacy of critical drugs; and third, the combined approach maintains optimal gut microbiota balance during pathogen clearance. By using environmentally derived phages with minimized antibiotic dosing, this strategy achieves targeted removal of resistant pathogens-including invasive biofilms-without collateral damage to commensal flora. Crucially, it prevents systemic inflammation and preserves intestinal barrier function. This ecologically sustainable paradigm provides a dual-defense mechanism against infections and microbiome dysbiosis, positioning phage-antibiotic synergy as a transformative tool for containing foodborne disease threats.},
}

@article {pmid41869825,
year = {2026},
author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G},
title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261428562},
doi = {10.1177/15578666261428562},
pmid = {41869825},
issn = {1557-8666},
abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.},
}

@article {pmid41869845,
year = {2026},
author = {Suk, K and Lee, WH},
title = {Peptidoglycan recognition proteins in the brain: Role in neuroinflammation and behavioral consequences.},
journal = {Histology and histopathology},
volume = {},
number = {},
pages = {25064},
doi = {10.14670/HH-25-064},
pmid = {41869845},
issn = {1699-5848},
support = {RS-2024-00408736//National Research Foundation of Korea (NRF), Korean government/ ; },
abstract = {Peptidoglycan recognition proteins (PGRPs) constitute an evolutionarily conserved family of pattern recognition molecules that detect bacterial peptidoglycan. While their antimicrobial functions have been well characterized in peripheral immunity, recent discoveries have unveiled critical roles for PGRPs in central nervous system inflammation and behavior. Among the four mammalian PGRP family members, PGLYRP1 exhibits unique expression in brain microglia and demonstrates potent pro-inflammatory properties in neurological contexts. Recently, PGLYRP1 has been shown to function as a key amplifier of neuroinflammation through a novel TREM1-Syk-Erk1/2-Stat3 signaling axis, establishing a positive feedback loop with TNF-α that perpetuates microglial activation. This review synthesizes current understanding of PGRP biology in the nervous system, with particular emphasis on molecular mechanisms of PGLYRP1, cellular sources, and behavioral consequences. We examine the structural basis of peptidoglycan recognition, cell-type-specific expression patterns, signaling pathways, and integration with other innate immune systems. Furthermore, we explore emerging connections between gut microbiome-derived peptidoglycan, blood-brain barrier penetration, and neuropsychiatric disorders. Critical knowledge gaps remain regarding physiological versus pathological roles of PGLYRP1, therapeutic targeting strategies, and translational potential. Understanding PGLYRP1-mediated neuroinflammation provides novel mechanistic insights into microbiome-brain communication and offers promising therapeutic avenues for neuroinflammatory and neurodegenerative diseases.},
}

@article {pmid41869887,
year = {2026},
author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J},
title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e20332},
doi = {10.1002/advs.202520332},
pmid = {41869887},
issn = {2198-3844},
support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; },
abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.},
}

@article {pmid41869963,
year = {2026},
author = {Zhong, X and Chen, W and Sun, Q and Zhang, S and Yang, J and Min, W and Li, W},
title = {Crisaborole Reduced the Staphylococci but Increased Cutibacterium on the Skin Microbiome of Children with Atopic Dermatitis.},
journal = {Dermatitis : contact, atopic, occupational, drug},
volume = {},
number = {},
pages = {17103568261431028},
doi = {10.1177/17103568261431028},
pmid = {41869963},
issn = {2162-5220},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a common, recurrent skin disease in children, associated with an imbalance in the skin microbiome. Topical corticosteroids (TCS) cream is the first-line drug for treating AD. However, its long-term use is prone to the development of adverse reactions. Crisaborole, a nonsteroidal medication, is effective and well-tolerated for long-term maintenance treatment and flare reduction in adult and pediatric patients with mild-to-moderate AD. However, the effect of crisaborole on the skin microbiome remains unknown.

OBJECTIVE: The study aimed to compare the effects of topical crisaborole treatment and TCS treatment on microbial abundance and diversity in AD lesions.

METHODS: A cross-sectional study was conducted involving 30 children with mild-to-moderate AD and 10 healthy controls. Patients with AD were divided into three groups (untreated, TCS, and crisaborole; n = 10 each) based on baseline status. Skin samples were collected directly from the healthy child, the untreated lesions, and after a 2-week treatment period. The skin microbiome was analyzed using 16S rRNA gene sequencing.

RESULTS: Compared to the untreated AD group, both TCS and crisaborole treatments significantly reduced the relative abundances of Staphylococcus and Pseudomonas, while increasing the abundances of Streptococcus and Cutibacterium (formerly Propionibacterium). Alpha diversity of the skin microbiome was significantly increased after both treatments. However, the microbial profile of the crisaborole group was more distinct from the healthy control group than the TCS group was. Furthermore, the crisaborole group showed significant enrichment of taxa from the phylum Actinobacteria, including the genus Cutibacterium and species acnes.

CONCLUSIONS: Although the efficacy of crisaborole in treating mild-to-moderate AD in children is not equivalent to that of TCS, crisaborole could still remarkably improve the clinical symptoms of patients and partially restore the microbial diversity on the skin surface of children with AD.},
}

@article {pmid41869966,
year = {2026},
author = {Yu, T and Fan, H},
title = {Host-microbiota interactions: a novel insight into the aryl hydrocarbon receptor in Parkinson's disease.},
journal = {Postgraduate medical journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/postmj/qgag017},
pmid = {41869966},
issn = {1469-0756},
abstract = {BACKGROUND: Parkinson's disease (PD) is regarded as the second most common neurodegenerative disease. Accumulating evidence suggested an emerging effect of the dysregulation of the gut-brain axis in the neurodegenerative disease pathogenesis, mediated particularly by microbiota-derived metabolites in PD. The aryl hydrocarbon receptor (AHR) is of great importance in regulating central nervous system inflammation by sensing microbiota-derived metabolites.

STRATEGY: AHR is a transcription factor activated by ligands, which can be activated locally or remotely by endogenous microbial metabolites. AHR signaling suppressed inflammation by activating anti-inflammatory and immunosuppressive responses, promoting intestinal host-microbiome homeostasis. The pathogenesis of PD is related to the activation of microglia and the occurrence of neuroinflammation. There is increasing attention that alterations in the intestinal flora and decreased AHR activity were closely associated with PD.

CONCLUSION: The AHR-gut microbiota axis garnered increasing attention in PD research. In this review, we synthesize current clinical and preclinical evidence linking the AHR-gut microbiota axis to PD pathogenesis, and we highlight that pharmacological targeting of this pathway represents an emerging therapeutic strategy for PD.},
}

@article {pmid41870062,
year = {2026},
author = {Weingarten, EA and Fernando, BM and Freitas, MR and Indest, KJ},
title = {Cave microbial communities are structured by environmental matrix and depth and can be characterized with field-portable assays.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0031226},
doi = {10.1128/aem.00312-26},
pmid = {41870062},
issn = {1098-5336},
abstract = {UNLABELLED: Terrestrial caves are unique ecosystems characterized by environmental stability, nutrient limitation, and absence of light, yet they host diverse microbial communities with ecological and public health relevance. Microbiome studies of caves have typically been limited in scope, sampling only select environments or cave depths. We conducted a broad survey of microbial diversity in three natural limestone caves and two abandoned mines spanning continental, subtropical, and arid climates in the United States. Using amplicon sequencing of 382 samples composed of soil, rock, water, air, and bat and rodent feces, microbiome composition was found to be primarily structured by cave location, followed by environmental matrix (soil, water, air, etc.), and transect distance from the cave entrance. Significant heterogeneity was observed both between and within caves, underscoring the need for spatially explicit and multi-matrix sampling to capture representative community profiles. Portable DNA extraction and quantitative PCR (qPCR) technologies for onsite detection of microbial pathogens were further validated, demonstrating comparable results to laboratory-based workflows and reducing sample-to-result turnaround time from several days to less than 2 h. Pathogen panels detected zoonotic and waterborne agents of human health concern, including Salmonella and Legionella, directly from cave environments. Collectively, our findings establish a methodological framework for robust microbiome characterization in subterranean ecosystems and highlight the feasibility of field-deployable genetic tools for both biodiversity mapping and rapid pathogen surveillance. These approaches will enable more systematic monitoring of cave environments, with applications for ecology, conservation, and public health.

IMPORTANCE: Caves and mines represent extreme and isolated environments that harbor unique microbial communities, yet they remain among the least studied environments on Earth. Understanding how these communities are structured across different habitats and locations is essential for both ecological research and public health monitoring. In this study, we surveyed microbiomes across multiple caves and environmental materials to reveal how location, substrate type, and depth shape microbial diversity. We also demonstrated that portable DNA extraction and analysis tools can be used in the field to rapidly detect microorganisms, including potential pathogens, without the need for laboratory infrastructure. These results provide new insight into how microbial life is distributed in subterranean ecosystems and establish practical methods for monitoring microbial diversity and detecting pathogens in remote environments.},
}

@article {pmid41870087,
year = {2026},
author = {Wang, X and Wu, W and Yang, B and Liu, Y and Xu, Y and Wang, L and Lv, X and Gao, J and Lu, M and Yu, A and Li, N and Chen, Q and Lu, L and Zhao, D},
title = {Additive effects of fecal microbiota transplantation and infliximab on gut microbiome and metabolome in refractory inflammatory bowel disease patients.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0077425},
doi = {10.1128/msystems.00774-25},
pmid = {41870087},
issn = {2379-5077},
abstract = {UNLABELLED: Fecal microbiota transplantation (FMT) is an emerging therapy for inflammatory bowel disease (IBD), yet its efficacy in patients refractory to conventional treatments and its underlying mechanisms require further elucidation. We studied 37 IBD patients (15 ulcerative colitis [UC], 22 Crohn's disease [CD]) refractory to conventional therapies and 16 healthy donors. FMT monotherapy from a single donor induced week-4 clinical response in 12 UC and 9 biologic-naïve CD patients, with all responders sustaining remission and most achieving endoscopic remission by week 14. Integrated multi-omics revealed FMT restored microbial diversity and profoundly reorganized host-microbiota-metabolite networks. In nine refractory CD patients (7 infliximab [IFX] non-responders, 2 FMT non-responders), IFX-FMT combination led to week-4 response in 6 patients, all of whom attained clinical and endoscopic remission by week 14, with more complete microbial-metabolic restoration than monotherapy. Our findings establish that FMT induces remission in refractory IBD via ecosystem network rewiring, and that IFX-FMT exhibits additive effects, supporting further trials of microbiome-directed adjunctive strategies.

IMPORTANCE: This study provides mechanistic and clinical insights into the therapeutic effects of fecal microbiota transplantation (FMT) in inflammatory bowel disease (IBD), particularly when combined with the anti-tumor necrosis factor (anti-TNF) biologic infliximab (IFX). While both FMT and IFX achieve response in approximately 60% of IBD patients, their combined influence on the gut microbial and metabolic landscape in refractory disease has been poorly understood. Here, we demonstrate that FMT monotherapy restores gut microbial diversity and reconfigures host-microbiota-metabolite networks, correlating with clinical and endoscopic remission in patients refractory to conventional treatments. Furthermore, in Crohn's disease patients unresponsive to either therapy alone, combined IFX-FMT induced more complete microbial and metabolic normalization and achieved remission where monotherapy had failed. These findings reveal ecosystem-level network rewiring as a central mechanism of FMT efficacy and establish the additive potential of combining microbiome-targeted and immunomodulatory therapies. This work supports the development of microbiome-informed adjunctive strategies for severe or refractory IBD, highlighting an actionable path toward personalized, mechanism-based treatment regimens.

CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT07149441.},
}

@article {pmid41870088,
year = {2026},
author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S},
title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0010426},
doi = {10.1128/msystems.00104-26},
pmid = {41870088},
issn = {2379-5077},
abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.},
}

@article {pmid41870192,
year = {2026},
author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM},
title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261433762},
doi = {10.1177/15578100261433762},
pmid = {41870192},
issn = {1557-8100},
abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.},
}

@article {pmid41870248,
year = {2026},
author = {Deng, Y and Zhen, X and Xia, R and Zhu, R and Zhang, G and Chen, P and Lai, J and Tao, R},
title = {Integrated Microbiome and Metabolome Analysis for Characterization and Discrimination of Saliva, Semen, Vaginal Secretions, and Their Mixtures.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c05356},
pmid = {41870248},
issn = {1520-6882},
abstract = {Body fluid identification (BFID) and estimation of time since deposition (TsD) are valuable yet challenging in forensic practice. Previous studies have demonstrated that integrating microbial and metabolomic profiles provides complementary biological insights. Therefore, this study performed untargeted metabolomic profiling and full-length 16S rRNA sequencing on fresh saliva (SA), semen (SE), vaginal secretions (VF), and their mixtures (SA-VF and SE-VF), with additional microbial analysis after 15 and 30 days of indoor exposure. Results showed the single-fluid samples exhibited specific dominant bacterial taxa, whereas the two mixture samples contained detectable bacterial signatures from both constituent fluids. Untargeted UHPLC-QTOF/MS analysis revealed unique metabolic signatures for each body fluid, enriched in biologically relevant pathways like steroid and bile acid metabolism. Moreover, we putatively identified characteristic metabolites, including α-solanine, candicidin, and megalomicin C1, some of which are rare microbial antibiotics. Owing to the exploratory nature and associated constraints of nontargeted approaches, these results serve as a provisional reference for identifying potential candidates. Integration of metabolomic and microbiome data uncovered strong metabolite-microbe correlations, highlighting microbially influenced metabolic networks unique to each body fluid type. Using differential microbes and metabolites individually as input features, the random forest model achieved BFID accuracies of 80 and 83.1%, respectively; however, integrating both sets of features increased accuracy to 100%. In contrast, microbial-based TsD prediction performed well for single-fluid samples but showed reduced effectiveness for mixed samples. Overall, our research highlights the powerful predictive potential and improved predictive accuracy of the integration of microbiome and metabolome data in BFID.},
}

@article {pmid41870398,
year = {2026},
author = {Handoko, C and Singh, A and Dharmage, SC and Hu, YJ and Dashper, SG and Bertelsen, RJ and Lowe, AJ and Lopez, DJ},
title = {The Impact of Early Childhood Caries on Asthma Trajectories During the First 15 Years of Life.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70307},
pmid = {41870398},
issn = {1398-9995},
support = {//Australian Institute of Family Studies/ ; },
}

@article {pmid41870630,
year = {2026},
author = {da Costa, JP and Fraiz, GM and Bonifácio, DB and Milagro, FI and Bressan, J},
title = {Sex-specific differences in salivary microbiota composition and their associations with metabolic health in adults with excess body weight: a secondary cross-sectional analysis.},
journal = {Clinical oral investigations},
volume = {30},
number = {4},
pages = {},
pmid = {41870630},
issn = {1436-3771},
abstract = {OBJECTIVES: Growing evidence links the oral microbiome to obesity-related outcomes, yet the influence of sex-related biological differences on salivary microbial profiles remains insufficiently explored. This exploratory study aimed to characterize the composition, abundance, and diversity of the salivary microbiota in Brazilian men and women with excess body weight and to examine its associations with cardiometabolic markers.

MATERIALS AND METHODS: This cross-sectional secondary analysis of a randomized controlled trial (REBEC: RBR-9832wsx) included 59 adults with excess body weight. Salivary microbiota was profiled through amplification of the 16 S rRNA V4 region, and bioinformatics analyses were performed using the Microbiome Analyst (v2.0). Associations between microbial taxa and clinical variables were assessed using Spearman’s correlation.

RESULTS: Men exhibited greater alpha diversity at the family level by higher Shannon (p = 0.015, rrb = 0.4) and Simpson (p = 0.003, rrb = 0.5) indices. Sex-specific microbial differences were identified: men showed higher levels of genera Tannerella, Lachnoanaerobaculum, and Actinomyces, as well as the putative species-level taxons Tannerella serpentiformis and Lachnoanaerobaculum umeaense, whereas women demonstrated greater abundance of genera Campylobacter, Granulicatella, Moryella, and Scardovia. Among women, Granulicatella genera was positively associated with triglycerides and the TyG index.

CONCLUSION: Men and women with excess body weight exhibited distinct salivary microbiota profiles, with differences in both diversity and taxonomic composition.

CLINICAL RELEVANCE: Sex-specific differences in salivary microbiota composition may be associated with variations in metabolic markers. These findings are exploratory and hypothesis-generating, providing insight into sex-related patterns in the oral microbiome and may help inform future research exploring personalized approaches to cardiometabolic risk assessment.},
}

@article {pmid41870676,
year = {2026},
author = {Božac, E and Žučko, J and Braut, A and Špalj, S and Peršić Bukmir, R and Toplak, N and Hladnik, M and Vitezić, BM},
title = {Supragingival dental biofilm microbiomes of tobacco heating system smokers, cigarette smokers and non-smokers.},
journal = {Clinical oral investigations},
volume = {30},
number = {4},
pages = {},
pmid = {41870676},
issn = {1436-3771},
mesh = {Humans ; *Biofilms ; Cross-Sectional Studies ; Male ; Female ; Adult ; *Microbiota ; *Smokers ; RNA, Ribosomal, 16S ; *Non-Smokers ; Middle Aged ; *Gingiva/microbiology ; DNA, Bacterial ; Heating ; },
abstract = {OBJECTIVES: The study compared the bacterial composition of supragingival dental biofilm (SDB) among smokers and non-smokers (NS).

MATERIALS AND METHODS: This cross-sectional study included 60 subjects allocated into three groups: tobacco heating system smokers (THSS), cigarette smokers (CS) and NS. SDB samples were collected, and bacterial DNA was extracted and prepared for next generation sequencing of the 16s rRNA gene hypervariable regions. Bioinformatic pipelines were applied to assess microbial diversity and taxonomic composition.

RESULTS: No significant differences were observed in alpha diversity (Observed taxa and Shannon index) or beta diversity (Bray-Curtis index) among groups. In contrast, significant differences in microbiome bacterial composition were identified across multiple taxonomic levels. At the genus level, Alysiella (p = 0.016) and Propionibacterium (p = 0.025) were most abundant in THSS, whereas Actinobaculum (p = 0.004), Avibacterium (p = 0.015) and Haemophilus (p = 0.030) predominated in NS. At the species level: Alysiella filiformis (p = 0.006) and Streptococcus thermophilus (p = 0.025) were most abundant in THSS, Streptococcus lactarius (p = 0.05) in CS, and Prevotella multiformis (p = 0.016) and Lactobacillus salivarius (p = 0.018) in NS group.

CONCLUSIONS: Distinct differences in bacterial composition of SDB were observed among THSS, CS and NS. The increased abundance of anaerobic bacteria with cariogenic potential in THSS and CS suggests a more dysbiotic profile and increased pathogenic potential compared to NS.

CLINICAL RELEVANCE: Variations in SDB bacterial composition may influence the pathological potential of dental biofilms in smokers and non-smokers.},
}

Humans
*Biofilms
Cross-Sectional Studies
Male
Female
Adult
*Microbiota
*Smokers
RNA, Ribosomal, 16S
*Non-Smokers
Middle Aged
*Gingiva/microbiology
DNA, Bacterial
Heating

@article {pmid41870852,
year = {2026},
author = {Ellis, JR and Powell, EJ and Tomasovic, LM and Warman, A and Chien, A},
title = {The cutaneous microbiome as a dynamic photoprotective interface against solar radiation.},
journal = {Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology},
volume = {},
number = {},
pages = {},
pmid = {41870852},
issn = {1474-9092},
}

@article {pmid41871006,
year = {2026},
author = {Londoño-Sierra, DC and Restrepo-Mesa, SL and Costa Antunes, AE and Sivieri, K and Martínez-Galán, JP},
title = {Enhancing the microbiome in the maternal-infant dyad: Perspectives from maternal and infant nutrition.},
journal = {Archivos argentinos de pediatria},
volume = {},
number = {},
pages = {e202510860},
doi = {10.5546/aap.2025-10860.eng},
pmid = {41871006},
issn = {1668-3501},
abstract = {Establishing the microbiome is an important milestone for infant health. The type of delivery, gestational age, antibiotic use, and infant feeding practices significantly impact this process. However, interest in the effects of maternal diet and nutrition has grown. The objective of this review is to present an update on the microbiota in the mother-child dyad and the role of maternal nutritional status and diet in its modulation. Scientific articles in electronic databases were reviewed. Adherence to established dietary guidelines during pregnancy and lactation, as well as otherrecommendations based on the study of foods that are sources of fiber, unsaturated fatty acids, and fermented foods, is a good starting point for promoting a healthy microbiome from the early years of life.},
}

@article {pmid41871143,
year = {2026},
author = {Nguyen, AT and Kim, A and Fernando, C and Kularatne, BMDN and Palmer, DRJ and Hill, JE},
title = {Ligand-binding properties of substrate binding proteins of a maltose uptake system in Gardnerella swidsinskii.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {3},
pages = {},
pmid = {41871143},
issn = {1465-2080},
mesh = {*Maltose/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; Oligosaccharides/metabolism ; Glycogen/metabolism ; Operon ; Ligands ; Protein Binding ; Gene Expression Regulation, Bacterial ; Substrate Specificity ; *Maltose-Binding Proteins/metabolism/genetics ; },
abstract = {Glycogen and its breakdown products, maltose and malto-oligosaccharides, are important carbon sources for vaginal bacteria including Gardnerella species. MusEFGKI transport systems for maltose and malto-oligosaccharides have been identified in all Gardnerella species; however, unlike in other species, the Gardnerella swidsinskii operon encodes two substrate-binding proteins (SBPs) (MusE1345, MusE1346, ~60% amino acid identity). Two SBPs could allow binding of additional ligands, providing a competitive advantage to G. swidsinskii relative to other species with only one SBP. Our objectives were to determine if both genes are expressed in G. swidsinskii and compare the specificity and affinity of G. swidsinskii MusE SBPs for glycogen breakdown products. Gene expression analysis showed the presence of a polycistronic transcript spanning both SBP encoding genes; however, musE1346 transcripts were more abundant, likely due to the presence of an additional promoter identified in the intergenic region. No difference in the relative expression of either gene was observed in isolates grown in media supplemented with glycogen or maltotriose. Predicted structures of both SBPs were highly similar and characteristic of previously characterized maltose-binding proteins. Both proteins had a high affinity for maltose, maltotriose and maltotetraose (K d 10[-6] to 10[-7] M) and much lower affinities to maltopentaose and maltohexaose (K d 10[-3] to 10[-4] M). Our results demonstrate that the affinities of G. swidsinskii MusE SBPs for maltose and malto-oligosaccharides are similar under the same experimental conditions.},
}

*Maltose/metabolism
*Bacterial Proteins/metabolism/genetics/chemistry
Oligosaccharides/metabolism
Glycogen/metabolism
Operon
Ligands
Protein Binding
Gene Expression Regulation, Bacterial
Substrate Specificity
*Maltose-Binding Proteins/metabolism/genetics

@article {pmid41871593,
year = {2026},
author = {von Seth, E and Karlsen, TH and Tanaka, A and Ponsioen, C and Bergquist, A},
title = {Primary sclerosing cholangitis.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(25)02582-6},
pmid = {41871593},
issn = {1474-547X},
abstract = {Primary sclerosing cholangitis is a rare, chronic cholestatic liver disease characterised by biliary inflammation and fibrosis. Inflammatory bowel disease co-occurs in 50-80% of individuals with primary sclerosing cholangitis and there is an increased risk for hepatobiliary and colorectal cancers. Primary sclerosing cholangitis presentation is highly variable but there is usually a slowly progressive fibrosis of the bile ducts with strictures, development of liver fibrosis and cirrhosis, and eventually a need for liver transplantation, after which primary sclerosing cholangitis can reoccur. Primary sclerosing cholangitis is diagnosed mostly at the asymptomatic stage but, as the disease advances, people often have itching, fatigue, upper right abdominal pain, recurrent cholangitis, or complications related to portal hypertension. There are few treatment options and its exact cause and pathogenesis remain unclear. It is widely believed that both genetic and environmental factors are important, with the intestinal microbiome increasingly recognised as crucial to disease development, progression, and outcomes. This Seminar explores the clinical features of primary sclerosing cholangitis, summarises the current understanding of its pathogenesis, and gives insights into the challenges and opportunities in managing the disease.},
}

@article {pmid41871875,
year = {2026},
author = {Zhang, Y and Xu, X and Wang, S and Yin, X and Zhang, B and Zhu, Z and Ji, R and Zhu, J and He, H and Cheng, S and Han, Z and Xie, T and Zhang, X and Wang, Y and Shen, S and Kou, Y and Bao, S and Liu, Y and Cao, B and Bonny, C and Guo, X and Segal, E and Tan, Y and Shen, L and Peng, Z},
title = {Fecal microbiota transplantation combined with anti-PD-1 therapy in refractory microsatellite-stable gastric cancer: a phase I feasibility and safety study.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {3},
pages = {},
doi = {10.1136/jitc-2025-013823},
pmid = {41871875},
issn = {2051-1426},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; *Stomach Neoplasms/therapy/drug therapy ; Middle Aged ; Aged ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Feasibility Studies ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Adult ; },
abstract = {BACKGROUND: The discovery and therapeutic application of immune checkpoint inhibitors (ICIs) have significantly improved clinical outcomes in cancer treatment. However, the response rate is still low in gastrointestinal (GI) cancers. The gut microbiome's impact on immune modulation is a promising area for overcoming resistance to immunotherapy.

METHODS: This study (NCT04130763) is an open-label, single-arm, single-center, phase I study assessing the safety and efficacy of fecal microbiota transplantation (FMT) from healthy donors in 10 patients with advanced GI cancer resistant to anti-programmed death-ligand 1 (PD-(L)1) treatment. 10 patients with histologically confirmed, unresectable, or metastatic GI cancers (8 gastric, 2 colorectal) who were refractory to anti-PD-(L)1 treatment were enrolled. Patients received initial FMT treatment via oral capsules (60 capsules), followed by a combination therapy phase, where maintenance FMT (10 capsules per treatment) was paired with nivolumab at 3 mg/kg every 2 weeks for six cycles. Serial biomarker assessments were conducted through both fecal and blood sampling.

RESULTS: The combination of FMT and anti-PD-1 treatment was well tolerated with no serious adverse events. The objective response rate was 20% and the disease control rate was 40%. Clinical benefits were associated with colonization of donor-derived immunogenic microbes, and an activated immune status reflected by peripheral immune cell populations. Moreover, microbial signatures were identified for anti-programmed cell death protein-1 (PD-1) responsiveness and validated in an independent cohort.

CONCLUSIONS: This phase I study demonstrates the feasibility and safety of combining FMT with anti-PD-1 therapy in patients with ICI-refractory gastric cancer. The observed preliminary efficacy signals and identified microbial signatures generate hypotheses for future trials to investigate microbiome-based approaches to enhance immunotherapy efficacy.

TRIAL REGISTRATION NUMBER: NCT04130763.},
}

Humans
*Fecal Microbiota Transplantation/methods
Male
Female
*Stomach Neoplasms/therapy/drug therapy
Middle Aged
Aged
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Feasibility Studies
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Adult

@article {pmid41871943,
year = {2026},
author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB},
title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336675},
pmid = {41871943},
issn = {1468-3288},
abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.

OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.

DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] × interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.

RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7α-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.

CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.},
}

@article {pmid41871945,
year = {2026},
author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT},
title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337436},
pmid = {41871945},
issn = {1468-3288},
abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.

OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.

DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.

RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.

CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.},
}

@article {pmid41872049,
year = {2026},
author = {Carpay, NC and Kamphorst, K and van Elburg, RM and Vlieger, AM},
title = {Antibiotics in the first week of life are not associated with functional gastrointestinal disorders at 9-12 years of age.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70402},
pmid = {41872049},
issn = {1536-4801},
support = {//None/ ; },
abstract = {OBJECTIVES: Dysbiosis due to early-life antibiotics may contribute to the development of functional gastrointestinal disorders (FGIDs). This follow-up study of a birth cohort primarily investigates the association between antibiotic treatment in the first week of life and the presence of FGIDs at 9-12 years. Secondarily, it examines whether a history of infantile colic or current food allergy is associated with FGIDs.

METHODS: A prospective observational birth cohort of 436 term-born infants was followed up at the age of 9-12 years; 151 received intravenous antibiotics in the first week of life due to suspected early onset sepsis (AB+) and 285 did not (AB-). Participants filled out questionnaires on the presence of FGIDs (Rome IV questionnaire) and food allergies, and FGID diagnoses were reported by general practitioners. Statistical analyses included chi-squared tests and multivariable logistic regression.

RESULTS: 306 of 388 eligible participants (79.5%) participated in the follow-up study: 109 (35.6%) AB+ and 197 (64.4%) AB-. FGID prevalence at 9-12 years was similar in AB+ and AB- (any FGID: odds ratio [OR] 1.083, 95% confidence interval [CI] 0.608-1.932). Infantile colic was not significantly associated with FAPDs after adjusting for confounders (adjusted OR 2.007, 95% CI 0.978-4.003, p = 0.051). Children with a food allergy were more likely to have a functional abdominal pain disorder (FAPD) (adjusted OR 4.028, 95% CI 1.532-10.286).

CONCLUSIONS: No statistically significant association was observed between first-week antibiotics or infantile colic and FGIDs at 9-12 years of age, but FAPDs were significantly more prevalent in children with food allergies.},
}

@article {pmid41872068,
year = {2026},
author = {Ben-Assa, N and Naddaf, R and Carasso, S and Dagan, O and Sason, A and Gefen, T and Geva-Zatorsky, N},
title = {Intra-species competition combats vancomycin-resistant enterococci.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2647529},
pmid = {41872068},
issn = {1949-0984},
mesh = {Animals ; *Vancomycin-Resistant Enterococci/physiology/virology/drug effects/genetics/growth & development ; Mice ; *Enterococcus faecalis/physiology/virology/drug effects/genetics/growth & development ; *Gram-Positive Bacterial Infections/microbiology/therapy ; Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics/physiology ; Humans ; *Antibiosis ; Vancomycin/pharmacology ; Female ; },
abstract = {Vancomycin-resistant Enterococcus (VRE) is a leading cause of multidrug-resistant infections in hospitalized patients, yet no reproducible microbiota therapies exist to selectively displace it. Here we harness intra-species competition within Enterococcus to suppress VRE colonization. Through in vitro screening and mouse colonization models, we identified a single antibiotic-susceptible strain, E. faecalis X98, that significantly reduced VRE burden both in vitro and in mouse experiments, whereas multi-strain consortia failed due to competitive interference among consortium members. In parallel, we subjected the vancomycin-sensitive strain E. faecalis OG1RF to phage selection, which produced a prophage-integrated derivative with convergent glycosyltransferase mutations that secreted a VRE-killing factor, conferring enhanced antagonism even without exogenous phage. These findings reveal ecological and evolutionary principles for selecting strains as targeted microbial therapeutics. Exploiting intra-species antagonism and phage-driven evolution provides a practical framework for developing microbiota-based interventions that minimize collateral damage to the microbiome while addressing antibiotic-resistant pathogens.},
}

Animals
*Vancomycin-Resistant Enterococci/physiology/virology/drug effects/genetics/growth & development
Mice
*Enterococcus faecalis/physiology/virology/drug effects/genetics/growth & development
*Gram-Positive Bacterial Infections/microbiology/therapy
Anti-Bacterial Agents/pharmacology
Bacteriophages/genetics/physiology
Humans
*Antibiosis
Vancomycin/pharmacology
Female

@article {pmid41872195,
year = {2026},
author = {DeVito, VL and Karamched, BR},
title = {Signed, sealed, delivered: a generalizable model for living biotherapeutic dosing and metabolism.},
journal = {NPJ systems biology and applications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41540-026-00685-4},
pmid = {41872195},
issn = {2056-7189},
abstract = {Living Biotherapeutic Products (LBPs) offer a promising therapeutic strategy for metabolic disorders rooted in gut microbiome dysfunction, yet quantitative frameworks for predicting their efficacy remain underdeveloped. We introduce the Bacterial Compartment Absorption and Transit (BCAT) model, a pharmacokinetic-pharmacodynamic framework that couples probiotic transit, endogenous microbiome metabolism, and enzymatic transformation within a unified dose-optimization setting. Building on the classical CAT model, BCAT incorporates mechanistically-derived colon compartments and treats dosing time as a control variable. We validate BCAT against clinical data for native choline metabolism and SYNB1618 probiotic trials, achieving 5% mean prediction error compared to ~30% for prior two-compartment models. Applying BCAT to trimethylaminuria (TMAU), we predict that ~10[9] CFU of engineered probiotic, administered 3-4 h before meals, achieves 95% reduction in systemic trimethylamine, matching healthy hepatic clearance. Global sensitivity analysis identifies enzyme expression level as the dominant design parameter, enforcing the broad applicability of this model. The BCAT framework generalizes to any gut microbiome-mediated metabolic disorder and provides quantitative dosing targets to guide live biotherapeutic development.},
}

@article {pmid41872294,
year = {2026},
author = {Vaughn, SN and Pavlovsky, JC and Heiman, JA and Jackson, CR},
title = {Contrasting spatial and temporal structuring of seawater and sediment bacterial communities in coastal environments.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45076-1},
pmid = {41872294},
issn = {2045-2322},
}

@article {pmid41872423,
year = {2026},
author = {Papagiannidou, A and Mitropoulou, M and Papantzikos, K and Petropoulou, D and Tsilingiris, D and Magkos, F and Dalamaga, M},
title = {Hypomagnesemia: A Clinical and Nutritional Update.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {},
pmid = {41872423},
issn = {2161-3311},
abstract = {PURPOSE OF REVIEW: Hypomagnesemia, defined as low serum/plasma magnesium concentration, is a highly prevalent yet underrecognized electrolyte disorder with extensive clinical, metabolic, and nutritional implications. This review provides an updated synthesis of magnesium physiology, dietary determinants, homeostatic regulation, diagnostic challenges, and therapeutic strategies, with particular emphasis on recent meta-analyses and large-scale epidemiological evidence linking hypomagnesemia to multisystem disease.

RECENT FINDINGS: Accumulating evidence has shown consistent associations between low serum or dietary magnesium and increased risk of cardiometabolic disorders (hypertension, type 2 diabetes mellitus, metabolic syndrome, and cardiovascular disease), neuropsychiatric conditions (migraine, depression, cognitive impairment, and dementia), osteoporosis, immune dysregulation, and adverse outcomes in hospitalized, critically ill, and chronic kidney disease patients. Mechanistic studies have clarified the roles of TRPM6/7 channels, tight junction claudins, and basolateral magnesium transporters in intestinal and renal magnesium handling, elucidating pathways underlying both inherited and acquired deficiencies. Research has also highlighted the contribution of modern dietary patterns, food processing, mineral-depleted drinking water, medication use (notably proton pump inhibitors, diuretics and chemotherapeutic agents), and gut microbiome alterations to widespread subclinical deficiency. Meta-analyses of RCTs indicate that magnesium supplementation confers modest but clinically relevant improvements in blood pressure, glycemic control, inflammatory markers, endothelial function, migraine frequency, and depressive symptoms, particularly in individuals with baseline hypomagnesemia. However, serum magnesium remains an insensitive biomarker of total body magnesium status, and consensus on optimal diagnostic thresholds and replacement strategies is lacking.

SUMMARY: Magnesium deficiency contributes to a wide spectrum of multisystem disorders, and is driven by dietary insufficiency, gastrointestinal and renal losses, medication use, chronic disease, and altered microbiome function. Meta-analytic evidence supports its role as a modifiable risk factor across cardiovascular, metabolic, neurological, skeletal, and immune disorders. Dietary modification, optimized supplementation, and correction of underlying causes of deficiency remain central to management. Future research should focus on improved diagnostic tools, personalized dosing approaches and long-term outcomes of magnesium repletion. Enhancing clinical awareness and integrating magnesium evaluation into routine care may reduce the growing burden of hypomagnesemia.},
}

@article {pmid41872585,
year = {2026},
author = {Gokalp, S and Dinleyici, EC and Muluk, C and Inci, A and Aktas, E and Okur, I and Ezgu, F and Tumer, L},
title = {Alterations in gut microbiota composition in children with methylmalonic acidemia, propionic acidemia, and maple syrup urine disease.},
journal = {European journal of clinical nutrition},
volume = {},
number = {},
pages = {},
pmid = {41872585},
issn = {1476-5640},
support = {TGA-2021-7036//Gazi Üniversitesi (Gazi University)/ ; },
abstract = {AIM: Methylmalonic acidemia (MMA), propionic acidemia (PA), and maple syrup urine disease (MSUD) are rare monogenic disorders that are described as intoxication-type inborn errors of metabolism (IEMs). They usually present in early life, and long-term management requires strict dietary protein restriction, which may significantly alter gut microbiota composition. Despite growing interest in microbiome research, limited data exist on gut microbiota in these disorders, and no study is available for MMA and MSUD. We aimed to describe the gut microbiota compositions in children with MMA, PA, and MSUD.

METHOD: A total of eight patients (Five MMA, one PA, and two MSUD), and 11age-matched healthy controls were enrolled. All patients were following a medically supervised, protein-restricted diet. Fecal sample was collected from each participant, and gut microbiota composition was evaluated with 16S rRNA sequencing.

RESULTS: Patients with MMA, PA, and MSUD exhibited significantly altered gut microbiota composition compared to healthy controls. Alpha diversity analysis revealed reduced microbial richness in patients, with significantly lower Chao1 and observed OTU indices (p < 0.05). Beta diversity metrics demonstrated distinct clustering between groups, indicating significantly different microbial community structures. Higher relative abundances of opportunistic or dysbiotic taxa have been seen in patient group, while controls were enriched in beneficial taxa like Faecalibacterium prausnitzii, Ruminococcus, and Lactobacillus. LEfSe analysis identified 17 taxa enriched in patients-including members of Proteobacteria, Sphingobacteriia, and Streptococcus anginosus-and 6 taxa enriched in controls, notably Faecalibacterium prausnitzi.

DISCUSSION: This is the first descriptive study of the gut microbiota composition of MMA, PA, and MSUD patients. These findings indicate an association between long-term dietary management and altered microbiota composition, although causality cannot be inferred due to the cross-sectional study design. The observed alterations suggest that the gut microbiota may represent a novel therapeutic target in the management of IEMs.},
}

@article {pmid41872600,
year = {2026},
author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E},
title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41872600},
issn = {1546-170X},
abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.},
}

@article {pmid41872622,
year = {2026},
author = {Lee, H and Oh, Y and Seo, TW and Choi, YB and Kim, S and Cheon, S and Lee, DG and Kang, S and Han, K and Heo, YM and Mun, S},
title = {Exploring Cyclo (-Gly-Pro) for inflammation modulation in atopic dermatitis: a study on streptococcal postbiotics.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41872622},
issn = {2092-9293},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by intense itching and eczematous lesions, significantly affecting quality of life. Complex interactions involving genetic predispositions, environmental factors, and immune dysregulation contribute to AD pathogenesis, with impaired skin barriers and Staphylococcus aureus playing critical roles. Recent interest in postbiotics, beneficial compounds derived from probiotics, has opened potential therapeutic avenues.

OBJECTIVE: This study investigates the postbiotic solution derived from three human skin-derived Streptococcus isolates, to identify a core bioactive compound and its therapeutic role in AD.

METHODS: Using GC-MS and GC-FID, we quantified Cyclo (-Gly-Pro) and assessed its impact on inflammatory biomarkers in an AD-like keratinocyte cell model. The effect of different incubation temperatures on the compound's production was also analyzed. Furthermore, 16S V3-V4 amplicon sequencing was performed to analyze changes in the skin microbiome of AD patients following treatment.

RESULTS: Cyclo (-Gly-Pro) was consistently present across all strains, with production inversely related to incubation temperature, peaking at 25 °C. Our findings suggest that optimized production conditions and potential synergistic effects with other postbiotic components could enhance therapeutic efficacy.

CONCLUSION: These results support further in vivo research to elucidate the mechanisms and validate the compound's role in AD treatment strategies, potentially leading to novel dermatological therapies.},
}

@article {pmid41872902,
year = {2026},
author = {Rojas, CA and Smith, R and Oliver, R and Jospin, G and Corral, I and Ganz, HH},
title = {Temporal variability is an inherent feature of the healthy canine microbiome assessed by full-length 16S rRNA gene sequencing.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00546-9},
pmid = {41872902},
issn = {2524-4671},
}