@article {pmid42034994,
year = {2026},
author = {Chen, Y and Bao, R and Jin, W and Yin, X and Qin, L and Pan, J and Yao, Y and Shen, J and Fang, T and Ma, Y and Zhou, C and Miao, Q and Hu, B},
title = {Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {42034994},
issn = {1471-2334},
support = {SHDC22024315//Shanghai Shen Kang Hospital Development Center/ ; },
abstract = {INTRODUCTION: The incidence of Mycobacterium abscessus complex (MABC) infections is rising, becoming a major pathogen of nontuberculous mycobacteria responsible for pulmonary disease (PD) and extrapulmonary disease (ED). However, studies on the clinical characteristics of MABC-ED remain limited.

METHODS: A 7-year retrospective analysis was conducted on MABC-ED cases at Zhongshan Hospital in Shanghai, China. We analyzed predisposing factors, clinical features, metagenomic sequencing (MS) results, drug susceptibility testing (DST), and genomic characteristics of MABC-ED patients, comparing the data with those of PD cases.

RESULTS: Among 17 MABC-ED patients, 15 had predisposing risk factors and underlying conditions, with 2 of 3 patients with rheumatic disease showing poor prognosis. The diagnostic performance of metagenomic sequencing for MABC-ED was comparable to that for MABC-PD. However, MABC-ED samples exhibited distinct microbiome features and a more diverse mycobacterial community structure compared to PD. Resistance rates among extrapulmonary MABC isolates were observed as follows: 0% (amikacin), 20% (macrolides), 30% (linezolid), and 40% (cefoxitin). One case showed paradoxical results between erm (41) T28 sequevar and susceptibility phenotype. Genomic analysis revealed no specific dominant circulating clones (DCC) for MABC-ED isolates.

CONCLUSION: MABC-ED patients commonly present with risk factors and underlying diseases. Metagenomic sequencing diagnosis of MABC-ED poses challenges, and DST and whole genome sequencing data indicate diversity among MABC-ED isolates. Our study provides detailed data on MABC-ED, contributing to a better understanding of its disease characteristics.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-13117-9.},
}

@article {pmid42046020,
year = {2026},
author = {Zhou, Q and Huang, P and Zhou, R and Zeng, F and Jiang, J and Zhao, B and Zhao, B and Xu, H and Wei, W and Li, X},
title = {Multi-omics profiling of gut microbiota and host transcriptome identifies diagnostic signatures and mechanistic links in moyamoya disease.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42046020},
issn = {1471-2180},
support = {82171517; 82271556//National Natural Science Foundation of China/ ; ZNJC202245//Translational Medicine and Interdisciplinary Research Joint Fund of Zhongnan Hospital of Wuhan University/ ; PDJH202201//Climbing Project for Medical Talent of Zhongnan Hospital, Wuhan University/ ; },
abstract = {BACKGROUND: Moyamoya disease (MMD) features progressive intracranial artery stenosis and collateralization. Growing evidence implicates a dysregulated gut–brain axis in cerebrovascular pathology. We aimed to identify MMD-associated gut microbes and delineate the molecular mechanisms linking intestinal signals to vascular inflammation in MMD.

RESULTS: We profiled fecal microbiota using full-length 16S rRNA sequencing from 24 MMD patients and 20 matched controls, prioritizing taxa with LEfSe, LASSO, and random forest algorithms. A species-level diagnostic model showed robust discrimination in our cohort (ROC AUC = 0.9146), and DCA supported its clinical utility. To connect gut signals to host vascular responses, we integrated peripheral and vascular transcriptomes from GEO and a cross-disease cerebrovascular cohort. Differential expression, WGCNA, and LASSO analyses identified key MMD genes and their immune modules. We then intersected these with microbiome-derived, gut-related genes to nominate candidate mediators of gut–immune–vessel crosstalk. This multi-omics pipeline identified Fusobacterium nucleatum, Lachnoanaerobaculum cf. saburreum C27KA, and NK4A214_group as MMD-specific microbial markers. Crucially, these markers were associated with immune infiltration signatures and inflammatory pathway activation in diseased vessels. Further integration pinpointed QRFPR and HCAR2 as key mediators of gut-derived cerebrovascular inflammation, suggesting a potential microbiota–immune–vascular pathway along the gut–brain axis.

CONCLUSION: We characterized an MMD-associated microbiota profile and proposed QRFPR and HCAR2 as candidate genes linking intestinal microbes to vascular immune activation. By mapping the gut–brain axis from microbial taxa to host receptors and vessel-wall transcriptional programs, this study uncovers potential disease mechanisms and highlights new avenues for microbiome-informed biomarkers and therapeutic targeting in MMD.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05084-7.},
}

@article {pmid42259341,
year = {2026},
author = {Lim, LL and Jenkins, A and Prabhakaran, D and Sookoian, S and Bannuru, RR and Khunti, K},
title = {Biological and mechanistic pathways of cardiometabolic multiple long-term conditions.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(26)00607-0},
pmid = {42259341},
issn = {1474-547X},
abstract = {Cardiometabolic multiple long-term conditions (MLTC) arise from the complex interplay of biological, sociodemographic, environmental, and behavioural factors across the life course. Shared risk factors and mechanisms, including insulin resistance, adiposity, and chronic inflammation, underpin its development. Growing evidence also implicates that even low-level, long-term exposure to fine particulate matter, nitrogen dioxide, and related pollutants can accelerate the trajectory of cardiometabolic MLTC. Early-life exposures, including undernutrition and overnutrition, altered gut microbiome, and endocrine-disrupting chemicals, interact with social determinants of health to aggravate inflammatory and metabolic dysregulation. These mechanisms, together with genetic susceptibility, epigenetic modifications, and multiomics perturbations, shape disease progression, heterogeneity, and the clustering of cardiometabolic MLTC. Yet, fundamental gaps persist, whereby most mechanistic insights are derived from single-disease studies, leaving the temporal hierarchy, causal pathways, and population-level heterogeneity largely unresolved. Addressing these challenges will require life-course research, integrative systems approaches, and translational studies that link mechanistic insights to precision prevention and therapeutic strategies. By bridging discovery with actions, such efforts can enhance care for cardiometabolic MLTC and promote equitable health outcomes globally.},
}

@article {pmid42259432,
year = {2026},
author = {Hao, L and Li, ZF and Qu, YN and Zhao, FY and Lu, SY and Li, BQ and Zhang, HY and Wang, HQ},
title = {IUPHAR review. Gut microbial metabolites as remote regulators of behavior and neuropsychiatric disease.},
journal = {Pharmacological research},
volume = {230},
number = {},
pages = {108284},
doi = {10.1016/j.phrs.2026.108284},
pmid = {42259432},
issn = {1096-1186},
abstract = {The gut-brain axis has emerged as a fundamental pathway through which gut-derived microbial metabolites exert remote control over brain development, neural circuit function and behavior. This Review synthesizes evidence that key microbial metabolites including short-chain fatty acids, tryptophan derivatives, bile acids and trimethylamine N-oxide modulate neuroimmune, neuroendocrine and synaptic signaling in a context-dependent manner, influencing whether the brain maintains homeostasis or progresses toward pathology. We critically evaluate how these metabolites contribute to the etiology and symptomatology of neurodevelopmental and psychiatric disorders such as autism spectrum disorder, major depressive disorder, anxiety and post-traumatic stress disorder. Causal insights are highlighted by studies demonstrating that fecal microbiota transplantation from affected individuals to rodents transfers core behavioral phenotypes. It is important to note, however, that while FMT and gnotobiotic studies establish causality in animal models, evidence from human studies remains predominantly correlative, and we have explicitly distinguished these evidence tiers throughout. We also explore the translational potential of microbiome-derived biomarkers for diagnosis and the challenges in developing targeted therapeutics, including probiotics, postbiotics and metabolite-sequestering agents. Moving forward, the field should prioritize decoding the contextual determinants of microbial influence and adopt personalized, function-based strategies to effectively modulate the gut-brain metabolic axis for brain health.},
}

@article {pmid42259440,
year = {2026},
author = {Lee, HS and Ibarra, LE and Zuo, B and Zhao, J and Fox, R and Read, QD and Gurung, M and Yeruva, L and Chen, C and Trudo, SP},
title = {Protective effect of apiaceous vegetables against Total Western Diet- and dextran sulfate sodium-induced colitis in mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101652},
doi = {10.1016/j.tjnut.2026.101652},
pmid = {42259440},
issn = {1541-6100},
abstract = {BACKGROUND: Western-style dietary patterns are associated with colitis and colon cancer. Existing data indicate intake of apiaceous vegetables (API; e.g., celery, parsnip) may prevent inflammation-associated diseases.

OBJECTIVE: We investigated in mice the effect of API supplementation to the Total Western Diet (TWD) against dextran sulfate sodium (DSS)-induced colitis.

METHODS: Male C57BL/6J mice (8-week-old; 15/group) were fed TWD supplemented with 21% or 42% fresh API (w/w) and given 2% DSS to induce colitis. Diet intake, body weight, and disease activity index (DAI) were monitored. Serum was collected for cytokine/chemokine analysis and colonic tissues for histology and Western blot. Fecal samples were analyzed by 16S rRNA gene sequencing and targeted/untargeted metabolomics. Phenotypic data were analyzed by ANOVA with Tukey's test. Microbiome data were Centered-Log Ratio (CLR) transformed and analyzed using linear mixed models with adjusted pairwise comparisons.

RESULTS: API supplementation attenuated colitis phenotypes including weight loss (44% recovery; P < 0.001), colon shortening (57% recovery; P < 0.01), disease activity (59% lower; P < 0.001), cytokine/chemokine release (35-73% reductions; P < 0.05), and mucosal F4/80+ cells infiltration (80% reduction; P < 0.001). API also improved gut microbiota diversity and composition, increasing alpha diversity metrics (4.4%-13.8%; P <0.05), suppressing pathogenic bacteria (Paraclostridium, Enterococcus, Eubacterium; estimated CLR difference: -1.8 to -6.7; P < 0.001), and enriching beneficial bacteria (Lachnospiraceae and Blautia; estimated CLR difference: +1.6 to +3.0; P < 0.05). Furthermore, metabolomics indicated TWD consumption increased arachidonic acid and aliphatic aldehydes (by 109%-510%; P < 0.001), and decreased short-chain and unsaturated fatty acids (by 30%-91%; P < 0.001). API supplementation also mitigated TWD-derived functional metabolites (including bile acids; P < 0.05).

CONCLUSIONS: These data indicate that API intake is beneficial for risk reduction of diseases associated with Western diets. However, further investigations are warranted to determine the mechanism behind these beneficial effects.},
}

@article {pmid42259836,
year = {2026},
author = {Galal, L and Eltokhy, MA and Abostate, HM and Omran, ME and Radwan, SMR},
title = {Comparative analysis of the sputum microbiota in different COPD clinical states.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42259836},
issn = {2045-2322},
abstract = {Chronic obstructive pulmonary disease (COPD) is a well-known respiratory illness. COPD patients oscillate between a stable state and an exacerbated state that leads to disease deterioration. Studies suggest that respiratory microbiome dysbiosis plays a vital role in COPD pathogenesis. However, the exact microbial composition among different clinical states of COPD is still elusive. To determine and compare the respiratory microbiota composition in different COPD clinical states, namely, the stable state (S-COPD) and the acute exacerbated state (AE-COPD). In this prospective study, 74 samples were collected from COPD patients. The sputum microbiota was analyzed via 16 S rRNA gene sequencing, and only 35 samples were included due to bad reads or not in accordance with inclusion criteria: S-COPD patients (n = 18), and AE-COPD patients (n = 17). Bioinformatics analysis was used to determine changes in the microbiota among the comparison groups. The most abundant phyla among all the samples were Proteobacteria, Fusobacteria, Firmicutes, and Actinobacteria, with Paracoccus, Streptomyces Leptotrichia Fusobacterium and Ruminococcaceae being the most prevalent genera. Dissimilarity in abundance across the studied COPD states was observed, with significantly greater abundance of Proteobacteria and Fusobacteria in S-COPD patients and greater abundance of Firmicutes in AE-COPD patients at the phylum level. At the genus level, Paracoccus, Fusobacterium, Streptococcus, Haemophilus, and Moraxella were significantly different between the two groups and were more prevalent in S-COPD, whereas Cellulosilyticum, Streptomyces, Leptotrichia, Ruminococcaceae_UCG_014, and Atopobium were more prevalent in exacerbated individuals. Alpha diversity revealed greater diversity in stable versus exacerbated patients, and a PCoA plot of Bray‒Curtis and weighted UniFrac distances revealed that stable patients were highly clustered, whereas exacerbated patients were more disseminated. At the genus level, LEfSe analysis revealed the dominance of Cellulosilytic, Liptotrichia, and Streptomyces in the AE-COPD group, whereas the S-COPD group microbiome was dominated by the genera Paracoccus, Fusobacterium, Streptococcus Haemophilus, and Moraxella (p < 0.05). The results of the present study suggest that COPD patients have unique microbial profiles that differ across different states, with increased abundances of Proteobacteria, chiefly Paracoccus. These findings need more research to clarify the definite role of microbiome dysbiosis in COPD pathogenesis.},
}

@article {pmid42259841,
year = {2026},
author = {Deng, F and Fan, Y and Yan, J and Zhang, X and Guo, Y and Li, M and Peng, Y and Zhao, L and Liu, F and Zheng, Y and Deng, B and Deng, J and Chen, S and Jiang, H and Chai, J and Zhao, J and Li, Y},
title = {Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01038-z},
pmid = {42259841},
issn = {2055-5008},
abstract = {Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.},
}

@article {pmid42259846,
year = {2026},
author = {Kakuk, B and Dörmő, Á and Taifi, A and Járay, T and Kurucsai, G and Gulyás, G and Prazsák, I and Boldogkői, Z and Tombácz, D},
title = {Canine Fecal Microbiome Dataset: Ultra-deep Multi-platform Sequencing Across Extraction and Library Protocols.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07594-5},
pmid = {42259846},
issn = {2052-4463},
support = {LP2020-8/2020//Magyar Tudományos Akadémia (Hungarian Academy of Sciences)/ ; FK 142676//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; },
abstract = {The canine gut microbiome is an important model for microbiome research, yet methodological variation in DNA isolation, library preparation, and sequencing complicates cross-study comparisons. Here we present a three-component dataset to evaluate methodological effects. First, an ultra-deep sequencing dataset was generated from a single dog fecal sample using both short- (Illumina NovaSeq) and long-read (Oxford Nanopore MinION) platforms. Second, fecal samples from eight co-housed dogs were collected over one year to compare two DNA extraction workflows across 40 samples. Third, three full-length 16S rRNA primer sets were evaluated using synthetic microbial community standards and human and canine fecal samples, all sequenced on the MinION platform. The dataset comprises 75.2 GB of raw sequencing data and quality control and taxonomic classification outputs. The single-sample multi-platform dataset contributes 9.19 GB, the longitudinal cohort 43.45 GB, and the primer comparison dataset 22.61 GB across two accessions. Together, these data provide a multi-platform resource for evaluating extraction, sequencing, and primer-associated methodological effects in canine fecal microbiome profiling.},
}

@article {pmid42259906,
year = {2026},
author = {Ling, X and Zhang, Y and Bui, CHT and Chan, HN and Peng, Y and Zhang, XJ and Yim, CC and Yau, JW and Kam, KW and Ip, P and Young, AL and Hon, KL and Tham, CC and Pang, CP and Chen, LJ and Yam, JC},
title = {Profiling of ocular surface microbiome and its ocular types in children and adolescents.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01667-7},
pmid = {42259906},
issn = {2730-664X},
support = {82425017 & 82171089//National Natural Science Foundation of China (National Science Foundation of China)/ ; 11220206//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; },
abstract = {BACKGROUND: The ocular surface microbiome is increasingly recognized for its role in eye health, but the complexity of its composition complicates personalized characterization. This study aims to define the ocular surface microbiome profile and identify distinct microbial community clusters, or Ocular Types, in a population of children and adolescents.

METHODS: In this population-based, cross-sectional study, conjunctival swabs from children and adolescents were processed with 16S ribosomal RNA gene amplicon sequencing. Microbial clusters were determined using a partitioning around medoids clustering approach, validated through internal cross-comparison and external datasets. Functional profiles of the clusters were predicted from the sequencing data.

RESULTS: Here we show that in 1246 samples from 1006 individuals aged 3 to 18 years, the predominant bacterial phyla are Proteobacteria (34.1%), Firmicutes (37.4%), and Actinobacteria (25.2%), with Staphylococcus, Corynebacterium, and Streptococcus as core microbiota. Five distinct Ocular Types are identified, characterized by the dominance of Staphylococcus, Corynebacterium, Streptococcus, uncultured Neisseriaceae, or Escherichia-Shigella. These Ocular Types demonstrate associations with host factors including age, ethnicity and ocular parameter, but not with sex. Functional prediction reveals considerable overlap in the metabolic pathways among the Ocular Types.

CONCLUSIONS: This study characterizes five distinct ocular surface microbiome types in pediatric population and establishes their association with host factors. These findings provide a structured framework for investigating microbial community dynamics and their potential implications for ocular health.},
}

@article {pmid42259958,
year = {2026},
author = {Yu, D and Zhang, L and Zhang, L and Damu, A and Gao, N and Xu, J and Hao, J and Xiao, Y and Zhang, J and Yan, J},
title = {A dual-marker approach for forensic age prediction: integrating the salivary microbiome and antibiotic resistome.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {42259958},
issn = {1437-1596},
support = {82030058//National Natural Science Foundation of China/ ; 82101977//National Natural Science Foundation of China/ ; 202503021211157//Natural Science Foundation of Shanxi Province/ ; },
abstract = {Age prediction is a critical challenge in forensic science. Current mainstream approaches, such as DNA methylation analysis, often involve complex sample processing (e.g., bisulfite conversion), which can be costly and time-consuming and may compromise DNA integrity, thereby limiting multi-analyte recovery from trace evidence. Recent studies have highlighted the potential of the human microbiome as a source of forensic biomarkers, including for age estimation. Notably, the profile of antibiotic resistance genes (ARGs) in the microbiome has been reported to vary with host age, yet their utility as forensic age biomarkers remains unexplored. To address this, we characterized the salivary microbiome of volunteers via 16S rRNA gene (V3-V4) amplicon sequencing and quantified the abundance of 32 preselected ARGs using high-throughput quantitative PCR (HT-qPCR). Our analysis identified six bacterial genera and seven ARGs whose relative abundances were significantly correlated with chronological age (P < 0.05). We then constructed and compared random forest regression models for age prediction based on (i) microbiome features (Amplicon Sequence Variants, ASVs), (ii) ARG abundances alone, and (iii) an integrated set combining both marker types. Our results showed that the microbiome-only and ARG-only models both yielded higher mean absolute error (MAE) than the integrated model. In contrast, the combined model, built on just 13 features (six bacterial genera and seven ARGs), achieved a test MAE of 6.22 ± 3.75 years (MAE ± SD). This study reveals that ARGs hold promise as novel biomarkers for forensic age estimation. More importantly, the dual‑marker "microbiome‑ARG" strategy achieves effective age prediction using only a small number of features, offering a highly efficient and promising new approach for forensic age estimation.},
}

@article {pmid42260063,
year = {2026},
author = {Álvarez-Bobillo, Z and Gracia-Cazaña, T and Gilaberte, Y and Lim, HW},
title = {What's New in Photoprotection?.},
journal = {American journal of clinical dermatology},
volume = {},
number = {},
pages = {},
pmid = {42260063},
issn = {1179-1888},
support = {Research group of Aragon Goverment B59_23D Dermatology//Departamento de Educación, Cultura y Deporte, Gobierno de Aragón/ ; Photobiology//Departamento de Educación, Cultura y Deporte, Gobierno de Aragón/ ; },
abstract = {It is well established that a complete package of photoprotection includes staying in the shade, wearing photoprotective clothing, hat, and sunglasses, and on otherwise exposed sites, applying sunscreen. Recent advances have modified photoprotection through new active ingredients, innovative formulations, complementary oral strategies, and personalized approaches. This review aims to summarize the latest new developments in photoprotection. A narrative review of the literature was conducted from January 2010 to October 2025 using terms related to photoprotection, sunscreen innovation, visible light, oral photoprotection, microbiome interaction, climate change, and personalized approaches. Articles in English and Spanish were selected based on scientific relevance. Advances in photoprotection include the development of new topical filters targeting UVA1 and visible light, as well as the incorporation of iron oxides and, in some formulations, pigmentary titanium dioxide in tinted sunscreens to enhance protection against visible light. In addition, the use of antioxidants and DNA repair enzymes has been explored to mitigate oxidative stress and address field cancerization. Natural and eco-friendly bioactive ingredients derived from botanical and marine sources show growing potential as photoprotective agents. Additional considerations such as the role of skin microbiome, and personalized photoprotection strategies tailored to skin phototype, lifestyle, diseases, and high-exposure conditions further refine preventive practice. Photoprotection is evolving into a multidimensional approach that integrates advanced topical formulations, oral agents, and individualized recommendations. This paradigm offers improved prevention of photoaging, pigmentary disorders, and photocarcinogenesis while promoting safer and more sustainable photoprotection practices.},
}

@article {pmid42260168,
year = {2026},
author = {Smith, J},
title = {Daily briefing: Lung microbiome linked to a mysterious tissue-scarring condition.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-026-01828-7},
pmid = {42260168},
issn = {1476-4687},
}

@article {pmid42260293,
year = {2026},
author = {Kuriyama, Y and Mizuno, F and Yamada, T and Kumagai, M and Tanaka, M and Naka, I and Hirata, K and Mizushima, S and Yonemoto, S and Funahashi, K and Seguchi, N and Sakaue, K and Kanazawa, E and Matsushita, M and Matsushita, T and Saso, A and Nara, T and Sawaura, R and Katagiri, C and Maekawa, T and Kurosaki, K and Saitoh, H and Namiki, S and Ueda, S and Ohashi, J},
title = {Insights into demographic and cultural influences on the oral microbiome from historical Japanese dental calculus.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42260293},
issn = {2045-2322},
support = {24K00163//JSPS KAKENHI/ ; 24K00163//JSPS KAKENHI/ ; 24K00163//JSPS KAKENHI/ ; 24K21381//JSPS KAKENHI/ ; 24K21381//JSPS KAKENHI/ ; 24K21381//JSPS KAKENHI/ ; 24K00163//JSPS KAKENHI/ ; },
abstract = {Recent advances in genomic technologies have enabled detailed analyses of ancient microbiomes using dental calculus. While most studies have focused on European and North American populations, ancient Japanese oral microbiomes remain largely unexplored. Here, we analyzed dental calculus primarily from Edo period individuals (17th-19th centuries) to investigate the compositional, functional, and phylogenetic diversity of ancient oral microbiomes. Our results revealed clear differences between ancient and modern Japanese microbiomes, as well as phylogenetic divergence between the Final Jomon (ca. 1000 BCE) and Edo periods. We also identified regional variation in ancient oral microbiomes and clade-level diversity within the periodontitis-associated archaeon Methanobrevibacter oralis. Interestingly, individuals with traces of tooth blackening (ohaguro), a custom practiced by Edo period women, were all assigned to the same clade, suggesting cultural influences on the oral microbiome. These findings highlight the important role of human culture and demography in shaping the evolutionary dynamics of microbiomes.},
}

@article {pmid42260348,
year = {2026},
author = {Gudra, D and Lunge, M and Skinderskis, E and Roga, A and Rubins, S and Fridmanis, D},
title = {Cyanoacrylate glue as an effective skin-decontamination method for hair follicle microbiome sampling: insights from a nonhuman model (Capreolus capreolus).},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05268-1},
pmid = {42260348},
issn = {1471-2180},
support = {LZP-2022/1-0119//Latvijas Zinātnes Padome/ ; LZP-2022/1-0119//Latvijas Zinātnes Padome/ ; LZP-2022/1-0119//Latvijas Zinātnes Padome/ ; LZP-2022/1-0119//Latvijas Zinātnes Padome/ ; LZP-2022/1-0119//Latvijas Zinātnes Padome/ ; LZP-2022/1-0119//Latvijas Zinātnes Padome/ ; },
abstract = {INTRODUCTION: In humans, microorganisms within hair follicles differ from those on the skin surface and may contribute to autoimmune skin diseases such as alopecia areata and vitiligo. Owing to the low biomass of hair follicle microorganisms, precise sample acquisition and strategies to avoid contamination with genetic material are critical. To address this, we developed and evaluated a sampling methodology using a nonhuman wildlife proxy model - the wild roe deer (Capreolus capreolus) - to identify effective approaches for minimizing skin contamination prior to biopsy. Animal was obtained during licenced hunts and frozen at -20°C shortly postmortem. Four sets of biopsy and skin surface swab samples were collected from the right front leg: 1) untreated skin; 2) skin cleaned with isopropyl alcohol (IPA) wipes; 3) skin treated with cyanoacrylate glue (CAG); and 4) skin treated with CAG followed by IPA wipes. Swabs were collected via Copan FLOQSwabs, whereas biopsies were obtained with single-use 1 mm biopsy punches. Nucleic acids were subjected to droplet digital PCR (ddPCR) for 16S rRNA and 18S rRNA gene copy number quantification. Additionally, the swab samples were subjected to 16S rRNA V3-4 region and ITS-1 sequencing.

RESULTS: ddPCR analysis revealed greater bacterial presence on the skin surface (11,661±5,181 copies/±L) than fungal presence (87±35 copies/μL), and the microbial load was greater in the swab samples (16S: 11,661±5,181; 18S: 87±35 copies/μL) than in the biopsy samples (16S: 76±56; 18S: 8±5 copies/μL). Notably, the use of CAG reduced the microbial load in biopsy samples by 3.7-fold. 16S and ITS sequencing analysis revealed slightly greater alpha diversity in swab samples than in biopsy samples, particularly in areas treated with CAG. Beta diversity revealed distinct clustering of swab and biopsy samples, with shorter distances between CAG-treated samples and untreated samples. Fewer bacterial (n = 8) and fungal (n = 1) genera were detected in CAG-treated biopsies compared with untreated (n = 21, n = 9, resp.) and IPA-treated (n = 45, n = 7, resp.) biopsies.

CONCLUSIONS: These results demonstrate a high probability of biopsy contamination with microbial DNA originating from the skin surface. They also confirmed that CAG effectively reduces such contamination and can serve as a practical decontamination step before biopsy. Although based on a nonhuman wildlife model, this feasibility study provides methodological insights that can inform the design of future human hair follicle microbiome investigations.},
}

@article {pmid42260510,
year = {2026},
author = {Babolin, S and Enea, R and Cicala, M and Di Giovanni, D and Mazzone, L and Emberti Gialloreti, L},
title = {Machine learning model to identify gut microbiome-derived metabolites as potential biomarkers of autism spectrum disorder: a pilot study.},
journal = {BMC psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12888-026-08178-8},
pmid = {42260510},
issn = {1471-244X},
abstract = {Autism Spectrum Disorder (ASD) arises from complex and not yet completely understood interactions between genetic and environmental factors. Alongside known hallmarks of neurobiological and structural changes in ASD brain, alterations in gut microbiota are frequently observed in ASD and may contribute to its pathophysiology. Identifying reliable biomarkers through multivariate analysis and machine learning offers promising avenues for improving ASD diagnosis and understanding comorbid gastrointestinal symptoms. In this study, a machine learning model was trained to identify ASD and healthy controls based on the theoretical production of metabolites for each gut bacterial species and each individual, combining the data collected from two global databases (GMRepo v2 and Agora2). Random Forest Classification models reach a mean accuracy of 85%, and a subsequent literature analysis of the 5% most significant metabolites showed a 40% correspondence with previously published in vivo studies. Some of the most relevant compounds detected by the theoretical model are amino acid and amino-acidic derivatives, volatile organic compounds, and short-chain fatty acids. Results are coherent with empirical evidence, supporting microbiota's role in ASD pathophysiology by contributing to neurotransmitters' biosynthesis and degradation, intestinal epithelial barrier integrity, immunological modulation. Future work will focus on stratified sampling, empirical validation, and developing personalized metabolic signatures for early diagnosis and precision medicine.},
}

@article {pmid42260597,
year = {2026},
author = {Rynikova, M and Gancarcikova, S and Lauko, S and Mudronova, D and Adamkova, P and Janicko, M and Demeckova, V},
title = {Exploring new animal models of ulcerative colitis: evaluating chemical and patient-derived microbial triggers to advance translational relevance.},
journal = {Laboratory animal research},
volume = {42},
number = {1},
pages = {},
pmid = {42260597},
issn = {1738-6055},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with multifactorial aetiology involving genetic, immune, environmental, and microbial factors. Alterations in the gut microbiome are a consistent feature of UC, yet their causal contribution to disease onset and progression remains unresolved. Current animal models rely largely on chemical or genetic induction and fail to capture the complexity of host-microbiome interactions characteristic of human disease. To address this limitation and enhance the translational relevance of preclinical research, this study employed patient-derived microbiota to model UC-associated dysbiosis and investigated its effects alone and in combination with chemical induction.

RESULTS: We compared three mouse models using different UC-induction triggers: dextran sulphate sodium (DSS), faecal microbiota transplantation (FMT) from a UC patient, and their combination (COMB). DSS and COMB treatments induced marked clinical symptoms, whereas FMT alone caused only mild changes, likely due to the short exposure period. Immunophenotyping revealed distinct immune profiles across all models, with leukocyte and neutrophil infiltration in the colonic mucosa of all groups, demonstrating that the microbiota alone can elicit localized immune activation. Transcriptomic analysis showed that FMT significantly modulated tight junction and mucin gene expression and induced microbiome shifts resembling those observed in human UC. In contrast, DSS triggered a strong pro-inflammatory transcriptional response and reduced microbial diversity, but with compositional changes mostly opposing those seen in UC patients. The COMB model combined features of both approaches - producing clinical symptoms and inflammatory activation similar to DSS and tight junction dysregulation resembling FMT.

CONCLUSIONS: This study investigated novel experimental models of ulcerative colitis by incorporating patient-derived microbiota as an inducing factor. DSS induced strong clinical and inflammatory responses, FMT primarily altered barrier gene expression and microbiome composition, and their combination merged both inflammatory and epithelial characteristics. These microbiota-based models show promise for more accurately reproducing UC pathophysiology and thereby improving translational relevance. Further optimization is needed, including adjustment of exposure duration and sequence of induction, as well as validation for reproducibility.},
}

@article {pmid42260689,
year = {2026},
author = {Wang, K and Peng, Q and Geng, L and Zhang, F and Liu, R and Liu, X and Zhang, J and Shu, C},
title = {Protaetia brevitarsis larvae frass affects substrate microecological systems via two suggestive pathways to enhance cherry tomato growth.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00915-6},
pmid = {42260689},
issn = {2524-6372},
support = {2023YFD1701502//National Key Research and Development Program of China/ ; 32570599//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The identification and development of high-quality humus sources to enhance the productivity and performance of substrate-based vegetable cultivation systems remains a significant challenge in sustainable agriculture. Protaetia brevitarsis larvae (PBL) exhibit exceptional efficiency in decomposing decaying crop straw and produce nutrient-rich frass with high humic acid content and a complex microbial community. However, its impacts on substrate microecological systems and the underlying functional mechanisms remain unclear, limiting its rational application in substrate cultivation. This study aimed to investigate the effects of PBL frass on substrate microecology and elucidate the associated mechanisms using cherry tomato (Lycopersicon esculentum Mill. var. cerasiforme Alef) pot experiments.

RESULTS: Incorporation of 2% or 4% (w/w) PBL frass into cherry tomato cultivation substrates significantly promoted plant growth, characterized by reduced plant height (indicating more robust, dwarf-type growth) and increased aboveground (stem) and belowground (root) biomass. Furthermore, PBL frass application enhanced substrate microbial diversity through two distinct, complementary pathways: (ⅰ) Frass-derived microbes, which possess specific colonization capabilities, directly augmented microbial communities in both the rhizoplane and bulk substrate; and (ⅱ) Organic compounds in PBL frass may have activated a broad range of microbes, enriching the rhizosphere microbiome. This enhanced microbial diversity was associated with an increased abundance of plant-beneficial taxa, which likely contributed to growth promotion and substrate health maintenance.

CONCLUSIONS: This study uncovers the multifaceted contributions of PBL frass to substrate microbial ecology and reveals its two suggestive regulatory pathways. These results provide a theoretical basis for the sustainable utilization of PBL frass and advance the development of eco-friendly amendments for modern vegetable production.},
}

@article {pmid42260913,
year = {2026},
author = {Shahid, M and Ilyas, T and Shafi, Z},
title = {Rhizobacterial Exopolysaccharides in Soil-Plant Systems: Molecular Mechanisms, Engineering Approaches, and Translational Challenges.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c02760},
pmid = {42260913},
issn = {1520-5118},
abstract = {Plant productivity has become increasingly affected by various abiotic and biotic factors such as drought, salinity, metal toxicity, heat/cold stresses, and pathogen pressure that disrupt soil-plant interactions. Plant growth-promoting rhizobacteria (PGPR)-secreted exopolysaccharides (EPSs) play a significant role in maintaining rhizosphere stability through promoting soil aggregation, increasing the soil water retention capacity, and proper ion management. In addition, EPSs provide extracellular binding sites for toxic metals and facilitate the formation of stress-tolerant biofilms. Production of EPSs is under the strict control of sophisticated regulatory systems, linking environmental conditions and adaptive mechanisms at the genetic level. Novel advancements in omics and genome editing techniques could be used in the development of improved EPS-secreting strains with enhanced stress-resistance capabilities. Potential applications include PGPR formulations for seed coating, bioinoculants, and soil treatments; however, strain heterogeneity and environmental variability represent important challenges.},
}

@article {pmid42261315,
year = {2026},
author = {Setyawan, HY and Widyastuti, E and Sugiarto, Y and Sunyoto, NMS and Ulandari, D and Dewi, J and Choirun, AU and Arwani, M and Okoye, C},
title = {Applications and mechanisms of biochar-mycorrhizal synergies in agriculture based on systematic review.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21336},
pmid = {42261315},
issn = {2167-8359},
abstract = {Biochar (BC) and arbuscular mycorrhizal fungi (AMF) have emerged as powerful tools for sustainable agriculture, offering significant benefits for soil health, crop productivity, and ecological resilience. Their combined application has shown synergistic effects; however, key gaps in our understanding remain. This systematic review synthesizes findings from recent studies (n = 72) published up to 2025 to examine the synergistic effects of biochar and AMF. A comprehensive search across Scopus, Web of Science, and PubMed employed database-specific Boolean operators combining keywords such as "biochar," "mycorrhizal fungi," "soil health," and "nutrient cycling." This review highlights the role of biochar in improving soil structure, nutrient availability, and microbial diversity, thereby providing favourable habitats for mycorrhizal colonization. Approximately 78% of reviewed studies reported yield or nutrient-uptake improvements ranging between 15-35% under combined BC-AMF treatments, particularly under environmental stresses like drought or salinity. Synergistic interactions also promoted microbiome shifts, notably increasing the dominance of Glomus and Rhizophagus, which were associated with biochar porosity and nutrient composition. However, uncertainties remain regarding the long-term sustainability of these effects, and the influence of biochar properties on AMF functionality. To fully realize the potential of BC-AMF synergies, future research must focus on standardizing biochar production, exploring molecular and soil-plant-microbe mechanisms, and conducting long-term studies. Collaboration among stakeholders is essential to ensure the scalability and adoption of these technologies, positioning BC-AMF systems as ecologically sustainable alternatives that can support resilient agricultural production while reducing dependence on conventional chemical inputs.},
}

@article {pmid42261381,
year = {2026},
author = {Sandra, KS and Vithalkar, MP and Beere, V and Bharath, HB and Satyanarayana, B and Rafiq, M and Nayak, Y},
title = {Oligosaccharide prebiotics in functional foods and therapeutics: innovations and challenges.},
journal = {3 Biotech},
volume = {16},
number = {7},
pages = {254},
pmid = {42261381},
issn = {2190-572X},
abstract = {Oligosaccharide prebiotics, such as inulin, fructooligosaccharides (FOS), and galactooligosaccharides (GOS), have demonstrated significant effects on gut microbiota and host health across in vitro, animal, and clinical studies. These studies consistently report an increase in beneficial bacteria, particularly Bifidobacterium and Lactobacillus, leading to higher production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These metabolic changes are linked to improved integrity of the epithelial barrier, reduced inflammatory signaling, modulation of immune responses, and enhanced metabolic balance. Biotechnological production methods, including enzymatic synthesis, microbial fermentation, and controlled depolymerization of plant polysaccharides, allow for precise control over the degree of polymerization and the types of glycosidic linkages. This control directly affects the fermentability, microbial selectivity, and functional effectiveness of the prebiotics. When incorporated into functional food systems, oligosaccharide prebiotics can enhance physicochemical properties such as texture, sweetness, and stability, all while maintaining their biological performance. Advanced delivery technologies, such as nano- and microencapsulation, improve thermal stability, resistance to gastrointestinal degradation, and targeted colon-specific release. Additionally, synbiotic formulations can further enhance the effectiveness of these prebiotics by promoting microbial colonization and sustained availability of SCFAs. Therapeutic benefits have been observed across various models of gastrointestinal health, metabolism, immune responses, and the gut-brain axis. These benefits involve mechanisms such as GPCR activation, histone deacetylase inhibition, and cytokine regulation. However, several challenges remain, including dose-dependent gastrointestinal intolerance, variability in individual microbiomes, degradation during processing, regulatory hurdles, and high costs of downstream processing. Overall, these findings highlight oligosaccharide prebiotics as versatile and scalable biotechnological ingredients, emphasizing the need for standardized production methods, precise dosing, and long-term clinical validation.},
}

@article {pmid42261608,
year = {2026},
author = {Shelat, VG},
title = {Microbial ecology and hepatocellular carcinoma: should a subset be viewed as a microbiome-conditioned malignancy?.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2026.2687711},
pmid = {42261608},
issn = {1747-4132},
}

@article {pmid42262083,
year = {2026},
author = {Lewin, GR and Khadempour, L},
title = {mGem: Tapping into the language of symbiosis to advance human microbiome research.},
journal = {mBio},
volume = {},
number = {},
pages = {e0366125},
doi = {10.1128/mbio.03661-25},
pmid = {42262083},
issn = {2150-7511},
abstract = {In human microbiome research, the term "commensal" is often used to describe organisms that benefit their hosts. In ecology, in host-microbe symbiosis, a commensal organism has no impact on its host, whereas a mutualist organism benefits its host. While others have recognized this discrepancy in terminology use, old habits are hard to break, and the human microbiome community has continued in this vein. This is our call to action for the human microbiome community to use more precise terminology that appropriately reflects the impact that these microbes have on their hosts. We should use the terms "commensal" and "mutualist" when we know the effect on the host, and "symbiont" when we do not. By using the same terminology as ecologists, we will be able to make use of, and contribute to the vast research in the field of symbiosis.},
}

@article {pmid42262087,
year = {2026},
author = {Barrack, KE and Surve, SV and de Sousa Bezerra, AV and Murphy, CE and Soucy, SM and Aguilar Ramos, MA and Valls, RA and Ruff, RD and Balskus, EP and Sanville, JL and Madan, JC and O'Toole, GA},
title = {A genotoxin associated with colorectal cancer linked to gut dysbiosis in children with cystic fibrosis.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0019026},
doi = {10.1128/jb.00190-26},
pmid = {42262087},
issn = {1098-5530},
abstract = {Cystic fibrosis (CF) alters the gastrointestinal microbiome from an early age, leading to significant changes in microbial composition and functionality. This study explores the physiological and microbiological factors contributing to dysbiosis in children with cystic fibrosis (cwCF), characterized by an increase in potentially pathogenic Escherichia coli and a decrease in beneficial anaerobes, such as Bacteroides. We employed an in vitro medium representative of the nutritional environment of the CF colon to test the role of factors, including mucin, fat, bile, pH, antibiotics, and features associated with inflammation (e.g., nitrate, sulfate, formate, and reactive oxygen species), on the growth of clinical isolates of E. coli and Bacteroides spp., with a focus on Bacteroides vulgatus. We further examined interactions between these two microbes under CF-like conditions and identified glycerol, a surrogate of increased fat, as a significant driver of altered microbial competition. Finally, we investigated genetic determinants influencing these microbial interactions by performing a transposon mutagenesis screen in E. coli. The results pointed to the role of colibactin, a DNA-damaging genotoxin associated with an increased risk of colorectal cancer (CRC), in mediating this microbial competition. This work enhances our understanding of the mechanisms of microbial competition in the CF gut and potential CRC risk in persons with CF through the identification of early-life microbial biomarkers.IMPORTANCEThe risk of CRC development in CF populations is significantly increased. This in vitro study examines the interplay of altered intestinal physiology in the microbial dysbiosis common in the CF gut, implicating the high-fat/glycerol environment in a competition-mediated depletion of immune-modulating Bacteroides vulgatus. This work identifies candidate features of the young CF intestine and gut microbiome that may contribute to dysbiosis, development of inflammation, and CRC in these populations, informing potential prognostic and therapeutic approaches.},
}

@article {pmid42262089,
year = {2026},
author = {Thianheng, P and Schroeter, KL and Larsbrink, J and McKee, LS},
title = {Exploring the native pulp and paper sludge microbiome to inspire new biotechnologies for waste minimization.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0135926},
doi = {10.1128/spectrum.01359-26},
pmid = {42262089},
issn = {2165-0497},
abstract = {Thousands of metric tonnes of diverse sludge wastes are generated annually in the pulp and paper industry. Due to a high moisture content and an abundance of inorganic material, many types of sludge are hard to recycle and instead accumulate in landfills, causing environmental damage. During storage, forestry sludge waste appears recalcitrant to natural attenuation, indicating limited degradation of wood- and process-derived fibers and polymers by environmental microbes. Intentional enzymatic or microbial hydrolysis of carbohydrates within the sludge may, however, be a feasible approach to reduce waste volume and prevent transfer to landfill. Here, we show that a previously validated biomass-degrading enzyme cocktail lacks efficacy on a metal-rich sludge obtained from a Swedish pulp and paper mill, possibly due to enzyme inhibition. Hypothesising that microbes dwelling within sludge may host enzymes better adapted to this complex contaminated substrate, we assessed whether a native sludge microbiome could be identified, and whether it degrades carbohydrates during incubation in microcosms. Marker gene profiling revealed diverse bacterial and fungal communities undergoing genus-level changes over time, and the most abundant species could be enriched via serial cultivation with pulp-derived carbon sources. Complementary chemical analyses showed that biopolymers were largely removed after a 10-week incubation, leading to sludge solubilization and volume reduction. This confirms the capacity for fiber degradation by native microbiomes and suggests the waste as a potential source of microbes and enzymes capable of sludge polymer degradation, the mechanism of which remains to be explored, but which could reduce the need for future landfilling.IMPORTANCEAccording to European and Swedish guidelines, the top priority in waste handling is prevention, followed by reuse, recycling, energy recovery, and, as a last resort, landfill. While effective in municipal contexts, these guidelines are difficult to apply to pulp and paper industries when managing heterogeneous sludge wastes. Process-derived sludges are hugely abundant but have low economic value as their high moisture content prevents combustion, and the complex mixture of organic fibers prevents metal recovery. According to industrial reports, less than 10% of sludge is used for energy, and under 50% is recycled. Our results demonstrate that biological treatment of sludge could be a method of waste reduction to reduce landfilling, specifically targeting hygroscopic carbohydrate-based polymers. Mapping the microorganisms in this under-explored industrial waste material, using combined "omic" technologies and chemical analysis, lays a foundation for discovering robust organisms and enzymes that withstand harsh conditions, such as low water activity and high metal content.},
}

@article {pmid42262103,
year = {2026},
author = {Heredia, MY and Knoll, LJ},
title = {Contributions of intestinal protists on the human gut landscape through the lens of Entamoeba spp.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0001126},
doi = {10.1128/msphere.00011-26},
pmid = {42262103},
issn = {2379-5042},
abstract = {Intestinal protists represent an underappreciated yet functionally significant component of the human gut microbiome. Historically dismissed as parasites or transient contaminants, many of these microbial eukaryotes, particularly Entamoeba spp., are now recognized as integral to gut ecosystem function and host immune homeostasis. This review examines the complex roles of Entamoeba spp. in the mammalian gut, positioning them as dynamic microbiome "landscapers" that influence host-pathogen interactions, immune tone, and microbial diversity. We explore the evolutionary adaptation of Entamoeba to the gut's anaerobic and immunologically active environment, highlighting both pathogenic (E. histolytica) and non-pathogenic species (E. dispar, E. coli) and their distinct immunomodulatory strategies. Special attention is given to the host immune responses shaped by E. histolytica, including inflammasome activation, macrophage polarization, and suppression of protective type-2 responses. The review also details Entamoeba's interactions with the gut microbiota, emphasizing their capacity for selective bacterial predation, disruption or enhancement of microbial community structure, and synergistic or antagonistic relationships with commensals and pathogens alike. Methodological challenges in protist detection, genome annotation, and cultivation are discussed, alongside promising advances in sequencing, host DNA depletion, and animal modeling. Taken together, current evidence reframes Entamoeba spp. not as mere pathogens but as key ecological players whose presence can signal resilience or susceptibility within the gut ecosystem. Understanding the context-dependent functions of intestinal protists may offer new insights into microbial therapeutics, immune modulation, and disease prevention strategies.},
}

@article {pmid42262118,
year = {2026},
author = {Sommer, AJ and Ferrandis-Vila, M and Mamerow, S and Berens, C and Menge, C and Wei, S and Wang, Q and Aarestrup, FM and Otani, S and Sapountzis, P},
title = {Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0050126},
doi = {10.1128/msystems.00501-26},
pmid = {42262118},
issn = {2379-5077},
abstract = {The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome, leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6, likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa.IMPORTANCECattle serve as natural reservoirs of zoonotic strains of Escherichia coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial-resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in the prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.},
}

@article {pmid42262124,
year = {2026},
author = {Tanca, A and De Diego, L and Deledda, MA and De Maio, F and Boru, C and Musella, M and Raffaelli, M and Silecchia, G and Delogu, G and Uzzau, S},
title = {Reshaping of the fecal proteome and metaproteome in obese patients 2 years after bariatric surgery.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0176425},
doi = {10.1128/msystems.01764-25},
pmid = {42262124},
issn = {2379-5077},
abstract = {Bariatric surgery provides effective and durable weight loss in patients with severe obesity. Both the surgical procedure and postoperative management, including dietary and behavioral changes, are known to induce long-term alterations in gut microbiota composition. However, their impact on microbial and host proteome profiles remains poorly understood. In this prospective, multicenter cohort study, we compared the fecal metaproteome profile of 45 patients with severe obesity at preoperative baseline (T0) and 2 years after surgery (T1). Patients were randomized to receive either Roux-en-Y gastric bypass or one anastomosis gastric bypass. At T1, the relative abundance of the bacterial genera Akkermansia, Anaerotignum, Desulfovibrio, Streptococcus, and Veillonella significantly increased, whereas that of Faecalibacterium and Romboutsia decreased. Furthermore, we observed a significant increase in the relative abundance of microbial enzymes involved in glycolysis, short-chain fatty acid biosynthesis, amino acid metabolism, and cofactor/vitamin biosynthesis, alongside various outer membrane proteins encoded by Enterobacterales. Conversely, several proteins involved in oxidative phosphorylation and sporulation were reduced. Moreover, 74 human proteins, primarily associated with immune functions, showed a significant increase in relative abundance at T1, while numerous digestive enzymes displayed a downward trend. Our data reveal that a distinct reshaping of the fecal proteome and metaproteome persists 2 years after bariatric surgery. Future studies are needed to elucidate the mechanistic aspects of host-microbiota interaction and to identify associations with long-term clinical outcomes.IMPORTANCEBariatric surgery is widely recognized as the most effective and durable intervention for severe obesity; however, its long-term molecular effects on gut microbiota-host interactions remain poorly understood. By applying shotgun metaproteomics to fecal samples collected before and 2 years after surgery, our study provides novel insights into the functional consequences of bariatric bypass procedures. We demonstrate sustained alterations in both microbial and host protein profiles, including metabolic enzymes, outer membrane proteins, and immune-related factors, revealing a long-lasting remodeling of gut ecosystem functions. These findings underscore the value of metaproteomics in uncovering molecular mechanisms underlying bariatric surgery outcomes and may ultimately guide the development of microbiome- or host-targeted strategies to optimize therapy and long-term patient care.},
}

@article {pmid42262136,
year = {2026},
author = {Iacovacci, J and Cannon, N and McCulloch, JA and Rancati, T and Trinchieri, G},
title = {Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0028426},
doi = {10.1128/msystems.00284-26},
pmid = {42262136},
issn = {2379-5077},
abstract = {UNLABELLED: The human microbiota plays a pivotal role in health, with widespread alterations implicated in conditions ranging from inflammatory disorders to cancer. While correlation-based network analyses have illuminated ecological interactions within these communities, the host environment uniquely mediates microbial relationships, demanding new methods to capture dynamic, condition-dependent modules of species interactions. Here, we present a statistical framework termed differential co-occurrence analysis, which identifies blocks of taxa whose collective presence is strengthened or weakened under distinct host states. By leveraging recent advances in metagenomics that enable detailed taxonomic profiling and higher-order interaction discovery, our method transcends traditional pairwise correlation constraints. Conceptually akin to associative rule mining, it diverges through the integration of robust statistical modeling, directly extracting interactions that differ significantly between conditions. This approach offers a refined lens to dissect microbiota ecology and could pave the way for new insights into microbiome-associated disease mechanisms.

IMPORTANCE: The research on the role of the intestinal microbiota in the onset of cancer and as a modulator of anticancer treatments, including chemotherapeutics and immune checkpoint inhibitors, is helping medicine to identify novel strategies for cancer prevention, for the delivery of more effective treatments, and in reducing treatment side effects and complications. Within this context, it is of crucial importance to approach the analysis of clinical microbiome data with an ecology-oriented perspective and to develop bioinformatics tools able to identify functional interactions in bacterial communities of patients from observational cohort studies. Clinical microbiome datasets are typically high dimensional, comprising numerous taxa measured across relatively few samples. This imbalance increases the risk of statistical overfitting and undermines the robustness of analytical findings. However, recent advances in metagenomic bioinformatics pipelines and reference databases have enabled the comprehensive extraction of genetic information from microbiome samples, facilitating the precise characterization of bacterial species presence and absence. In our manuscript, we describe a statistical computational method that we named differential co-occurrence analysis, which focuses on the analysis of the co-presence of microbiota taxa across samples associated with different host conditions. The proposed method can reveal modules of interacting taxa that are strengthened or weakened when the host condition changes (e.g., when passing from a healthy state to a disease state). The method is general and applicable to a broad range of ecological datasets featuring presence/absence data structures. Furthermore, the method accommodates the analysis of higher-order co-occurrence patterns beyond pairwise co-occurrence, thereby enabling the investigation of higher-order interactions, whose detection and identification are a major challenge in ecological network analysis.},
}

@article {pmid42262337,
year = {2026},
author = {Kadyan, S and Park, G and Khalili, L and Patoine, C and Mayonu, M and Wang, B and Salazar, G and Yamashiro, Y and Nagpal, R},
title = {Maternal diet shapes neonatal microbiome ontogenesis and neurometabolic resilience.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2684074},
pmid = {42262337},
issn = {1949-0984},
abstract = {Maternal diet high in saturated fatty acids (SFA) promote infant gut dysbiosis and impairs metabolic and neurocognitive outcomes; however, the protective potential of maternal polyunsaturated fatty acids (PUFA), particularly omega-3 (n3), remains unclear. This study examined how maternal diets enriched in SFA (20% milk fat), omega-6 (n6; 20% corn oil), or omega-3 (n3; 19% olive oil + 1% fish oil) influence neonatal metabolism, neurodevelopment, the gut microbiome, the gut-blood-brain metabolomes, and the brain lipidome in C57BL/6 mice. The offspring were exposed to these diets only during gestation and lactation and then maintained on a Western-style diet for 10 weeks. Compared to SFA, maternal PUFA-rich diets induced distinct and persistent microbiome signatures and reshaped the gut and systemic metabolomic profiles into adulthood. The offspring of n3-fed dams displayed higher lean-to-fat mass ratios, improved ileal morphology, and enhanced gut epithelial integrity. Chronic low-grade inflammation (MCP-1) along the gut-blood-brain axis was markedly reduced in n3 offspring. Moreover, maternal n3 intake enhanced synaptic plasticity, suppressed neuroinflammation, and enriched brain lipids and metabolites associated with membrane integrity, neuronal signaling, and anti-inflammatory pathways. Overall, maternal omega-3 intake confers long-term neuroprotective effects by modulating brain lipid remodeling and the gut-brain-immune axis.},
}

@article {pmid42262444,
year = {2026},
author = {Hemmatinafar, M and Tajanaki, AS and Jäger, R and Safari, K},
title = {Probiotics and the Gut Microbiome in Combat Sports: A Narrative Review of Performance, Recovery, and Health Pathways.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42262444},
issn = {1867-1314},
abstract = {Competitive combat athletes are routinely exposed to high training loads, rapid weight-making practices, psychological stress, and frequent injuries-all of which may adversely affect the gut microbiome and, consequently, multiple physiological systems relevant to performance. Growing scientific interest in the role of probiotics and host-microbiome interactions suggests that targeted modulation of gut bacteria may offer functional benefits for athletes. This narrative review synthesizes current evidence on probiotics and microbiome-mediated pathways influencing performance, recovery, and health in combat-sports athletes. A comprehensive literature search was conducted across PubMed, Web of Science, and Google Scholar, with no date limits, including studies published up to October 2025. Search terms covered the gut microbiome, probiotics, athletic performance, combat sports, gastrointestinal barrier function, immune responses, psychological factors, nutrient absorption, hypoxia, weight cutting, and sex-specific considerations. Reference lists of relevant reviews and grey literature were manually screened. Across the available literature, probiotic supplementation has been associated with a range of effects that could be relevant to combat athletes. Evidence, largely from non‑combat and mixed‑population studies, suggests that probiotics may influence several physiological systems, including: (1) inflammatory and oxidative stress responses and injury rehabilitation; (2) immune function and upper respiratory tract infection outcomes; (3) gastrointestinal permeability and nutrient absorption, particularly after rapid weight loss; (4) psychological factors via the gut-brain axis; (5) muscle recovery through inflammatory and metabolic pathways; (6) body composition and weight regulation; (7) oral and skin microbiome composition; and (8) gut microbial changes during hypoxia or hormonal fluctuations. However, most of these findings are indirect, with very few studies conducted specifically in competitive combat‑sport athletes, and the overall evidence base remains heterogeneous. Probiotic and gut microbiome-targeted strategies may serve as potential adjunctive strategies to support health, recovery, and performance in combat athletes. However, because the current evidence is largely derived from non-combat and predominantly male populations, strain-, dose-, and sport-specific recommendations cannot yet be made. There is a clear need for randomized controlled trials in combat-sport athletes-including women-that employ standardized probiotic protocols and sport-specific outcome measures.},
}

@article {pmid42262446,
year = {2026},
author = {Cruz Neto, JPR and Godet, M and da Costa, PCT and de Luna Freire, MO and de Albuquerque Lemos, DEC and de Oliveira Coutinho, D and Sampaio, KB and Brasil, JMA and Meugnier, E and Vidal, H and Magnani, M and de Brito Alves, JL},
title = {Combined Probiotics and Phenolics in Western Diet-fed Rats Enhance Parasympathetic Tone in the Gut-Brain Axis by Attenuating Inflammasome Signaling, and Reshaping Gut Microbiome.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42262446},
issn = {1867-1314},
abstract = {Western dietary patterns are major drivers of cardiometabolic dysfunction, partly mediated by gut microbiome dysbiosis and sustained inflammation along the gut-brain axis. In this study, we investigated whether a synbiotic formulation combining Limosilactobacillus (L.) fermentum strains with polyphenols, quercetin, and resveratrol could mitigate cardiovascular and neuroinflammatory alterations induced by a Western diet. Male Wistar rats were assigned to three groups receiving a standard diet, a Western diet, or a Western diet supplemented with the synbiotic. Arterial pressure and cardiac autonomic function were assessed, alongside gut microbiome diversity and composition, and gene expression analyses of intestinal permeability and inflammatory markers in colonic tissue and in the brainstem. Synbiotic supplementation prevented the Western diet-induced cardiac autonomic imbalance. These functional benefits were accompanied by marked modulation of the gut microbiome, characterized by increased abundance of beneficial bacterial taxa (Gemmiger formicilis, Lactobacillus acidophilus, Flavonifractor plautii, Blautia glucerasea, Blautia stercoris, Roseburia faecis, Marvinbryantia formatexigens, and Romboutsia timonensis) and significant shifts in microbial community structure. In parallel, synbiotic supplementation attenuated pro-inflammatory gene expression in both peripheral and central tissues associated with the gut-brain axis (Nlrp3, Casp1, Il-1β). These findings demonstrate that synbiotic supplementation exerts integrated anti-inflammatory and neuroautonomic protective effects through the gut-brain axis. Our results support the therapeutic potential of combined probiotic-phenolic strategies to counteract cardiometabolic dysfunction induced by Western diets.},
}

@article {pmid42262562,
year = {2026},
author = {Wood, CM},
title = {A 30-year retrospective on the respirometric method for measuring instantaneous metabolic fuel use in fish.},
journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology},
volume = {},
number = {},
pages = {},
pmid = {42262562},
issn = {1432-136X},
support = {RGPIN-2023-03714//NSERC/ ; },
abstract = {In 1996, based on the ideas of Max Kleiber, we proposed a respirometric method in this journal for the quantitative determination of the roles of protein, lipid and carbohydrate as substrates for fueling aerobic metabolism in fish on an instantaneous basis. Here I provide a 30-year retrospective on its performance, explaining how it works, methodological challenges, the applications for which it has been used, its strengths and potential flaws, and the important issues to be addressed going forward. The approach is based on the simultaneous measurement of the rates of O2 consumption (ṀO2), CO2 excretion (ṀCO2) and N-waste excretion (ṀN = Ṁamm + Ṁurea-N) under steady-state conditions in the whole fish when anaerobic metabolism is not occurring. These allow the calculation of the Respiratory Quotient (RQ = ṀCO2/ṀO2) and the Nitrogen Quotient (NQ = ṀN /ṀO2), and from these, the fractional contributions of each of the three fuels. Principal methodological challenges arise from the difficulties of measuring ṀCO2, and to a lesser extent ṀN, in water. To date, the approach has been used mainly to study fuel use during feeding, fasting, starvation, sustainable exercise, and at different temperatures. In general, lipid and carbohydrates have emerged as the major fuels burned in ammoniotelic fish (where ammonia is the predominant N-waste product), while protein is conserved, though protein metabolism may be more important in ureotelic fish (where urea-N is the predominant N-waste product) and air-breathers. Possible unidentified N- products of protein oxidation, the action of the anaerobic gut microbiome in generating ṀN in the absence of ṀO2, and the ability of the gill microbiome to convert N-waste to di-nitrogen (N2) are highlighted as potential flaws.},
}

@article {pmid42263007,
year = {2026},
author = {Chen, Y and Liu, Z and Chen, Y and Zhong, J and Li, X and Song, P},
title = {Correlation of hs-CRP and T lymphocyte subsets with severity and prognosis in elderly pulmonary infection.},
journal = {Journal of infection in developing countries},
volume = {20},
number = {5},
pages = {743-749},
doi = {10.3855/jidc.22001},
pmid = {42263007},
issn = {1972-2680},
abstract = {INTRODUCTION: This study aimed to investigate the correlation between high-sensitivity (hs)-CRP, T lymphocyte subset profiles, disease severity, and treatment outcomes in elderly patients with pulmonary infection.

METHODOLOGY: The study included 85 elderly patients with respiratory infections (46 non-severe, 39 severe) and 79 healthy controls. The levels of hs-CRP, T lymphocyte subsets (CD4+/CD8+, CD4+, CD8+), and clinical pulmonary infection score (CPIS) were measured. Correlations with disease severity and CPIS were analyzed. Additionally, pre- and post-treatment levels of hs-CRP and T lymphocyte subsets were compared in patients with different treatment responses.

RESULTS: Patients had lower CD4+ counts and CD4+/CD8+ ratios, but higher hs-CRP, CD8+, and CPIS levels (p < 0.05) compared to controls. Severe cases had lower CD4+ and CD4+/CD8+, but higher CD8+, hs-CRP, and CPIS, than non-severe cases (p < 0.05). CD4+ and CD4+/CD8+ were negatively correlated with disease severity and CPIS, while hs-CRP and CD8+ were positively correlated (p < 0.05). The patients who responded to treatment (responders) had higher increases in hs-CRP, CD4+, and CD4+/CD8+ after 7 days of treatment, compared to non-responders; while CD8+ levels were lower (p < 0.05). Receiver operating characteristic (ROC) analysis showed that an hs-CRP difference cutoff of 5.31 had the highest predictive value for treatment outcomes, with 86.67% sensitivity and 68.57% specificity.

CONCLUSIONS: hs-CRP and T lymphocyte subsets are closely associated with disease severity and treatment response in elderly patients with pulmonary infection, and their dynamic monitoring may aid in clinical prognosis evaluation.},
}

@article {pmid42263027,
year = {2026},
author = {Cuevas-Sierraa, A and Tomé-Carneirob, J and Marques da Silva, MM and Tavares da Silva, MI and de Cuevillas, B and Silvestre, MP and Martínez, JA},
title = {Inflammation and Chronic Disease: The Mediterranean Diet in Precision and Personalized Nutrition.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-19},
doi = {10.1159/000551530},
pmid = {42263027},
issn = {1421-9697},
abstract = {Low-grade chronic inflammation (LGCI) is a shared biological pathway for noncommunicable diseases (NCDs) and clinical manifestations, including atherosclerotic cardiovascular disease, type 2 diabetes, obesity-related complications, some cancers, and neurodegenerative conditions. Diet is a powerful modulator of inflammatory status. This summary article synthesizes mechanistic and clinical evidence linking LGCI to NCDs, with emphasis on the role of the Mediterranean dietary pattern (MedDiet) and outlines pragmatic prescription guidelines within precision and personalized nutrition bases. Meta-analytic evidence indicates that MedDiet interventions reduce interleukin(IL)-6 and IL-1β, with a trend toward lower C-reactive protein. The Mediterranean diet promotes beneficial shifts in gut microbiota (gut microbiome) composition, increasing short-chain fatty acid production and supporting epithelial barrier integrity, which contributes to its anti-inflammatory effects. Taken together, these data endorse the Mediterranean Diet as a primary cardiometabolic protective approach, emphasizing the importance of integrating straightforward, equity-focused strategies to translate biological potential into measurable benefits at the population level.},
}

@article {pmid42263077,
year = {2026},
author = {Spochacz-Santoro, M and Szeliga, A and Durda-Masny, M and Morańska, K and Englert-Golon, M and Sadowski, W and Bocheńska, M and Doijad, S and Dutilh, BE and Brouns, R and Grabowska, M and Sajdak, S and Męczekalski, B and Szwed, A},
title = {Higher BMI is associated with vaginal microbiome alterations in women with PCOS.},
journal = {Reproduction & fertility},
volume = {},
number = {},
pages = {},
doi = {10.1530/RAF-26-0051},
pmid = {42263077},
issn = {2633-8386},
abstract = {ABSTRACT: Polycystic ovary syndrome (PCOS) is commonly associated with obesity and metabolic disturbances. Although gut and vaginal microbiome changes have been linked to PCOS, the independent role of body mass index in these alterations remains unclear. This study aimed to compare gut and vaginal microbiomes in women with PCOS and healthy controls, emphasizing the impact of body mass index. Seventy-five women were enrolled, including 55 with PCOS and 20 healthy controls. Participants were stratified into normal-weight (<25) and overweight (≥25) groups. Vaginal and anorectal swabs were analyzed using full-length 16S rRNA Nanopore sequencing. Microbial diversity and composition were assessed with alpha diversity indices, principal component analysis, Analysis of Composition of Microbes, PERMANOVA and Vaginal Community State Types classification. Without body mass index stratification, women with PCOS showed differences in several vaginal taxa compared with healthy controls. Within the PCOS cohort, overweight women exhibited higher vaginal alpha diversity, reduced Lactobacillus dominance, and enrichment of anaerobic taxa compared with normal-weight women with PCOS. Differences in vaginal microbial composition were also observed between healthy and PCOS women with normal body mass index. In contrast, gut microbiome alterations were limited and less consistent across analytical approaches. Vaginal community State Types analysis revealed predominance of Class IV communities in both healthy women and women with PCOS. These findings suggest that higher body mass index is associated with vaginal microbiome alterations in women with PCOS, although PCOS-related factors independent of body weight may also contribute to the observed microbial differences.

LAY SUMMARY: Polycystic ovary syndrome is a common condition that affects hormones, fertility, and metabolism in women. Many women with this condition are also overweight, but it is not fully understood how body weight influences the bacteria living in the body. In this study, we compared bacteria present in vaginal and anorectal samples from women with and without polycystic ovary syndrome, while also considering body weight. We found that women with higher body weight had more noticeable changes in vaginal bacterial composition, including lower amounts of protective Lactobacillus bacteria and higher diversity of anaerobic bacteria. At the same time, some bacterial differences were also observed in women with polycystic ovary syndrome who had normal body weight. Changes in gut bacteria were smaller and less consistent. These findings suggest that both body weight and polycystic ovary syndrome may influence vaginal bacterial composition and should be considered in future studies of women's reproductive health.},
}

@article {pmid42263170,
year = {2026},
author = {Sigvardsson, I and Ludvigsson, J and Lerchova, T and Imberg, H and Størdal, K and Mårild, K},
title = {Timing of complementary food introduction is not associated with inflammatory bowel disease risk: A prospective birth cohort study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag093},
pmid = {42263170},
issn = {1536-4844},
support = {S20-0007//Birgitta och Göran Karlssons Stiftelse: Swedish Society for Medical Research/ ; 2020-01980//Swedish Research Council/ ; ALFGBG-915661//Swedish Research Council/ ; //Swedish Child Diabetes Foundation/ ; FAS2004-1775//Swedish Council for Working Life and Social Research/ ; FAS2004-1775//Swedish Council for Working Life and Social Research/ ; K2005-72X-11242-11A//Swedish Research Council/ ; K2008-69X-20826-01-4//Swedish Research Council/ ; K2008-69X-20826-01-4//Swedish Research Council/ ; //Medical Research Council of Southeast Sweden (FORSS)/ ; K 98-99D-12813-01A//JDRF Wallenberg Foundation/ ; //Region Östergötland and Linköping university/ ; //Joanna Cocozza Foundation/ ; //Ministry of Health and Care Services/ ; //Norwegian Institute of Public Health/ ; },
abstract = {BACKGROUND: Complementary feeding (ie, food introduction besides formula or breast milk) imprints on the developing gut microbiome and immune system, which may have durable influences on disease risk. This study aimed to prospectively assess the association between the timing of complementary feeding and subsequent inflammatory bowel disease (IBD) risk.

METHODS: We followed 94 238 participants from the All Babies in Southeast Sweden (ABIS) (n = 11 947) and the Norwegian Mother, Father and Child (MoBa) (n = 82 291) cohorts from birth (1997-2009) through 2023 (mean age 16.5 [MoBa] to 25.2 [ABIS] years). National patient registers identified IBD diagnoses. The timing of complementary food introduction (<4, 4-5, or ≥6 months) was assessed using early-life food diaries and questionnaires. Latent class analyses identified 4 patterns across introductions of major food groups (eg, cereals and dairy). Cox regression estimated hazard ratios (aHRs) for IBD adjusted for socio-demographics and parental IBD. Sensitivity analysis additionally adjusted for breastfeeding duration, formula feeding, and perinatal factors.

RESULTS: Over 1 562 350 person-years of follow-up, 400 participants developed IBD (ABIS, n = 124; MoBa, n = 276). Overall timing of complementary food introduction was not associated with IBD (<4 months: aHR, 1.04 [95% CI, 0.67-1.60]; 4-5 months: aHR, 0.83 [95% CI, 0.63-1.10] vs ≥6 months). Also, aHRs for IBD by latent class analyses-defined introduction patterns approached 1. Results were consistent across cohorts, sensitivity analyses, and Crohn's disease and ulcerative colitis subtypes.

CONCLUSIONS: The findings from this binational birth cohort study indicate that neither the timing nor the pattern of complementary food introduction is a major risk factor for later development of IBD.},
}

@article {pmid42263421,
year = {2026},
author = {Liu, Z and Zhao, X and Guo, Y and Qin, C},
title = {Ontogenetic and spatial variation in the feeding habits of Tripneustes gratilla.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108170},
doi = {10.1016/j.marenvres.2026.108170},
pmid = {42263421},
issn = {1879-0291},
abstract = {As a keystone species in coral reef ecosystems, the collector sea urchin Tripneustes gratilla maintains its ecological balance by regulating algal populations; however, a systematic understanding of its role as a primary consumer in tropical marine environments remains limited. In this study, we investigated T. gratilla populations in coastal waters near Wuzhizhou Island, Sanya city, Hainan Province, China. Using 18S rDNA and 16S rDNA high-throughput sequencing, we analyzed differences in the T. gratilla diet in autumn across different habitats and body size classes. The analysis revealed that Tripneustes gratilla has a diverse diet spanning multiple phyla, including Arthropoda, Rhodophyta, Apicomplexa, and Cyanobacteriota. Distinct spatial dietary patterns were observed across different benthic habitats. In offshore rocky substrates, the gut contents primarily consisted of Rhodophyta (red algae) and Arthropoda (crustaceans), collectively accounting for more than 40% of the ingested material. Conversely, nearshore sandy-gravel substrates showed remarkable dietary specialization, with Arthropoda and Rhodophyta constituting more than 70% of the total dietary composition. Body size influenced the T. gratilla diet: large individuals (500-600 g) consumed specialized diets dominated by Eukaryota and Rhodophyta (>80%), whereas medium and small individuals presented greater dietary diversity. The gut microbiota demonstrated regional universality, with Proteobacteria and Bacteroidetes constituting the core microbiome. Environmental factors (e.g., pH) significantly affect T. gratilla feeding behavior. In this study, we identified habitat heterogeneity and ontogenetic shifts as critical drivers of T. gratilla trophic ecology, providing novel insights into its functional role in ecosystem dynamics.},
}

@article {pmid42263473,
year = {2026},
author = {Wu, C and Chen, X and Zhang, Y and Li, X and Yang, D and Dou, E and Zhang, F},
title = {Vertically transmitted seed core endophytes enhance the drought tolerance of Ambrosia artemisiifolia.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128575},
doi = {10.1016/j.micres.2026.128575},
pmid = {42263473},
issn = {1618-0623},
abstract = {Seed endophytes play a pivotal role in shaping plant microbiota, with certain species being vertically transmitted throughout the plant's life history. Nevertheless, their transmission patterns and contributions to drought adaptation remain poorly understood. In this study, through comparative analysis of microbial communities in seeds and in vitro plantlets from five geographic populations, Pseudomonas and Bacillus were identified as vertically transmitted core endophytes. Analysis of endophytic communities in leaves and roots of plants grown in a common garden further revealed that these genera not only dominated the microbiota but also served as potential keystone taxa. Moreover, pot experiments demonstrated that these genera remained dominant under drought. Representative culturable isolates associated with core vertically transmitted OTUs, including Pseudomonas benzopyrenica and Bacillus cereus, carried multiple antioxidant-related genes based on whole-genome sequencing, and qRT-PCR analysis further showed that most of these genes were upregulated under drought stress. The pot experiment revealed that both strains enhance plant drought tolerance, with altered NCED expression associated with modulated ABA levels, and changes in GST, SOD2, and CAT expression correlated with reduced accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) in inoculated plants. These findings advance our understanding of the role of vertically transmitted core endophytes in the adaptation of invasive plants and offer new perspectives for microbiome-based management strategies.},
}

@article {pmid42263474,
year = {2026},
author = {Xie, T and Hao, Y and Qin, L},
title = {The skin microbiome as a key regulator of psoriasis: From dysbiotic drivers to host-directed therapeutics.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128577},
doi = {10.1016/j.micres.2026.128577},
pmid = {42263474},
issn = {1618-0623},
abstract = {The skin harbors diverse microbial communities. Compared with gut microbiome dysbiosis, perturbations in the skin microbiome may be more directly implicated in the onset and progression of psoriasis (PSO). More than twenty studies reveal microbial dysbiosis within psoriatic lesions, which is manifested by elevated abundances of pro-inflammatory taxa such as Corynebacterium and Staphylococcus aureus, declined levels of commensal microbes including Cutibacterium, increased total bacterial load and decreased microbial community diversity. Such cutaneous microbial dysbiosis accelerates disease progression via multiple biological pathways, involving impairment of the skin barrier, dysregulation of the innate and adaptive immunity, as well as multifaceted biological effects mediated by microbial metabolites. Microbiome-based diagnostic strategies have emerged as novel tools for evaluating disease prognosis, and targeted modulation of the skin microbiome holds promising prospects for clinical translation. In-depth exploration of skin microbial signatures in PSO enables the skin microbiome to serve as clinically valuable biomarkers for predicting subtype transformation and disease progression and fluctuation. Future research priorities lie in the integration of multi-omics strategies to dissect the potential causal mechanisms underlying host-microbe crosstalk, establish optimized bioengineering techniques and further promote the advancement of individualized therapeutic regimens. Collectively, the skin microbiome not only sheds new light on the pathogenic mechanisms of PSO, but also identifies promising candidate targets for auxiliary diagnosis and precise microbiome-based therapeutic interventions.},
}

@article {pmid42263665,
year = {2026},
author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, AM and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, D and Bleakley, M and Holmberg, LA and Peled, JU and Schenk, J and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA},
title = {Plant-based whole-food diets are feasible during auto-HCT and are associated with dose-dependent microbiome modulation.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2026020270},
pmid = {42263665},
issn = {2473-9537},
abstract = {Plant-based whole foods may represent a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing auto-HCT for multiple myeloma, a population in whom intestinal dysbiosis has been linked with inferior survival. We conducted a single-arm clinical trial at our center, in which participants undergoing auto-HCT (n = 22) received fresh, pre-prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting the consumption of nutrient-dense, high-fiber foods. The primary endpoints were feasibility and tolerability, defined by successful enrollment, and patient-reported intake of study meals. Dietary intake was quantified using prospective food diaries and 24‑hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming delivered meals to some degree, with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. The trial is registered at ClinicalTrials.gov (NCT06559709).},
}

@article {pmid42263820,
year = {2026},
author = {Rindchen, A and Schneider-Daum, N and Lehr, CM},
title = {Microphysiological ("organ-on-a-chip") models of pulmonary infections for developing novel anti-infectives.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115917},
doi = {10.1016/j.addr.2026.115917},
pmid = {42263820},
issn = {1872-8294},
abstract = {Infectious diseases are among the leading death causes globally, with the lung being particularly vulnerable due to its continuous exposure to inhaled pathogens. Yet, anti-infective research and drug development are hampered by the lack of models that accurately recapitulate the lung's complex immunological and pathophysiological responses to infections. Microphysiological ("Organ-on-a-chip", OoC) models allow elegant incorporation of multiple cell types, biological barriers, mechanical stress and perfusion, not only in healthy, but also in diseased state. Besides enabling the evaluation of drug efficacy and safety, these models provide a platform to investigate host-pathogen interactions and their modulation by pharmaceutical interventions. This review examines microphysiological systems (MPS) designed to mimic pulmonary infections and highlights how these models capture key hallmarks of such diseases, including disruption of barrier integrity, changes of mucus, mucociliary clearance and surfactant, as well as the recruitment and stimulation of immune cells. Specific design considerations will be explained regarding the challenges of viral and bacterial pulmonary infections. Emphasis is further placed on how MPS may be implemented for repurposing established drugs, as well as for developing new small molecules, biologicals and delivery systems. Remaining challenges, such as incorporation of the microbiome, vaccine development and requirements for standardization and validation, are critically examined. These insights underscore the potential of MPS to bridge preclinical gaps in infection research, accelerate clinical translation, and guide the development of novel anti-infective drugs and delivery systems.},
}

@article {pmid42263891,
year = {2026},
author = {Bibi, R and Swayamsiddhi, and Saishree, S and Sobti, M and Reddy, S and Sarkar, K},
title = {Involvement of immunomodulators in the development of cancer vaccines.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {},
number = {},
pages = {168321},
doi = {10.1016/j.bbadis.2026.168321},
pmid = {42263891},
issn = {1879-260X},
abstract = {Previous research shows that cancer vaccines hold great potential as immunotherapeutic agents which activate the body's tumor-cell elimination powers through immune recognition. Cancer vaccines encounter restricted success because of three limiting factors that include immunosuppressive tumor microenvironment (TME) dynamics and deficient antigen presentation and tumor immune evasion methods. Immunomodulators function as vital instruments which help patients overcome vaccination resistance barriers in addition to strengthening vaccine-generated immunity. The review investigates how different immunomodulatory agents such as cytokines and checkpoint inhibitors as well as TLR agonists and STING pathway activators, oncolytic viruses enhance the effectiveness of cancer vaccines. The immune response derives additional advantages from these agents. They enhance antigen presentation, activate T cells, counteract immune suppression, and improve the structural integrity of the tumor microenvironment (TME). The review examines modern treatment developments that include individualized neoantigen vaccines and nanoparticle delivery vehicles alongside microbiome modification strategies as promising methods for customized effective cancer treatments. Although cancer vaccines face obstacles from toxicity and heterogeneous tumors and limitations in manufacturing there is potential to combine them with immunomodulators for creating sustainable and specific cancer treatments. Further research along with innovative work needs to occur to develop clinically effective patient-specific treatments from existing therapeutic breakthroughs.},
}

@article {pmid42263966,
year = {2026},
author = {Nazir, MJ and Hussain, MM and Ali, S and Otwil, P and Iddi, AT and Li, T and Wu, Z and Wei, J and Yu, L},
title = {Nucleic acid dynamics at the plant-rhizosphere interface: Regulatory mechanisms, and implications for future food security: A review.},
journal = {International journal of biological macromolecules},
volume = {370},
number = {},
pages = {152977},
doi = {10.1016/j.ijbiomac.2026.152977},
pmid = {42263966},
issn = {1879-0003},
abstract = {Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are no longer regarded solely as carriers of hereditary information or intermediates of gene expression. They are now increasingly recognized as structurally distinct biological macromolecules that regulate plant development, stress adaptation, intercellular communication, and rhizosphere interactions. Recent advances in genome editing, pan-genomics, transcriptomics, epitranscriptomics, and long non-coding RNA (lncRNA) biology have expanded the translational potential of nucleic-acid research for climate-resilient agriculture. Concurrently, the rhizosphere has emerged as a molecular interface in which plant-derived extracellular DNA (exDNA) and extracellular RNA (exRNA) influence microbiome assembly, nutrient signaling, and cross-kingdom communication. Although, these themes are often treated separately in the existing literature, with few reviews integrate intracellular and extracellular nucleic acid functions within a unified plant-soil, particularly rhizosphere, framework. The present review synthesizes current knowledge by linking the macromolecular properties of nucleic acids with their intracellular regulatory functions, extracellular release and fate in soil, roles in rhizosphere communication, and translational relevance for crop improvement and future food security. Particular emphasis is given to biotic and abiotic stresses, including drought, salinity, nutrient limitation, pathogen pressure, and overall climate instability. We propose that plant and rhizosphere nucleic acids constitute a single adaptive continuum connecting intracellular regulation with extracellular ecological function, thereby providing a broader conceptual basis for climate-resilient and resource-efficient agriculture.},
}

@article {pmid42264044,
year = {2026},
author = {Han, F and Guo, Y and Lei, J and Zhang, L and Zhao, C and Li, Y and Zhou, W},
title = {Micro-sized aerobic heterotrophic ammonium assimilation granules and microbial community assembly under varying hydraulic shear force.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135139},
doi = {10.1016/j.biortech.2026.135139},
pmid = {42264044},
issn = {1873-2976},
abstract = {Heterotrophic ammonium assimilation (HAA) represents an emerging biological nitrogen removal strategy for saline wastewater treatment. Developing halophilic HAA microbiome into granular form enables simultaneously improve the sludge settleability and robustness. However, the regulatory mechanism of hydraulic shear force (HSF) on granule characteristics and microbial community ecology of the HAA microbiome remain unclear. This study investigated the effects of HSF, controlled by reactor height-to-diameter ratios (H/D = 1, 2.5, 5, and 10), on the nitrogen removal performance, granule morphology, and microbial community assembly. The constructed aerobic HAA granules were uniformly micro-sized (230-280 μm) yet exhibited high density (1030-1115 kg/m[3]) and excellent settleability. Notably, under moderate HSF condition (H/D = 5), the abundance of key HAA-related genes (glnA, gltB, and gdhA) and the enzyme activities of GS, GOGAT, and GDH were maximized, corresponding to highest ammonium removal efficiency. Across all four systems, the constructed aerobic HAA granules strictly performed assimilation function, with no detectable ammonia-oxidizing genes (AMO), nitrifying bacteria, or nitrogen loss. Increasing HSF imposed strong selective pressure on the aerobic HAA granules, resulting in a linear increase in deterministic community assembly while reducing microbial diversity. In system with an H/D of 5, the dominant genera Ponticoccus and Marinobacillus acted as network hubs, maintaining microbial community stability. Overall, this study successfully established micro-sized aerobic HAA granules, and revealed the regulatory effects of HSF on their granule characteristics, microbial community assembly, and nitrogen metabolism. This study provides valuable insights for the design and optimization of stable HAA-based systems for saline wastewater treatment.},
}

@article {pmid42264080,
year = {2026},
author = {Abdullah, M and Jayadevan, K and Therayil, A and Kumaraguruparan, N and Kavyasree, PKV and Dilna, P and Faiza, A},
title = {Pharmaco-microdynamics (PMD): Redefining Dose, Exposure, and Control for Living Drug Carriers.},
journal = {Annales pharmaceutiques francaises},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pharma.2026.06.002},
pmid = {42264080},
issn = {2772-803X},
abstract = {Living drug delivery systems including probiotics, engineered microbial therapeutics, and live biotherapeutic products represent a rapidly emerging therapeutic modality whose behavior fundamentally diverges from the assumptions underlying classical pharmacokinetics and pharmacodynamics (PK/PD). Unlike chemically defined, non-replicating drugs, living therapeutics persist, replicate, adapt, and generate bioactive molecules in situ, such that therapeutic exposure is not externally imposed but biologically generated over time. As a result, administered dose functions only as an initiating condition, while realized exposure emerges from population dynamics, ecological establishment, spatial localization, and regulated functional output. These properties render concentration-based PK/PD frameworks insufficient for predicting efficacy, safety, and controllability of living drug carriers. We introduce pharmaco-microdynamics (PMD) as a quantitative delivery-science framework designed to define, measure, and control exposure for living therapeutics. PMD is operationalized through a set of formal metrics including the functional exposure integral (F-AUC), colonization efficiency (CE), residence-time-weighted activity (RTWA), effective functional concentration (EFC50), and the genetic stability index (GSI)that serve as living-system analogues of AUC, bioavailability, mean residence time, EC50, and product-identity specifications. PMD reconceptualizes exposure as a time-integrated biological process governed by four interdependent axes: population kinetics, functional output kinetics, spatial pharmacology, and evolutionary dynamics. By integrating principles from pharmacology, microbial ecology, synthetic biology, biomaterials science, and systems modeling, PMD provides an operational vocabulary for translating adaptive biological agents into predictable and engineerable delivery systems. We further delineate PMD from adjacent frameworks such as quantitative systems pharmacology (QSP) and ecological microbiome modeling, and critically discuss boundary conditions under which classical PK/PD remains applicable to non-replicating or transient microbial interventions. This review critically examines the limitations of classical PK/PD in modeling living drug carriers, formalizes the core principles of PMD, and illustrates them through three quantitative case studies: SYNB1618 for phenylketonuria, synchronized-lysis bacterial tumor therapies, and fecal microbiota transplantation for recurrent Clostridioides difficile infection. Regulatory and clinical implications are addressed, emphasizing the need to shift from dose- and concentration-centric evaluation toward functional biomarkers, persistence metrics, and model-informed assessment of biological activity. Collectively, pharmaco-microdynamics establishes a unifying conceptual and quantitative foundation for the rational development of living medicines.},
}

@article {pmid42264124,
year = {2026},
author = {Vandersanden, S and van Leeuwen, J and Vangronsveld, J and Thijs, S},
title = {Integrated physicochemical and microbial analyses reveal redox-driven microbial community structure in a polycyclic aromatic hydrocarbon-polluted subsurface.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128559},
doi = {10.1016/j.envpol.2026.128559},
pmid = {42264124},
issn = {1873-6424},
abstract = {Hydrocarbon-polluted sites are a global environmental concern. Although bioremediation is a cost-effective and sustainable remediation method, its efficiency is often impaired by various environmental and microbial factors. Further advancements in bioremediation require a deeper understanding of the relationship between the soil microbiome and the physicochemical parameters that limit biodegradation. Here, we investigated a 3-meter-deep polycyclic aromatic hydrocarbon (PAH)-polluted soil core from a historically polluted site in The Netherlands. Soil samples were taken from six depths at 50 cm intervals, followed by a physicochemical characterisation, including measurements of PAH, electron acceptors, pH and electrical conductivity. These analyses were complemented by a detailed microbial community analysis. Our findings suggest that microbial communities are primarily shaped by a combination of the availability of electron acceptors and pollution levels. Additionally, groundwater level fluctuations appear to play an important role in the transport and replenishment of electron acceptors. In-depth community analysis further revealed a diversity of metabolic strategies employed by the different communities to cope with the oversupply of electrons. Collectively, these results demonstrate that microbial communities in PAH-polluted soils vary according to habitat-specific redox environments. Therefore, microbial community analysis can serve as an additional diagnostic tool to infer the specific physicochemical constraints that limit efficient biodegradation. Our findings provide a detailed, integrated interpretation of physicochemical and microbial field data, offering insight into the heterogeneous nature of in situ biodegradation. They further highlight the value of comprehensive and integrated microbial community and physicochemical analyses in identifying biodegradation-limiting factors in the field.},
}

@article {pmid42264152,
year = {2026},
author = {Gibbons, JA and Nelson, RM and Dabrowski, CN and Narkhede, A and Szalacha, LA and Kneusel, ML and Maru, JS and Huszar, MR and Hoang, LK and Schiavo, V and Eddins, AC and Georgieff, MK and Neu, J and Donovan, SM and Groer, MW and Ho, TTB},
title = {Enteral Iron Dose Effect on Iron Storage, Intestinal Barrier, and Gut Microbiome in Preterm Infants: A Randomized Clinical Trial.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101389},
doi = {10.1016/j.ajcnut.2026.101389},
pmid = {42264152},
issn = {1938-3207},
abstract = {BACKGROUND: Preterm infants routinely receive enteral iron supplementation to support growth, replace phlebotomy losses, and prevent iron deficiency. However, concerns regarding potential harms, including those on the gut microbiome, have contributed to recommendations for lower dosing.

OBJECTIVE: To compare the effects of two enteral iron doses on gut health in very-low-birth-weight preterm infants. We hypothesized that higher iron dose would increase abundances of pathogenic bacteria, intestinal inflammation, and barrier dysfunction.

METHODS: This randomized, double-blind clinical trial assigned preterm infants born <1500 g to receive either the recommended dose, 2 mg/kg/day, or a higher dose of 6 mg/kg/day of total enteral iron. The primary outcome was the fecal microbiome after 2 weeks on iron, assessed by metagenomic sequencing. Secondary outcomes included biomarkers of intestinal inflammation and barrier function (fecal calprotectin, urinary claudin-3, and urinary intestinal fatty acid-binding protein). Iron status, adverse events, and auditory brainstem response latencies at 36 weeks postmenstrual age were also evaluated.

RESULTS: Among 151 randomized infants who received study iron (77 low-dose; 74 high-dose), bacterial diversity, individual taxa, virulence potential, bacterial overgrowth, and iron-related functional genes were not significantly different between the treatment groups. In subgroup analysis of singletons, treatment groups demonstrated significant differences in temporal shifts in overall bacterial community structure. Infants receiving 2 mg/kg/day had higher post-treatment urinary claudin-3 concentrations, indicating possible differences in intestinal permeability, and a higher prevalence of iron deficiency than those receiving 6 mg/kg/day. Other biomarkers, clinical outcomes, adverse events, and auditory latencies did not differ between groups.

CONCLUSIONS: Enteral iron supplementation at 6 mg/kg/day was associated with improved iron status and lower intestinal barrier dysfunction, without evidence of harms on gut microbiome compared with the recommended 2 mg/kg/day dose. These findings do not support concerns regarding gut microbiome disruption as a justification for lower iron dosing in preterm infants.

TRIAL REGISTRATION: Clinicaltrials.gov NCT04497012.},
}

@article {pmid42264215,
year = {2026},
author = {Hou, P and Che, Y and Han, J and Deming, C and Amirkhani, A and Kim, CS and Taylor, ME and Velez, D and Cho, E and Holmes, CJ and Suh, G and Castelo-Soccio, L and , and McDermott, DH and Murphy, PM and Segre, JA and Kong, HH},
title = {Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.05.024},
pmid = {42264215},
issn = {1523-1747},
abstract = {Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a rare inborn error of immunity (IEI) caused by hyperfunctional pathogenic variants in CXC chemokine receptor 4 (CXCR4), predisposing individuals to recurrent bacterial skin and airway infections and warts. The targeted CXCR4 antagonist plerixafor has shown efficacy in wart regression and potential reduction in bacterial infection frequency. Here, we investigated skin microbiomes of 11 patients with WHIM syndrome using shotgun metagenomics, compared to healthy controls. WHIM skin microbial communities displayed greater inter-individual variability, with highly diverse human papillomavirus profiles and expansion of airway-associated pathogens on the skin. Among patients receiving plerixafor therapy, we observed shifts in the viral composition and a downward trend in viral abundances. Together, these findings demonstrate the distinctive and permissive skin microbiome in WHIM syndrome and highlight the potential microbiome-modulating effects of targeted CXCR4 antagonism.},
}

@article {pmid42264216,
year = {2026},
author = {Guo, L and Li, J and An, J and Miao, J and Yi, Y and Zhu, K and Cai, Q and Wang, S and Su, Z and Ye, X and Wang, Y and Pan, M and Lu, Q and Cui, B and Zhang, F and Mao, J and Liu, X and Lu, Y and Ding, D},
title = {Neuroprotective role of Faecalibacterium prausnitzii-derived butyrate in diabetic gastrointestinal autonomic neuropathy.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2026.06.005},
pmid = {42264216},
issn = {1673-8527},
abstract = {Diabetic gastrointestinal autonomic neuropathy (DGAN) is a common yet poorly understood complication of diabetes that is characterized by gastrointestinal dysmotility and enteric neurodegeneration. Here, we investigate whether gut microbiota dysbiosis contributes to DGAN pathogenesis and explore the potential involvement of microbiota-derived metabolites in enteric nervous system (ENS) injury. Gut microbiota profiling reveals disease-associated compositional alterations in patients with DGAN, including depletion of Faecalibacterium-associated signals, with Faecalibacterium prausnitzii identified as a putative species-level annotation and negatively associated with gastrointestinal symptom severity. Fecal microbiota transplantation from patients with DGAN into db/db mice aggravates gut dysmotility and increases apoptosis of ChAT[+] and nNOS[+] myenteric neurons. Further experiments indicate that butyrate, the predominant metabolite produced by F. prausnitzii, attenuates neuronal apoptosis under high-glucose conditions. This biological process is accompanied by enhanced BCL2 expression, downregulation of cleaved caspase-3, and activation of the PI3K/Akt signaling cascade. Collectively, our findings support the presence of a gut microbiota-ENS axis in DGAN and identify butyrate as an important candidate neuroprotective metabolite associated with F. prausnitzii. These results provide a rationale for microbiota-targeted therapeutic strategies for diabetic enteric neuropathy.},
}

@article {pmid42264348,
year = {2026},
author = {Zaccaria, E and Honerlagen, H and Šebek, L and Wind, T and Kar, SK and van der Valk, E and van Gastelen, S},
title = {Effects of feeding grass silage- and corn silage-based diets in phenotypically low and high methane emitting Holstein-Friesian dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28444},
pmid = {42264348},
issn = {1525-3198},
abstract = {The objectives of this study were to determine (1) whether replacing grass silage with corn silage reduced methane (CH4) emissions equally effectively in dairy cows with a low or high CH4 emission level, (2) whether low or high CH4 emitting cows remained low and high CH4 emitters irrespectively of the diet fed, and (3) whether the diet and CH4 emission level affected lactation performance, feed intake, and rumen microbiome. Emissions of CH4 of 192 lactating dairy cows were measured with the GreenFeed system in a screening phase to select the 12 highest and the 12 lowest CH4 emitting cows (i.e., 15.9 ± 1.49 vs. 24.0 ± 1.43 g CH4/kg DMI). These 24 cows were subsequently enrolled in a crossover design trial with a grass silage-based diet (GS) and a corn silage-based diet (CS). The GS diet consisted of 58.0% grass silage, 19.3% corn silage, and 22.7% concentrate, and CS consisted of 19.3% grass silage, 58.0% corn silage, and 22.7% concentrate (DM basis). Treatment periods lasted 4 weeks and consisted of a 2-week adaptation period followed by a 2-week measurement period. No interaction between diet and CH4 emission level was observed. Hence, the reduction in CH4 emissions by CS compared with GS did not differ between the low (-23%) and high (-18%) CH4 emitting cows. The CH4 emission level of low-emitting cows was 27% lower than that of high-emitting cows, and was persistent irrespective of the type of diet fed. The community structure and diversity of the rumen microbiome responded to diet and CH4 emission level, but no interactions were observed except for 1 low-abundance bacterial genus accounting for less than 0.6% of total bacterial relative abundance. Replacing grass silage with corn silage resulted in increased milk yield and DMI, decreased milk fat content and CH4 emissions, and a shift from acetate to propionate. The latter aligned with the changes in rumen microbiota, shifting from a more fibrolytic, acetate-oriented community with GS toward a more amylolytic, propionate-oriented community with CS. Other than in CH4 emissions, the low and high CH4 emitting cows did not differ from each other in feed intake level, lactation performance, and body measures. Despite these similar production responses, low CH4 emitting cows had distinct ruminal bacterial and archaeal communities compared with high CH4 emitters across both diets. Low CH4 emitters were enriched in Succinivibrionaceae_UCG-001, which was positively associated with ruminal molar proportion of propionate. High CH4 emitters showed higher archaeal diversity and a greater relative abundance of Methanomethylophilaceae. The molar proportions of butyrate and carbon dioxide (CO2) yield were higher in high-emitting cows compared with low-emitting cows. In conclusion, this study shows that replacing grass silage with corn silage effectively reduces CH4 emissions regardless of the cow's CH4 emission level, and that CH4 emission levels in Holstein Friesian cows are persistent regardless of diet fed.},
}

@article {pmid42264710,
year = {2026},
author = {Li, Y and Li, M and Meng, Q and Zhang, J and Yang, Z and Zhang, Q and Yan, M},
title = {Coinoculation with Bacillus mojavensis BA23 and Rhizobium indicum RH64 protects red kidney bean from root rot by activating plant systemic defense-related responses and modulating the rhizosphere microbial community.},
journal = {Pesticide biochemistry and physiology},
volume = {221},
number = {},
pages = {107111},
doi = {10.1016/j.pestbp.2026.107111},
pmid = {42264710},
issn = {1095-9939},
abstract = {Root rot is a major threat to red kidney beans (Phaseolus vulgaris), caused mainly by Fusarium oxysporum. This study tested single/combined inoculation of Bacillus mojavensis BA23 and Rhizobium indicum RH64 on disease control, plant growth, and systemic defense in greenhouse pots. Both single strains reduced disease index and improved growth, but coinoculation was better: vs single BA23/RH64, it increased plant biomass by 11.05%/23.81% and reduced disease index by 18.87%/40.27%. BA23 inhibited F. oxysporum (80.54% in vitro) and activated plant defense (e.g., boosted antioxidant enzyme activity), while RH64 had nitrogen-fixing activity (253.22 U·L[-1]) and recruited beneficial rhizobacteria. Coinoculation enriched taxa like Sphingomonadaceae and Vicinamibacteraceae (key for disease suppression and growth promotion) and enhanced rhizosphere microbial network stability (e.g., higher modularity and average degree). Partial least squares path modeling (PLS-PM) showed that bacterial community structure was significantly correlated with reduced disease index and increased plant biomass. In conclusion, coinoculating BA23 and RH64 effectively controls red kidney bean root rot and promotes plant growth by inducing systemic defense-related responses and beneficially reshaping the rhizosphere microbiome.},
}

@article {pmid42265111,
year = {2026},
author = {Campese, L and Longo, A and Pelletier, E and Delmont, TO and Ambrosino, L and Miralto, M and Mele, BH and Alberti, A and Labadie, K and Oliveira, PH and Perdereau, A and Wincker, P and , and Iudicone, D},
title = {Eukaryotic MAGs from the NEREA observatory: expanding the coastal microbiome dataset.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07571-y},
pmid = {42265111},
issn = {2052-4463},
support = {101082021//MARCO-BOLO/ ; ID: 862923//AtlantECO/ ; 101081642//OBAMA-NEXT/ ; },
abstract = {Marine ecosystems are hotspots of biodiversity and biogeochemical activity, yet much of their complexity remains largely inaccessible without genome-resolved data. Here we present a curated dataset of 52 eukaryotic metagenome-assembled genomes (MAGs) reconstructed from samples collected between April 2019 and January 2020 at three NEREA (Naples Ecological REsearch for Augmented observatories) sites in the Gulf of Naples. NEREA is a coastal observatory integrating physical, chemical and biological measurements with state-of-the-art metagenomics. The eukaryotic MAGs have an average completeness of ~55% and genome size of ~20 Mb. Predicted proteins were functionally annotated against UniProtKB, InterPro, and eggNOG databases, and each MAG was taxonomically classified using a curated RNA polymerase A reference dataset. The recovered MAGs encompass diverse eukaryotic lineages, primarily Ochrophyta, Chlorophyta and Haptophyta. Building on the Tara Oceans eukaryotic MAG legacy, this release represents the first reconstruction of eukaryotic MAGs from a coastal time series, enabling temporal and functional analyses of eukaryotic plankton.},
}

@article {pmid42265593,
year = {2026},
author = {Liu, T and Wang, N and Hao, J and Hong, J and Han, Y and Yang, L and Zhang, H and Zhou, J and Tan, Y and Li, L and Yang, R},
title = {Integrated culturomics and 16S rDNA sequencing reveal a functional microbiome signature in endometrial cancer.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05242-x},
pmid = {42265593},
issn = {1471-2180},
support = {2021YFC2301000//National Key Research and Development Program of China/ ; 32394054//National Natural Science Foundation of China/ ; },
abstract = {OBJECTIVE: Endometrial cancer (EC) is a common gynecologic malignancy globally, but the role of the intratumoral microbiome remains poorly defined. While microbial dysbiosis is increasingly linked to cancer, the composition, function, and clinical relevance of the microbiota in EC are underexplored. This study aims to systematically profile the microbiome in EC patients by integrating culturomics and 16S rDNA sequencing, and to evaluate the functional properties of key bacterial strains in relation to tumor progression.

METHODS: We collected cancerous tissues (CATs), non-cancerous adjacent tissues (NATs), and vaginal swabs from 32 EC patients. Culturomics was performed on 57 samples from 19 patients to isolate and identify bacteria, while 16S rDNA sequencing assessed microbial diversity and composition. Functional assays, including flow cytometry for invasion efficiency and ELISA, were used to evaluate pro-inflammatory capacity.

RESULTS: Culturomics identified 79 bacterial species, with Staphylococcus, Streptococcus, and Cutibacterium emerging as core genera shared across the vagina, NATs, and CATs. Functional analysis revealed that strains such as Staphylococcus epidermidis and Streptococcus anginosus exhibited high invasion efficiency (up to 84.8%) and significantly upregulated pro-inflammatory responses. 16S rDNA sequencing showed that Lactobacillus dominated the vaginal microbiota, whereas endometrial tissues were enriched with opportunistic pathogens (e.g., Stenotrophomonas). Critically, specific genera were associated with aggressive clinical features: Slackia with poorly differentiated (G3) tumors and Porphyromonas with deep myometrial invasion (≥ 50%).

CONCLUSION: This study uncovers a distinct, translocally disseminated core microbiota in EC, with key strains demonstrating invasive and pro-inflammatory capacities that may play a role in tumor progression. These findings provide a foundation for microbial biomarkers and targeted interventions, highlighting the transformative potential of microbiome research in gynecologic oncology.},
}

@article {pmid42265613,
year = {2026},
author = {Hu, Y and Pan, L and Liu, B and Su, C and Zhang, L and Li, W and Fu, T and Gao, T and Lian, H and Wang, L and Zhang, Y and Liu, K},
title = {Eucommia ulmoides leaves improving growth by regulating the rumen microbiome in sheep.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05089-2},
pmid = {42265613},
issn = {1471-2180},
support = {252102110017//Henan Province Science and Technology Research Project (2025)/ ; 2024YFD1300204//Key technologies for efficient utilization of cattle and sheep feed and forage and carbon emission reduction/ ; },
abstract = {BACKGROUND: Ruminants have the ability to convert agricultural byproducts into valuable resources. However, the influence of functional roughage with medicinal value on production performance and rumen function in ruminants remains unclear. This study aimed to examine the role of Eucommia ulmoides leaves (EUL) in the growth performance and rumen microbiome of sheep.

RESULTS: Twenty-one healthy female sheep were randomly divided into three groups, in which the EUL feeding amounts were 0% (CON), 5% (Diet 1), and 10% (Diet 2) on a dry matter basis. The results revealed that body weight gain, dry matter intake, and feed conversion efficiency were significantly greater in the Diet 1 group than in the CON and Diet 2 group. The metatranscriptome annotation results indicated that feeding EUL to sheep altered the rumen microbial community. Compared with those in the other two groups, the abundances of butyrate-producing bacteria, such as Coprobacillus, significantly increased in the Diet 1 group. Functional enrichment analysis of the metatranscriptome indicated higher metabolic activity in the carbohydrate and amino acid pathways in the Diet 1 group than in the control group, which might be due to improved nutrient utilization in the Diet 1 group.

CONCLUSIONS: In conclusion, feeding 5% EUL to sheep enhanced production performance, feed conversion efficiency, and microbial metabolism. These findings suggest that EUL plays a critical role in sustainable livestock farming as a promising functional roughage.},
}

@article {pmid42265709,
year = {2026},
author = {Li, Y and Zhang, Y and Liu, W and Tao, T},
title = {Bridging gut microbiota and polycystic ovary syndrome: the mediating role of metabolites and immune pathways via Mendelian randomization and mediation analysis.},
journal = {Journal of ovarian research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13048-026-02162-2},
pmid = {42265709},
issn = {1757-2215},
support = {82370797//National Natural Science Foundation of China/ ; J202103E006//Bethune Charitable Foundation/ ; RJTJ23-ZD-005//National Nature Promotion Project, Renji Hospital, Shanghai Jiao Tong University School of Medicine/ ; },
abstract = {BACKGROUND: Polycystic Ovary Syndrome (PCOS) is a common reproductive metabolic disorder impacting women of reproductive age, with its etiology influenced numerous factors. Recent research indicates that the gut microbiota, along with its metabolites and associated immune-inflammatory responses, may contribute to the pathogenesis of PCOS. However, there is finite understanding of the potential intermediate impacts of circulating metabolites, immune cells, and inflammatory proteins on the linkage between intestinal flora and PCOS. This study seeks to explore the interrelationships among the gut microbiome, immune-inflammatory responses, and the metabolome within the context of PCOS.

METHODS: Aggregated statistics pertaining to individual traits were derived from genome-wide association studies accessible to general public. To elucidate mediation mechanisms, a two-step MR mediation framework was applied. In the first step, univariable MR was used to identify causal effects of gut microbial taxa on circulating metabolites, immune cells, and inflammatory proteins. In the second step, multivariable MR and mediation analyses were employed to estimate indirect effects of these mediators on PCOS. All analyses were performed using the inverse variance weighted (IVW) method as the primary model, complemented by MR-Egger, weighted median, and MR-PRESSO sensitivity tests.

RESULTS: MR analysis identified the causal impacts of 11 intestinal flora taxa on PCOS, among which 4 taxas (Class Betaproteobacteria, Genus Eubacterium eligens group, Genus Ruminiclostridium6 and Order Burkholderiales) may exert positive effects on PCOS, 7 taxas (Family Bifidobacteriaceae, Genus Bilophila, Genus Holdemania, Genus Hungatella, Genus Ruminococcaceae UCG004, Genus Veillonella, and Order Bifidobacteriales) may act as protective factors on PCOS. Meanwhile, 124 plasma metabolites, 45 circulating immune cell types, and 5 inflammatory proteins exhibited causal effects on PCOS. Notably, the circulating metabolites predominantly involved in PCOS were correlative of androgenic steroids, leucine, isoleucine and valine metabolism, glutathione metabolism, and secondary bile acid metabolism, and other metabolic pathways. Mediation analysis elucidated 34 metabolites-mediated path-ways linking gut microbiota and PCOS, with 13 immune cells/inflammatory proteins-mediated pathways interconnecting gut flora and PCOS.

CONCLUSIONS: According to MR analysis, circulating metabolites, immune cells, and inflammatory proteins play a role in the correlation between intestinal flora and PCOS. The findings shed new light on the underlying pathophysiological mechanisms of PCOS.},
}

@article {pmid42265811,
year = {2026},
author = {Xiang, FM and Tang, XT and Brandón, MG and Henawy, AR and Jiang, S and Xu, X and Chen, X and Zhang, Z},
title = {Dismissing-then-recruiting: a unique mechanism for symbiont recruitment and lignocellulose degradation in gut of black soldier fly larvae.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02441-6},
pmid = {42265811},
issn = {2049-2618},
abstract = {BACKGROUND: Black soldier fly larvae (Hermetia illucens L., BSFL) efficiently degrade lignocellulosic waste despite lacking endogenous lignocellulolytic enzymes, indicating a critical dependence on gut-associated microbiota. However, how BSFL are associated with the enrichment and spatial organization of lignocellulose-degrading symbionts within the gut remains poorly understood.

RESULTS: We show that BSFL establish a spatially structured microbiome through gut compartment-specific immune regulation. Axenic larvae showed negligible lignocellulose degradation, whereas microbiota-associated larvae achieved ~ 33.3%, confirming microbial dependence. Antimicrobial peptides, including cecropin and defensin, were highly expressed in the anterior midgut, forming a selective barrier. In contrast, the posterior midgut showed reduced immune activity via peptidoglycan recognition proteins (PGRP-LB, PGRP-SC). Concurrently, host glycosylation-related genes (C1galt1, GlcAT-P, FUT8/11) were significantly upregulated in the posterior midgut (17-19 TPM), representing a 4-fivefold increase relative to the anterior region (p < 0.01). This region was correspondingly enriched in carbohydrate-active symbionts producing glycoside hydrolases, including galactosidases, fucosidases, and mannosidases, suggesting that upregulated glycan biosynthesis may provide sustained nutrient availability for microbial taxa with corresponding carbohydrate-utilizing capacities. Such compartmentalized immune-metabolic coordination is consistent with a potentially conserved strategy for modulating immune tolerance and fostering symbiont recruitment.

CONCLUSIONS: Collectively, our findings define a compartmentalized "Dismissing-then-Recruiting" strategy for microbiome assembly in BSFL, which is associated with the structuring of functional symbiont communities for efficient lignocellulose bioconversion, thereby elucidating novel principles for sustainable waste management. Video Abstract.},
}

@article {pmid42265904,
year = {2026},
author = {Rashid, SS and Dahchi, M and Jafarian, F},
title = {Combined Antibiotic, Steroid, and Moisturizer Therapy in Eczema Treatment: Balancing Short-Term Relief with Long-Term Risks.},
journal = {Journal of cutaneous medicine and surgery},
volume = {},
number = {},
pages = {12034754261455695},
doi = {10.1177/12034754261455695},
pmid = {42265904},
issn = {1615-7109},
abstract = {Combined antibiotic-corticosteroid-moisturizer therapy, often referred to as the Aron Regimen has gained popularity for managing atopic dermatitis (AD). While this therapy has been shown in some studies to provide short-term improvement in symptoms, evidence for its long-term utility is limited, and its widespread use raises concerns about promoting antibiotic resistance and disrupting the skin microbiome. Studies suggest that topical antibiotics provide limited benefit for most eczema cases, with only modest or context-specific benefits reported in more severe or treatment-resistant situations. Importantly, current clinical guidelines do not recommend the routine use of topical antimicrobials in the absence of clear infection. This review contextualizes the Aron Regimen within current evidence and emphasizes a more cautious, limited role for antibiotic-containing therapies in AD.},
}

@article {pmid42265922,
year = {2026},
author = {Uriot, O and Deschamps, C and Etienne-Mesmin, L and Brun, M and Pouget, M and Chalancon, S and Durif, C and Chaudemanche, C and Alric, M and Boirie, Y and Blanquet-Diot, S},
title = {Colonic nutritional and physicochemical parameters drive gut microbiota dysbiosis in obesity: what we learned from the Ob-M-ARCOL model development.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2685908},
doi = {10.1080/19490976.2026.2685908},
pmid = {42265922},
issn = {1949-0984},
abstract = {BACKGROUND: Obesity has reached epidemic proportions worldwide with a substantial burden on both individual health and society. Alterations in gut microbiota are increasingly recognized as a key contributor in disease pathogenesis. However, mechanistic understanding at the ecosystem level remains limited. In line with EU and US regulations, in vitro gut systems can be useful to address these questions, but up to now, there is no validated in vitro model of the obese human colon.

RESULTS: To address this gap, we performed dietary surveys and conducted an extensive analysis of 250 articles to set-up and validate a unique in vitro colonic model, based on human in vivo data and reproducing obese-specific nutritional, physicochemical, and lumen vs mucus-associated microbial parameters. Then, in an original experimental set-up, we cross-compared data on gut microbiota structure and activities during fermentations performed with fecal microbiota from healthy (n = 4) or obese (n = 5) donors and operated under healthy or newly designed obese parameters. Interestingly, applying obese parameters on healthy fecal samples resulted in a significant reduction in microbial α-diversity and in taxa associated with health (e.g., Akkermanciaceae, Rikenellaceae, and Archaea), together with a tendency toward increased production of short-chain fatty acids and associated energy, in full agreement with in vivo data. Conversely, applying healthy parameters on obese fecal samples led to gut microbiota resilience.

CONCLUSIONS: These findings highlight the importance of nutritional and physicochemical environment in shaping colonic bacterial and archaeal populations in obesity. This innovative validated model represents a robust and useful platform for mechanistic investigations on gut microbiome in the absence of the host cells, as well as for preclinical evaluation of food and pharmaceutical strategies aiming to restore microbiota eubiosis in a personalized manner.},
}

@article {pmid42266133,
year = {2026},
author = {Duggar, M and Leardini, D and Muratore, E and Margolis, EB and Masetti, R},
title = {Gut Microbiome-Immune Interactions During Pediatric Hematopoietic Cell Transplantation: From Conditioning to GvHD Prevention.},
journal = {Pediatric transplantation},
volume = {30},
number = {6},
pages = {e70371},
doi = {10.1111/petr.70371},
pmid = {42266133},
issn = {1399-3046},
abstract = {Hematopoietic stem cell transplantation (HCT) offers curative potential for children with high-risk hematologic malignancies. However, this treatment carries significant risks, particularly acute graft-versus-host disease (aGvHD), which affects 30%-60% of pediatric recipients and causes 15%-20% of post-transplant deaths. The gut microbiome has emerged as a critical factor in aGvHD development, yet pediatric microbiome dynamics differ substantially from adult patterns. This review seeks to evaluate the current state of knowledge of how the gut microbiome impacts aGvHD pathogenesis and the methods of microbiome modulation that may lead to aGvHD prevention and treatment. Children's microbiomes undergo more rapid compositional shifts and contain distinct bacterial compositions enriched in taxa like Bifidobacterium and Lactobacillus. During transplant, conditioning regimens and antibiotics cause dramatic microbiome disruption in children. This eliminates beneficial bacteria that normally maintain intestinal barrier integrity and produce immunomodulatory metabolites. Consequently, this disruption triggers inflammatory cascades through bacterial translocation, impaired immune education, and altered metabolite production. Unlike adults, where low diversity consistently predicts poor outcomes, pediatric studies show inconsistent diversity-outcome relationships, with only pre-transplant microbiome patterns reliably predicting aGvHD risk. Several promising interventions have emerged from this research. These include enteral nutrition to preserve beneficial bacteria, targeted antibiotic strategies, and fecal microbiota transplantation. Fecal microbiota transplantation has shown remarkable response rates in pediatric steroid-resistant aGvHD cases. Nevertheless, significant knowledge gaps remain regarding pediatric-specific mechanisms, optimal biomarkers, and age-appropriate therapeutic approaches for microbiome-directed aGvHD prevention.},
}

@article {pmid42266457,
year = {2026},
author = {Stach, TL and Deep, A and Madge Pimentel, I and Buchner, D and Borton, MA and Soares, AR and Starke, J and Bornemann, TLV and Rehsen, PM and Dreger, KL and Boenigk, J and Vos, M and Leese, F and Beisser, D and Probst, AJ},
title = {Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf079},
pmid = {42266457},
issn = {2730-6151},
abstract = {Rivers face constant anthropogenic stress, resulting in significant changes in microbial community composition. What remains unclear is whether stream microbiomes exhibit distinct resilience patterns in composition and/or activity upon exposure to different stressors. By subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to low flow velocity. This stress results in altered community compositions incapable of mitigating the applied stressor within a two-week timeframe despite functional stability (inferred via metagenomics). Transcriptomics revealed a systematic heat shock response in the community and a highly active, metabolically versatile, uncharacterized anaerobic keystone species. Increases in temperature (+ 3.5°C) or salinity (+ 0.5 mS/cm) elicited minor responses at community and transcriptomic levels (e.g. upregulation of photosystems). Following a two-week recovery, transcriptomic-inferred stress responses vanished completely, underscoring the river microbiome resilience. Given the complex community responses observed at the activity and compositional levels, we conclude that maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.},
}

@article {pmid42266459,
year = {2026},
author = {Van Landuyt, J and Oosterlinck, J and De Vrieze, J},
title = {The anaerobic digestion microbiome is robust toward variation in the waste activated sludge feed.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf072},
pmid = {42266459},
issn = {2730-6151},
abstract = {Anaerobic digestion stands out as the foremost technology for maximizing the valorization of waste activated sludge (WAS) to recover energy and recover resources. The physical/chemical and microbial makeup of WAS is susceptible to seasonal fluctuations, due to the open-air nature of wastewater treatment facilities, potentially impacting subsequent digester performance and the quality of the resulting digestate. This study delved into a comprehensive analysis of both the initial WAS and the digestate produced by 12 full-scale digesters during both a summer and winter sampling campaign. A significant influence of seasonal variations was observed on the physical/chemical and microbial composition of WAS. Interestingly, the digestate microbiome exhibited a high resilience with minimal seasonal fluctuations, but instead showed variations between different digesters. In summary, this research demonstrates that while WAS composition manifests in specific physical/chemical attributes, it does not exert a discernible influence on the microbial composition of the resulting digestate.},
}

@article {pmid42266461,
year = {2026},
author = {Jang, S and Ryu, CM},
title = {A new role for an old actor: plant small RNAs orchestrate the phytobiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf060},
pmid = {42266461},
issn = {2730-6151},
}

@article {pmid42266611,
year = {2026},
author = {Yang, H and Liu, Y and Zhu, T and Xiao, Z and Wang, H and Zhu, S and Chen, Y},
title = {Gut Microbiome-Metabolite Interactions Contribute to Esophageal Cancer Risk: Evidence From Mendelian Randomization and Multiomics Integration.},
journal = {International journal of genomics},
volume = {2026},
number = {},
pages = {5967802},
pmid = {42266611},
issn = {2314-4378},
abstract = {BACKGROUND: Growing evidence implicates gut microbiota (GM) in the pathogenesis of esophageal cancer (EC). However, the causal nature of this association-particularly the potential mediating role of circulating metabolites-remains insufficiently clarified, especially across EC subtypes.

METHODS: We applied a two-sample Mendelian randomization (MR) framework to investigate the causal associations of GM and blood metabolites with EC and esophageal adenocarcinoma (EAC). The primary analysis was conducted using the inverse-variance weighted method, with complementary MR approaches and genetic risk score (GRS) validation to ensure robustness. Mediation analyses were further performed to assess whether metabolites mediate the effects of GM on EC and EAC.

RESULTS: Twenty-five GM taxa showed significant associations with EC, including 11 with risk-promoting and 14 with protective effects. For EAC, 15 taxa were implicated, with 11 increasing and 4 decreasing disease risk. In addition, five metabolites were causally linked to EC (two risk-related and three protective), and six to EAC (five risk-related and one protective). Mediation analyses revealed that specific metabolites partially mediated the effects of GM on both EC and EAC.

CONCLUSIONS: Our findings provide genetic evidence for a causal GM-metabolite-cancer axis in EC pathogenesis. These results highlight the role of circulating metabolites as potential intermediaries linking GM to EC and EAC, and suggest new avenues for biomarker discovery and microbiome-targeted interventions.},
}

@article {pmid42266650,
year = {2026},
author = {Yu, Z and Zhang, S and Lu, Z and Wang, H and Liu, H and Li, Y and Pan, Y},
title = {Crosstalk between iron metabolism dysregulation and the oral microbiome in periodontitis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2682975},
pmid = {42266650},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease caused by periodontal pathogens. The impact of periodontitis is not only limited to the oral cavity, but also related to a variety of systemic diseases. Iron is a kind of redox metal, which may be deleterious to cells by producing damaging free radicals. Iron homeostasis dysregulation, especially ferroptosis, involves in the progression of periodontitis.

OBJECTIVE: This review aims to systematically summarize the crosstalk between iron metabolism dysregulation and the oral microbiome in periodontitis, focusing on alterations in iron-related biomarkers, iron-mediated tissue damage, the role of ferroptosis, and the potential of iron-targeted therapies.

DESIGN: A narrative review of recent advances in iron metabolism and ferroptosis, with emphasis on studies investigating molecular mechanisms, clinical correlations, and therapeutic interventions in periodontitis.

RESULTS: In periodontitis, serum iron and transferrin levels are decreased, while ferritin, hepcidin, and ceruloplasmin are elevated. Dysregulated iron metabolism promotes periodontal pathogen survival, amplifies inflammatory responses, induces ferroptosis in periodontal ligament cells, and contributes to alveolar bone resorption. Iron disorders also link periodontitis to systemic diseases such as anemia of inflammation, type 2 diabetes, and cardiovascular disease. Preclinical studies show that iron chelators (e.g. deferoxamine) and lactoferrin can inhibit bacterial growth, alleviate ferroptosis, and promote periodontal regeneration.

CONCLUSIONS: Iron metabolism dysregulation and ferroptosis play critical roles in the initiation and progression of periodontitis and its systemic comorbidities. Targeting iron homeostasis represents a promising therapeutic strategy, but further well-designed clinical trials are needed to validate efficacy and safety.},
}

@article {pmid42266651,
year = {2026},
author = {Hamada, M and Matsuoka, Y and Ogaya, Y and Kadota, T and Ikeda, S and Akitomo, T and Nomura, R and Nakano, K},
title = {Effects of multiple tongue conditions on the diversity and composition of the oral microbiota.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2684141},
pmid = {42266651},
issn = {2000-2297},
abstract = {OBJECTIVE: The present study examined the effects of multiple tongue conditions on the diversity and composition of the oral microbiota to obtain a more detailed understanding of their potential role in health and disease.

METHOD: Ninety-three subjects were classified according to tongue conditions, such as a yellow tongue coating, the presence or absence of swelling of the sublingual vein, a red tongue or red tongue tip, a fissured tongue, enlarged tongue, geographic tongue, and tooth marks. The oral microbiota was examined using α- and β-diversity metrics and taxonomic composition analyses.

RESULTS: α-Diversity was significantly lower in subjects with a fissured tongue than in those without. A β-diversity analysis revealed distinct microbial community structures between these subjects. Taxonomic profiling showed a higher abundance of Firmicutes and sulfur-metabolizing bacteria in subjects with a fissured tongue. However, these differences were not retained after age adjustment. Age-restricted sensitivity analyses identified age-independent microbial signatures associated with a fissured tongue, including a reduced abundance of Veillonella and Granulicatella in saliva samples.

CONCLUSION: Morphological abnormalities of the tongue are associated with distinct oral microbiome profiles. These features may reflect oral microbial dysbiosis and could be relevant for future studies exploring non-invasive markers of oral health.},
}

@article {pmid42266671,
year = {2026},
author = {Zhang, Y and Xue, J and Lin, H and Wang, K and Tan, X and Jiao, X and Jiang, H},
title = {Persistent dysbiosis of intestinal and oral microbiota after neoadjuvant radiotherapy for rectal cancer: Implications for surgery and microbiome intervention.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1786044},
pmid = {42266671},
issn = {2234-943X},
abstract = {BACKGROUND: Neoadjuvant radiotherapy represents a conventional approach for managing locally advanced rectal carcinoma. Although this regimen has many benefits, radiation injury is associated with intestinal mucosal injury and gut microbiota dysbiosis. The long-term dynamics of inflammation and microbial recovery, including oral microbiota alterations, remain unclear.

METHODS: Intestinal mucosal specimens were obtained from patients with rectal cancer who underwent surgical treatment without radiotherapy or at predetermined time intervals (4 ± 1 weeks, 8 ± 1 weeks and 12 ± 1 weeks) after radiotherapy. The levels of TNF-α, IL-4 and IL-6 in the intestinal mucosa were determined using ELISA. Meanwhile, the intestinal mucosa and saliva of 18 recruited rectal cancer patients were subjected to 16S rRNA gene sequencing (radiotherapy group, n=9; non-radiotherapy group, n=9) for analysis of the gut and oral microbial communities.

RESULTS: Mucosal IL-4 levels were still significantly elevated at 12 weeks post-radiotherapy with respect to the non-radiotherapy group (p<0.05), while TNF-α and IL-6 were back at baseline levels. The gut microbiota composition of radiotherapy patients differed from that of non-radiotherapy patients, with a significant reduction in Chao1 diversity index (p<0.01) and distinct β-diversity clustering (ANOSIM R = 0.614, p=0.001). These differences were still present at 12 weeks post radiotherapy. The oral microbiota changes were limited, with only a few taxa that showed significant differences (ANOSIM R = 0.38, p=0.009).

CONCLUSION: Neoadjuvant radiotherapy is associated with persistent intestinal mucosa inflammation and prolonged disruption of gut microbiota and this dysbiosis does not fully normalize within 12 weeks after treatment. Changes in oral microbiota appeared less pronounced. These findings provide the biological context for understanding intestinal recovery after radiotherapy and indicate that more studies are needed to direct future efforts towards the peri-operative manipulation of gut microbiota.},
}

@article {pmid42266678,
year = {2026},
author = {Rao, X and Zou, L and Cai, X and Yao, Y and Zhong, L},
title = {Microbiome-orchestrated cross-organ immunity in autoimmunity: from metabolites to therapeutic targets.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1761834},
pmid = {42266678},
issn = {1664-3224},
abstract = {Autoimmune diseases are systemic disorders in which barrier-site immune activation, especially in the gut, can reshape inflammatory programs in distant organs. This review advances a metabolite-centered, cross-organ framework for understanding how gut microbial ecology influences autoimmunity beyond individual gut-organ axes. We synthesize evidence that short-chain fatty acids, bile acid derivatives, tryptophan catabolites, polyamines and related microbial products act as mobile biochemical checkpoints linking intestinal barrier integrity, pattern-recognition signaling, immune-cell metabolism and tissue-specific inflammation in joints, kidneys, skin, lungs and the central nervous system. Across these axes, shared mechanisms include barrier failure, altered microbial metabolite pools, dysregulated MAMP sensing, trafficking or systemic conditioning of lymphoid and myeloid cells, and local stromal imprinting in target organs. We also discuss sex-dependent microbiome-immune interactions, including the microgenderome concept, as a framework for explaining why microbiome composition, hormone metabolism and immune responses may shape autoimmune risk and treatment response differently in females and males. Finally, we evaluate multi-omics, single-cell and spatial profiling, organ-on-chip platforms and causal computational tools, and we outline translational strategies ranging from diet, probiotics, fecal microbiota transplantation and engineered consortia to pharmacologic targeting of metabolite receptors. By treating microbial metabolites as actionable cross-organ immune checkpoints, this review highlights opportunities and limitations for biomarker-guided, metabolite-focused precision therapy in autoimmunity.},
}

@article {pmid42266929,
year = {2026},
author = {Stoia, O and Anderco, P and Badiu, T and Todor, SB and Ichim, C},
title = {Artificial intelligence in optimizing antimicrobial therapy for gastro-renal disorders.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1792361},
pmid = {42266929},
issn = {2235-2988},
abstract = {Antimicrobial therapy remains central to the management of gastrointestinal and urinary tract infections, yet its effectiveness is increasingly compromised by antimicrobial resistance and antibiotic-induced microbiome disruption. These challenges are particularly pronounced in gastro-renal settings, where recurrent infections, altered drug absorption and impaired renal clearance generate substantial pharmacokinetic variability and narrow therapeutic margins. Empiric, guideline-based regimens may therefore contribute to treatment failure, resistance selection, and disease recurrence. Artificial intelligence (AI) and machine learning offer novel opportunities to optimize antimicrobial therapy by integrating clinical, microbiological and multi-omics data to predict resistance, guide antibiotic selection and dosing, and support antimicrobial stewardship. However, clinical translation remains limited by data heterogeneity, insufficient prospective validation, regulatory constraints, and the need for continued human oversight. This review synthesizes current AI-driven strategies relevant to gastro-renal infections, highlighting shared pathophysiological challenges, practical clinical applications and key limitations. An integrated framework for AI-assisted antimicrobial optimization is proposed to enhance therapeutic efficacy while mitigating antimicrobial resistance and preserving microbiome integrity.},
}

@article {pmid42266934,
year = {2026},
author = {Bautista, J and Lara-Hernández, ME and Hidalgo-De La Cruz, M and Andino-Araque, V and León-Rivera, M and López-Cortés, A},
title = {Host-microbiome interactions in breast cancer progression and treatment response.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1827694},
pmid = {42266934},
issn = {2296-858X},
abstract = {Breast cancer (BC) is a biologically heterogeneous disease in which tumor progression and therapeutic response vary substantially across patients and molecular subtypes. Alongside genetic, endocrine, and immunological determinants, microbial ecosystems have been proposed as components of the host environment that interact with tumor biology. Microorganisms detected in breast tissue, the gastrointestinal tract, and the oral cavity coexist with epithelial and immune compartments and participate in metabolic and inflammatory processes relevant to mammary physiology. Differences in microbial composition have been reported between non-malignant and malignant breast tissue, while intestinal microbial metabolism generates bioactive compounds capable of interacting with immune regulation and systemic endocrine signaling. Microbial enzymatic activity involved in estrogen deconjugation further connects intestinal ecology with hormone-responsive disease. Microbiome-related variation has also been examined in relation to systemic therapies, where differences in microbial composition have been observed alongside variability in therapeutic outcomes. This review examines current knowledge on host-microbiome interactions across breast, gut, and oral environments and discusses how microbial ecology intersects with inflammatory signaling, metabolic regulation, and endocrine pathways relevant to breast cancer progression and treatment response. Methodological challenges and future research directions for microbiome-informed oncology are also considered.},
}

@article {pmid42267107,
year = {2026},
author = {Mathyk, BA and Shukla, R and Kumar, V and Mishra, SP and Pandya, S and Patten, N and Gerardi, K and Beatty, HW and Persad, AH and Imudia, AN and Yadav, H and Jain, S},
title = {Parabolic flight induces site specific microbiome changes in women.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1817099},
pmid = {42267107},
issn = {1664-302X},
abstract = {INTRODUCTION: The vaginal microbiome plays a central role in women's health by supporting immune function, maintaining mucosal homeostasis, and preventing infections. Spaceflight and its analogs can induce acute physiological stress, which can alter host microbiome interactions. While other studies have analyzed the microbiome changes at certain body sites, the female-specific microbiome changes have not been explored in depth in space medicine research.

METHODS: Pre- and post-parabolic flight vaginal and oral microbiome were analyzed via metagenomic shotgun sequencing to assess taxonomic composition and metabolic pathways. Host DNA and bad quality sequences were removed using the KneadData tool. Taxonomic and functional profiles were analyzed with MetaPhlAn and HUMAnN. Microbiome data were integrated with stress response parameters including cortisol, proinflammatory cytokines, and urinary short-chain fatty acids.

RESULTS: Both alpha- and beta diversity analysis showed minimal impact of parabolic flight on oral microbiome while vaginal microbiome showed significant differences. Taxonomic profiling showed marked restructuring of the vaginal microbiome, characterized by increased Firmicutes dominance and enrichment of Lactobacillus species, particularly Lactobacillus crispatus and Lactobacillus jensenii, whereas oral microbiome stayed relatively stable. Overall, only 2.54% of oral species showed significant postflight changes compared to 57.9% of vaginal species (p < 0.0001). Random Forest model identified L. crispatus as a key discriminator of postflight vaginal microbiome composition. Metabolic pathway analysis revealed minimal postflight pathway redistribution in saliva samples but greater number of changes in the vaginal microbiome, with significant postflight enrichment of fatty acid biosynthesis and nucleotide metabolism. Vaginal samples demonstrated a threefold greater proportion of altered metabolic pathways compared to oral samples. In addition, urinary acetate, butyrate, and valeric acid levels were significantly reduced postflight. Salivary cortisol increased postflight and positively correlated with L. jensenii.

CONCLUSION: Parabolic flight induces body site-specific microbiome changes in reproductive age women, with greater taxonomic and functional metabolic remodeling in the vaginal microbiome than in the oral microbiome. These findings highlight the sensitivity of the vaginal microbial ecosystem to spaceflight stressors and underscore the need for longitudinal and mechanistic studies to determine the persistence, clinical significance, and potential health implications of these changes during longer duration space missions.},
}

@article {pmid42267108,
year = {2026},
author = {Seo, JH and Seo, YJ and Ryu, HY and Shin, M and Lee, CY},
title = {Current insights into bacterial secondary infection following influenza A virus infection.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1851115},
pmid = {42267108},
issn = {1664-302X},
abstract = {Influenza A virus (IAV) continues to pose a substantial challenge to global health, not merely through primary viral pneumonia but largely due to lethal secondary bacterial complications. Pathogens such as Streptococcus pneumoniae, Staphylococcus aureus, and Haemophilus influenzae capitalize on the physiological "storm" induced by IAV, leading to significantly exacerbated morbidity. This review provides a comprehensive synthesis of the multifaceted mechanisms that dismantle host antibacterial defenses. Beyond the classical understanding of respiratory epithelial damage and the compensatory upregulation of bacterial adhesion receptors, we delve into the sophisticated dysregulation of innate immune signaling, specifically the collateral damage caused by interferon responses and impaired phagocytic function. Furthermore, we examine the complex roles of direct virus-bacterium synergism and the disruption of the respiratory microbiome (dysbiosis). By integrating these established paradigms, we extend the discussion to the rising clinical concern of nosocomial and multidrug-resistant (MDR) infections in critically ill patients. We conclude by identifying critical knowledge gaps and emphasizing the need for targeted strategies to mitigate the host vulnerabilities that permit opportunistic MDR colonization in the wake of viral insult.},
}

@article {pmid42267126,
year = {2026},
author = {Quan, W and Qi, Y and Liu, Y and Sun, X and Wang, H and Zeng, C and Chen, H and Gao, S and Xu, Y and Zhao, Q and Du, T},
title = {Soil-borne diseases in medicinal plants: linking allelopathy and host immunity to microbiome-based interventions.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1797910},
pmid = {42267126},
issn = {1664-462X},
abstract = {The rising global demand for natural medicines has intensified the cultivation of Chinese medicinal herbs, exacerbating continuous cropping obstacles and constraining the sustainable development of Chinese medicinal materials. A defining manifestation is a severe soil-borne disease that limits long-term productivity and stable medicinal quality. Despite progress in understanding individual diseases or host species, integrative syntheses of the coupled "pathogen-environment-host" network remain limited. Here, we synthesize the current understanding of soil-borne disease development under continuous cropping and evaluate ecological management options by integrating evidence on pathogen virulence, continuous-cropping-driven edaphic shifts, host immunometabolism (the coupled reprogramming of immunity and metabolism), and microbiome-based interventions. We summarize the major soil-borne pathogens and their virulence determinants and explain how allelochemical accumulation reshapes the rhizosphere microbiome, weakens the barrier functions, and facilitates pathogen ingress. We further discuss how allelochemical stress reprograms defense hormone networks (notably salicylic acid and jasmonic acid pathways) with downstream consequences for innate immune competence. Building on these insights, we assessed microbiome-guided strategies to restore rhizosphere function, including synthetic community design, recruitment of probiotic taxa, and induction of disease-suppressive soils. By integrating microbiology, chemical ecology, and plant pathology, this review provides a conceptual framework and actionable directions for the precise and sustainable control of soil-borne diseases in Chinese medicinal herb production.},
}

@article {pmid42267128,
year = {2026},
author = {Daurova, A and Daurov, D and Sapakhova, Z and Kanat, R and Abilda, Z and Toishimanov, M and Isgandarov, I and Mukhametov, A and Volkov, D and Shamekova, M and Zhambakin, K},
title = {Rhizosphere microbiome dynamics and plant adaptation to abiotic stress in major oilseed crops: a review.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1832403},
pmid = {42267128},
issn = {1664-462X},
abstract = {Abiotic stresses, such as drought, salinity, extreme temperatures, nutrient deficiencies, and heavy metal contamination, severely limit oilseed crop productivity under accelerating climate change. This review synthesizes recent advances in understanding the critical role of soil and plant-associated microbiomes in conferring stress tolerance to major oilseed species, including rapeseed (Brassica napus), sunflower (Helianthus annuus), soybean (Glycine max), and sesame (Sesamum indicum). Beneficial microorganisms, particularly plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and endophytes, enhance plant tolerance through an integrated network of biochemical, physiological, and molecular mechanisms. Biochemically, they modulate phytohormone levels (e.g., IAA and ABA), produce osmoprotectants, and regulate antioxidant systems (e.g., SOD, CAT, POD) to mitigate oxidative damage. Physiologically, these processes contribute to improved root architecture, water-use efficiency, nutrient acquisition, and ion homeostasis under stress conditions. At the molecular level, microorganisms influence gene expression and signaling pathways associated with stress responses, including activation of stress-responsive genes and metabolic adjustments. These interconnected mechanisms collectively strengthen plant resilience by coordinating metabolic regulation, cellular protection, and adaptive responses within the plant-microbiome system. Agroecological practices (soil type, crop rotation, tillage, fertilization) strongly shape microbial community assembly and functional potential, while multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) reveal stress-driven restructuring and adaptive metabolic shifts in the rhizosphere. Emerging tools such as synthetic microbial consortia (SynComs) and targeted microbiome engineering offer promising, sustainable alternatives to conventional breeding and chemical interventions, enhancing soil health, nutrient cycling, and agroecosystem resilience with reduced environmental footprint. This review presents a comprehensive synthesis with a specific focus on oilseed crops, integrating current knowledge on microbiome dynamics under multiple abiotic stress conditions-an area that remains comparatively underrepresented in the literature. It examines key microbial groups driving adaptation, evaluates omics-based insights into plant-microbiome interactions, identifies critical research gaps, and outlines future directions for microbial inoculants and climate-resilient oilseed production systems.},
}

@article {pmid42267559,
year = {2026},
author = {Xu, T and Xing, J and Lin, X and Yang, Y and Yang, T and Xu, XS and Yuan, M},
title = {Genus-level oral microbiome composition and Dietary Approaches to Stop Hypertension dietary adherence in relation to hypertension.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000004377},
pmid = {42267559},
issn = {1473-5598},
abstract = {BACKGROUND: Hypertension (HTN) remains a leading global health burden and a key risk factor for cardiovascular disease. While the Dietary Approaches to Stop Hypertension (DASH) diet is an established strategy for blood pressure control, the interplay between dietary patterns and the oral microbiome in the etiology of HTN is not well understood.

OBJECTIVE: To investigate the independent and joint associations of genus-level oral microbiome composition and adherence to the DASH diet with hypertension in a nationally representative sample of US adults.

METHODS: We analyzed data from the 2009-2010 and 2011-2012 National Health and Nutrition Examination Survey (NHANES), including 5371 adults with complete oral microbiome, dietary, blood pressure, and covariate data. Genus-level oral microbiome profiles were derived from oral rinse samples using 16S rRNA sequencing and transformed with the centered log-ratio method. DASH adherence was assessed from 24-h dietary recalls using a validated score. Hypertension was defined as self-reported diagnosis, antihypertensive medication use, or measured blood pressure meeting 2017 American College of Cardiology/American Heart Association (ACC/AHA) criteria (systolic ≥130 mmHg or diastolic ≥80 mmHg). Analyses employed a multistage design: differential abundance testing to identify hypertension-associated genera; survey-weighted multivariable logistic regression to examine independent and joint associations, adjusting for demographic, lifestyle, and clinical covariates; subgroup analyses by sex, age, and microbial characteristics; and sensitivity analyses to assess robustness.

RESULTS: Greater adherence to the DASH diet was associated with lower odds of hypertension [high vs. low tertile odds ratio (OR) ≈0.62; P < 0.005]. Several oral bacterial genera - Actinomyces, Rothia, Lactobacillus, and Veillonella - showed independent associations with increased hypertension risk (OR range: 1.302-1.468; P < 0.05). Higher Faith's Phylogenetic Diversity was inversely associated with hypertension (OR = 0.742; P = 0.037). Stratified analyses suggested effect modification: the protective DASH-hypertension association was strongest among individuals with low Lactobacillus abundance and intermediate microbial diversity and Rothia abundance, more pronounced in women, and attenuated in adults aged at least 60 years. Sensitivity analyses confirmed these patterns, highlighting the consistent risk associated with Actinomyces and the stability of joint DASH-microbiome associations.

CONCLUSION: Genus-level oral microbiome composition and DASH dietary adherence were independently and jointly associated with hypertension risk. These results support a potential oral-dietary axis in cardiovascular risk and underscore the need for integrated microbiome-dietary approaches to hypertension prevention.},
}

@article {pmid42267567,
year = {2026},
author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL},
title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.},
journal = {Zoological research},
volume = {47},
number = {3},
pages = {827-842},
doi = {10.24272/j.issn.2095-8137.2025.141},
pmid = {42267567},
issn = {2095-8137},
abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.},
}

@article {pmid42267822,
year = {2026},
author = {Khalil, SB and Kowalski, CH},
title = {The cutaneous microbiome: microbial remodeling of the skin lipid landscape.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0064825},
doi = {10.1128/msphere.00648-25},
pmid = {42267822},
issn = {2379-5042},
abstract = {The human skin microbiome exists within a lipid-rich environment that profoundly shapes microbial colonization, metabolism, and interactions with the host. Resident microbes not only consume host-derived lipids for energy but also transform them into bioactive compounds that influence microbial competition, immune responses, and skin barrier function. In turn, microbially generated lipids become part of the skin lipid landscape, including short-chain fatty acids and cell envelope lipids, and contribute to maintaining homeostasis or, in some cases, influence disease processes such as acne and atopic dermatitis. Despite increased recognition of their importance, the diversity, origins, and bioactivities of microbially derived lipids on skin remain underexplored. Here, we highlight recent advances in understanding how cutaneous microbes shape and are shaped by the skin lipid landscape, emphasizing the potential of microbial lipids as mediators of skin health, disease, and novel therapeutic strategies.},
}

@article {pmid42267833,
year = {2026},
author = {Hauza, E and Mutai, IJ and Necel, A and Kamya, D and Śliwka, P and Dusza, I and Węgrzyn, A and Skaradzińska, A},
title = {Bacteriophages in the treatment of cutaneous infections and skin disorders: therapeutic advances and future directions.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0004826},
doi = {10.1128/cmr.00048-26},
pmid = {42267833},
issn = {1098-6618},
abstract = {SUMMARYSkin and soft tissue infections represent a major clinical challenge. This is particularly true given the rise in antimicrobial resistance, the increasing prevalence of chronic wounds, and the growing number of immunocompromised patients. Conventional antibiotic therapies are frequently compromised by multidrug-resistant pathogens, biofilm formation, and disruption of the skin microbiome, underscoring the urgent need for alternative or adjunctive antibacterial strategies. Bacteriophages, viruses that specifically infect and lyse bacteria, have re-emerged as promising therapeutic agents due to their high specificity, activity against antibiotic-resistant strains, and capacity to target biofilm-associated infections. This review provides a comprehensive overview of current advances in bacteriophage-based approaches for the treatment of cutaneous infections and skin disorders. We discuss the biological principles of phage therapy, its advantages and limitations, and the regulatory and manufacturing challenges associated with clinical translation. Particular emphasis is placed on topical and biomaterial-based phage delivery platforms, including hydrogels, nanocarriers, and adhesive wound dressings, designed to enhance phage stability, local bioavailability, and therapeutic efficacy. Furthermore, we summarize experimental and clinical evidence supporting the use of bacteriophages against the most clinically relevant skin pathogens. By integrating data from in vitro studies, animal models, clinical trials, and compassionate-use cases, this review highlights both the therapeutic potential and current limitations of phage-based interventions in dermatology. Collectively, the available evidence supports the use of bacteriophages as a viable component of future precision antimicrobial therapies for skin infections, while emphasizing the need for well-designed clinical trials, standardized production protocols, and optimized delivery systems to enable broader clinical adoption.},
}

@article {pmid42267859,
year = {2026},
author = {Shittu, OE and Enagbonma, BJ and Babalola, OO},
title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70307},
pmid = {42267859},
issn = {2045-8827},
support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; },
abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.},
}

@article {pmid42267869,
year = {2026},
author = {Wojakowicz, K and Pielech, AK and Kowalińska, JE and Stypka, R and Rabczyński, M},
title = {Gut microbiome in type 2 diabetes mellitus: A literature review.},
journal = {Advances in clinical and experimental medicine : official organ Wroclaw Medical University},
volume = {},
number = {},
pages = {},
doi = {10.17219/acem/218917},
pmid = {42267869},
issn = {1899-5276},
abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder influenced by genetic, environmental, and lifestyle factors. Emerging evidence highlights the crucial role of the gut microbiota (GM) in the pathophysiology of T2DM, with alterations in microbial diversity and composition contributing to insulin resistance, systemic inflammation, and metabolic dysregulation. This review explores the current literature on the role of the GM, its metabolites, including short-chain fatty acids (SCFAs), bile acids (BAs), and branched-chain amino acids (BCAAs), as well as the impact of diet and body mass index (BMI) on the progression of T2DM. We examine how dietary patterns, including fiber intake, fat composition, and the use of prebiotics and probiotics, modulate the GM. Furthermore, we analyze evidence regarding the influence of the microbiome on host metabolism, gut permeability, and the pathophysiology of T2DM. Understanding the dynamic interactions among the GM, microbial metabolites, diet, and BMI may provide promising avenues for the development of personalized therapeutic strategies targeting microbiome-mediated mechanisms in the prevention and management of T2DM. Such approaches may facilitate more effective patient-centered interventions.},
}

@article {pmid42268644,
year = {2026},
author = {Lieberman, OJ and Nittala, S and Rojas-Valencia, L and Baranzini, SE and Singhal, NS and Hemphill, JC and Amorim, E and Ferguson, AR and Hinson, HE},
title = {Circulating Short-Chain Fatty Acid Profile Predicts Functional Outcome After Moderate-to-Severe Traumatic Brain Injury.},
journal = {Critical care explorations},
volume = {8},
number = {6},
pages = {e1433},
pmid = {42268644},
issn = {2639-8028},
support = {5K23NS110828-05/NS/NINDS NIH HHS/United States ; },
abstract = {OBJECTIVES: Short-chain fatty acids (SCFAs) are immunometabolites produced by the gut microbiome. In animal models, SCFAs affect traumatic brain injury (TBI) severity by modulating the immune response and serving as an energy source. The goal of this study was to assess whether SCFAs are associated with functional outcome in adult patients with moderate-to-severe TBI (msTBI).

DESIGN: Prospective cohort study.

SETTING: Urban Trauma Center.

PATIENTS: Adults (age ≥ 15 yr) who had TBI with Glasgow Coma Scale 3-12, intracranial hemorrhage on head CT scan, and at least one reactive pupil. Blood samples had to be collected within 3 hours of trauma.

INTERVENTIONS: None.

MEASUREMENTS AND MAIN RESULTS: Univariate and multivariate analyses demonstrated that plasma SCFAs were associated with better functional outcomes at discharge and 6 months, an association driven primarily by differences in plasma acetate and propionate. K-means clustering of acetate and propionate levels identified two patient clusters with distinct discharge and 6-month functional outcomes but similar clinical, biomarker, and radiographic injury severity. Cluster 1 (n = 47) had higher SCFA levels compared with cluster 2 (n = 76) and cluster 1 had more favorable outcomes at discharge (Glasgow Outcome Scale 4-5: 83% vs. 55%; p = 0.003) and 6 months (Extended Glasgow Outcome Scale 4-8: 78% vs. 45%; p = 0.005). Multivariable logistic regression adjusting for the International Mission for Prognosis and Analysis of Clinical Trials in TBI (IMPACT)lab model identified an independent association between the SCFA cluster and functional outcome at discharge (p = 0.001) and 6 months (p = 0.03). Adding the SCFA cluster to the IMPACTlab model improved the area under the receiver operating characteristic curve for the prediction model for a favorable outcome.

CONCLUSIONS: Our study suggests that SCFA levels are associated with functional outcome after msTBI. Future studies will focus on identifying mechanisms through which SCFAs may improve msTBI outcomes and what drives interpatient variation in their levels, which could position SCFAs as prognostic biomarkers and therapeutic targets in TBI.},
}

@article {pmid42268676,
year = {2026},
author = {Viniotis, AF and Jameson, GS and Wertheim, BC and Roe, DJ and Lee, K and Tsai, FY and Gordon, MS and Sharma, S and Guarnieri, CM and Snyder, CE and Thosani, AJ and Amini, A and Sckolnik, SE and Garrick, JM and Korn, RL and Rahmanuddin, S and Evans, RM and Downes, M and Truitt, M and Von Hoff, DD and Borazanci, EH},
title = {A phase II clinical trial of albumin-bound paclitaxel, cisplatin, gemcitabine (NABPLAGEM) and paricalcitol as neoadjuvant therapy in pancreatic cancer.},
journal = {The oncologist},
volume = {},
number = {},
pages = {},
doi = {10.1093/oncolo/oyag232},
pmid = {42268676},
issn = {1549-490X},
abstract = {BACKGROUND: For patients with untreated pancreatic ductal adenocarcinoma (PDAC), chemotherapy before surgery ("neoadjuvant therapy") has shown benefit in reducing recurrence and prolonging survival. Targeting the vitamin D receptor (VDR) with analogs such as paricalcitol may improve chemotherapy effectiveness. This study evaluated the efficacy and safety of neoadjuvant albumin-bound paclitaxel (nab-paclitaxel) plus cisplatin plus gemcitabine (NABPLAGEM) plus paricalcitol (NCT03138720).

METHODS: Participants were ≥18 years, had stage I-III PDAC without prior chemotherapy or radiation, Karnofsky Performance Status ≥70, and elevated CA 19-9. Study treatment included nab-paclitaxel (125 mg/m2), cisplatin (25 mg/m2), gemcitabine (1000 mg/m2), and paricalcitol (25 mcg) on days 1 and 8 of a 21-day cycle for up to six months. The primary outcome was CA 19-9 normalization. Secondary outcomes included margin-negative resection (R0), pathologic complete response (pCR), radiologic response, safety, and survival. Microbiome was analyzed as an exploratory outcome.

RESULTS: Thirty-two participants were enrolled with median age 69.4 years, 56.2% male, and 93.8% white. Patients had resectable (cohort A, n = 10) and borderline resectable/locally advanced (cohort B, n = 22) tumors. CA 19-9 normalization occurred in 14 patients (43.8%). Two patients (6.2%) achieved pCR, and 19 (59.4%) achieved R0. Complete or partial radiologic response occurred in 39.3% of patients. Adverse events included grade 3-4 anemia (43.8%) and thrombocytopenia (59.4%). Median (95% CI) overall survival was 43.2 (7.5-upper bound not achieved) and 18.4 (10.9-41.2) months for cohorts A and B, respectively.

CONCLUSION: Neoadjuvant NABPLAGEM plus paricalcitol demonstrated a high CA 19-9 normalization rate and was fairly well tolerated.},
}

@article {pmid42268809,
year = {2026},
author = {Ruschman, GL and Bittor, JA and Charnock-Jones, DS and Day-Walsh, PE},
title = {Toward Microbiome-Informed Strategies for Predicting and Preventing Pregnancy Complications.},
journal = {Reproduction & fertility},
volume = {},
number = {},
pages = {},
doi = {10.1530/RAF-26-0009},
pmid = {42268809},
issn = {2633-8386},
abstract = {ABSTRACT: Despite the prevalence of pregnancy complications, including miscarriage, stillbirth, preeclampsia (PE), fetal growth restriction (FGR), and preterm birth (PTB), current predictive tools remain limited. This underscores an urgent need for novel molecular biomarkers and mechanistic insights. The microbiome regulates host physiology, and its disruption correlates with adverse pregnancy outcomes such as PE, PTB, and gestational diabetes mellitus (GDM), and thus holds promise for predictive insights and therapeutic interventions. However, these associations are largely correlative, based on taxonomic rather than protein or metabolite-based functional changes. Additionally, they are often derived from cross-sectional studies, and the underlying mechanisms remain poorly understood. Given the evidence-based view of a sterile intra-uterine environment, understanding the factors that mediate host-microbial interactions is crucial for improving pregnancy outcomes. Maternal immune and hormonal changes can influence the composition and functional capacity of the microbiome, while the microbiome in turn, modulate immune, neuroendocrine responses, nutrient bioavailability and metabolic processes, impacting placental development and pregnancy physiology. We explore direct and indirect mediators of host-microbiome interactions and discuss how these may be targeted to improve pregnancy outcomes. We briefly consider the potential influence of the paternal microbiome and maternal preconception microbial states on pregnancy physiology and outcomes. Finally, we critically evaluate existing methodologies and databases for studying microbial variation in pregnancy-related disorders and propose strategies to better harness microbiome-based research for clinical application. By integrating current evidence and identifying key knowledge gaps, this review aims to highlight microbiome-informed strategies for improving pregnancy outcomes and lifelong health.

LAY SUMMARY: Understanding How Microbes Influence Pregnancy Outcomes Pregnancy complications such as miscarriage, stillbirth, preeclampsia (PE), fetal growth restriction (FGR), and preterm birth (PTB) are common, yet we still lack reliable tools to predict who is at risk. This makes it essential to identify new biological markers and better understand the underlying mechanisms. One promising area is the microbiome; the community of microorganisms that live in and on our bodies including bacteria, viruses and fungi. The microbiome plays a major role in regulating health, and changes in its composition have been linked to pregnancy disorders including PE, PTB, and gestational diabetes (GDM). However, most of what we know comes from studies that only identify which microbes are present, rather than what these microbes are doing. Many studies are also cross-sectional, capturing only a single time point, which limits our ability to understand cause and effect. Because the uterus is generally considered a sterile environment, the key question is how the maternal body and microbiome communicate. During pregnancy, the immune system and hormone levels change dramatically, and these shifts can alter the composition and function of the microbiome. In turn, the microbiome can influence maternal immunity, hormone signalling, nutrient availability, and metabolism. These interactions may shape how the placenta develops and how the pregnancy progresses. In this review, we examine how the body and the microbiome interact both directly and indirectly, and how these pathways might be targeted to improve pregnancy outcomes. We also touch on the possible influence of the paternal microbiome and the mother's pre-conception microbiome on fertility, early development, and long-term pregnancy health.},
}

@article {pmid42268876,
year = {2026},
author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR},
title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351562},
doi = {10.1371/journal.pone.0351562},
pmid = {42268876},
issn = {1932-6203},
abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.

METHODS: BAL specimens from healthy control volunteers (n = 20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n = 52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).

RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p < 0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p = 0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q < 0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.

CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.},
}

@article {pmid42269302,
year = {2026},
author = {Zheng, M and Lun, W and Wang, P and Ren, C and He, Y and Huo, M},
title = {The correlation between vaginal microbiome dysbiosis and recurrent spontaneous abortion.},
journal = {Journal of reproductive immunology},
volume = {176},
number = {},
pages = {104918},
doi = {10.1016/j.jri.2026.104918},
pmid = {42269302},
issn = {1872-7603},
abstract = {In recent years, the role of the vaginal microbiota in pregnancy maintenance has garnered increasing attention. Extensive research indicates that vaginal dysbiosis is closely associated with various adverse pregnancy outcomes, including ectopic pregnancy, miscarriage, preterm birth, and premature rupture of membranes. Recurrent spontaneous abortion (RSA) affects approximately 1-5% of women of childbearing age and has a complex etiology, with infection implicated in about 4% of cases. This systematic review examines the compositional characteristics of the vaginal microbiota, its dynamic changes during pregnancy, and the underlying mechanisms linking it to RSA. It focuses on the protective role of lactobacilli, ascending pathogen infection, and local immune regulation, aiming to provide a novel theoretical foundation for the prevention, risk prediction, and personalized treatment of RSA.},
}

@article {pmid42269309,
year = {2026},
author = {Barbudo-Lunar, M and Arjona, GL and Trombini, C and Pérez-González, L and Chica, AF and Martín, MÁ and Blasco, J and Michán, C and Siles, JÁ and Alhama, J},
title = {A multidisciplinary approach to risk assessment enables the identification of deteriorated sections within a major waterway: The Guadalquivir River as a case study.},
journal = {Journal of contaminant hydrology},
volume = {282},
number = {},
pages = {105019},
doi = {10.1016/j.jconhyd.2026.105019},
pmid = {42269309},
issn = {1873-6009},
abstract = {To date, few studies have assessed the quality of the Guadalquivir River, the main hydrographic basin of the Southern Iberian Peninsula. Here, we present the first comprehensive study to integrate physico-chemical characterisation, bacterial community assessment, and quality indices along its entire course. The Water Quality Index showed a gradual, progressive deterioration in water quality downstream, with 10% of the stations showing fair quality, signs of eutrophication (∼400 mg/m[3] chlorophyll), and microbiological contamination (Escherichia coli, up to 3000 CFU/100 mL). The lower-middle section showed significant changes in the levels of organic carbon, metals, suspended solids and turbidity, as well as high nitrate (up to 19 mg L[-1]) and ammonia (up to 1.4 mg L[-1]) levels influenced by agricultural activities. Water quality may also be negatively influenced by the impact of tributaries. Since microorganisms are ubiquitous and play indispensable environmental roles, changes in water microbiome composition, structure and functionality were evaluated. Metabarcoding analysis revealed significant alterations, particularly in the upper reaches, despite the prevalence of parameters associated with good quality. In this section, a considerable decrease in α-diversity, very high values of microgAMBI ecological index, and potential functional changes revealed signs of environmental degradation. In addition, the predicted high prevalence of "ABC transporters" and the "two-component system" suggests a response to adverse conditions, driven by a small number of tolerant opportunistic microorganisms, notably the family Comamonadaceae. This area, characterised by extensive olive monoculture, has traditionally been exposed to contamination from biocides. In practical terms, this research confirmed that although widely recognised indices may report high overall water quality, complementary microbiome analyses might help reveal undetected hazards affecting the whole ecosystem. This multidisciplinary study could be used as a model for designing risk maps that identify "hotspots" for action to improve the management of essential water resources.},
}

@article {pmid42269396,
year = {2026},
author = {Stylianakis, D and Bertaglia, V and Sangiolo, D and Podda, M and Saba, G and Stylianakis, I and Denaro, N and Pisanu, A and Agelaki, S and Scartozzi, M and Novello, S and Solinas, C},
title = {The antibiotic-immunotherapy interaction in NSCLC: a systematic review and meta-analysis of 54,250 patients across three outcomes.},
journal = {Cancer treatment reviews},
volume = {148},
number = {},
pages = {103162},
doi = {10.1016/j.ctrv.2026.103162},
pmid = {42269396},
issn = {1532-1967},
abstract = {BACKGROUND: Approximately 20-28% of NSCLC patients receiving ICIs also receive systemic antibiotics. Whether this reflects a true microbiome-mediated pharmacological interaction or confounding by indication remains unresolved.

METHODS: We searched PubMed, Scopus, and CENTRAL (2013-2025) for NSCLC studies reporting OS, PFS, or ORR by antibiotic exposure. Random-effects meta-analysis was performed, with mostly non-pre-specified subgroup analyses by study design, ICI class, antibiotic timing, and line-of-therapy, plus leave-one-out, exposure-window, and adjustment-status sensitivity analyses and meta-regression of heterogeneity sources. Risk of bias was assessed with ROBINS-I and ROB 2, and certainty of evidence was rated with GRADE.

RESULTS: Forty-one studies including 54,250 patients were analyzed, 27.8% of whom were antibiotic-exposed. Antibiotic exposure was associated with worse OS (HR 1.47, 95% CI 1.30-1.66; p < 0.00001; I[2] = 79%) and PFS (HR 1.32, 95% CI 1.18-1.47; p < 0.00001; I[2] = 65%), but not ORR (OR 0.95, 95% CI 0.67-1.35; p = 0.77; I[2] = 88%). RCT post-hoc estimates were non-significant (OS HR 1.20, p = 0.07; PFS HR 1.09, p = 0.41; I[2] = 0%), whereas observational estimates were larger and driven by less-adjusted cohorts. Subgroup, sensitivity, and meta-regression analyses indicated that heterogeneity was explained mainly by study design and line of therapy. In chemo-free ICI analyses, only mixed ICI regimens remained significant for OS and PFS. GRADE certainty was very low for observational outcomes and low for RCT-based estimates.

CONCLUSIONS: The strongest available evidence does not support a clear antibiotic-related reduction in ICI efficacy in NSCLC. The observational signal is more compatible with confounding and exposure heterogeneity than with a uniform pharmacological interaction, although a context-specific biological effect cannot be excluded.},
}

@article {pmid42269588,
year = {2026},
author = {Massey, WJ and Brown, JM},
title = {The expanding role of the microbiome in GLP-1 pharmacology.},
journal = {Cell host & microbe},
volume = {34},
number = {6},
pages = {989-990},
doi = {10.1016/j.chom.2026.05.006},
pmid = {42269588},
issn = {1934-6069},
abstract = {There is now overwhelming evidence that glucagon-like peptide 1 (GLP-1) receptor agonists have many health benefits. In this issue of Cell Host & Microbe, Bian et al. find that the gut microbiome is implicated in the psychological effects of these drugs. These findings have broad implications for drug-microbe-host interactions.},
}

@article {pmid42269618,
year = {2026},
author = {Eriksson, D and Schiller, J and Schickele, A and Priest, T and Mankowski, A and Faucher, E and Ustick, LJ and Kuhn, M and Miravet-Verde, S and Ruscheweyh, HJ and Clerc, C and Gruber, N and Sunagawa, S and Bork, P and Vogt, M},
title = {Variations in the latitudinal diversity gradients of the ocean microbiome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.016},
pmid = {42269618},
issn = {1934-6069},
abstract = {Latitudinal diversity gradients (LDGs), which typically decline from the equator to the poles, are a pervasive macroecological pattern. However, their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed-layer microbiomes exhibit diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) show no latitudinal diversity structuring. Taxonomic resolution reveals that the mixed-layer LDG is underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibit distinct or contrasting LDGs. Diversity structuring also varies by seasons and regions and is governed by temperature and nutrient availability. Together, these findings highlight that, within the ocean microbiome, LDGs are not universal but reflect lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.},
}

@article {pmid41975402,
year = {2026},
author = {Zhu, Y and Xiao, C and Zhang, Z and Zhou, Y and Xu, L and Zhang, L and Qu, K and Yu, B and Yan, H},
title = {Association between oral microbiota and suicidal ideation among vocational high school students in China.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {41975402},
issn = {1472-6831},
support = {82204073//the National Natural Science Foundation of China/ ; 22YJC840037//the Ministry of Education of Humanities and Social Science project/ ; WY22B09//the Wuhan Health Science Research Funding/ ; },
abstract = {OBJECTIVE: To investigate the association between oral microbiome characteristics and suicidal ideation (SI) in vocational high school students.

METHODS: The oral microbiota composition and abundance of the SI group (N = 45) and the matched healthy control group (N = 45) were analyzed using 16S rRNA sequencing. Demographic variables and SI assessments (measured by the Columbia Suicide Severity Rating Scale) were obtained. Bioinformatics analyses (e.g., alpha and beta diversity indices, PCoA, NMDS, and LEfSe) were performed to compare oral microbiota characteristics between the SI group and the control group.

RESULTS: The vocational high school students with SI exhibited significantly lower alpha diversity indices in oral microbiota compared to the control group, including PD whole tree (20.56 [19.45, 21.38] vs. 21.37 [20.17, 23.27]), Chao1 (621.82 ± 66.99 vs. 672.24 ± 68.52), and observed species (426.91 ± 54.59 vs. 466.42 ± 69.75) (all p values < 0.01). Beta diversity analysis revealed distinct microbial composition between groups (p < 0.05), with greater homogeneity in the SI group. LEfSe analysis identified increased abundances of Enterobacter, Escherichia_Shigella, and Parabacteroides in the SI group, while controls showed enrichment of Rikenellaceae and Alistipes.

CONCLUSION: A decrease in oral microbiota diversity and alterations in the abundance of specific bacterial genera (Enterobacter, Escherichia_Shigella, and Parabacteroides) are associated with SI among vocational high school students. Longitudinal studies are needed to elucidate the underlying mechanisms and potential health impacts.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-08317-3.},
}

@article {pmid42254517,
year = {2026},
author = {Liu, S and Luo, X and Zhou, J and Wang, L and Li, R and Luo, Z and Li, N and Xiao, S and Zhang, P},
title = {A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1801806},
pmid = {42254517},
issn = {1664-302X},
abstract = {BACKGROUND: Geographic variations in climate and lifestyle may be associated with hypertension (HTN) through alterations in the gut microbiota and its metabolites. This study aimed to comparatively analyze the gut microbiome and fecal metabolome of hypertensive patients from two Chinese cities characterized by distinct climatic conditions: Daqing (middle-temperate climate) and Haikou (tropical climate). The objective was to identify gut microbial and metabolic characteristics associated with geographic differences and to provide insights into HTN prevention and management.

METHODS: A cross-sectional study was conducted between May and December 2024, involving hypertensive patients from Daqing and Haikou. Fecal samples were collected from 28 hypertensive patients in Daqing (DQ group) and 32 in Haikou (HK group), and analyzed using shotgun metagenomic sequencing and untargeted metabolomics.

RESULTS: Differences in microbial composition and metabolite profiles were observed between the two groups. Using ALDEx2 analysis at the genus level, 34 genera were identified as differentially abundant between the DQ and HK groups. After adjusting for potential confounding variables, including age, body mass index, smoking, and drinking status, 6 genera remained significantly associated with geographic grouping. A logistic regression model based on these genera achieved an area under the curve (AUC) of 0.8069, with Pseudescherichia showing the highest individual discriminatory performance (AUC = 0.7925). Functional analysis suggested that pathways such as xylene degradation and biofilm formation were relatively reduced in the DQ group. Metabolomic analysis identified 38 differentially abundant metabolites, including 15-hydroxyeicosatetraenoic acid (15-HETE), 7α,25-dihydroxycholesterol, the putative metabolite (3-hydroxypentadecanoyl) lysine, and ginsenoside Rg3. Dysregulated pathways were mainly involved in glycerophospholipid metabolism, ABC transporters, and choline metabolism. Correlation analysis revealed potential associations between differential microbes and metabolites.

CONCLUSION: Distinct gut microbiome and metabolome profiles were observed between hypertensive patients from the two geographic regions. These findings suggest potential associations between environmental factors and host-microbiome-metabolite interactions.},
}

@article {pmid42254525,
year = {2026},
author = {Chen, J and Zhou, Q and Cao, X and Jin, S and Wu, Y and Ren, T and Xu, C and Chen, H and Zhang, H and Zhang, Y and Liu, J},
title = {The outcome of Infliximab induction in patients with severe ulcerative colitis may be related to intestinal microbiota.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779143},
pmid = {42254525},
issn = {1664-302X},
abstract = {BACKGROUND AND OBJECTIVE: Although infliximab (IFX) is endorsed for induction therapy in severe ulcerative colitis (SUC), its therapeutic response remains heterogeneous. We conducted a comprehensive analysis of fecal and mucosal microbiota, coupled with targeted metabolomics, to delineate microbial and metabolic signatures predictive of IFX induction efficacy and to explore mechanistic pathways underlying differential treatment responses.

METHODS: This study was a prospective cohort study (clinical study registration number: ChiCTR2300071816). It enrolled adult patients aged ≥ 18 years who were first diagnosed with SUC at the First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital between February 2022 and December 2023. None of these patients had received any medication for UC, including antibiotics. Clinical data, fecal samples, and rectal mucosal samples were collected for analysis. High-throughput sequencing of the 16S rRNA gene and non-targeted metabolomics analysis were performed on both fecal and rectal mucosal samples. All patients underwent IFX (5 mg/kg) induced remission therapy at weeks 0, 2, and 6. Based on their clinical response at week 14, they were categorized into two groups: response and unresponse. Significant differences in bacterial composition between the two groups were identified by screening fecal and mucosal samples. The gut microbiota of feces and intestinal mucosa were combined with clinical data to create four prediction models and conduct comparisons. Furthermore, different metabolites from fecal and mucosal samples of the two groups were screened and compared with KEGG and PubChem databases to identify metabolic pathways associated with the efficacy of IFX-induced therapy.

RESULTS: Compared with non-responders, IFX responders harbor distinct gut microbiota. Clinical indices alone poorly forecast induction response (AUC 0.6429). Augmenting clinical variables with fecal or mucosal microbiota improves prediction to AUC 0.795 and 0.900, respectively; combining both compartments further elevates performance to AUC 0.964, indicating that integrated microbiome profiling is essential for optimal IFX response prediction. IFX responders and non-responders differ metabolically, with more discriminatory features in mucosa than feces. The most enriched differential pathways in feces included nicotinate and nicotinamide metabolism, butyrate metabolism, biosynthesis of valine, leucine, and isoleucine, pantothenate and coenzyme A biosynthesis, histidine metabolism, and alanine, aspartate, and glutamate metabolism. In mucosa, the most enriched differential pathways included alanine, aspartate, and glutamate metabolism, sphingolipid metabolism, ascorbate and aldarate metabolism, tryptophan metabolism, and D-glutamine and D-glutamate metabolism. The common pathway enriched in both feces and mucosa was alanine, aspartate, and glutamate metabolism.

CONCLUSION: The intestinal microbiota may be a predictive factor for IFX induction outcome in patients with SUC. The metabolic pathway of alanine, aspartate, and glutamate may be associated with the 14-week clinical response to IFX treatment in SUC.},
}

@article {pmid42254837,
year = {2026},
author = {Schmelz, P and Eckensperger, S and Osvatic, J and Séneca, J and Alzubaidy, H and Petersen, JM},
title = {Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag082},
pmid = {42254837},
issn = {2730-6151},
abstract = {All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health; however, such efforts are often hindered by the dominance of host-derived material in, e.g. DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome DNA Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.},
}

@article {pmid42254838,
year = {2026},
author = {Kobayashi, R and Shiba, T and Nagai, T and Komatsu, K and Matsumura, S and Watanabe, T and Nemoto, T and Takada, K and Takeuchi, Y and Iwata, T},
title = {Metatranscriptomic insights into microbial network modulation and pathogen dynamics underlying healing outcomes in non-surgical periodontal treatment.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag092},
pmid = {42254838},
issn = {2730-6151},
abstract = {Gingivitis and periodontitis are caused by oral microbiome dysbiosis. Post-treatment alterations in bacterial community structure are uncharacterized in situ, including how these alterations may differ between resolved and unresolved disease states. Understanding these treatment-induced microbial shifts and identifying prognostic markers in situ associated with favorable or unfavorable outcomes are crucial for developing diagnostic tools and refining therapeutic strategies. Therefore, we performed metatranscriptomic analysis on subgingival plaque samples from the anterior teeth of individuals, including healthy, gingivitis, and periodontitis sites, before and after non-surgical treatment in 28 patients. We revealed a new bacteriological characteristic of periodontitis, where periodontal pathogens emerge within the bacterial network alongside excessive and skewed associations among bacterial taxa, such as those in the Streptococcus and Actinomyces genera. Furthermore, these imbalances were found improvable through non-surgical treatment. However, even in clinically resolved gingivitis or periodontitis, the bacterial networks did not fully revert to the state observed in healthy sites. This was due to the persistence of periodontal pathogens, absent in the networks at healthy sites. By comparing groups in which periodontitis resolved and those in which it did not, specific bacterial taxa, such as Neisseria elongata and Rothia aeria, were suggested to play a role in the periodontitis healing process, while increases in genes related to glycine degradation and bacterial adhesion, including glycine dehydrogenase β-subunit and cleaved adhesin domain were implicated in inhibiting the healing process. These findings provide insights for the development of treatment strategies targeting specific bacteria and functional genes involved in the resolution of periodontitis.},
}

@article {pmid42254885,
year = {2026},
author = {Targino, AJM and da Silva Vilarinho, JLP and Carneiro, VMA and Greggianin, BF and Guimarães, MDCM},
title = {Periodontal Ecosystem and Clinical Implications of the Oral Microbiome: A Narrative Review.},
journal = {International journal of dentistry},
volume = {2026},
number = {},
pages = {1479982},
pmid = {42254885},
issn = {1687-8728},
abstract = {BACKGROUND: Periodontal disease, although widely documented, remains one of the leading causes of tooth loss worldwide. This situation can be attributed to patients' difficulty in following treatment protocols and to an incomplete understanding of the disease's mechanisms, which could be explored to develop new therapies.

OBJECTIVE: The present study aimed to summarize the main advances in understanding the periodontal microbiome, especially concerning the development of genetic sequencing technologies and metabolite analysis, as well as new treatment methods that have emerged from these innovations.

METHODS: A narrative literature review was conducted through searches in the PubMed, Scopus, Web of Science, and SciELO databases, prioritizing publications from the past 15 years while also including classic and foundational studies relevant to the theoretical framework.

CONCLUSIONS: Periodontal microbiome results from the synergistic interaction among different microorganisms, rather than just the sum of their individual metabolites. This synergy can create structural microarrangements that resist biofilm disruption, such as fungal barriers surrounding Gram-negative bacteria. Innovative treatments-such as host response modulation with resolvins and oral microbiome modulation, particularly using prebiotics derived from plant extracts (nitrate metabolism)-offer promising prospects. However, limitations remain regarding their clinical use and the challenge of managing refractory cases, highlighting the need for further research to support these findings.},
}

@article {pmid42254896,
year = {2026},
author = {Vaggi, C and Vötterl, JC and Lerch, F and Yosi, F and Koger, S and Ricci, S and Verhovsek, D and Metzler-Zebeli, BU},
title = {Characterization of fecal bacterial microbiomes according to fecal color, consistency, and sample type in piglets before and after weaning.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1815748},
pmid = {42254896},
issn = {2297-1769},
abstract = {Fecal samples are widely used as a proxy for the large intestinal microbiota; however, phenotypic characteristics (e.g., color and consistency) may be associated with divergent microbial profiles, especially around weaning, when diet and physiological adaptation rapidly alter gut function. The relationship between fecal phenotype, sample type, and piglet gut microbiota under physiological conditions remains poorly understood. This study investigated the bacterial communities in different fecal phenotypes of piglets shortly before and immediately after weaning. The fecal consistency of 192 piglets across two replicate batches was scored daily from day of life (DoL) 28 to 36, and fecal or rectal swab samples were collected at DoL28 and DoL33. The samples were classified by type (feces/swab), color (brown/yellow), and consistency (balls/liquid). DNA was extracted for quantification of total bacterial gene copies and 16S rRNA gene sequencing, and microbial composition was analyzed using Quantitative Insights Into Microbial Ecology 2 (QIIME2), Statistical Analysis System (SAS), and R. Fecal consistency changed markedly over time, shifting from predominantly ball-shaped on DoL28-32 to softer feces thereafter (p < 0.001). Age strongly influenced microbiota structure, with marked increases in relative abundance of Prevotella and Alloprevotella from DoL28 to DoL33, whereas the abundance of Escherichia, Methanobrevibacter, and Fusobacterium declined. Microbial communities differed between sample types, with swabs potentially reflecting mucosa-associated taxa more closely than fecal samples. Shannon and Simpson indices indicated reduced diversity in yellow and liquid feces on DoL28 (p < 0.001). Swabs and yellow liquid feces on DoL28 showed higher relative abundances of Escherichia, Bacteroides, and Fusobacterium, whereas brown ball-shaped feces were enriched in Lachnospiraceae, Prevotella, and Lactobacillus on both sampling days (p < 0.05). Overall, each fecal phenotype exhibited a distinct bacterial signature, and the sample type influenced the composition of the captured community. Monitoring fecal phenotypes alongside selecting appropriate sample types may enhance the interpretation of microbiome data and offer a practical, non-invasive approach to assess gut health during the critical weaning period.},
}

@article {pmid42254901,
year = {2026},
author = {Adegbeye, MJ and Sadarman, S and Poonooru, R and Alvarado-Ramírez, ER and Widiawati, Y},
title = {Editorial: Natural compounds/products and livestock productivity: enhancing antioxidant levels, gut health, mitigating greenhouse gas emissions, and disease control, volume II.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1867705},
pmid = {42254901},
issn = {2297-1769},
}

@article {pmid42254910,
year = {2026},
author = {Al-Ardhi, SA and Al-Waeli, SK and Osman, MA and Al-Shahari, EA and Siddig, NH and Ahmed, AE and Hazzazi, Y and Sumayli, M and Al-Rasheed, M and Alanazi, IMM},
title = {Modeling of growth performance, physiological response, and intestinal microbiota shift in growing Japanese quail fed olive leaf powder.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1824857},
pmid = {42254910},
issn = {2297-1769},
abstract = {INTRODUCTION: Due to the anti-inflammatory, antioxidant, and antibacterial properties of olive leaf powder (OLP), it may serve as a beneficial feed supplement for birds. This study aimed to evaluate the effect of adding OLP to feed on growth efficiency, carcass traits, blood parameters, antioxidant activity, and cecal microbial load in growing Japanese quail.

METHODS: Three hundred and seventy-five one-day-old quail chicks were randomly assigned to five experimental groups, each containing five replicates of 15 birds: a control group fed a basal feed and four experimental groups given 3, 4, 5, and 6% OLP per kg of quail diets for the 6 weeks.

RESULTS: The results showed a significant (P < 0.05) improvement in growth performance, with increased live body weight (LBW) and an insignificantly improved feed conversion ratio in the 6% OLP group. Carcass yield and total edible meat also substantially improved (P < 0.05). Blood parameters showed improved (P < 0.05) protein and lipid levels and increased liver enzyme activity; moreover, the use of the OLP led to a decrease in TC, TG, LDL, and VLDL levels, as well as an increase in HDL. Additionally, the activity of antioxidant enzymes increased (P < 0.001), along with higher levels of GSH and SOD activity. All meat quality attributes, including cooking loss %, water-holding capacity, PH values, and meat color, improved (P < 0.05) with the use of OLP. Furthermore, intestinal microbiota analysis showed a significant improvement in Lactobacillus count and a decrease in pathogenic bacteria (total bacterial count, coliforms, E. coli, and Salmonella). However, the Bacillus count was not significantly affected by OLP supplementation.

DISCUSSION: The findings of this study demonstrate that OLP is a promising natural feed additive for growing Japanese quail, enhancing growth performance and the gut microbiome, thereby establishing it as a safe and natural growth promoter.},
}

@article {pmid42255244,
year = {2026},
author = {Saadatkhah, A and Nicholson, L and Buchholz, TA and Hong, L},
title = {Beyond the tumor: the role of the gut microbiome in triple-negative breast cancer.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1832176},
pmid = {42255244},
issn = {2234-943X},
abstract = {The gut microbiome, a metabolically active community of microorganisms in the gastrointestinal tract, regulates host immunity, metabolism, and inflammation. Dysbiosis, or disruption of this ecosystem, has been linked to cancer initiation, progression, and therapy resistance. Triple-negative breast cancer (TNBC) accounts for 10-15% of breast cancers and is managed primarily with chemotherapy and immune checkpoint inhibitors; however, treatment responses remain variable and these patients are at higher risk of cancer recurrence compared to patients with hormone receptor-positive or HER2-positive breast cancer. Emerging evidence suggests that the gut microbial composition and its diversity can influence outcomes and therapeutic efficacy of systemic treatments in TNBC. We review the current epidemiologic, mechanistic, and clinical evidence on how the gut microbiome influences TNBC biology, with particular attention to the tumor immune microenvironment and response to therapy. We highlight protective and pro-tumorigenic microbial signatures, the impact of antibiotics and obesity, and emerging strategies, such as dietary modulation and microbiome-targeted interventions, that may ultimately be used to optimize TNBC management and improve patient outcomes.},
}

@article {pmid42255295,
year = {2026},
author = {Ranjan, P and Das, D and Bundela, V and Ramesh, A and Verma, RK and Nargund, R and Manandhar, U and Drijber, R and Upadhyay, RK and Sharma, MP},
title = {Role of rhizosphere specific microbiome in enhancing soybean productivity across contrasting soil and crop management systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1830235},
pmid = {42255295},
issn = {1664-462X},
abstract = {Soybeans are a globally significant legume and oilseed crop with a diverse rhizospheric microbiome that can enhance sustainable agriculture by reducing the need for chemical fertilizers. These microbes can potentially impact plant growth and development through symbiotic (rhizobium and mycorrhizae) and non-symbiotic (plant growth-promoting rhizobacteria and fungi) interactions with soybean roots under optimal crop and soil management practices. During the production of soybeans, practices such as excessive use of fertilizers and pesticides, mono-cropping, and intensive tillage are often employed to achieve higher yields. However, these practices can alter the rhizomicrobiome communities and their interactions with soybean crops. Implementing optimal soil and crop management techniques can create a more favorable environment for rhizomicrobial communication with soybean roots, ultimately enhancing nutrient uptake for the soybean plants. In this review, we address how the soil rhizomicrobiome communicates with soybean roots, its role in promoting plant health and yield, and approaches to enhance soil rhizomicrobiome diversity and function through improved crop and soil management practices. Herein we synthesize current literature on soybean-microbe interactions, including both symbiotic and non-symbiotic relationships with an emphasis on how plant-microbe interactions within soybean cropping systems are influenced by agricultural practices such as crop rotation, intercropping, integrated nutrient management, and no-tillage. Greater understanding of the complexity underlying rhizosphere microbiome relationships will enable design of local cropping systems enhancing soybean yield along with improving soil health.},
}

@article {pmid42255425,
year = {2026},
author = {Hu, R and Deng, J and Tu, L and Jiang, T and Xu, J},
title = {Integration of tongue image features and tongue coating microbiome for differentiating dampness patterns in MASLD.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1851610},
pmid = {42255425},
issn = {1664-2392},
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a prevalent metabolic disorder that can progress to hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. Traditional Chinese medicine (TCM) has therapeutic effects in MASLD. In TCM, dampness patterns predominate in MASLD and are further classified into damp heat (DH) and cold dampness (CD) subtypes based on distinct pathogenic mechanisms. However, the characteristics of the tongue image and tongue coating microbiome across different dampness patterns and their associations with clinical features remain poorly understood.

MATERIALS AND METHODS: This study enrolled 320 participants, including 214s dampness patterns patients with MASLD, further classified into DH pattern (n = 110) and CD pattern(n = 104), along with 106 healthy controls. Tongue images and tongue coating samples were collected; tongue image segmentation was performed using a customized Tongue-InSPyReNet framework and extract quantitative features, while tongue coating microbiota were profiled using 16S rRNA gene sequencing. To distinguish between patterns, five machine learning models were developed and evaluated based on integrated tongue image features and microbiome data.

RESULTS: Significant differences in tongue features and microbial composition were observed between groups. The DH pattern was characterized by a red-crimson tongue with yellow coating and enrichment of Prevotella (P < 0.05). In contrast, the CD pattern more frequently exhibited a pale tongue with petechiae and higher abundances of Streptococcus and Rothia (P < 0.05). Integration of tongue image features and tongue coating microbiome effectively distinguished DH and CD patterns, achieving an AUC of 0.871 and an accuracy of 79.1%.

CONCLUSION: Our study highlights the contributions of tongue image features and the tongue coating microbiome to differentiating two TCM patterns in MASLD, and may provide the rationale for adopting different treatment strategies for different TCM syndromes of MASLD in the future.},
}