@article {pmid42402956,
year = {2026},
author = {Wang, Y and Jin, S and Xu, L and Yan, C},
title = {The Relation Between Antibiotic Use and Gastrointestinal Cancer: A Systematic Review and Meta-Analysis.},
journal = {Journal of biochemical and molecular toxicology},
volume = {40},
number = {7},
pages = {e71006},
doi = {10.1002/jbt.71006},
pmid = {42402956},
issn = {1099-0461},
mesh = {Humans ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; *Gastrointestinal Neoplasms/chemically induced/epidemiology ; },
abstract = {Cancer remains a major cause of premature mortality worldwide, with incidence and mortality rates continuing to rise. Antibiotic use, while essential for treating infections, has been linked to an increased risk of certain cancers, particularly colorectal cancer (CRC), possibly through microbiome disruption. Although previous studies and meta-analyses have reported modest but consistent associations, variations in study design and antibiotic exposure limit the certainty of these findings. Given the widespread use of antibiotics and the growing global cancer burden, a systematic synthesis of the evidence is needed to better understand this relationship and inform preventive strategies. Relevant studies on the relationship between antibiotic use and gastrointestinal (GI) cancer were retrieved from PubMed, Web of Science, Scopus, and Embase. After removing duplicate records, the remaining studies were assessed based on predefined inclusion and exclusion criteria. Data analysis was performed using Comprehensive Meta-Analysis software (version 2). Publication bias was evaluated using Egger's test, and heterogeneity across studies was assessed using the I[2] statistic. The analyses were conducted using odds ratios (OR) with 95% confidence limits. A total of 12 studies met the inclusion criteria and were incorporated into the meta-analysis. Pooled estimates from a random-effects model (I[2] = 97.2%) indicated that antibiotic use was associated with an 18.7% higher risk of GI cancers compared with non-use (OR = 1.187, 95% CI: 1.018-1.386, p = 0.029), with no significant evidence of publication bias. Subgroup analysis revealed a significant association with CRC risk (OR = 1.208, 95% CI: 1.027-1.420, p = 0.022), but not with gastroesophageal cancers, likely reflecting limited data in the latter group. Stratification by exposure intensity demonstrated a dose-response relationship: 1-5 antibiotic prescriptions (OR = 1.077, 95% CI: 1.043-1.112) and > 5 prescriptions (OR = 1.154, 95% CI: 1.124-1.186) were both significantly associated with elevated risk. Similarly, short-term (1-15 days), intermediate-term (15-60 days), and long-term (> 60 days) antibiotic use were linked to progressively higher risks, ranging from 11% to 13% increases. Meta-regression confirmed that a greater number of prescriptions was significantly associated with higher GI cancer risk, although the effect size per prescription was small. No significant linear relationship was detected between duration of exposure (days) and risk, and substantial heterogeneity persisted across studies. This systematic review and meta-analysis provide evidence of a modest but statistically significant association between antibiotic use and an increased risk of GI cancers, including CRC. The observed dose-response patterns suggest that repeated or prolonged exposure may confer greater risk. Potential biological mechanisms include antibiotic-induced alterations in gut microbiome composition, promotion of chronic inflammation, and impairment of immune surveillance, all of which may contribute to carcinogenesis. While the relative increases in risk are moderate, the widespread and often indiscriminate use of antibiotics globally amplifies their potential public health impact. These findings underscore the importance of judicious antibiotic prescribing practices and highlight the need for well-designed longitudinal studies with robust control for confounding factors to clarify causality further, identify high-risk subgroups, and inform targeted prevention strategies.},
}

Humans
*Anti-Bacterial Agents/adverse effects/therapeutic use
*Gastrointestinal Neoplasms/chemically induced/epidemiology

@article {pmid42402960,
year = {2026},
author = {Shi, R and Zhi, Y and Gao, L and Li, SM and Zhi, KQ and Ren, WH},
title = {Artificial intelligence and oral microbiome: Reshaping the diagnostic and therapeutic paradigm of OSCC.},
journal = {Clinical and translational medicine},
volume = {16},
number = {7},
pages = {e70723},
doi = {10.1002/ctm2.70723},
pmid = {42402960},
issn = {2001-1326},
support = {ZR2022MH223//Natural Science Foundation of Shandong Province/ ; },
mesh = {Humans ; *Microbiota/physiology ; *Artificial Intelligence/trends/standards ; *Mouth Neoplasms/diagnosis/therapy/microbiology ; *Mouth/microbiology ; *Carcinoma, Squamous Cell/diagnosis/therapy ; },
abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) remains a major clinical challenge, with delayed diagnosis, frequent resistance to therapy, and poor long-term survival.

METHODS: This review systematically evaluates the methodological framework for applying AI to oral microbiome data in OSCC. Emerging paradigms, including self-supervised learning for leveraging unlabelled data and explainable AI (XAI) techniques for model interpretability, are also discussed. Model evaluation relies on cross-validation, hyperparameter optimisation, and performance metrics such as AUC, accuracy, sensitivity, specificity, and F1-score.

RESULTS: Multiple studies demonstrate that AI-based classifiers, especially random forest models built on salivary or tissue-derived microbial features, achieve outstanding discrimination between OSCC patients and healthy controls in retrospective, single-centre cohorts, with reported AUC values exceeding 0.99 and accuracy >95%. However, these exceptional metrics should be interpreted with caution, as they are susceptible to cohort size, sampling site heterogeneity, batch effects, feature-selection bias, and the absence of independent external validation. Beyond binary diagnosis, AI has been successfully applied to predict lymph node metastasis, explore tumour metabolic reprogramming, and assess environmental interactions. Integrated multi-omics approaches further enhance the specificity and clinical relevance of microbial biomarkers.

CONCLUSIONS: The convergence of AI and oral microbiome analysis is reshaping the diagnostic and therapeutic landscape of OSCC, and explore microbiome-targeted combination therapies. Addressing these challenges will be pivotal to realising truly intelligent, personalised management and ultimately improving outcomes for OSCC patients.},
}

Humans
*Microbiota/physiology
*Artificial Intelligence/trends/standards
*Mouth Neoplasms/diagnosis/therapy/microbiology
*Mouth/microbiology
*Carcinoma, Squamous Cell/diagnosis/therapy

@article {pmid42403177,
year = {2026},
author = {Choi, BY and Kim, HJ and Kim, MJ and Roh, YJ and Hong, JY and Park, KY and Sul, WJ},
title = {Adipose tissue-derived stem cell exosomes enhance skin barrier function and show exploratory associations with the skin mycobiome in aging skin.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {6},
pages = {e2603020},
doi = {10.71150/jm.2603020},
pmid = {42403177},
issn = {1976-3794},
support = {//Korea Health Industry Development Institute/ ; H12300860//Ministry of Health and Welfare/ ; //Chung-Ang University Graduate Research Scholarship/ ; 2024-ER2116-00//Korea National Institute of Health/ ; },
mesh = {Humans ; *Skin Aging/physiology/drug effects ; Skin Microbiome ; Female ; *Skin/microbiology ; Male ; Aged ; *Stem Cells/cytology/metabolism ; Middle Aged ; *Exosomes/metabolism ; *Adipose Tissue/cytology ; Adult ; RNA, Ribosomal, 16S/genetics ; Water Loss, Insensible ; },
abstract = {Skin aging increases transepidermal water loss (TEWL), reduces elasticity, and perturbs the skin microbiome. Adipose tissue-derived stem cell exosomes (ASCE) show regenerative potential; however, their clinical effects on skin physiology and microbiome remain unclear. We conducted a split-face, randomized controlled trial in 16 adults aged ≥ 40 years with visible facial aging. One facial side received ultrasound-assisted transdermal delivery of a human ASCE-containing solution (HACS), whereas the other side received normal saline, at two-week intervals for three sessions. Biophysical outcomes (TEWL, stratum corneum hydration, and elasticity parameters R2/R5/R7) were assessed at baseline and week 2, 4, and 8. Wrinkles, pigmentation, and sebum levels were quantified using Mark-Vu imaging, and the Physician's Global Aesthetic Improvement Scale (PGAIS) and patient satisfaction assessment scores were recorded. Skin swabs from ten participants were subjected to 16S rRNA and ITS1 sequencing. HACS treatment significantly reduced TEWL (p = 0.006 at week 2; p = 0.009 at week 8) and increased hydration (p < 0.001 at all time points) with a significant increase in elasticity (R2/R5/R7 values, p < 0.001). Both the PGAIS and patient satisfaction scores were significantly higher on the experimental side. Bacterial α/β-diversity remained largely unchanged, and no bacterial taxa remained significantly associated with skin parameters after FDR correction. In contrast, several fungal taxa showed significant positive associations with skin parameters after FDR correction, detectable only on the HACS-treated side. No significant adverse events were observed. HACS improved barrier function, elasticity, and aesthetic outcomes, whereas microbiome analyses suggested a modest fungal response associated with treatment-related skin changes in aging skin.},
}

Humans
*Skin Aging/physiology/drug effects
Skin Microbiome
Female
*Skin/microbiology
Male
Aged
*Stem Cells/cytology/metabolism
Middle Aged
*Exosomes/metabolism
*Adipose Tissue/cytology
Adult
RNA, Ribosomal, 16S/genetics
Water Loss, Insensible

@article {pmid42403302,
year = {2026},
author = {Ielo, S and Carriera, L and Mari, PV and Barone, R and Cefaloni, F and Loperfido, A and Coppola, A and Baglioni, S and De Corso, E and Scala, R},
title = {Upper and lower airway crosstalk in acute exacerbations of COPD: a clinical and biological overview.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/17476348.2026.2699459},
pmid = {42403302},
issn = {1747-6356},
abstract = {INTRODUCTION: Acute exacerbations of chronic obstructive pulmonary disease (AE-COPD) are acute worsening events characterized by increased dyspnea, cough, and sputum production. Although traditionally viewed as lower airway events, growing evidence suggests that AE-COPD may reflect broader pan-airway dysfunction involving both upper and lower respiratory compartments.

AREAS COVERED: This overview examines upper - lower airway crosstalk in AE-COPD across three domains: pan-airway inflammation, epithelial alarmin/cytokine networks, and the continuous airway microbiome. We discuss the coexistence of COPD with sinonasal inflammation, chronic rhinitis, and chronic rhinosinusitis, and their possible contribution to symptom burden, impaired quality of life, and exacerbation risk. We also review mechanisms linking upper and lower airways, including epithelial barrier dysfunction, impaired antiviral responses, innate immune activation, alarmin release, and microbiome-driven dysbiosis.

EXPERT OPINION: Recognizing AE-COPD as a manifestation of pan-airway dysfunction may have relevant clinical implications. Systematic assessment of upper airway symptoms and comorbidities could improve phenotyping, risk stratification, and therapeutic targeting, particularly in frequent exacerbators. Future longitudinal and multi-omic studies are needed to validate upper airway biomarkers and determine whether targeted treatment of upper airway disease can modify COPD outcomes.},
}

@article {pmid42403425,
year = {2026},
author = {Mirowski, K and Ciszowski, K and Zwolinska-Wcislo, M},
title = {Environmental shaping of tolerance failure in autoimmune liver diseases: a phenotype-specific framework with primary biliary cholangitis as the strongest model.},
journal = {Journal of translational autoimmunity},
volume = {13},
number = {},
pages = {100376},
pmid = {42403425},
issn = {2589-9090},
abstract = {Autoimmune liver diseases (primary biliary cholangitis, PBC; primary sclerosing cholangitis, PSC; autoimmune hepatitis, AIH) are three distinct, organ-specific autoimmune disorders that share loss of tolerance as the central pathophysiological mechanism but differ in target tissue, age of onset, genetic background, and environmental susceptibility. This review examines how environmental exposures modulate tolerance failure and tissue-directed injury across the three phenotypes. The signal is most coherent in PBC, where epidemiological evidence (smoking, recurrent urinary tract infections), neoantigen-focused mechanistic work on xenobiotic modification of PDC-E2, cholangiocyte apotope biology, and emerging exposomic data converge. PSC is better understood through gut-liver-microbiome interactions. AIH, including pediatric AIH, shows a weaker and more heterogeneous environmental signature complicated by overlap with drug-induced autoimmune-like hepatitis (DI-ALH). We outline the limitations of current exposomic methodology and propose phenotype-resolved research priorities. Environmental modulation does not replace loss of tolerance as the central paradigm; it provides context for how tolerance failure becomes durable and tissue-selective.},
}

@article {pmid42403700,
year = {2026},
author = {Coury, SM and Lopez, SD and Savoca, PW and Gaines, EM and Parenti, B and Razon, A and Dosanjh, KK and Labus, JS and Jacobs, JP and Eich, TS and Wong, MD and Callaghan, BL and Silvers, JA},
title = {Does sex moderate health and Alzheimer's disease risk tied to early educational experiences? The reducing inequities through social and educational change follow-up in early adulthood extension study protocol.},
journal = {Brain, behavior, & immunity - health},
volume = {55},
number = {},
pages = {101294},
pmid = {42403700},
issn = {2666-3546},
abstract = {Alzheimer's disease (AD) -a progressive neurodegenerative disorder that is characterized by insidious cognitive decline and distinct neuropathological features- significantly impacts daily life functioning and behavior and is disproportionally prevalent in women compared to men. The reasons and risk factors for sex-based disparities in AD prevalence are still largely unclear, however early life exposures (e.g., education and stress) may be important contributing factors. Therefore, it is increasingly important to disentangle the complex interactions between known early environmental protective and risk factors and genetic susceptibility and uncover how these factors might impact and shape neurobiological processes. Moreover, it is critical to assess how these processes, in turn, influence later cognitive and brain health outcomes that may confer sex-specific pathways of risk for developing AD. In this paper we describe the rationale and study protocol for The Reducing Inequities through Social and Educational Change Follow-Up in Early Adulthood Extension (RISE-Up EA+; R01AG089426) study, a follow-up study of 300 participants aged 24-26 years old that leverages a natural quasi-experimental cohort to investigate how health outcomes tied to socioeconomic mobility opportunity may contribute to sex-specific vulnerability for developing AD later in life. To examine how sex-specific vulnerabilities related to early educational experiences may set the stage for later AD risk, we will assess self-report, cognitive, biological (e.g., inflammation and microbiome), and brain health measures. Results from this work provide the opportunity to better understand how adolescent mobility opportunities might contribute to later life health outcomes and influence sex-specific developmental pathways important for later AD risk.},
}

@article {pmid42403898,
year = {2026},
author = {Hu, M and Xiang, J and Hou, X and Shao, Y and Peng, Q and Li, C},
title = {Gut frailty in chronic heart failure: clinical determinants and distinct microbial signatures.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1779873},
pmid = {42403898},
issn = {2297-055X},
abstract = {BACKGROUND: Gut frailty is a critical yet under-recognized sub-phenotype in chronic heart failure (CHF) that may exacerbate systemic inflammation. This study aimed to identify risk factors for gut frailty in CHF and characterize associated gut microbiome alterations.

METHODS: In this cross-sectional study of 270 CHF patients, gut frailty was defined as a Gastrointestinal Symptom Rating Scale score of ≥3. Clinical determinants were identified via multivariable logistic regression. 16S rRNA sequencing was performed on a balanced sub-cohort (n = 60) to analyze microbial diversity, taxonomy, and predicted metabolic functions.

RESULTS: A meat-rich diet independently increased gut frailty risk (OR = 3.995; 95% CI: 1.107-16.110; P = 0.041), while vegetarian adherence was protective (OR = 0.148; 95% CI: 0.024-0.883; P = 0.035). Alpha-diversity was significantly reduced across all indices (Observed ASVs, Shannon, Chao1, ACE; all P < 0.0001), with distinct beta-diversity clustering (ANOSIM R = 0.2766, P = 0.001). The frail phenotype harbored fewer unique ASVs (76 vs. 142) and exhibited depletion of short-chain fatty acid producers (Faecalibacterium, Coprococcus) alongside enrichment of pathobionts and trimethylamine-producers (Lachnoclostridium, Enterobacteriaceae). Functionally, the microbiome shifted toward stress-responsive xenobiotic biodegradation, notably cytochrome P450 (log2 fold change = 2.82).

CONCLUSION: Gut frailty in CHF constitutes a distinct syndrome modulated by diet and characterized by profound dysbiosis and metabolic reprogramming. Targeting the gut-heart axis through nutritional or microbiome-directed interventions may offer a novel strategy to mitigate frailty in heart failure.},
}

@article {pmid42403914,
year = {2026},
author = {Llorente, C},
title = {Intestinal neutral ceramidase, microbial metabolites and epithelial fucosylation in MASH.},
journal = {eGastroenterology},
volume = {4},
number = {2},
pages = {e100458},
pmid = {42403914},
issn = {2976-7296},
}

@article {pmid42403915,
year = {2026},
author = {Wang, T and Chen, L and Lei, C and Song, X and Tuohongerbieke, A and Feng, J and Gasparetto, R and Zhang, X and McClain, CJ and Tan, Y and Deng, Z},
title = {Intestinal neutral ceramidase exacerbates MASH pathogenesis.},
journal = {eGastroenterology},
volume = {4},
number = {2},
pages = {e100417},
pmid = {42403915},
issn = {2976-7296},
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease and its more severe manifestation, metabolic dysfunction-associated steatohepatitis (MASH), are intimately linked to genetic factors, gut microbiota and barrier alteration. Ceramidases and ceramides are associated with MASH, yet the role of intestinal neutral ceramidase in MASH development remains unclear.

METHODS: Murine models with intestinal epithelial cell (IEC)-specific depletion of neutral ceramidase (Asah2[ΔIEC]) or aryl hydrocarbon receptor (AhR [ΔIEC]) were subjected to either a Western diet (WD) at 6 weeks old for 10-12 months to induce MASH, or a hydrogenated vegetable oil, sucrose, palmitate and cholesterol (HSPC) diet to accelerate MASH progression. Fecal microbiota transplantation was performed in germ-free mice.

RESULTS: MASH is associated with the induction of neutral ceramidase, which reshapes the intestinal microbiota and metabolite profiles, leading to increased production of 2-hydroxyhippuric acid (2-HHA). We identified 2-HHA as an inhibitor of AhR signalling, a pathway that normally promotes intestinal fucosylation. Elevated 2-HHA suppresses AhR activity, reduces fucosylation and contributes to MASH and associated airway inflammation in mice fed WD or HSPC diet. Notably, IEC-specific deletion of neutral ceramidase decreases 2-HHA levels, restores AhR signalling, enhances fucosylation and protects against MASH. Consistently, intestinal AhR deficiency exacerbates MASH by reducing intestinal fucosylation, whereas supplementation with fucoidan increases fucosylation, improves barrier function and attenuates MASH.

CONCLUSIONS: These findings identify intestinal neutral ceramidase as a key driver of MASH through a microbiota-2-HHA-AhR axis that impairs intestinal fucosylation and barrier function, highlighting a potential therapeutic target.},
}

@article {pmid42403930,
year = {2026},
author = {Loria, F and Kattel, A and Junusova, M and Brucale, M and Valle, F and Bergese, P and Kobrin, EG and Chiesi, A and Guazzi, P and Korulu, S and Stulova, I and Zarovni, N and Vilu, R},
title = {Investigating the Effect of Ginger-Derived Nanovesicles on the Growth and Metabolic Activity of Bacteroides thetaiotaomicron: An Isothermal Microcalorimetric Study.},
journal = {Journal of extracellular biology},
volume = {5},
number = {7},
pages = {e70163},
pmid = {42403930},
issn = {2768-2811},
abstract = {Plant-derived extracellular vesicles (EVs) have shown numerous health benefits, including modulation of the human gut microbiota. Herein, we employed isothermal microcalorimetry (IMC) to explore the effects of ginger-derived nanovesicles (G-NVs) on the growth and metabolic activity of Bacteroides thetaiotaomicron (Bt), a dominant saccharolytic commensal with promising next-generation probiotic potential. Bt was exposed to either G-NVs or the ginger extract separated from G-NVs (G-CTL) in defined media under anaerobic conditions. Both ginger samples enhanced bacterial specific growth rate and maximum metabolic activity, inducing the latter earlier. However, higher biomass production and greater secretion of acetic, succinic and propionic acids occurred only in response to the G-CTL. Complete sugar depletion and unchanged free amino acid levels indicated preferential carbohydrate utilisation by Bt. Overall, these findings revealed that Bt's metabolic state is shaped by both G-NVs and G-CTL, yet through distinct mechanisms, with G-NVs inducing rapid stimulation without increasing total metabolic output and G-CTL providing a sustained, dose-dependent effect. To our knowledge, this is the first study applying IMC to monitor in real-time the impact of EVs on microbial growth and metabolism, underscoring IMC's utility for mechanistic studies of EV-microbe interactions. Furthermore, this research sets the ground for innovative strategies in nutraceutical and microbiome-targeted therapy development.},
}

@article {pmid42404004,
year = {2026},
author = {Chen, J and Chen, J and Wang, Z},
title = {Targeting the Gut Microbiota with Herbal Compounds from Traditional Chinese Medicine: A Mechanistic Synthesis of a Novel Therapeutic Approach for Ulcerative Colitis.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {590456},
pmid = {42404004},
issn = {1178-7031},
abstract = {Ulcerative colitis (UC) represents a chronic relapsing inflammatory bowel disease characterized by substantial unmet clinical needs and limited curative modalities. Accumulating evidence implicates gut microbiota dysbiosis as a pivotal pathogenic driver, positioning microbiota-targeted interventions as promising therapeutic strategies. This review systematically delineates the mechanisms by which herbal compounds from Traditional Chinese Medicine ameliorate UC through the restoration of microbial and metabolic homeostasis-including the modulation of beneficial commensals and their bioactive metabolites-thereby reinforcing intestinal barrier integrity and dampening mucosal inflammation. Although translational bottlenecks persist, integrative multi-omics frameworks coupled with advanced pharmaceutical engineering offer viable pathways to bridge preclinical findings and clinical application. Taken together, deciphering the bidirectional crosstalk between herbal compounds and the gut microbiome paves the way for mechanism-based, personalized botanical therapeutics in UC management.},
}

@article {pmid42404061,
year = {2026},
author = {Molina, MA and Dai, W},
title = {Microbiome-Metabolome Crosstalk in HPV Pathogenesis: From Ecosystem Dynamics to Translational Biomarkers.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0158},
pmid = {42404061},
issn = {2001-0370},
abstract = {High-risk human papillomavirus (hrHPV) infection alters the cervicovaginal microenvironment, driving metabolic reprogramming that influences viral persistence and progression to cervical cancer. This review adopts a systems-level perspective to synthesize findings from recent metabolomic studies across urine, vaginal swabs, and cervicovaginal fluids, highlighting consistent trends from cervicovaginal health through hrHPV infection, persistence, cervical lesion development, and cancer. HPV infection is characterized by increased microbial amines and oxidative stress, whereas viral persistence and high-grade cervical lesions exhibit disrupted metabolism of amino acids, lipids, and nucleotides. Cervical cancer is associated with distinct metabolic signatures involving sphingolipids, ketone bodies, and intermediates of the tricarboxylic acid cycle. Collectively, metabolic profiles emerge as functional readouts of host-microbiome interactions, often showing stronger associations with clinical outcomes than microbial composition alone. Integrative multiomics approaches combining metabolomics with microbiome- and host-derived data are beginning to uncover coordinated biological pathways underlying HPV pathogenesis and may improve risk stratification and biomarker discovery. Despite methodological heterogeneity, converging evidence supports the potential of metabolic profiling for early detection of cervical neoplasia and stratification of hrHPV-positive women, although reproducibility across studies remains limited. Future longitudinal and integrative studies, supported by standardized analytical frameworks and computational modeling, are needed to clarify causal mechanisms and enable the development of clinically actionable biomarkers and targeted interventions.},
}

@article {pmid42404236,
year = {2026},
author = {Davis, JM and Ogbewekon, A and Gordon, DM and Kipp, ZA and Martinez, GJ and Stefater-Richards, MA and Wagner, KH and Hinds, TD},
title = {Microbiome-derived cancer: the catabolism of bilirubin to urobilin in the liver-gut axis and its consequences.},
journal = {Gastroenterology report},
volume = {14},
number = {},
pages = {goag065},
pmid = {42404236},
issn = {2052-0034},
abstract = {Colorectal cancer (CRC) is the second leading cause of cancer-related deaths globally and is associated with factors, such as obesity, inflammation, and metabolic disorders. Bilirubin, a byproduct of heme degradation, is increasingly recognized as a signaling molecule with antioxidant properties that protect against obesity by reducing oxidative stress, decreasing inflammation, and activating the nuclear receptor PPARα, which enhances fat metabolism and utilization. The gut microbiome converts bilirubin to urobilinogen via bilirubin reductase, which is then rapidly oxidized to urobilin, thereby influencing colon cancer outcomes. Urobilin may contribute to CRC by being linked to insulin resistance and inflammation in obese individuals, and it could cause DNA damage. Additionally, it may serve as a biomarker for CRC, obesity, insulin-resistant diabetes, and irritable bowel syndrome. This review covers enzymes in the heme oxygenase pathway (HMOX, BVR, UGT1A1) that regulate bilirubin production and excretion, as well as the microbiome-driven breakdown of bilirubin into urobilinogen and its subsequent oxidation to urobilin. It highlights the inverse relationships among CRC, obesity, and inflammation and suggests that urobilin pathways influence CRC risk. Restoring bilirubin's protective signaling and reducing circulating urobilin could open new avenues for prevention and treatment.},
}

@article {pmid42404294,
year = {2026},
author = {Gao, W and Liu, Y and Wang, Q and Xiao, H and Wang, F and Wang, L},
title = {Vaginal Microecological Imbalance, Human Papillomavirus Infection, and Cervical Carcinogenesis: Mechanisms and Clinical Implications.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {621765},
pmid = {42404294},
issn = {1178-7074},
abstract = {The vaginal microecology serves as a critical barrier for female reproductive tract health, with its dysbiosis being closely linked to persistent HPV infection and the initiation and progression of cervical cancer. This review systematically outlines the composition and functions of the vaginal microbiota and delves into the multifaceted mechanisms by which microecological imbalance promotes human papillomavirus (HPV) acquisition, persistence, and oncogenic transformation. These mechanisms include dysregulation of local and systemic immunity, chronic inflammation, alterations in microbial metabolites, and disruption of the epithelial barrier. Furthermore, the article synthesizes recent advancements in novel strategies for cervical cancer prevention, auxiliary diagnosis, and treatment based on microecological modulation. The overarching aim is to provide a consolidated theoretical foundation and identify potential therapeutic targets for the precise prevention and management of cervical cancer, highlighting the pivotal role of maintaining or restoring vaginal microbial homeostasis.},
}

@article {pmid42404342,
year = {2026},
author = {Karaskova, E and Friedecky, D and Kleparnik, D and Palkovska, A and Brumarova, R and Karasek, D},
title = {Cardiovascular risk in inflammatory bowel disease: focus on lipids and visceral adipose tissue.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1860937},
pmid = {42404342},
issn = {1664-2392},
mesh = {Humans ; *Cardiovascular Diseases/etiology/metabolism/epidemiology/pathology ; *Inflammatory Bowel Diseases/complications/metabolism ; *Intra-Abdominal Fat/metabolism/pathology ; Heart Disease Risk Factors ; *Lipid Metabolism ; Risk Factors ; *Lipids/blood ; Animals ; Atherosclerosis ; },
abstract = {Inflammatory bowel diseases (IBD), including Crohn's disease and ulcerative colitis, are chronic immune-mediated diseases that are increasingly recognized as systemic diseases with significant cardiovascular consequences. Growing epidemiological evidence suggests that patients with IBD face an increased risk of atherosclerotic cardiovascular disease (ASCVD) that cannot be fully explained by traditional cardiovascular risk factors. This excess risk is most pronounced in younger patients and during periods of active intestinal inflammation. This review summarizes current knowledge on common pathogenic mechanisms linking IBD and ASCVD. Chronic systemic inflammation plays a central role, promoting endothelial dysfunction, hypercoagulability, immune cell activation, and accelerated atherogenesis. Other factors include intestinal barrier disruption with microbial translocation, dysbiosis of the gut microbiome, dysfunctional visceral adipose tissue, and adverse metabolic effects of some IBD therapies. Particular emphasis is placed on lipid abnormalities observed in IBD, including the "lipid paradox", a phenomenon in which reduced circulating lipid levels paradoxically coexist with increased cardiovascular risk due to inflammation-mediated changes in lipid metabolism leading to lipoprotein dysfunction, and emerging lipidomic biomarkers that suggest causal relationships between specific lipid species, inflammatory mediators, and cardiovascular risk. Attention is also given to current strategies for the assessment and prevention of cardiovascular risk in IBD, emphasizing the importance of controlling disease activity, minimizing corticosteroid exposure, and aggressive treatment of modifiable cardiovascular risk factors. Traditional risk calculators may underestimate risk in this population, highlighting the need for tools that integrate inflammatory burden and imaging of subclinical atherosclerosis. Optimization of anti-inflammatory therapy along with individualized cardiovascular prevention strategies may improve long-term outcomes in patients with IBD.},
}

Humans
*Cardiovascular Diseases/etiology/metabolism/epidemiology/pathology
*Inflammatory Bowel Diseases/complications/metabolism
*Intra-Abdominal Fat/metabolism/pathology
Heart Disease Risk Factors
*Lipid Metabolism
Risk Factors
*Lipids/blood
Animals
Atherosclerosis

@article {pmid42404519,
year = {2026},
author = {Nawara-Węgrzyn, N and Cichy, Ł and Kowalska-Duplaga, K and Morka, A},
title = {Protein-losing enteropathy after the Fontan procedure - A cardiologist's and gastroenterologist's perspective.},
journal = {Annals of pediatric cardiology},
volume = {19},
number = {2},
pages = {198-204},
pmid = {42404519},
issn = {0974-2069},
abstract = {Protein-losing enteropathy (PLE) is a severe, multifactorial complication of Fontan circulation that affects approximately 12% of patients with single-ventricle physiology. Because no universal standard therapy exists, management is individualized and guided by the dominant hemodynamic and lymphatic drivers, clinical severity, and local expertise. Chronically elevated central venous pressure and impaired lymphatic drainage promote lymph congestion and leakage into the intestinal lumen, leading to hypoalbuminemia, edema, diarrhea, malnutrition, and immune dysfunction. Treatment is multimodal and includes optimization of Fontan hemodynamics, symptomatic and anti-inflammatory pharmacotherapy, and targeted nutritional strategies (high-protein diet, medium-chain triglycerides, and supplementation). Advances in lymphatic imaging have enabled phenotype-based, lymphatic-directed interventions such as lymphatic embolization and thoracic duct decompression, which can improve outcomes in selected patients. When conservative and interventional strategies fail, heart transplantation remains the definitive option. Emerging evidence also highlights the potential contribution of the gut-liver axis, including intestinal barrier dysfunction and alterations in the microbiome, which may influence inflammation and disease persistence. This review summarizes current concepts in PLE pathophysiology and therapeutic approaches, with emphasis on lymphatic dysfunction and evolving adjunctive targets.},
}

@article {pmid42404574,
year = {2026},
author = {Campione, E and Simonelli, A and Pistoia, ES and Cosio, T and Artosi, F and Diluvio, L and Bianchi, L and Gaziano, R},
title = {The role of dupilumab in skin microbiome shifts in the Netherton genodermatosis: a case report and review of literature.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1854027},
pmid = {42404574},
issn = {2296-858X},
abstract = {Skin dysbiosis plays a crucial role in inflammatory skin diseases, particularly in genodermatoses such as Netherton syndrome (NS). This case report aimed to investigate changes in the skin microbiome of a patient with Netherton syndrome before and during dupilumab therapy, with the goal of expanding the limited evidence currently available on this topic. We report the case of a 35-year-old woman diagnosed with NS at birth, who, prior to dupilumab therapy, presented with atopic dermatitis (AD), ichthyosis linearis circumflexa, and severe pruritus. Dupilumab therapy was initiated, and skin swabs were collected from lesional sites at three different time points: at baseline, after 1 month, and after 1 year of continuous dupilumab therapy. At baseline, a microbiome analysis revealed low microbial diversity with a predominance of Pantoea and Pseudomonas species. After 1 year, a significant increase in microbial diversity, with a predominance of Staphylococcus species and an increase in Malassezia species, was observed. Clinically, the patient experienced remission in parallel with these microbiome shifts. Post-treatment, the skin microbiome showed increased microbial diversity and re-establishment of beneficial commensals, more closely resembling healthy skin. The findings of this case report underscore the role of dupilumab in restoring a healthy skin microbiome along with symptomatological and clinical improvement in the genodermatosis Netherton syndrome.},
}

@article {pmid42404584,
year = {2026},
author = {Singkham-In, U and Pedcharat, S and Saisorn, W and Sawaswong, V and Phuengmaung, P and Leelahavanichkul, A},
title = {Pseudomonas aeruginosa Virulence Bacteriophage Isolated From Inflammatory Mouse Feces Exhibits Bactericidal Activity in Infected Wounds of a Mouse Model.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {4451708},
pmid = {42404584},
issn = {1687-918X},
abstract = {BACKGROUND: Recently, bacteriophages have risen as a potent therapy for superbug infections. The mammal gut demonstrates an interesting source of virulence bacteriophages. The gut with inflammation is phage-rich; therefore, we primarily aimed to prove the concept that an inflammatory gut is a possible source of effective phages and to evaluate the efficacy of the candidate phage against Pseudomonas aeruginosa in vitro and in a mouse model of infected wounds.

RESULTS: The gut microbiome of cecal ligation and puncture (CLP) sepsis mice, an animal model of inflammation, showed a dominant presence of Podoviruses. CLP bacteriophages (CLP Φ1-Φ4), of which the CLP Φ4 possessed the broadest bactericidal activity (viable bacterial cell reduction in time-kill study) against P. aeruginosa isolates. The CLP Φ4 specifically killed the Pseudomonas aeruginosa clinical (PACL) strain with two huge burst events. Although the CLP Φ4 had no effect on ex vivo mouse bone marrow-derived macrophage (BMDM) cytokine gene expression and cytokine production, the CLP Φ4 attenuated the severity of the P. aeruginosa-infected wound mouse model after treatment. P. aeruginosa PACL exhibited significantly pathogenic characteristics in a mouse model, including excessive bacterial loads (in wounds and internal organs, indicating the systemic infection due to localized infected wound with P. aeruginosa), increased IL-6 cytokine (in serum), upregulated IL-6 expression (in wounds), and immune cell infiltration (in wounds), indicating severe inflammation. In the CLP Φ4 treatment alone, the wound tissues upregulated IL-10 expression and recruited inflammatory cells. Interestingly, the three-day CLP Φ4 treatment was adequate to eradicate P. aeruginosa PACL in the wounds and other internal organs. After treatment, the mouse serum cytokine showed a remarkably decreased IL-6. Likewise, IL-6 downregulation and IL-10 upregulation were demonstrated in the treated wounds, suggesting an anti-inflammatory shift. These results demonstrated the effectiveness (bacterial wound and internal organ clearance and cytokine modulation) of the CLP Φ4 in the P. aeruginosa-infected wound and systemic infection. Finally, the CLP Φ4 isolation verified a proof of concept that the irritated gut acts as a source of bacteriophages.

CONCLUSIONS: The gut virome was a promising and interesting source of antimicrobial and immunomodulating bacteriophage.},
}

@article {pmid42404619,
year = {2026},
author = {Ramani, RR and Baskaran, S and Arun, KV and Alamelu, S and Arumugamnainar, D},
title = {Salivary metagenomic profiling of Neisseria , Dialister , and Filifactor species in periodontal health and disease using next-generation sequencing.},
journal = {Journal of oral biology and craniofacial research},
volume = {16},
number = {4},
pages = {101482},
pmid = {42404619},
issn = {2212-4268},
abstract = {BACKGROUND: Periodontal diseases represent a complex dysbiosis-driven inflammatory condition, where the transition from health to gingivitis and periodontitis is accompanied by distinct microbial shifts. Emerging evidence highlights the significance of less-studied genera such as Neisseria, Dialister, and Filifactor in shaping periodontal outcomes. This study aimed to investigate the salivary distribution of Neisseria, Dialister, and Filifactor species across periodontal health, gingivitis, periodontitis, and gingival recession using next-generation sequencing (NGS).

METHODS: Whole saliva samples were collected from 40 participants (10 per group) classified according to the American Academy of Periodontology criteria. Microbial DNA was extracted and subjected to 16S rRNA sequencing (V3-V4 region, Illumina MiSeq). Species-level classification was performed using the Human Oral Microbiome Database. Frequency distributions were compared across groups using Fisher's exact test, with significance set at p < 0.05.

RESULTS: Distinct patterns were observed. Several commensal Neisseria species, including N. subflava (p = 0.001), N. elongata(p = 0.015), and N. polysaccharea (p = 0.001), showed significantly reduced prevalence in periodontitis compared with health and gingivitis. In contrast, Dialister pneumosintes exhibited a sharp increase in all diseased groups (p = 0.002). Filifactor alocis was markedly enriched in gingivitis, recession, and periodontitis (p = 0.011), suggesting its strong association with disease states.

CONCLUSION: The findings demonstrate a characteristic microbial shift in saliva: health-associated Neisseria species decline with disease progression, while anaerobic taxa such as D. pneumosintes and F. alocis expand. These results align with the polymicrobial synergy and dysbiosis model and underscore the potential of these species as salivary biomarkers for early detection and monitoring of periodontal disease.},
}

@article {pmid42404621,
year = {2026},
author = {Dorado-González, GE and Muro-Reyes, A and de Los Santos-Villalobos, S and García-Cervantes, D and García-Olivares, JG and Robles-Berlanga, HM and Gutiérrez-Bañuelos, H},
title = {Microbial drivers of soil health: Integrating physical, chemical and biological properties for food security under climate change.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100636},
pmid = {42404621},
issn = {2666-5174},
abstract = {Climate change is intensifying heat, drought/flooding extremes, salinity, and CO2-driven shifts that disrupt soil structure, chemistry, and biological activity, with cascading consequences for crop productivity and food security. This review synthesizes evidence that soil health results from the interconnected interactions among physical structure (aggregation, porosity, bulk density, and pore connectivity), chemical constraints (pH, salinity, nutrient availability, cation exchange capacity, and redox heterogeneity), and biological activity (microbial biomass, diversity, and functional pathways). A central conclusion is that climate impacts are frequently mediated through pore-scale microhabitats (oxygen and moisture gradients, redox microsites, and substrate accessibility), which reorganize microbial functional guilds and regulate C-N-P transformations, organic matter turnover, and aggregation dynamics. We highlight mechanistic pathways by which microbiomes actively shape soil resilience, including EPS/biofilm-mediated aggregate stabilization, extracellular enzyme systems that control depolymerization and nutrient acquisition, and metabolite-driven nutrient mobilization (e.g., organic acids and siderophores), alongside nitrogen and phosphorus cycling processes that are highly sensitive to aeration and moisture regimes. Evidence across agroecosystems indicates that effective climate-smart soil management is most robust when "habitat-first" practices (reduced disturbance, continuous plant inputs, organic amendments) are combined with context-dependent microbiome steering (diversified rotations/cover crops and targeted inoculants). Overall, integrating cross-domain indicators with mechanistic understanding offers actionable pathways to strengthen soil multifunctionality, stabilize yields under climate variability, and support sustainable food systems.},
}

@article {pmid42404749,
year = {2026},
author = {Bhuiyan, MNI and Rahman, MS and Rahman, MM and Saha, BK},
title = {Rhizospheric Microbes and Nanoparticles Synergize to Enhance Plant Immune Responses.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {7},
number = {4},
pages = {e70183},
pmid = {42404749},
issn = {2575-6265},
abstract = {Sustainable crop production increasingly requires innovative strategies that can enhance plant resilience while reducing dependence on synthetic agrochemicals. Recent advances in nanotechnology and rhizosphere microbiome research have created new opportunities to strengthen plant defense systems through integrated biological and material-based approaches. This review introduces the concept of nanobiotic synergies, defined as the strategic combination of engineered or biologically synthesized nanoparticles with beneficial rhizospheric microorganisms to improve plant immunity, stress tolerance, nutrient acquisition, and overall crop performance. We critically examine the individual and interactive roles of nanoparticles and plant-associated microbiomes in regulating immune signaling, rhizosphere communication, nutrient dynamics, and adaptation to biotic and abiotic stresses. Particular emphasis is placed on the mechanistic pathways underlying plant-microbe-nanoparticle interactions, including immune priming, modulation of root exudates, microbiome restructuring, antioxidant regulation, and stress-responsive signaling networks. The review further evaluates emerging evidence supporting nanobiotic applications in disease suppression, stress mitigation, and sustainable crop management while addressing key challenges related to environmental safety, regulatory oversight, scalability, and long-term ecosystem impacts. Finally, we propose a systems-level framework integrating multi-omics technologies, systems biology, and predictive computational approaches to guide the rational design of next-generation nanobiotic agricultural inputs. Collectively, this review highlights the potential of nanobiotic strategies as a promising avenue for advancing climate-resilient and environmentally sustainable agriculture.},
}

@article {pmid42404766,
year = {2026},
author = {Liu, Y and Li, C and Zhao, Y and Zhong, LQ and Li, Y and Xiao, Z and Liu, Q and Chen, X},
title = {From health to periodontitis: dynamic changes in the subgingival microbiome and their association with systemic inflammation levels.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1864541},
pmid = {42404766},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Female ; *Gingiva/microbiology ; Male ; *Periodontitis/microbiology/pathology ; Adult ; *Inflammation ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Biomarkers/blood ; Disease Progression ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {INTRODUCTION: This study aims to characterize the dynamic progression of the subgingival microbiome across different stages of periodontitis and to explore its association with levels of systemic chronic inflammation.

METHODS: A total of 148 subjects were enrolled based on predefined inclusion and exclusion criteria. Participants were classified into five groups according to diagnostic criteria: Stage I (n = 25), Stage II (n = 30), Stage III (n = 31), Stage IV (n = 30), and a healthy control group (n = 32). Subgingival samples were collected from all participants and subjected to the 16S rRNA gene sequencing. Peripheral venous blood was obtained to determine blood cell counts and to calculate systemic inflammatory markers. The Spearman's correlation analysis was performed to evaluate associations between subgingival microbial communities and systemic inflammatory markers.

RESULTS: Patients with Stage IV periodontitis exhibited significantly higher levels of WBC, NEUT, NLR, and SII compared to those with Stage I disease. Notably, NLR and SII were markedly elevated (P < 0.01), while WBC and NEUT also showed statistically significant increases (P < 0.05). Further analysis revealed a positive correlation between the abundance of multiple periodontitis-associated bacterial genera and systemic inflammatory markers.

DISCUSSION: This study demonstrates that the progression of periodontitis is associated with distinct changes in the subgingival microbial community, and that this microbial dysbiosis is positively correlated with elevated levels of systemic chronic inflammation.},
}

Humans
*Microbiota
RNA, Ribosomal, 16S/genetics
Female
*Gingiva/microbiology
Male
*Periodontitis/microbiology/pathology
Adult
*Inflammation
Middle Aged
Bacteria/classification/genetics/isolation & purification
Biomarkers/blood
Disease Progression
DNA, Bacterial/genetics
DNA, Ribosomal/genetics/chemistry

@article {pmid42404767,
year = {2026},
author = {Abdelaal, R and Anwar, N and Moustafa, A and Abdelnaser, A},
title = {Skin microbiome characterization in acne vulgaris across urban and rural Egyptian populations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1816205},
pmid = {42404767},
issn = {2235-2988},
mesh = {Humans ; *Acne Vulgaris/microbiology/epidemiology ; *Skin Microbiome ; Egypt/epidemiology ; Rural Population ; RNA, Ribosomal, 16S/genetics ; Male ; Urban Population ; Female ; Adult ; Young Adult ; Adolescent ; *Skin/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Severity of Illness Index ; },
abstract = {BACKGROUND: Cutibacterium acnes is recognized as a key contributor to acne, but recent evidence suggests that shifts in skin microbial diversity, rather than simple overgrowth, are critical in disease progression. Despite the unique genetic and environmental characteristics of the Middle East and North Africa, microbiome data on acne remain scarce.

OBJECTIVE: To characterize the skin microbiome associated with acne vulgaris in Egyptian urban and rural populations and assess the influence of acne severity and lifestyle factors on microbial diversity.

METHODS: We recruited 45 acne patients (urban n=37, rural n=8) and 25 healthy urban controls. Skin swabs were collected and analyzed by 16S rRNA sequencing. Microbial community profiles were generated with QIIME2, while differential taxa and functional pathways were evaluated using ANCOM-BC and PICRUSt2.

RESULTS: In urban patients, moderate-to-severe acne was associated with greater microbial evenness and diversity, though species richness was unchanged. Community composition differed significantly by severity. Functional analysis revealed enrichment of amino acid biosynthesis pathways. Rural patients showed greater diversity, distinct microbial structures, and functional enrichment in amino acid and lipid metabolism pathways, with reduced enrichment in energy metabolism pathways. A depletion of C. acnes ASVs in patients with more severe acne across both cohorts was observed, possibly indicating a strain-specific behavior of C. acnes.

CONCLUSION: Interventions that selectively eliminate pathogenic C. acnes strains while conserving beneficial ones may prove more efficacious for managing acne than broad-spectrum approaches. Environmental context significantly shapes the acne-associated skin microbiome. It influences both the taxonomic composition and potential function.},
}

Humans
*Acne Vulgaris/microbiology/epidemiology
*Skin Microbiome
Egypt/epidemiology
Rural Population
RNA, Ribosomal, 16S/genetics
Male
Urban Population
Female
Adult
Young Adult
Adolescent
*Skin/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Severity of Illness Index

@article {pmid42404769,
year = {2026},
author = {Wang, Y and Wu, J},
title = {Intratumoral microbiome: a key regulator and novel therapeutic target for chemoresistance in pancreatic cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1860523},
pmid = {42404769},
issn = {2235-2988},
mesh = {Humans ; *Pancreatic Neoplasms/drug therapy/microbiology/pathology ; *Drug Resistance, Neoplasm ; Tumor Microenvironment ; *Microbiota ; Antineoplastic Agents/therapeutic use/pharmacology ; Animals ; Signal Transduction ; },
abstract = {Pancreatic cancer is a highly lethal gastrointestinal malignancy with chemotherapy resistance as a major obstacle to improving prognosis. Emerging evidence indicates that the intratumoral microbiome is closely implicated in the development, progression, and therapeutic response of pancreatic cancer. The intratumoral microbiome of pancreatic cancer is mainly composed of Proteobacteria and Firmicutes, and its composition is significantly correlated with patient survival. Intratumoral microbes drive tumor progression by remodeling the immune microenvironment, inducing DNA damage, and activating oncogenic signaling pathways. Meanwhile, they exacerbate chemotherapy resistance via multiple mechanisms, including remodeling the extracellular matrix, establishing an immunosuppressive microenvironment, and metabolically inactivating chemotherapeutic agents. This review systematically summarizes the community composition of the intratumoral microbiome in pancreatic cancer, its regulatory effects, and underlying mechanisms on chemotherapy resistance, as well as the latest advances in targeted therapeutic strategies.},
}

Humans
*Pancreatic Neoplasms/drug therapy/microbiology/pathology
*Drug Resistance, Neoplasm
Tumor Microenvironment
*Microbiota
Antineoplastic Agents/therapeutic use/pharmacology
Animals
Signal Transduction

@article {pmid42404775,
year = {2026},
author = {Mallick, S and Chakkalakkal, GJ and Heryanto, C and Alqassar, JD and Martin, A and Lažetić, V and Eleftherianos, I},
title = {Photorhabdus symbiotic bacteria drive stronger microbiome restructuring in Plodia interpunctella larvae during infection with Heterorhabditis nematodes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1838162},
pmid = {42404775},
issn = {2235-2988},
mesh = {Animals ; *Photorhabdus/physiology ; *Symbiosis ; Larva/microbiology/parasitology ; *Microbiota ; *Moths/microbiology/parasitology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rhabditoidea/microbiology ; },
abstract = {The insect microbiome can influence host physiology and responses to infection, yet how it changes during interactions with pathogens remains underexplored. The Indianmeal moth, Plodia interpunctella, a major global pest of stored food products, can be targeted for biological control using the entomopathogenic nematodes (EPNs) Heterorhabditis bacteriophora. Understanding whether H. bacteriophora infection alters the P. interpunctella larval microbiome is crucial, since changes in microbial diversity, measured by alpha diversity indices (Faith's Phylogenetic diversity, Observed Amplicon Sequence Variants, Shannon diversity, and Pielou's evenness), can affect how the infection develops and influence the success of the EPNs as biological control agents. However, the response of the P. interpunctella larval microbiome to H. bacteriophora infection has not been well-characterized. Here, we investigated how the P. interpunctella larval microbiome changes following infection with either symbiotic (carrying the symbiotic bacteria Photorhabdus luminescens) or axenic (lacking bacterial symbionts) H. bacteriophora. Beta diversity analyses (Bray-Curtis dissimilarity, PERMANOVA) revealed shifts in ASV richness (number of observed amplicon sequence variants) and community evenness in the P. interpunctella larvae infected with either symbiotic or axenic nematodes. P. interpunctella larvae were sampled at 36h and 60h post-infection for 16s rRNA sequencing (READS/SAMPLE). We analyzed 150 P. interpunctella larval microbiomes per time point (60 larvae infected with symbiotic H. bacteriophora, 60 larvae infected with axenic H. bacteriophora, and 30 uninfected larvae). Illumina paired-end sequencing of 16S rRNA V3-V4 libraries yielded a mean sequencing depth of approximately 3.76 × 10^5 read pairs per sample. The UpSet analyses of shared ASVs across uninfected larvae and larvae infected with either symbiotic or axenic H. bacteriophora identified distinct ASVs unique to each infection type. LEfSe analysis further identified differentially expressed taxa observed in the microbiome of larvae infected with either symbiotic or axenic H. bacteriophora. Notably, larvae infected with symbiotic H. bacteriophora showed the highest number of unique ASVs, indicating that larval microbiome restructuring correlates with the presence of the symbiotic bacteria P. luminescens. These results indicate that the bacterial symbiont associated with EPNs is an important driver of host microbiome changes during infection, which may influence infection outcomes and the effectiveness of EPN-based biological control.},
}

Animals
*Photorhabdus/physiology
*Symbiosis
Larva/microbiology/parasitology
*Microbiota
*Moths/microbiology/parasitology
Phylogeny
RNA, Ribosomal, 16S/genetics
*Rhabditoidea/microbiology

@article {pmid42404783,
year = {2026},
author = {Zhang, T and Tang, B and Yu, Z and Zhang, C and Pan, Z and Liang, C and Zheng, H and Wang, Q},
title = {Gut microbiota-immune crosstalk in osteoarthritis: pathogenic mechanisms and emerging therapeutic opportunities.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1869199},
pmid = {42404783},
issn = {1664-302X},
abstract = {Osteoarthritis (OA) has traditionally been viewed as a degenerative joint disorder primarily associated with mechanical stress and progressive structural damage. Increasing evidence, however, indicates that immune imbalance and persistent low-grade inflammation are critically involved in disease initiation and progression. In this context, alterations in the gut microbiota have attracted growing attention due to their capacity to influence systemic immune responses. Here, we provide an integrated overview of the interactions between the gut microbiota and the immune system in OA and introduce the concept of a "gut microbiota-immune-joint axis" to describe this interconnected regulatory network. Disruption of the gut microbial ecosystem may impair intestinal barrier function and facilitate the entry of microbe-derived signals into the circulation. These signals subsequently activate inflammatory pathways, including TLR4/NF-κB and JAK/STAT cascades, leading to immune cell reprogramming, altered macrophage polarization, and imbalanced T-cell responses. The resulting chronic inflammatory state can extend beyond the intestine and contribute to pathological changes in synovial tissue, cartilage, and subchondral bone. In addition, we summarize current progress in microbiota-oriented therapeutic strategies, particularly the use of probiotics and prebiotics, and discuss their potential roles in modulating immune responses and restoring systemic homeostasis. Finally, we highlight existing challenges and propose future directions, emphasizing the importance of multi-omics integration and longitudinal clinical studies to better understand the dynamic nature of microbiota-immune interactions and to support the development of targeted interventions in OA.},
}

@article {pmid42404789,
year = {2026},
author = {Luo, Z and Zhu, S and Lu, Y and Yili, W and Xu, J},
title = {Gut microbiota-mediated cardiovascular effects of Gastrodia elata polysaccharides: resolving the bioavailability-efficacy paradox.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1868003},
pmid = {42404789},
issn = {1664-302X},
abstract = {BACKGROUND: Growing evidence suggests that many plant-derived polysaccharides exert systemic effects through gut microbiota-mediated mechanisms rather than direct absorption. Gastrodia elata polysaccharides (GEPs) represent a promising but mechanistically complex class of bioactive compounds with potential cardiovascular relevance.

OBJECTIVE: This review aims to examine the role of gut microbiota in mediating the biological effects of GEPs, with particular focus on resolving the bioavailability-efficacy paradox through host-microbe interactions.

METHODS: A narrative synthesis of recent literature was conducted, integrating data on microbiota-polysaccharide interactions, microbial fermentation processes, metabolite production, and downstream host signaling pathways.

RESULTS: Due to limited systemic bioavailability, GEPs undergo extensive fermentation by gut microbiota, generating bioactive metabolites such as short-chain fatty acids and secondary bile acids. These metabolites modulate key host pathways including inflammation, oxidative stress, endothelial function, and lipid metabolism. Emerging evidence highlights the central role of the gut-heart axis in mediating these effects.

CONCLUSION: The biological activity of GEPs is best understood within a microbiota-centered framework. This perspective provides new insights into polysaccharide pharmacology and supports the development of microbiome-targeted therapeutic strategies.},
}

@article {pmid42404794,
year = {2026},
author = {Putumbaka, S and Thorgersen, MP and Schut, GJ and Poole, FL and Barrow, CE and Glass, JB and Adams, MWW},
title = {Classification of tungsten-containing oxidoreductases provides insights into their biochemical and physiological diversity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1849799},
pmid = {42404794},
issn = {1664-302X},
abstract = {Tungsten-containing oxidoreductases (WORs) are a diverse family of enzymes with over 4,000 known members that can be subdivided into 92 clades based on the phylogeny of the large pyranopterin cofactor-containing large subunit (WorL). Despite being widespread in Bacteria and Archaea, particularly in members of the human microbiome, only five of the 92 WOR clades contain a WOR with a defined physiological role in cellular metabolism, primarily-but not exclusively-involved in oxidation of various aldehydes. However, this phylogenetic-based organizational system lacks a perspective on the diversity and complexity of WOR enzymes. Herein, we propose a non-phylogenetic classification system for WORs based on predicted subunit composition and electron carrier specificity that provides insight into potential physiological roles. WORs can be divided into five classes that range in complexity and predicted function. The simpler cytoplasmic Class I-III WORs are involved in aldehyde detoxification, a modified glycolysis pathway and cold adaptation. More complex multimeric WORs are proposed to use multiple electron carriers in bifurcating reactions (Class IV) or interact with various respiratory systems via associations with the cell membrane (Class V). We characterized two new WORs, one Class I and one Class V, from the human gut bacterium Cetobacterium somerae, and showed that the former enzyme had aldehyde oxidation activity but the latter did not. By combining phylogenetic information with the new WOR classification system, we can predict structural and functional characteristics of as-yet uncharaterized WORs and identify unique and novel enzymes for future studies.},
}

@article {pmid42404795,
year = {2026},
author = {Tang, J and Chen, L and Wang, Q and He, X and Hang, D and Chen, G and Feng, L},
title = {Optimized fecal microbiota transplantation using membrane-filtered bacterial concentrates as adjunctive therapy for mild-to-moderate ulcerative colitis: a retrospective cohort study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1805799},
pmid = {42404795},
issn = {1664-302X},
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic approach for ulcerative colitis (UC). This single-center retrospective cohort study evaluated the clinical effectiveness and safety of an optimized FMT protocol, in which donor bacteria were concentrated by tangential-flow micropore membrane filtration and delivered after pre-FMT antibiotic preconditioning, as adjunctive therapy in adults with mild-to-moderate UC.

METHODS: We analyzed prospectively collected data from 156 patients with mild-to-moderate active UC treated between December 2022 and December 2024. Treatment allocation was determined by a shared clinical decision between the gastroenterologist and patient based on disease severity, prior medication exposure, and patient preference. Patients were grouped into four pre-specified treatment strata: aminosalicylates alone (Group A, n = 42), aminosalicylates plus corticosteroids/immunosuppressants (Group B, n = 38), aminosalicylates plus FMT (Group FMT1, n = 40), and aminosalicylates plus corticosteroids/immunosuppressants plus FMT (Group FMT2, n = 36). Donor stools were processed using a validated tangential-flow 0.22-μm membrane filtration workflow that retains and concentrates viable bacteria in the retentate while clearing soluble metabolites and host debris in the permeate. Confounding was addressed using multivariable logistic regression and inverse probability of treatment weighting (IPTW) as a sensitivity analysis. The primary outcome was clinical response at 12 weeks; effect sizes are reported as risk differences with 95% confidence intervals.

RESULTS: Clinical response rates at 12 weeks were 31.0% (Group A), 52.6% (Group B), 72.5% (Group FMT1), and 77.8% (Group FMT2). Clinical remission rates were 19.0%, 34.2%, 55.0%, and 61.1%, respectively. FMT-containing regimens were associated with higher response and remission than aminosalicylates alone (risk difference for response: 41.5%, 95% CI 22.7-60.3% for FMT1 vs. A; 46.8%, 95% CI 28.0-65.6% for FMT2 vs. A; both P < 0.001). Microbiome analysis using 16S rRNA gene sequencing showed that responders had increased Bacteroides-related amplicon sequence variants and increased alpha diversity comparable to donor profiles, while non-responders maintained dysbiotic profiles. Adverse events were mild and comparable across all groups.

CONCLUSIONS: In this retrospective cohort, an optimized FMT protocol using membrane-filtered bacterial concentrates was associated with higher rates of clinical response, clinical remission and endoscopic improvement at 12 weeks compared with conventional therapy, with an acceptable short-term safety profile. Given the observational design, these findings should be interpreted as hypothesis-generating and require confirmation in randomized controlled trials.},
}

@article {pmid42404798,
year = {2026},
author = {Yao, M and Li, X and Li, L and Yan, H and Li, X and Xu, E and Zhou, H},
title = {Synergistic modulation of the gut microbiome-liver-host metabolome axis associates with the therapeutic efficacy of Danlou tablet against metabolic syndrome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1808318},
pmid = {42404798},
issn = {1664-302X},
abstract = {BACKGROUND: Obesity drives chronic diseases such as cardiovascular disease and diabetes. Danlou tablet (DLT), a traditional Chinese medicine formula, is used to treat coronary heart disease by regulating lipid metabolism, suggesting potential for addressing obesity-related metabolic dysfunction. However, its role in obesity and insulin resistance remains unexplored.

OBJECTIVES: We investigated the efficacy and mechanisms of DLT against high-fat diet (HFD)-induced obesity and insulin resistance.

METHODS: C57BL/6N mice were fed an HFD for 22 weeks and treated with DLT. A comprehensive phenotypic assessment was conducted, including body weight, glucose tolerance, insulin sensitivity, serum biochemistry, and histopathology of key tissues. To elucidate the therapeutic mechanism, we integrated 16S rRNA gene sequencing of gut microbiota, serum metabolomics (UPLC-Q-TOF-MS), and hepatic transcriptomics.

RESULTS: DLT treatment counteracted HFD-induced metabolic dysfunction, reducing body weight, adiposity, dyslipidemia, and insulin resistance, while ameliorating hepatic steatosis, inflammation, and oxidative stress. At the microbial level, DLT restored gut microbial diversity, corrected the Firmicutes/Bacteroidota ratio, and modulated key genera. Metabolomics linked these changes to restored fatty acid β-oxidation. In the liver, transcriptomics showed that DLT reversed HFD-induced gene expression, suppressed inflammatory pathways and enhanced fatty acid oxidation and xenobiotic metabolism. Integrated multi-omics analysis revealed a strong correlative relationship that DLT's therapeutic benefits are associated with the modulation of the gut-liver axis, where remodeling of the gut microbiome is closely linked to the reprogramming of hepatic metabolic pathways.

CONCLUSION: DLT counteracts HFD-induced obesity and insulin resistance via a multi-level regulatory mechanism that is closely associated with the modulation of the gut-liver axis, which involves suppressing pathogenic gut microbes, restoring fatty acid metabolism, and enhancing hepatic lipid catabolism and antioxidant defense. This comprehensive preclinical evidence supports the clinical translation of DLT as a novel therapeutic option for obesity and type 2 diabetes mellitus.},
}

@article {pmid42404879,
year = {2026},
author = {Dai, P and Feng, J and Cao, J and Fan, D},
title = {Integrative multi-omics profiling reveals coordinated immunometabolic reprogramming and host-microbiome interactions in acute pancreatitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1828633},
pmid = {42404879},
issn = {1664-3224},
mesh = {Humans ; Multiomics ; *Pancreatitis/metabolism/microbiology/immunology ; Metabolomics ; Gene Expression Profiling ; *Host Microbial Interactions/immunology ; Biomarkers ; Metabolic Reprogramming ; *Gastrointestinal Microbiome/immunology ; Acute Disease ; Female ; Transcriptome ; Male ; Metabolome ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) is a life-threatening inflammatory disorder characterized by diverse etiologies and complex pathophysiological mechanisms involving immune dysregulation, systemic metabolic reprogramming, and gut microbiota disturbances. Although single-omics studies have provided partial insights into AP pathogenesis, comprehensive integrative multi-omics analyses investigating the intricate interactions among immunity, metabolism, and the microbiome in AP remain limited.

METHODS: We conducted an integrative multi-omics analysis of peripheral blood transcriptomics, untargeted plasma metabolomics, and fecal whole-metagenome sequencing in 15 patients with AP and 15 age- and sex-matched healthy controls. Differentially expressed genes (DEGs), metabolites (DEMs), and gut microbial species (DGMs) were identified. Subsequently, functional enrichment analysis, correlation network analysis, and exploratory machine learning approaches were employed to investigate molecular interactions and identify candidate biomarkers.

RESULTS: Transcriptomic profiling identified 4, 776 DEGs, including 409 immune-related genes significantly enriched in the NF-κB, IL-17, and cytokine-cytokine receptor interaction pathways, indicating pronounced inflammatory activation. Metabolomic analysis detected 296 DEMs, with prominent alterations in amino acid and lipid metabolism, mong which 9 metabolites showed potential discriminatory value (AUC > 0.75), with representative metabolites including xanthine, homocarnosine, and tetradecanedioic acid. Metagenomic sequencing revealed significant microbial compositional and functional remodeling, characterized by enrichment of pro-inflammatory taxa such as Escherichia coli and Streptococcus anginosus, alongside depletion of SCFA-producing commensals including Faecalibacterium prausnitzii and Blautia wexlerae. Functional profiling demonstrated disrupted amino acid metabolism, gut-brain signaling, and SCFA synthesis. Multi-omics integration revealed 215 significant correlations between host genes, metabolites, and microbes, highlighting key interaction hubs. An exploratory random forest model identified Lachnospira pectinoschiza, Megamonas funiformis, and SRGN as candidate biomarkers, showing promising classification performance within the current cohort (AUC = 0.951).

CONCLUSIONS: This study provides a systems-level characterization of the immune, metabolic, and microbial alterations in AP. The identified molecular signatures and cross-omics interaction networks offer mechanistic insights into AP pathogenesis and highlight candidate biomarkers that warrant further validation in larger, independent cohorts.},
}

Humans
Multiomics
*Pancreatitis/metabolism/microbiology/immunology
Metabolomics
Gene Expression Profiling
*Host Microbial Interactions/immunology
Biomarkers
Metabolic Reprogramming
*Gastrointestinal Microbiome/immunology
Acute Disease
Female
Transcriptome
Male
Metabolome

@article {pmid42404902,
year = {2026},
author = {Yin, Z and Gong, G and Yin, J},
title = {Bidirectional communication between spinal cord injury and gut microbiota, from the bench to the bedside.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1742885},
pmid = {42404902},
issn = {1664-3224},
mesh = {*Spinal Cord Injuries/microbiology/therapy/metabolism/immunology ; Humans ; Animals ; *Gastrointestinal Microbiome ; *Dysbiosis ; Blood-Spinal Cord Barrier ; Neuroinflammatory Diseases ; },
abstract = {Spinal cord injury (SCI) is a type of central nervous system damage that often results in motor, sensory, and autonomic dysfunction, and can lead to death, with currently no effective treatment available. As research on the microbiome in central nervous system disorders progresses, the role of gut microbiota in spinal cord injury has garnered significant attention. Spinal cord injury disrupts intestinal function and triggers an imbalance in gut microbiota, while metabolites produced by gut microbiota can cross the blood-spinal cord barrier into the central nervous system, exacerbating neuroinflammation in the spinal cord. The relationship between gut microbiota dysbiosis and spinal cord injury is bidirectional. In recent years, the proposal of the 'gut microbiota-gut-spinal cord' axis theory has led to increased interest in the impact of gut microbiota on spinal cord injury. Gut microbiota not only serve as biomarkers for the severity of spinal cord injury but also represent potential therapeutic targets. Current research primarily focuses on the alterations in gut microbiota following spinal cord injury and the potential effects of microbiota-derived metabolites-such as aryl hydrocarbon receptor agonists and short-chain fatty acids-on secondary inflammatory responses post-injury. Although numerous studies have utilized various approaches to modulate gut microbiota to promote functional recovery after spinal cord injury, standardized and effective clinical treatments remain elusive. This review synthesizes laboratory and clinical perspectives on the mechanisms underlying the interaction between spinal cord injury and gut microbiota, aiming to provide novel insights for the therapy of spinal cord injury.},
}

*Spinal Cord Injuries/microbiology/therapy/metabolism/immunology
Humans
Animals
*Gastrointestinal Microbiome
*Dysbiosis
Blood-Spinal Cord Barrier
Neuroinflammatory Diseases

@article {pmid42404992,
year = {2026},
author = {Szilagyi, A and Galiatsatos, P and Margolese, N and Hilzenrat, N},
title = {Microbiome alternative treatments for hepatic encephalopathy: Reassessment of the potential use of lactose in lactase non-persistent cirrhosis patients.},
journal = {Canadian liver journal},
volume = {9},
number = {2},
pages = {319-327},
pmid = {42404992},
issn = {2561-4444},
abstract = {BACKGROUND: Hepatic encephalopathy is secondary to liver failure and is prevalent in 20%-40% of cirrhosis patients. The cause involves ammonia toxicity, gut-brain interactions, and inflammation usually involving the microbiome. The aim was to review succinct management of microbiome disturbances. The purpose includes an argument for further research into the possible selective benefit of lactose and dairy products in managing chronic hepatic encephalopathy in lactose maldigesters.

METHODS: Articles from 1970 to June 2025 were sought on PubMed and Google Scholar, as well as individual articles, regarding using altered microbiome and hepatic encephalopathy management.

RESULTS: Non-digestible disaccharides and synthetic polymers, often combined with non-absorbable antibiotic rifaximin, have been found to benefit hepatic encephalopathy. It is of note that after a few reports, lactose was abandoned as a potential treatment in lactase non-persistent cirrhotic patients. After abandonment for unclear reasons, colonic adaptation in lactase non-persistent populations was clearly defined to be associated with microbiome changes similar to other non-absorbable disaccharides.

CONCLUSIONS: While current treatment is acceptable to most patients, the potential role of lactose and dairy products likely deserves further studies in patients with lactase non-persistence. The process of colonic adaptation may favour improvement in hepatic encephalopathy by altering the bacterial milieu. Use of dairy foods could also improve nutrition in cirrhosis. As such, use of lactose or dairy products could have a wide application since cirrhosis is common in parts of the world where lactose maldigestion is also widespread.},
}

@article {pmid42405211,
year = {2026},
author = {Jung, SM and Sunwoo, W and Son, YM},
title = {Respiratory Microbiome Remodeling in Aging: Implications for Immunosenescence and Therapeutic Intervention.},
journal = {Immune network},
volume = {26},
number = {3},
pages = {e23},
pmid = {42405211},
issn = {1598-2629},
abstract = {Aging involves progressive declines in lung structure and immune function, increasing the incidence and severity of respiratory diseases and reducing vaccine responsiveness. Meanwhile, the respiratory tract harbors a dynamic microbial ecosystem that contributes to immune homeostasis and colonization resistance. Growing evidence indicates that aging disrupts this host-microbe balance within the respiratory tract; however, the mechanisms and therapeutic implications remain incompletely integrated. This review summarizes age-related remodeling of the respiratory microbiome. Beyond compositional shifts, aging alters microbial functions, including metabolic output and resilience to perturbation, exhibiting downstream effects on epithelial barriers, mucus clearance, and immune priming. Furthermore, as the microbiome-immune axis is modifiable, microbiome-targeted therapies represent key opportunities to restore respiratory homeostasis during aging. These interventions, combined with senescence- and cytokine-directed immunomodulation and vaccine optimization using adjuvants and mucosal immune-informed designs, may reduce infection burden and chronic lung disease progression in older populations. Together, this review highlights that a deeper understanding of age-related respiratory microbiome remodeling and its interplay with immunosenescence will be essential for the rational design of microbiome-informed therapies.},
}

@article {pmid42405256,
year = {2026},
author = {Amillano-Cisneros, JM and Raggi, L and Hernández-Rosas, PT and Gomez-Gil, B and Navarrete-Ramírez, P and Ríos-Durán, MG and Martínez-Chávez, CC and Fonseca-Madrigal, J and Martínez-Palacios, CA},
title = {Dietary prebiotics and synbiotics modulate gut microbiota and improve growth performance of Mexican pike silverside Chirostoma estor.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21435},
pmid = {42405256},
issn = {2167-8359},
mesh = {Animals ; *Prebiotics/administration & dosage ; *Synbiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Animal Feed ; Dietary Supplements ; Lactobacillus acidophilus ; Diet/veterinary ; Probiotics ; Inulin/administration & dosage ; Aquaculture/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Aquaculture is the fastest-growing food production sector worldwide and is vital for a sustainable animal protein supply. However, optimizing fish performance in captivity remains a major challenge, requiring functional diets that support a healthy holobiont. This study evaluated the effects of balanced experimental diets supplemented with inulin or yeast cell wall (prebiotics), Lactobacillus acidophilus (probiotic), or their combination (synbiotics) on juvenile pike silverside (Chirostoma estor). Growth performance was monitored, and gut microbiota composition was characterized by 16S rRNA gene metabarcoding. Synbiotic and yeast cell wall supplementation significantly improved growth parameters, including weight gain, final body weight, and specific growth rate, compared to the control. Microbiota profiling revealed a core community of nine genera (Bacillus, Citrobacter, Cutibacterium, Lactobacillus, Pseudomonas, Spiroplasma, Stenotrophomonas, Streptococcus, and Thermogemmatispora), with each treatment inducing distinct shifts in bacterial composition. Candidate probiotic taxa, including Lactobacillus spp., were also identified as part of the gut microbial response to dietary treatments. Functional predictions further indicated an enrichment of bacterial biosynthetic pathways in synbiotic and yeast cell wall treatments, aligning with the observed improvements in growth and feed efficiency. These findings indicated that yeast cell wall and synbiotic supplementation modulated gut microbial composition and were associated with improved growth performance in C. estor, underscoring the role of microbiome-targeted nutrition in this species.},
}

Animals
*Prebiotics/administration & dosage
*Synbiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
Animal Feed
Dietary Supplements
Lactobacillus acidophilus
Diet/veterinary
Probiotics
Inulin/administration & dosage
Aquaculture/methods
RNA, Ribosomal, 16S/genetics

@article {pmid42405327,
year = {2026},
author = {Kusuma, SAF},
title = {Selective Modulation of Cutibacterium acnes Biofilms in Acne: Limitations of Conventional Therapies and Emerging Anti-Virulence Strategies.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {621646},
pmid = {42405327},
issn = {1178-7015},
abstract = {Acne vulgaris is a multifactorial inflammatory skin disorder in which Cutibacterium acnes biofilm formation contributes to disease persistence, antimicrobial tolerance, and treatment failure. Conventional therapies primarily target bacterial viability but often fail to address biofilm-associated resilience and strain-specific virulence. Emerging strategies have therefore shifted toward the selective modulation of bacterial behavior rather than broad-spectrum eradication, with the aim of attenuating pathogenicity while minimizing disruption of the skin microbiome. This review critically evaluates selective modulation approaches targeting biofilm integrity, virulence pathways, and microbial ecology, including anti-virulence therapy, quorum-sensing inhibition, biofilm disruption, nanocarrier-based delivery systems, and microbiome-informed interventions. Preclinical studies suggest that these strategies may disrupt biofilm architecture, attenuate virulence factor expression, and potentially reduce selective pressure associated with conventional antimicrobial therapies. Approaches such as antimicrobial peptides, quorum-sensing inhibitors, and advanced delivery systems have demonstrated promising in vitro, ex vivo, and early preclinical outcomes; however, clinical evidence remains limited. Significant challenges remain, including insufficient in vivo validation, formulation instability, biofilm-associated delivery barriers, regulatory considerations, and limited long-term safety data. Overall, selective modulation represents a promising emerging framework for acne management, although its successful clinical translation will require robust clinical validation, improved disease-relevant models, and the integration of personalized strategies based on microbiome profiling and advanced delivery technologies.},
}

@article {pmid42405387,
year = {2026},
author = {Sharma, S and Saini, A and Kalra, D and Bhushan, B and Dhanawat, M and Malik, G},
title = {Human Papillomavirus (HPV)-The Interplay between Vaginal Microbiota and HPV, along with its Prevention.},
journal = {Current HIV research},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570162X461254260618050011},
pmid = {42405387},
issn = {1873-4251},
abstract = {INTRODUCTION: Human Papillomavirus (HPV) is considered one of the leading causes of cervical cancer and other anogenital malignancies. While most infections are considered short-term, persistent infection with some high-risk strains of HPV, such as HPV-16 and HPV-18, can lead to oncogenesis. This review explores the inter-relationship between HPV and the vaginal microbiota. It focuses on how the microbial imbalance influences viral persistence.

METHODS: The article is a narrative review for which a narrative literature search was conducted across PubMed, Elsevier, Scopus, and Web of Science for peer-reviewed English language publications (2000-2025). Boolean operators were used, and research was filtered for original studies and meta-analyses covering HPV prevention, diagnosis, molecular pathways, and treatment.

RESULTS: Preventive strategies include vaccinations such as Cervarix and Gardasil that are considered to be the most effective when they are administered between the ages of 9 and 14. A healthy vaginal microbiome is considered to strengthen the immune system and reduce persistence of the virus. Emerging future trends include AI-based screening, multi-omics, and precision therapies.

DISCUSSION: Regardless of the available interventions, cervical cancer remains a topic of concern in low- and middle-income countries. Oncogenesis is driven by E6 and E7 oncoproteins, which disrupt cell regulation and metabolism. Beyond host immunity, the microbiota composition is a key factor in progression. AI and Personalized treatment strategies can also help in the optimisation of the treatment.

CONCLUSION: The relationship between the vaginal microbiome and HPV shows that preventive strategies such as probiotics and vaccination may significantly reduce infection risk and cancer progression.},
}

@article {pmid42405448,
year = {2026},
author = {Cheng, Z and Zhang, C and Li, X and Wei, Y and Zhang, Z and Li, M and Yu, Q and Fang, Y and Zhang, D},
title = {Bridging Organ-on-a-Chip and Omics: A Multi-Dimensional Frontier in Biomedical Research.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70280},
pmid = {42405448},
issn = {1097-0290},
support = {2023030//Integrated Traditional Chinese and Western Medicine Research Project of Tianjin/ ; 2023ZD027//Science & Technology Development Fund of Tianjin Education Commission for Higher Education/ ; 2025004//Tianjin Key Area Scientific Research Project of Traditional Chinese Medicine of Tianjin Health Commission/ ; QN20230231//Young Scientific and Technological Talents (Level Two) in Tianjin/ ; YJSKC-20240022//Graduate Research Innovation Project of TUTCM/ ; 202510063040//College Students' Innovation and Entrepreneurship Training Program of Tianjin Municipality/ ; },
abstract = {Organ-on-a-Chip (OOC) technology offers a powerful platform for replicating human tissue-specific microenvironments, thereby narrowing the translational gap between conventional biomedical models and actual human physiology. Concurrently, omics technologies deliver comprehensive molecular-level insights into biological systems. This review highlights the transformative potential of integrating OOC platforms with high-throughput omics methodologies. We systematically examine the classification, structural configurations, and engineering principles underlying OOC systems, alongside the defining attributes of key omics domains-genomics, transcriptomics, proteomics, and metabolomics. The convergence of dynamic OOC models with advanced omics technologies enables high-resolution, multi-dimensional analyses across numerous biomedical applications, including drug metabolism, disease mechanisms, environmental toxicity assessments, and host-microbiome interactions. This interdisciplinary integration is driving a paradigm shift in precision and translational medicine. However, several challenges remain to be addressed, such as the development of whole-organ mimetics, adaptation of sample collection techniques, and real-time artificial intelligence-based integration of biosensor data with multi-omics datasets. Addressing these hurdles will be vital for unlocking the full potential of this technological synergy in biomedical science.},
}

@article {pmid42405543,
year = {2026},
author = {Anggraini, D and Yovi, I and Elliyanti, A and Safari, D and Syah, NA and Jati, AP and Sarassari, R and Simatupang, ETM},
title = {Metagenomic Analysis of Thoracic Empyema Etiology Through Next-Generation Sequencing Enhances Conventional Culture Techniques.},
journal = {Infection & chemotherapy},
volume = {58},
number = {2},
pages = {214-223},
doi = {10.3947/ic.2025.0159},
pmid = {42405543},
issn = {2093-2340},
abstract = {BACKGROUND: This study aimed to analyze the microbiome of thoracic empyema using metagenomic methods and compare the results with conventional culture methods to increase diagnostic accuracy and enhance antibiotic therapy.

MATERIALS AND METHODS: This study involved 30 patients with thoracic empyema from hospitals in Riau Province, Indonesia. Pleural fluid samples were collected for culture analysis and identification using the Vitek 2 compact system and metagenomic analysis. Patient clinical data were also collected.

RESULTS: Culture methods showed a 40.0% positive rate, with Gram-negative bacteria (Klebsiella pneumoniae and Pseudomonas aeruginosa) predominating. Metagenomics showed a 56.7% positive rate, identifying a more diverse microbiome, including fungi (29.4% abundance), other Gram-negative bacteria (26.5%), and anaerobic bacteria (22.5%). Comparison of the two methods showed 36.7% complete agreement and 23.3% partial agreement, with 40% disagreement, with a Kappa coefficient of 0.416 and P-value of 0.016 (P<0.050).

CONCLUSION: Metagenomic NGS offers significant advantages in detecting the microbiome of thoracic empyema, particularly fungi and anaerobic bacteria, which are often missed by conventional culture methods. This has the potential to improve diagnostic accuracy and optimize antibiotic therapy. Further research with larger sample sizes is needed.},
}

@article {pmid42405702,
year = {2026},
author = {Garcia, BM and Grim, SL and Jia, Y and Weber, L and Becker, CC and Kastner, M and Swarr, GJ and Kido Soule, MC and Brown, A and Zhang, W and Kujawinski, EB and Apprill, A},
title = {Spatiotemporal and hydrodynamic influences on microbial and exometabolite dynamics in coral reef and seagrass ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag177},
pmid = {42405702},
issn = {1751-7370},
abstract = {Coral reef and seagrass ecosystems provide critical storm protection and economic revenue to tropical coastal communities, and therefore effective monitoring and restoration strategies are essential. Microorganisms, and the metabolites they produce and consume, are key drivers of coastal ecosystem function. However, microbially-mediated metabolite recycling remains poorly understood, limiting its inclusion in conservation and restoration strategies. Here we examine how seawater exometabolites and microorganisms vary in coastal ecosystems, across spatial and temporal scales and in relation to hydrodynamics. We characterized benthic seawater from two St. John, U.S. Virgin Islands coral reefs (Yawzi and Tektite) and one seagrass meadow at dawn and mid-day over four consecutive days in January 2021. Using quantitative metabolomics and SSU rRNA gene amplicon sequencing, we found that exometabolite and microbial community composition differed between sites. By applying hydrodynamic modeling, we determined that the daily changes and system variability were strongly influenced by water source origins. Mid-day offshore water intrusion at Yawzi reef likely drove exometabolite and microbial shifts towards oligotrophic taxa (eg, SAR11, SAR86), whereas a high percentage of coastal source water in the seagrass site maintained stable exometabolite pools and supported diverse microorganisms. These findings demonstrate that geographically constrained site-level differences and hydrodynamics significantly impact exometabolite and microbial assemblages over short timescales. Integrating exometabolites, microorganisms, and hydrodynamics provides new insights into coastal ecosystem functioning useful for environmental monitoring and restoration strategies.},
}

@article {pmid42405765,
year = {2026},
author = {Blumer, LS and Beck, CW},
title = {Illuminating the "black boxes" of microbiome sequencing.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0008326},
doi = {10.1128/jmbe.00083-26},
pmid = {42405765},
issn = {1935-7877},
abstract = {Research on microbiomes is becoming common in undergraduate laboratory courses. These course-based undergraduate research experiences (CUREs) address many important microbiology and bioinformatics learning objectives related to science process skills. However, certain steps of the process for studying microbiomes represent "black boxes" for students. They never actually see any bacteria, but just extract bacterial DNA. Furthermore, how sequence data get translated into bacterial taxonomy tables is often opaque. We describe a protocol for evaluating communities of cultured bacteria that are sequenced with Oxford Nanopore technology. Then, students use BLAST on a subset of sequencing reads to identify the bacteria in the community. This approach illuminates these black boxes in typical microbiome CUREs.},
}

@article {pmid42405768,
year = {2026},
author = {Berryhill, BA and Gil-Gil, T and Burke, KB and Fontaine, J and Brink, CE and Harvill, MG and Goldberg, DA and Navas, JN and Grabowicz, M and Konstantinidis, KT and Levin, BR and Woodworth, MH},
title = {Enteric populations of Escherichia coli are likely to be resistant to phages due to O antigen expression.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0038626},
doi = {10.1128/msphere.00386-26},
pmid = {42405768},
issn = {2379-5042},
abstract = {Metagenomic data provide evidence that bacteriophage (phage) abound in the enteric microbiomes of humans. However, the contribution of these viruses in shaping the bacterial composition of the gut microbiome and how these phages are maintained remain unclear. We performed experiments with 756 combinations of 54 Escherichia coli and nine phage isolates from four fecal microbiota transplantation (FMT) doses and five laboratory phages as samples of non-dysbiotic human enteric microbiota. We also developed a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our experiments predict that as a consequence of the production of the O antigen, most of the E. coli in the human enteric microbiome will be resistant to infections with the array of co-occurring phages. Our modeling suggests that phages are maintained in these enteric communities due to the high rates of transition between the O antigen-resistant and -sensitive states. Based on our observations and predictions from this theory, we postulate that the phage found in the human gut are likely to play a little role in shaping the strain composition of E. coli of healthy individuals. Although we only investigated E. coli, the mechanism of resistance described here is shared among most of the gram-negative bacteria. Evidence is provided that, as a consequence of O antigen-mediated resistance, the genetically diverse array of bacteriophage in the gut microbiome of humans plays little or no role in determining the densities and distribution of the genetically diverse strain E. coli in this habitat. Our mathematical model predicts and our experiments support the hypothesis that the phage present in the gut microbiome are maintained by replication on the minority of sensitive bacteria generated by the leakiness of O antigen-mediated resistance.IMPORTANCEBacteriophages (phages) are abundant in the human gut, yet whether these viruses shape the bacterial communities living there remains unresolved. Using Escherichia coli and phages isolated from the stool of healthy fecal microbiota transplantation (FMT) donors, together with a mathematical model, we show that the vast majority of gut E. coli are resistant to co-occurring phages because they express the O antigen, a surface structure that masks the receptors phages use to attach. Despite this widespread resistance, phages persist by replicating on a small, continually regenerated subpopulation of sensitive cells, a phenomenon we term leaky resistance. These findings suggest that phages play a little role in determining which E. coli strains dominate the healthy human gut. Because the O antigen is broadly expressed across gram-negative bacteria, this mechanism likely extends well beyond E. coli and helps explain why isolating therapeutic phages against many pathogens is difficult.},
}

@article {pmid42405797,
year = {2026},
author = {Good, BH},
title = {Limited codiversification of the gut microbiota within humans.},
journal = {mBio},
volume = {},
number = {},
pages = {e0372725},
doi = {10.1128/mbio.03727-25},
pmid = {42405797},
issn = {2150-7511},
abstract = {UNLABELLED: Gut bacteria exhibit striking variation across different human populations, but the evolutionary forces that have shaped this diversity are less well understood. Recent work has argued that many species of gut bacteria have codiversified with modern humans, based on the phylogenetic correlations between human and microbial genomes. Here, I re-analyze these data and show that the correlations between human and microbial phylogenies are often substantially weaker than those between unlinked human chromosomes and that similar correlations can arise through geographic structure alone. These results suggest that traditional codiversification has been limited in recent human history and highlight alternative strategies for quantifying the extent of human-microbe coevolution.

IMPORTANCE: There is widespread interest in understanding the evolutionary history of our gut microbiota and how it varies within and among different human population groups. This Observation critically re-examines the hypothesis that many commensal gut bacteria have evolved in parallel (or "codiversified") with modern humans, providing new evidence that the correlations between human and microbial genealogies are weaker than previously supposed. These findings have important evolutionary implications and also practical consequences, from the sourcing of probiotic therapies to the design of sequencing-based diagnostics.},
}

@article {pmid42406070,
year = {2026},
author = {Charamis, J and Katzilakis, N and Stiakaki, E and Kyriakidis, I},
title = {Off-target anti-leukemic effects of antibiotics: mechanisms and therapeutic insights.},
journal = {Cancer chemotherapy and pharmacology},
volume = {96},
number = {1},
pages = {},
pmid = {42406070},
issn = {1432-0843},
mesh = {Humans ; *Leukemia/drug therapy/pathology ; Animals ; *Anti-Bacterial Agents/pharmacology/adverse effects/therapeutic use ; Cytopenia ; *Antibiotics, Antineoplastic/pharmacology/adverse effects/therapeutic use ; },
abstract = {Antibiotics are among the transformative advances in medicine, but many interact with mammalian cellular targets and pathways beyond their antimicrobial activity. A clinically important expression of these off-target effects is hematologic toxicity, including immune-mediated cytopenias and direct bone marrow suppression. This narrative review examines whether the same biology that injures normal hematopoietic cells can, in selected contexts, reveal therapeutically exploitable vulnerabilities in leukemia. We synthesize molecular, clinical, and preclinical evidence and organize it into an integrative framework linking mitochondrial translation inhibition, mitonuclear imbalance, oxidative phosphorylation failure, reactive oxygen species generation, DNA/topoisomerase stress, autophagy and lysosomal-flux blockade, and apoptosis modulation with both hematotoxicity and antileukemic activity. The strongest preclinical evidence supports selected tetracyclines, macrolides, and oxazolidinones, whereas evidence for beta-lactams, glycopeptides, polymyxins, rifamycins, fluoroquinolones, and folate-pathway agents remains more limited or largely hypothesis-generating. Importantly, antibiotic-induced cytopenia should not be interpreted as proof of leukemia selectivity: immune-mediated toxicity, supratherapeutic in vitro exposure, normal progenitor injury, pharmacokinetic constraints, microbiome effects, and resistance mechanisms all narrow the translational window. Overall, antibiotic hematotoxicity is best viewed as a biologically informative signal that can guide mechanism-based repurposing and combination strategies, but clinical development requires rigorous pharmacokinetic/pharmacodynamic validation, normal hematopoietic comparators, and biomarker-driven patient selection.},
}

Humans
*Leukemia/drug therapy/pathology
Animals
*Anti-Bacterial Agents/pharmacology/adverse effects/therapeutic use
Cytopenia
*Antibiotics, Antineoplastic/pharmacology/adverse effects/therapeutic use

@article {pmid42406122,
year = {2026},
author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B},
title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02817-z},
pmid = {42406122},
issn = {1432-184X},
support = {REIG-FPS-2025/038//UCSI University/ ; },
abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.},
}

@article {pmid42406142,
year = {2026},
author = {Dendooven, L and López-Vázquez, S and Pérez-Hernández, V and Hernández-Guzmán, M and Montoya-Ciriaco, NM and Luna-Guido, M and Thalasso, F and Navarro-Noya, YE},
title = {A nitrification bioreactor applied solely with ammonium and inorganic C maintains a highly diverse bacterial and archaeal community even after nine years.},
journal = {Biodegradation},
volume = {37},
number = {4},
pages = {},
pmid = {42406142},
issn = {1572-9729},
mesh = {*Bioreactors/microbiology ; *Nitrification ; *Archaea/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification ; *Ammonium Compounds/metabolism ; *Carbon/metabolism ; Oxidation-Reduction ; Ammonia/metabolism ; },
abstract = {The archaeal and bacterial community was determined in a continuous aerobic nitrifying reactor maintained under similar conditions for > 9 years, applied solely with ammonium as energy source and carbonate as C source. The high-throughput shotgun analysis revealed 4483 bacterial and 245 archaeal species that thrived on the metabolites provided by the autotrophic nitrifying population, mostly the ammonia oxidizing bacteria Nitrosomonas europaea and archaea Candidatus Nitrosocosmicus exaquare, and the nitrite oxidizing bacteria Nitrobacter winogradskyi and N. hamburgensis. Candidatus Nitrospira inopinata capable of oxidizing ammonia to nitrate was also detected. Although the reactor was supplied with sufficient O2, the anaerobic bacteria Candidatus Kuenenia stuttgardiensis capable of oxidizing ammonium to dinitrogen gas using nitrite as the electron acceptor under anoxic conditions (anammox) and four archaeal genera of the strict Methanobacteriaceae were detected in the reactor. A wide range of genes encoding for the different processes involved in N cycling were detected including the hzo gene encoding for the hydrazine oxidoreductase participating in the anaerobic anammox process. It was found that a bioreactor applied only with ammonium as energy source and maintained for > 9 years under steady state conditions contained a highly diverse bacterial and archaeal population and a wide range of metabolic processes related to the N cycle, which has not been reported before. This provides us with comprehensive insights into the dynamics of microbial communities in these types of systems.},
}

*Bioreactors/microbiology
*Nitrification
*Archaea/metabolism/genetics/classification
*Bacteria/metabolism/genetics/classification
*Ammonium Compounds/metabolism
*Carbon/metabolism
Oxidation-Reduction
Ammonia/metabolism

@article {pmid42406144,
year = {2026},
author = {Garrigós, M and Veiga, J and Garrido, M and García-López, MJ and Morales-Yuste, M and Marín, C and Recuero, J and Rosales, MJ and Moreno-Indias, I and Martínez-de la Puente, J},
title = {Drivers of Mosquito Microbiome Composition: Effects of Species, Locality, Season, and Plasmodium Infection.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02801-7},
pmid = {42406144},
issn = {1432-184X},
abstract = {Mosquito microbiota influences mosquito physiology and pathogen development, finally affecting their vectorial capacity. Identifying the factors that affect the composition of mosquito microbial communities in nature is essential for designing effective strategies to control vector-borne pathogens. Here, we used a 16 S rRNA metabarcoding approach to analyse the microbiome of 196 mosquito pools (four females per pool) of three common species: Culex pipiens, Aedes albopictus, and Culiseta longiareolata. Mosquitoes were collected from spring to autumn 2022 in five sampling localities of southern Spain. Mosquito bacterial alpha diversity was higher in Cs. longiareolata compared to Cx. pipiens and Ae. albopictus. In addition, beta diversity and the relative abundance of different bacterial taxa differed among mosquito species. Wolbachia dominated the bacterial community of Cx. pipiens and Ae. albopictus, but were virtually absent in Cs. longiareolata. Furthermore, using Cx. pipiens -the most extensively sampled species here- we further investigated differences in the microbiome composition according to sampling localities, seasons, and avian Plasmodium infection status. Locality and season affected the bacterial alpha and beta diversity, with mosquitoes collected in autumn from the Fuengirola locality showing a higher observed richness. Differences in beta diversity among localities and seasons could be, at least in part, influenced by differences in beta dispersion. The relative abundance of different taxa in Cx. pipiens varied by locality, season, and avian Plasmodium infection status. In sum, both intrinsic and environmental factors influence mosquito microbiome, yet the potential consequences for pathogen transmission should be further addressed. This study provides a comprehensive framework to understand the ecological drivers of wild mosquito microbiome, a key step for predicting vector-pathogen interactions and improving strategies for vector-borne disease control.},
}

@article {pmid42406180,
year = {2026},
author = {Gautam, S and Sharma, J and Sharma, M and Sharma, S and Kumar, R and Sheel, V and Gautam, P and Umar, A and Alkhanjaf, AAM and Ibrahim, AA and Baskoutas, S},
title = {Next-generation biodegradation of chlorpyrifos: integrative microbial strategies, molecular mechanisms, and environmental impacts.},
journal = {Biodegradation},
volume = {37},
number = {4},
pages = {},
pmid = {42406180},
issn = {1572-9729},
mesh = {*Chlorpyrifos/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism ; *Insecticides/metabolism ; *Soil Pollutants/metabolism ; },
abstract = {Chlorpyrifos (CP) belongs to organophosphate pesticide group. It is extensively applied in agricultural and household settings due to its broad-spectrum insecticidal properties. However, its persistence, bioaccumulative behavior, and toxicological effects on non-target organisms, including humans, pose significant environmental and public health concerns. CP and its metabolites, particularly two including 3,5,6-trichloropyridinol (TCP) and chlorpyrifos-oxon (CPO), have been recently reported to be widely found various samples such as in soils, sediments, water bodies, crops, and even human biological fluids. These compounds disrupt biogeochemical cycles, alter soil microbial communities, inhibit enzyme activities, and are linked to neurotoxicity, endocrine disruption, and genotoxic effects. Conventional remediation strategies such as photodegradation, ultrasonication, and filtration remain ineffective due to incomplete degradation and secondary pollution risks. Recent studies highlight the efficiency of microbial degradation, especially by bacteria such as Bacillus, Klebsiella, Pseudomonas and Enterobacter as a promising, eco-friendly alternative. These microorganisms utilize CP as a only carbon source, and degradation calibre is greatly governed by various abiotic factors like pH, temperature, and moisture. The genetic as well as enzymatic analyses reveal key roles of organophosphorus hydrolases encoded by genes such as opd and mpd. The integration of plant growth-promoting traits and laccase activity further enhances their bioremediation capability. Additionally, recent advancements in biosensing techniques for CP detection offer improved sensitivity and real-time monitoring. This review provides a comprehensive analysis of CP's environmental fate, toxicological impact, degradation pathways, and the emerging role of bacterial bioremediation, highlighting its potential for sustainable environmental detoxification.},
}

*Chlorpyrifos/metabolism
Biodegradation, Environmental
*Bacteria/metabolism
*Insecticides/metabolism
*Soil Pollutants/metabolism

@article {pmid42406610,
year = {2026},
author = {Leng, J and Tait, C and Alsubaie, B and Van Vliet, AHM and Sells, P and La Ragione, RM and Proudman, C},
title = {Rapid bacterial community profiling of equine faecal, skin, milk and saliva samples using Oxford Nanopore long-read 16S rRNA amplicon sequencing.},
journal = {Journal of medical microbiology},
volume = {75},
number = {7},
pages = {},
doi = {10.1099/jmm.0.002176},
pmid = {42406610},
issn = {1473-5644},
mesh = {Animals ; Horses/microbiology ; RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *Saliva/microbiology ; *Milk/microbiology ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; *Skin/microbiology ; Nanopore Sequencing/methods ; Skin Microbiome ; Sequence Analysis, DNA ; },
abstract = {Introduction. The composition of the equine gut microbiome is associated with many aspects of gastrointestinal, respiratory and musculoskeletal health that have been reported in the horse. Scientific studies exploring the microbiome non-intestinal ecological niches in or on horses are lacking. The clinical use of bacterial community profiling in horses is currently limited by cost and by slow analytical workflows.Hypothesis/Gap Statement. Most equine microbiome studies have relied on 16S rRNA amplicon sequencing of bacterial DNA, using high-throughput short-read sequencing technologies. This is often provided by an external service due to the cost of Illumina and other sequencers. Analysis of such sequencing files relies upon the researcher to have prior experience of coding-based programs.Aim. To explore the utility of Oxford Nanopore long-read sequencing in the analysis of microbiomes from several anatomical sites of the horse as a quicker and cheaper alternative to short-read sequencing.Methodology. Bacterial DNA was extracted from horse (udder) skin swabs, saliva swabs, faecal samples and milk samples. Samples were prepared for Oxford Nanopore long-read sequencing and sequenced using a flow cell on the MinION Mk1D. Sequencing data were analysed using EPI2ME, along with extra analyses on exported taxa abundance data in R.Results. Diversity measures and taxonomic relative abundance from phylum to family level were comparable to previously published equine studies that used Illumina sequencing. Sequencing data were acquired within 3 days costing around £30 per sample. Long-read sequencing gave accurate taxa assignment for two positive controls included at phylum, class, order and family levels of taxonomic classification.Conclusion. This work demonstrates that long-read technologies such as Oxford Nanopore MinION sequencing can provide a reliable, quick and cost-effective alternative to short-read Illumina sequencing when characterizing microbial communities from a range of anatomical locations on/in the horse.},
}

Animals
Horses/microbiology
RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Bacteria/genetics/classification/isolation & purification
*Microbiota/genetics
*Saliva/microbiology
*Milk/microbiology
High-Throughput Nucleotide Sequencing/methods
DNA, Bacterial/genetics
*Skin/microbiology
Nanopore Sequencing/methods
Skin Microbiome
Sequence Analysis, DNA

@article {pmid42406620,
year = {2026},
author = {Mohanty, S and Panda, P and Mohapatra, R},
title = {The skin microbiome-immune-barrier axis: implications for inflammatory skin disorders and immunotherapeutic strategies.},
journal = {Immunotherapy},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/1750743X.2026.2697682},
pmid = {42406620},
issn = {1750-7448},
abstract = {The skin microbiome is a complex and dynamic ecosystem that plays a pivotal role in maintaining skin barrier integrity and immune homeostasis. This review provides a comprehensive synthesis of current knowledge on the composition, diversity, and functional significance of the skin microbiota, with particular emphasis on site-specific and temporal variations, as well as intrinsic and extrinsic factors influencing microbial balance. Relevant literature was identified through comprehensive searches of PubMed, Scopus, Web of Science, and Google Scholar databases covering publications from 2018 to 2026. We discuss the multilayered architecture of the skin barrier, encompassing chemical, physical, microbial, and adaptive immune components, and highlight how commensal microorganisms contribute to barrier maintenance, lipid homeostasis, immune modulation, and colonization resistance against pathogens. Dysbiosis of the skin microbiome is critically examined in common dermatological disorders, including wound infections, atopic dermatitis, acne, and psoriasis, where microbial imbalance is closely linked to inflammation and disease progression. This review further explores emerging microbiome-targeted therapeutic strategies aimed at restoring microbial equilibrium and strengthening skin barrier function. Emerging therapies including bacteriotherapy, probiotics, phage therapy, and microbiome transplantation show promise, while challenges involving safety, ethics, and clinical translation remain important considerations.},
}

@article {pmid42406681,
year = {2026},
author = {Romero, R},
title = {Molecular, genetic, and pharmacological advances in type 2 diabetes (2015-2025).},
journal = {Biomolecular concepts},
volume = {17},
number = {1},
pages = {},
pmid = {42406681},
issn = {1868-503X},
mesh = {Humans ; *Diabetes Mellitus, Type 2/genetics/drug therapy/metabolism ; *Hypoglycemic Agents/therapeutic use/pharmacology ; Epigenesis, Genetic ; Glucagon-Like Peptide-1 Receptor Agonists ; },
abstract = {Type 2 diabetes (T2D) is a multifactorial metabolic disorder driven by the interplay of insulin resistance, β-cell dysfunction, and complex genetic and epigenetic factors. Over the past decade (2015-2025), advances in molecular biology, genomics, and pharmacology have reshaped our understanding of its pathogenesis and treatment. Large-scale GWAS and functional genomics have clarified genetic risk loci and epigenetic mechanisms, while novel biomarkers, including circulating microRNAs and metabolomic signatures, offer potential for early detection and risk stratification. Therapeutically, incretin-based drugs, especially GLP-1 receptor agonists and dual agonists, as well as SGLT2 inhibitors, have transformed outcomes by targeting both glycemic control and cardiovascular-renal protection. These insights have also informed prevention strategies, emphasizing weight reduction, microbiome modulation, and precision interventions based on genetic risk. Yet major gaps remain, including functional annotation of risk loci, understanding of β-cell dedifferentiation and recovery, and equitable implementation across diverse populations. This review synthesizes molecular, genetic, and pharmacological progress from 2015 to 2025, highlights clinical translation, and identifies priorities for the next decade of research.},
}

Humans
*Diabetes Mellitus, Type 2/genetics/drug therapy/metabolism
*Hypoglycemic Agents/therapeutic use/pharmacology
Epigenesis, Genetic
Glucagon-Like Peptide-1 Receptor Agonists

@article {pmid42406847,
year = {2026},
author = {Erdős, B and Chatzis, C and Thorsen, J and Stokholm, J and Smilde, AK and Rasmussen, MA and Acar, E},
title = {Extracting host-specific developmental signatures from longitudinal microbiome data.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014486},
doi = {10.1371/journal.pcbi.1014486},
pmid = {42406847},
issn = {1553-7358},
abstract = {Longitudinal microbiome studies provide critical insights into microbial community dynamics and their relation to host health. Tensor decompositions offer a powerful framework for the unsupervised analysis of such data, yielding interpretable low-dimensional temporal patterns. However, existing approaches based on the CANDECOMP/PARAFAC (CP) model assume common temporal dynamics for all subjects and therefore cannot capture subject-specific trajectories. To address this limitation, we introduce a novel analytical framework based on PARAFAC2 to explicitly model subject-specific variations, such as shifts and delays in temporal patterns. Through systematic comparisons on simulated and real-world datasets-including studies of infant gut maturation and dietary interventions-we demonstrate that PARAFAC2 outperforms CP in capturing subject-specific temporal trajectories, and enables the discovery of biologically relevant patterns that are overlooked by CP. Furthermore, we introduce replicability as a robust criterion for selecting the number of model components, ensuring that the extracted patterns are replicable.},
}

@article {pmid42406892,
year = {2026},
author = {Alam, S and Hadju, V and Ansariadi, A and Jafar, N and Abdullah, MT and Manyullei, S},
title = {Clostridium Abundance and Lower Weight-for-Age z Scores Among 6-Month-Old Infants: Nested Cross-Sectional Study.},
journal = {JMIR pediatrics and parenting},
volume = {9},
number = {},
pages = {e87452},
doi = {10.2196/87452},
pmid = {42406892},
issn = {2561-6722},
abstract = {BACKGROUND: The gut microbiota plays a crucial role in infant nutrition through its effects on energy metabolism, nutrient absorption, and immune regulation. However, evidence from Indonesian infants remains limited.

OBJECTIVE: This study aimed to examine the association between genus-level gut microbiota abundance and weight-for-age z scores (WAZ) among 6-month-old infants in coastal Banggai District, Central Sulawesi, Indonesia.

METHODS: We conducted a nested follow-up cross-sectional observational analysis of 88 six-month-old infants, including 42 (47.7%) who were born to mothers who were assigned to receive Moringa oleifera enriched with royal jelly group and 46 (52.3%) who were assigned to receive a multiple micronutrient supplement in a previous maternal supplementation trial. Maternal and infant characteristics were collected via structured interviews and standardized anthropometric measurements. WAZ was calculated using the World Health Organization Child Growth Standards, and underweight (WAZ <-2 SD) was reported as a secondary indicator. Stool samples were analyzed using genus-specific quantitative polymerase chain reaction to quantify Bifidobacterium, Lactobacillus, Bacteroides, Clostridium, and Escherichia coli (log10 colony-forming unit/mL). Associations between bacterial abundance and WAZ were assessed using multivariable linear regression adjusted for maternal supplementation allocation and relevant maternal, environmental, and infant covariates.

RESULTS: The pooled mean WAZ was -0.47 (SD 1.09), and 8% (7/88) of the infants were underweight. The combined abundance of beneficial genera was higher than that of opportunistic bacteria (E coli and Clostridium; Wilcoxon signed-rank test; P=.002). Higher Clostridium abundance was inversely associated with WAZ (unadjusted β=-.094, 95% CI -0.173 to -0.015; P=.02; adjusted β=-.091, 95% CI -0.172 to -0.010; P=.03). No statistically significant associations were observed for Bifidobacterium (P=.13), Lactobacillus (P=.19), Bacteroides (P=.70), or E coli (P=.18) in adjusted models.

CONCLUSIONS: Among 6-month-old infants in coastal Central Sulawesi, higher genus-level Clostridium abundance was independently associated with lower WAZ. Given the cross-sectional design and genus-level quantitative polymerase chain reaction assessment, temporality and species-level mechanisms cannot be established. Longitudinal studies using more comprehensive microbiome profiling are warranted to clarify potential pathways linking gut microbiota and early-life growth.},
}

@article {pmid42407193,
year = {2026},
author = {Zhang, Y and Zhang, H and Song, L and Xing, F and Jing, MZ and Wang, C and Deng, X and Liao, Y and Xing, N and Zhang, W},
title = {The dual role of the microbiome in sepsis: A complex interplay between pathogenicity and protection.},
journal = {Physics of life reviews},
volume = {58},
number = {},
pages = {131-163},
doi = {10.1016/j.plrev.2026.07.001},
pmid = {42407193},
issn = {1873-1457},
abstract = {Sepsis is an infection-induced syndrome characterized by systemic immune dysregulation and has traditionally been treated primarily with antibiotics. Although antibiotics remain essential for pathogen control, they rarely reverse immune dysfunction, barrier disruption, or microbial ecological imbalance in sepsis, suggesting that a purely anti-infective paradigm may be insufficient. In such phenotypes, microbiome-centered approaches may complement conventional anti-infective strategies by supporting microbial ecological restoration, host immune recalibration and disease tolerance. There is increasing evidence that the microbiome plays an important role in sepsis pathogenesis and immune modulation, both as a byproduct of immune perturbation and as a context-dependent mediator of immune maladaptation. Such insights underpin therapeutic strategies that integrate immune reprogramming with ecological restoration beyond infection control. Recent progress in single-cell omics, spatial transcriptomics and metabolomics is starting to uncover the complex interactions between microbial communities and the host immune system, providing new conceptual and translational pathways. Precise microbiome modulation combined with targeted immune recalibration may help shape future sepsis therapy, centered on restoring immune-microbial homeostasis rather than simply suppressing inflammation.},
}

@article {pmid42407345,
year = {2026},
author = {Shi, Y and Xue, Q and Yuan, Y and Li, Y and Zhu, X and Niu, D and Jin, C},
title = {WD-3 improves anti-PD-L1 therapy by remodeling the tumor immune microenvironment through gut microbiota.},
journal = {Immunobiology},
volume = {231},
number = {4},
pages = {153215},
doi = {10.1016/j.imbio.2026.153215},
pmid = {42407345},
issn = {1878-3279},
abstract = {BACKGROUND: Gastric cancer (GC) ranks as the fifth most prevalent malignancy globally. Emerging evidence implicates gut microbiome as a key modulator of anti-tumor immunity and immunotherapy response. Traditional Chinese Medicine (TCM) presents a promising yet underexplored avenue for microbiome modulation.

METHODS: 16S rDNA sequencing of fecal samples was used to detect changes of gut microbiota in advanced GC patients. GC models were established in huPBMC-NOG-dKO mice after fecal microbiota transplantation (FMT) to investigate the potential synergy between Number 3 Prescription (WD-3) and anti-PD-L1 monoclonal antibody (mAb) in treatment of non-responders.

RESULTS: In this study, WD-3 combined with αPD-L1 showed additive benefit after the FMT of non-responders in the humanized mouse model model. WD-3 combination therapy correlated with reduced proportion of Treg cell infiltration in tumors. WD-3 combination was also associated with increased species richness and improved gut microbiota community structure compared to αPD-L1 alone, with increased relative abundances of Enterobacteriaceae and Lachnospiraceae.

CONCLUSION: Our data provide correlative evidence that WD-3 supplementation combined with αPD-L1 treatment may attenuate GC progress in the FMT mouse model, indicating association with the modulation of gut microbiota. These findings aim to provide treatment strategies for the clinical treatment of advanced GC.},
}

@article {pmid42407790,
year = {2025},
author = {Silva, ZRJD and Cedrola, F and Senra, MVX and Rossi, MF and Dias, RJP},
title = {The ITS-rDNA region as a complementary or alternative phylogenetic marker to 18S-rDNA in rumen ciliates (Alveolata, Ciliophora).},
journal = {Zootaxa},
volume = {5716},
number = {3},
pages = {409-420},
doi = {10.11646/zootaxa.5716.3.7},
pmid = {42407790},
issn = {1175-5334},
abstract = {Rumen ciliates are important constituents of gastrointestinal microbiome of herbivorous mammals. They are traditionally classified based on morphological characteristics. However, molecular markers-mainly the 18S rRNA gene-have increasingly been used to investigate their evolutionary relationships. While the 18S gene provides reliable phylogenetic resolution at higher taxonomic levels, it lacks variability to distinguish closely related taxa. In this study, we evaluated the potential of the internal transcribed spacer (ITS) rDNA region as an alternative or complementary marker to the 18S rRNA gene for phylogenetic reconstruction of rumen ciliates. We generated and analyzed ITS sequences from rumen ciliate species and compared topologies obtained using three datasets: ITS alone, 18S alone, and a concatenated ITS+18S dataset. The concatenated dataset consistently showed improved resolution and support across several key clades, supporting its utility in Trichostomatia phylogeny. Some differences were observed, such as the variable placement of Troglodytella abrassarti, highlighting the importance of multi-marker approaches. Our findings demonstrate that the ITS region is a robust complementary marker that enhances phylogenetic resolution, especially when combined with 18S data.},
}

@article {pmid42409075,
year = {2026},
author = {Tsante, K and Petrou, E and Tsalas, S and Tsantes, AG and Lianou, A and Kartelias, G and Kyriakou, E and Kokoris, S and Nikolopoulos, G and Bonovas, S and Sokou, R},
title = {Gut Microbiome-Associated Thrombosis: Approaching Validation?.},
journal = {Seminars in thrombosis and hemostasis},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2900-7086},
pmid = {42409075},
issn = {1098-9064},
abstract = {Gut microbiome has emerged as an important modulator of thrombotic disease through complex immunometabolic and interorgan pathways. Microbiome-derived metabolites have been associated with platelet activation, endothelial injury, and adverse cardiovascular outcomes. However, evidence remains stronger for arterial than for venous thrombosis, although accumulating data suggest that dysbiosis may represent an important yet underrecognized contributor to the pathogenesis of venous thromboembolism. While current evidence supports a biologically plausible association between the gut microbiome and thrombosis, further studies are needed to clarify the underlying mechanisms and determine their clinical significance.},
}

@article {pmid42409099,
year = {2026},
author = {Jin, BJ and Chen, SC and Ji, BX and Wang, HB and Li, XY and Zhao, Y and Ding, K and Li, G},
title = {Manure-Free Organic Fertilization-Derived Lignin Alters the Dissemination of Antibiotic Resistance Genes from Soil to the Rhizosphere.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125194},
doi = {10.1016/j.envres.2026.125194},
pmid = {42409099},
issn = {1096-0953},
abstract = {Organic fertilizers significantly influence soil antibiotic resistance genes (ARGs); however, the impact of manure-free organic amendments on ARG dissemination from bulk soil to the rhizosphere remains unclear. This study investigated dissolved organic matter (DOM) composition and ARG profiles in bulk soil and the radish rhizosphere using three manure-free organic fertilizers with varying hydrochar contents (0%BC, 10%BC, and 30%BC). Under non-fertilized conditions, the rhizosphere harbored lower ARG abundances than bulk soil. Organic fertilization significantly elevated rhizospheric ARG enrichment, driven primarily by rhizosphere bacterial community shifts and antibiotic-resistant bacteria (ARB) accumulation rather than direct exogenous ARG inputs. Notably, the 10%BC treatment effectively mitigated this enrichment, maintaining absolute ARG abundances in the rhizosphere that were 69.5% and 72.5% lower than those in the 0%BC and 30%BC treatments, respectively. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) revealed that 10%BC selectively enriched low-molecular-weight, highly oxidized lignin-like molecules with higher aromaticity. In contrast, 0%BC and 30%BC accumulated higher-molecular-weight, more bioavailable lignins. Network analysis and structural equation modeling (SEM) demonstrated that these chemically distinct lignins exerted contrasting effects: highly oxidized lignins under 10%BC potentially suppressed horizontal gene transfer (HGT) and ARB accumulation, whereas bioavailable lignins under 30%BC promoted them. Overall, fertilizer-derived lignins serve as crucial molecular mediators steering resistome dynamics across the soil-rhizosphere interface, with their oxidation states and molecular weights exhibiting contrasting roles in modulating HGT and ARG dissemination.},
}

@article {pmid42409242,
year = {2026},
author = {Hutchinson, NT and Pang, Z and Chimezie, C and Hamp, B and Haley, A and Li, J},
title = {Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {115160},
doi = {10.1016/j.jconrel.2026.115160},
pmid = {42409242},
issn = {1873-4995},
abstract = {Despite the vast opportunities for therapeutic manipulation of the gut microbiome, recent late-stage clinical failures of engineered live biotherapeutic products (eLBPs) highlight critical knowledge gaps in ecological barriers and community dynamics. In this review, we propose repurposing the current eLBP toolkit as a set of discovery instruments that yield quantitative outputs for predictive modeling. We examine cutting-edge approaches in microbiome engineering and outline opportunities for their use in tandem with systems engineering methodology to conduct functional probing that establishes quantitative parameters describing community resilience, metabolic flux, and host-microbe interactions. Next, in light of FDA guidance on New Approach Methodologies, we detail how in silico and in vitro modeling approaches can be combined and leveraged not only for a priori triage of unviable designs, but can also be integrated into design-build-test-learn (DBTL) pipelines for functional forecasting. Building off an emerging cellular kinetics/pharmacodynamics (CK/PD) framework, we develop a Bayesian updating workflow that encapsulates eLBP-adapted equivalents of pharmacological parameters such as Cmax, Tmax, and AUC. Further, we adapt this framework for adaptive or prospective use, rather than purely retrospective application, supporting trial design rather than post-hoc analysis. This approach repositions eLBP development from an empirical, intuition-based process toward a predictive, model-informed pipeline that aligns with emerging regulatory frameworks.},
}

@article {pmid42409268,
year = {2026},
author = {Pirovano, E and Silva, IP and Camacho, M and Çanak, A and Aktas, B and Crompton, D and Gökçe, E and Tan, FM and Marino, F and Domingos, J and Almeida, MF and Comi, C and Dragic, M and Figueira, I},
title = {Non-pharmacological interventions modulating immune response in Parkinson's Disease: where do we stand for future preventive approaches.},
journal = {Neurochemistry international},
volume = {},
number = {},
pages = {106211},
doi = {10.1016/j.neuint.2026.106211},
pmid = {42409268},
issn = {1872-9754},
abstract = {Parkinson's disease (PD) imposes a growing socioeconomic burden due to its increasing prevalence and lack of a cure. Existing treatment options primarily manage motor and nonmotor symptoms but do not halt or slow disease progression, underscoring the urgent need for more effective and preventative strategies. Growing evidence suggests a strong link between immune system dysfunction, chronic inflammation, and the early pathogenesis of Parkinson's disease, often occurring years before the onset of motor symptoms, thereby indicating a critical window for early intervention. In this review, we examine current evidence on non-pharmacological approaches such as dietary changes, physical activity, and gut microbiome regulation, focusing on their potential to modulate both peripheral and central immune responses, thereby influencing the progression of PD. Besides being complementary to standard pharmacological treatments, these approaches not only reduce systemic inflammation but may also help delay, prevent, or improve clinical management of PD by targeting and modulating its immunological foundations.},
}

@article {pmid42409355,
year = {2026},
author = {Nguyen, HT and Bez, C and Tran, MQ and Tran, LT and Pham, VT and Bertani, I and Venturi, V and Dinh, HT},
title = {Rhizospheric Fungal Communities and Their Role in Biocontrol of Fusarium in Robusta Coffee (Coffea canephora) in Vietnam.},
journal = {The plant pathology journal},
volume = {},
number = {},
pages = {},
doi = {10.5423/PPJ.OA.12.2025.0186},
pmid = {42409355},
issn = {1598-2254},
abstract = {Rhizospheric microbial communities are critical to the health and productivity of coffee plantations. This study investigated the microbiome of robusta coffee (Coffea canephora) across three major cultivation areas in Vietnam (Dak-Nong, Dak-Lak, and Gia-Lai) to assess its role in Fusarium suppression. Using ITS ampliconbased metagenomics and culture-dependent approaches, we analyzed fungal community structure in relation to location, plant age, and health status. Metagenomic analysis revealed no significant differences in bacterial communities between healthy and diseased rhizospheres, whereas fungal communities showed clear distinctions, particularly in young plants (<2 years). These differences diminished in mature plants (≥2 years) but continued to vary with age (2-10 years). Healthy rhizospheres were enriched with beneficial fungi, while diseased soils contained more phytopathogenic genera. Fusarium was prevalent in all regions, with higher abundance in diseased soils, whereas Trichoderma, a known biocontrol agent, was more abundant in healthy soils but declined with plant age. Of 343 fungal isolates, 46 strains exhibited strong antagonistic activity against Fusarium, representing 10 genera, including Aspergillus, Penicillium, Gongronella, and Talaromyces. Although Trichoderma isolates were less frequent, they showed promising biocontrol potential. These findings underscore the role of rhizospheric fungi in managing Fusarium wilt and identify candidate biocontrol agents for sustainable robusta coffee cultivation.},
}

@article {pmid42409358,
year = {2026},
author = {Su, Z and Li, M and Zuo, Y and Guo, J and Wei, Y and Fan, S and Wang, Y},
title = {Preliminary Strain‑Specific and Non‑Additive Effects of Single Versus Mixed DSE Inoculation on Rhizosphere Microbiome and Nutrient Cycling Relative to Plant Biomass in Chinese Yam.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag165},
pmid = {42409358},
issn = {1365-2672},
abstract = {AIMS: To mitigate Chinese yam continuous cropping obstacles, this study assessed single and mixed dark septate endophyte (DSE) inoculation effects on yam growth, soil characteristics and rhizosphere microbial communities, offering references for optimizing rhizosphere microenvironment of continuously cropped medicinal plant soils.

METHODS AND RESULTS: 9 DSE strains were isolated from yam roots for single/mixed seedling pot inoculation; We found that growth-promoting effects differed by strain. Acrocalymma and Setophoma terrestris were the most commonly isolated DSE species, but strains with lower isolation rates Paraphoma ledniceana, Amesia atrobrunnea, and Zopfiella pilifera exhibited the most pronounced positive effects on yam root biomass. Increasing the number of co-inoculated strains did not proportionally enhance yam growth but progressively restructured soil microbial communities. However, mixed DSE inoculation as a whole showed no obvious growth promotion compared with the control. Fungal co-occurrence networks exhibited higher modularity and clustering, while bacterial communities had greater connectivity, especially under P. ledniceana and Fusarium sp. inoculation. Biosynthesis was the most abundant predicted function of rhizosphere microbes, with bacteria predicted to be enriched in detoxification and fungi in degradation-related pathways. Two strains of Chaetomiaceae and Periconia epilithographicola increased soil pH, organic carbon and available phosphorus, while available nitrogen decreased after DSE inoculation. Importantly, P. epilithographicola inoculation enhanced mycorrhizal fungi and mitigated microbial imbalance.

CONCLUSIONS: Single and mixed DSE inoculations regulate rhizosphere microbial assembly and nutrient cycling via species-specific effects. Screening beneficial DSE consortia and characterizing their influence on rhizosphere networks provides preliminary theoretical insights and and candidate strains that may relieve yam replant obstacles in future applications.},
}

@article {pmid42409534,
year = {2026},
author = {García, V and Vega-Gálvez, A and Bernal, G and Ramírez-Rivera, S and Bernal, C and Stucken, K},
title = {Temperature-modulated microbial succession governs sulforaphane bioconversion during natural enriched fermentation of broccoli.},
journal = {Food research international (Ottawa, Ont.)},
volume = {240},
number = {},
pages = {119594},
doi = {10.1016/j.foodres.2026.119594},
pmid = {42409534},
issn = {1873-7145},
abstract = {Sulforaphane, a potent anti-cancer isothiocyanate from broccoli, shows limited bioavailability in raw vegetables, restricting functional food applications. This study suggests for the first time that native lactic acid bacteria fermentation systematically enhances sulforaphane bioconversion through controlled temperature and matrix optimization. Broccoli inflorescences were fermented at 20-35 °C with different pretreatments (raw, blanched, sterilized), followed by HPLC-DAD quantification, 16S rRNA gene amplicon sequencing, and biochemical characterization including myrosinase activity and glucosinolate-isothiocyanate conversion efficiency. Fermentation at 35 °C with blanching achieved high sulforaphane concentrations of 84,000 μg/kg d.w. a 44-fold increase over unfermented raw broccoli values. Pearson correlation analysis revealed a strong positive association (r = 0.93, p < 0.01) between sulforaphane accumulation and microbial succession from Lactococcus to Lactiplantibacillus plantarum dominance across three distinct fermentation phases. This work supports the potential of natural fermentation biotransforms cruciferous vegetables into sulforaphane-enriched functional foods without chemical extraction, enabling sustainable microbiome-driven bioprocessing strategies for nutraceutical development and cancer chemoprevention applications.},
}

@article {pmid42409699,
year = {2026},
author = {Petrullo, L and Albery, GF and Raulo, A and Sweeny, AR},
title = {Microbial contributions to host life history trade-offs.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2026.06.008},
pmid = {42409699},
issn = {1872-8383},
abstract = {All organisms must allocate finite resources among growth, maintenance, and reproduction, generating trade-offs that constrain adaptation. Host-associated microbiomes are dynamic resource engines capable of generating and reallocating energy and resources for their hosts. In doing so, we argue they may recalibrate the trade-offs fundamental to host life history evolution.},
}

@article {pmid42409829,
year = {2026},
author = {Roh, M and Barat, B and Gilbert, JA and Karrison, T and Rouhani Ravari, M and Wild, C and Suss, NR and Gaines, S and Morgan, R and Martinez-Guryn, K and Martini, AM and Zaborina, O and DeLeon, O and Shogan, BD},
title = {A virulent bacterial signature is associated with the development of recurrence following colorectal cancer surgery.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74889-x},
pmid = {42409829},
issn = {2041-1723},
support = {Young Investigator Awared//Cancer Research Foundation (CRF)/ ; 1K08CA248957-01A1//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {The primary treatment for non-metastatic colorectal cancer is surgical resection. Despite the use of neoadjuvant and/or adjuvant chemoradiation, up to 30% of patients undergoing surgery for colorectal cancer will develop a postoperative recurrence. Why patients develop postoperative tumors despite all known cancer being resected at the time of surgery is largely unknown, and novel biomarkers that can predict the development of recurrence are lacking. Here, we report a unique bacterial signature present in the gut during the perioperative period that is strongly associated with the development of postoperative tumors. By studying patients undergoing resection for colorectal cancer, we demonstrate that the gut microbiome on the day of surgery is enriched with collagenase-producing bacteria in patients who later develop a recurrence. This bacterial community demonstrated enhanced antimicrobial resistance, was not eradicated by the standardized perioperative bowel preparation, and could promote cancer cell migration and invasion. Our study establishes that microbiota may contribute to postoperative colorectal cancer recurrence and serve as a prognostic biomarker for postoperative oncologic outcomes.},
}

@article {pmid42409865,
year = {2026},
author = {Garcia Mendez, DF and Rowley, C and Lodge, S and Egan, S and Zeng, AX and Campbell, MA and Jones, J and D'Vaz, N and Holmes, E and Christophersen, CT},
title = {High adherence to a Mediterranean diet is associated with a diverse faecal microbiome and reduced systemic inflammation in a cohort of pregnant women.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-55564-z},
pmid = {42409865},
issn = {2045-2322},
support = {FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; FL200100220//Australian Research Council/ ; },
abstract = {The Mediterranean diet (MD), known for its high intake of fruits, vegetables, whole grains, legumes, and healthy unsaturated fats, has been linked to a diverse and beneficial gut microbiome. However, its effect on the gut microbiome during pregnancy remains understudied. This study aimed to investigate the impact of high adherence to a Mediterranean diet on gut microbiome composition and function in pregnant women by analysing their metabolic profiles and faecal microbiome composition. Stool, serum, and urine samples were collected from 48 pregnant women at weeks 20/28 and at week 36. Participants were stratified based on MD adherence using a validated questionnaire. Stool samples underwent 16 S rRNA gene amplicon sequencing, and serum short-chain fatty acids (SCFAs) were measured using UPLC-MS. Women with high MD adherence showed significantly higher α-diversity in their faecal microbiomes at both time points. Significant differences in microbiome composition were observed between low and high adherence groups at weeks 20/28, but not at week 36. No significant differences in serum short-chain fatty acid concentrations were found between the groups. Our findings suggest that adherence to the Mediterranean diet during pregnancy is associated with changes in gut microbiome diversity and function. These results contribute to a better understanding of how dietary patterns during pregnancy may influence gut microbiome ecology.},
}

@article {pmid42409884,
year = {2026},
author = {Studer Silva Gutierrez, FAO and Morandi, SC and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Influence of smoking on the human ocular surface microbiome and tear proteome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60743-z},
pmid = {42409884},
issn = {2045-2322},
abstract = {The ocular surface hosts microbes of low abundance and their genomes, collectively called the ocular surface microbiome (OSM). The OSM is involved in maintaining health and protecting the eye from infection. Although disruption of this microbial balance has been linked to various eye diseases, the effect of smoking, a known risk factor for ocular conditions, on the OSM remains unclear. We analysed ocular samples from smokers (n = 17) and non-smokers (n = 24) using metagenomic sequencing and proteomics approaches to assess both microbial composition and functions, as well as the host protein profiles. Microbial DNA was examined for bacterial, fungal, and viral taxa, with contaminants removed using microDecon. Statistical analyses showed no significant differences in microbial diversity or tear proteins between groups, apart from one bacterial gene. No bacterial, fungal, or viral species were uniquely associated with smoking status. While no clear smoking-related effects were observed in microbial communities or tear proteome composition, the overall stability of tear proteins may reflect intrinsic resilience dynamics that maintain low microbial abundance on the ocular surface.},
}

@article {pmid42409886,
year = {2026},
author = {Liu, XL and Meng, SC and Hung, YJ and Hsu, SH and Huang, MC and Wu, LS},
title = {Gut microbiome dynamics and alcohol use outcomes during naltrexone treatment: a 12 week follow-up study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59750-x},
pmid = {42409886},
issn = {2045-2322},
support = {114-2314-B-532-003-MY3//National Science and Technology Council, Taiwan/ ; },
abstract = {Alcohol use disorder (AUD) is a heterogeneous condition. Growing evidence highlights the role of the gut-brain axis in alcohol-related behaviors; however, longitudinal changes in the gut microbiome during pharmacological treatment for AUD remain poorly understood. In this 12-week study, we investigated gut microbiome composition and functional profiles in individuals with AUD undergoing naltrexone treatment. Seventy-two patients meeting DSM-5 criteria for AUD were enrolled. Stool samples were collected at baseline, week 4, and week 12 and analyzed using high-throughput 16 S rRNA gene followed by bioinformatic analyses. Of the 72 enrolled participants, 32 and 23 completed stool sampling at weeks 4 and 12, respectively. Despite significant improvements in drinking behavior over the treatment period, no significant changes in α- or β-diversity were observed, and no distinct clustering of gut microbial communities emerged across timepoints. Notably, the relative abundance of the Eubacterium hallii group increased from baseline and remained elevated through week 12. Several specific bacterial taxa were significantly associated with drinking outcomes and craving severity, particularly abstinence days (or inversely drinking days). At week 12, β-diversity, but not α-diversity, differed significantly between abstinence and non-abstinence groups. Functional enrichment analyses indicated that naltrexone treatment predicted functional reorganization of the gut microbiome based on 16 S inference, characterized by enhanced xenobiotic degradation and remodeling of cofactor-dependent antioxidant metabolism. Naltrexone treatment had limited effects on overall gut microbiota structure. In contrast, AUD patients who achieved sustained abstinence exhibited a distinct gut microbiota profile, suggesting that microbiome functional dynamics may contribute to AUD recovery and reflect treatment response to naltrexone. The absence of a placebo or untreated AUD control group precludes conclusions about the independent effects of naltrexone on gut microbiome changes.},
}

@article {pmid42410152,
year = {2026},
author = {Kay, W and Carrasco, J and Kusari, S and Krijger, M and Carpio, MJ and Barnes, T and Cruz, MSR and van der Wolf, J and Bebenroth, T and Preston, GM},
title = {Biocontrol of mushroom crop mycoparasites by novel Bacillus velezensis strains.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13938-3},
pmid = {42410152},
issn = {1432-0614},
support = {GA: 101000651//HOZIZON 2020/ ; },
abstract = {The cultivation of button mushroom (Agaricus bisporus) requires the design of tailor-made substrates that nourish the crop and promote morphology changes from mycelium to basidiome. The agronomic stages of mushroom development are also influenced by the microbiota present in the mushroom crop microcosm. These microbes can have a beneficial impact on mushroom growth, development and quality, or a detrimental impact through reduction of yield or quality (parasites, competitors or disease vectors). In this report, we describe the isolation of multiple strains of Bacillus velezensis from mushroom casing material and basidiomes. We show that these strains exhibit antifungal activity towards major mushroom mycoparasites in vitro and further characterise their mode of action. Full genomes of B. velezensis CM5, CM19, CM35, EM5 and EM39 were sequenced and annotated, which together with metabolic profiling of specialised metabolites produced by CM5, CM19 and CM35 suggested that the antifungal activity of these strains is likely to be linked to the production of the lipopeptide fengycin. The addition of these B. velezensis strains to a growth chamber trial with crops infected by Zarea fungicola strain 150/1 did not result in a statistically significant reduction in disease incidence compared to the chemical fungicide prochloraz-Mn. Despite in vitro results, no negative effect on mushroom yield was observed. The analysis of the quantitative microbiome during this trial suggests that microbial dynamics is consistent with a regular crop cycle. Additionally, the application of B. velezensis strain CM5 resulted in increased Gram-negative and Gram-positive bacteria. Genomic and analytical tools were designed and used to evaluate B. velezensis persistence in casing soil when the selected strains were artificially applied. B. velezensis population levels decreased significantly after application, potentially contributing to the lack of biocontrol activity observed in growth chamber crop trials. KEY POINTS: • Bacillus velezensis strains isolated from peat-based microcosms show significant inhibitory effects against major fungal parasites of mushrooms in vitro. • Genome sequencing and metabolic profiling correlated antifungal activity with the production of lipopeptides, particularly fengycin. • Novel strains did not significantly limit dry bubble disease under growth chamber crop trials-potentially due to low bacterial persistence.},
}

@article {pmid42410155,
year = {2026},
author = {Ali, H and Khaleque, A and Sadia, T and Azmuda, N and Parvez, MAK and Adnan, N and Akter, S and Ahmed, MF},
title = {Cross-domain microbial differences across freshwater and marine habitats in a tropical delta.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61157-7},
pmid = {42410155},
issn = {2045-2322},
abstract = {Microbial communities are central to aquatic ecosystem functioning, yet integrated cross-domain comparisons of prokaryotic and microeukaryotic microbiomes remain underexplored in tropical regions, particularly in Bangladesh. Here, we investigated habitat-associated differences in microbial community structure across freshwater and marine ecosystems of the Bangladesh tropical delta using 16S and 18S rRNA gene amplicon sequencing and assessed inferred functional potential for prokaryotic communities. Six freshwater and ten seawater samples were analyzed, comprising eight newly generated datasets (six freshwater and two seawater) and eight previously published seawater datasets. Prokaryotic communities exhibited significantly higher alpha diversity in freshwater, whereas microeukaryotic diversity showed no significant habitat-associated differences after correction, despite a weak freshwater enrichment trend. Beta diversity revealed clear compositional separation between habitats for both domains, with prokaryotes exhibiting centroid shifts and microeukaryotes showing greater within-group dispersion. Taxonomic profiles showed seawater dominance by Gammaproteobacteria and Alphaproteobacteria, whereas freshwater communities were more evenly distributed across Bacteroidota, Actinomycetota, and Verrucomicrobiota. Microeukaryotic assemblages also displayed pronounced habitat-associated restructuring. Functional inference of prokaryotic communities indicated conservation of core pathways across habitats despite taxonomic turnover. Exploratory cross-domain correlation analysis identified mixed positive and negative associations, although none remained significant after multiple-testing correction. Collectively, these findings reveal consistent habitat-associated microbial differentiation across tropical freshwater and marine ecosystems and provide a comparative baseline for understanding cross-domain microbial biogeography in climate-sensitive aquatic environments.},
}

@article {pmid42410374,
year = {2026},
author = {Zhang, J and Zhang, H and Xu, Y and Wang, C and Li, X and Ni, Y},
title = {Exploratory urinary microbiome and metabolome profiles in patients with calcium oxalate kidney stones: a pilot cross-sectional study.},
journal = {BMC nephrology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12882-026-05100-y},
pmid = {42410374},
issn = {1471-2369},
support = {LHXM2023ZD12004//Shandong Provincial Third Hospital Research Fund/ ; 202404050251//Shandong Province Medicine and Health Science and Technology Development Program Project/ ; },
abstract = {BACKGROUND: Kidney stones represent a common urological disorder affecting approximately 14.8% of the global population, with calcium oxalate (CaOx) stones constituting nearly 80% of all cases. Recent studies have revealed a potential association between the gut microbiome and the risk of forming CaOx stones. Additionally, urinary microbiota has been implicated to influence stone development, although the relationship between urinary microbiota and urinary metabolites in patients with calcium oxalate kidney stones remains incompletely characterized.

METHODS: In this pilot cross-sectional study, we used 2bRAD sequencing for microbiome profiling (2bRAD-M) and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to characterize urinary microbial and metabolic features. We analyzed urine samples from a pilot cohort of 12 patients with calcium oxalate kidney stones and 10 healthy controls. Statistical analyses of microbial diversity and metabolomic profiles were conducted to explore between-group differences. To explore microbiome-metabolite associations, we performed Spearman correlation analysis with multiple-testing correction and provided stratified correlation heatmaps as supplementary analyses. This study is registered in the National Medical Research Registry filing system of China (https://www.medicalresearch.org.cn) (No. MR-37-23-016317).

RESULTS: Compared with healthy controls, patients with calcium oxalate kidney stones showed exploratory differences in urinary microbial diversity and community composition. Shannon and Simpson diversity were nominally higher in the CaOx group but did not remain significant after multiple-testing correction. At the genus level, Lactobacillus showed a nominally lower relative abundance in the CaOx group, whereas Escherichia showed a nominally higher relative abundance; however, no genus remained significant after BH-FDR correction. Untargeted metabolomics identified 131 candidate metabolites using exploratory screening criteria of VIP > 1 and nominal P < 0.05, including 33 higher-abundance and 98 lower-abundance candidates in the CaOx group; however, no metabolite remained significant after BH-FDR correction. Microbiome-metabolome correlation analyses suggested exploratory association patterns but did not establish direct biological interactions.

CONCLUSIONS: This pilot cross-sectional study describes exploratory voided urine-associated microbiome and metabolome profiles in patients with calcium oxalate kidney stones. The findings are hypothesis-generating and require validation in larger, multicenter, longitudinal studies with rigorous contamination-control strategies and paired urine, stone, and fecal sampling.},
}

@article {pmid42402030,
year = {2026},
author = {Qi, K and Zhang, S and Su, X and Chen, J and Huang, S and Chen, Y and Li, W and Ni, G and Duo, J and Yang, S and Shen, Q and Wang, X and Liu, Y and Wu, P and Yang, H and Ji, L and Wang, X and Zhang, W},
title = {Comparative analysis of gut viromes in four penguin species reveals diverse novel viruses and host-associated differences.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0084825},
doi = {10.1128/msphere.00848-25},
pmid = {42402030},
issn = {2379-5042},
abstract = {Penguins, as distinctive marine birds, play important roles in polar and sub-Antarctic ecosystems, yet the diversity and species-specific distribution of their gut viromes remain insufficiently understood. Here, we used viral metagenomics to characterize the cloacal viromes of four penguin species-Spheniscus humboldti (S. humboldti), Pygoscelis papua (P. papua), Pygoscelis adeliae (P. adeliae), and Aptenodytes forsteri (A. forsteri)-collected at Chimelong Ocean Kingdom. A total of 219 viral sequences representing potentially novel lineages were identified, with more than 94% sharing <80% amino acid similarity with previously known viruses. These sequences were assigned to several viral families, including Parvoviridae, Caliciviridae, Anelloviridae, Circoviridae, and Microviridae, among others. Marked interspecies differences in virome composition were observed: Parvoviridae dominated in S. humboldti, Microviridae were enriched in P. papua, Caliciviridae accounted for a substantial proportion in A. forsteri, and P. adeliae displayed the greatest overall virome diversity. Multiple-virus co-detections, particularly involving Parvoviridae, were frequent in S. humboldti. Phylogenetic analyses showed that many penguin-associated viruses clustered with viruses infecting other avian and fish hosts, suggesting possible dietary or environmental origins of some detected viral sequences. These findings expand current knowledge of penguin gut virome diversity and host-associated differences and provide a valuable foundation for evaluating the ecological roles, health implications, and transmission risks of penguin-associated viruses.IMPORTANCEThis study uncovers significant diversity in the gut viromes of four penguin species, revealing over 219 viral sequences representing potentially novel lineages, many of which showed host-associated distribution patterns. Using viral metagenomics, we identified notable interspecies differences, with Parvoviridae predominating in Spheniscus humboldti and Microviridae being enriched in Pygoscelis papua. These findings highlight the complexity of viral community structures in penguins, including frequent viral co-detections, which could impact host health and ecological adaptation. Additionally, novel bacteriophage communities were identified, emphasizing their potential role in shaping the gut microbiome and influencing viral dynamics. This work provides new insights into viral diversity in wildlife and lays the groundwork for future studies on viral transmission risks and ecological conservation.},
}

@article {pmid42402034,
year = {2026},
author = {Wu, Y and Wang, Y and Qin, R and Liu, L and Wang, L and Liu, Y and Wang, W and Diao, Q},
title = {Dietary supplementation with fermented compound Chinese herbal medicine reshapes the gastrointestinal microbiota and enhances growth in suckling lambs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0388925},
doi = {10.1128/spectrum.03889-25},
pmid = {42402034},
issn = {2165-0497},
abstract = {UNLABELLED: This study investigated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth performance, antioxidant capacity, immune function, and gastrointestinal microbiota in suckling lambs. FCHM consisted of 10 herbs fermented with Candida utilis and Bacillus subtilis. Sixty twin Hu lambs (15 days) were randomly fed a basal diet (CON) or the diet supplemented with 0.6% FCHM (Treat) for 45 days. The results indicated that the Treat group exhibited a significant increase in average daily gain (ADG) (P < 0.05). Serum analyses revealed elevated levels of growth hormone (GH), insulin-like growth factor-1 (IGF-1), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glucose (GLU), whereas malondialdehyde (MDA) and pro-inflammatory cytokines (IL-6 and TNF-α) were reduced (P < 0.05). In the duodenal mucosa, SOD and GSH-Px activities and T-AOC levels were significantly elevated, while MDA content was notably decreased (P < 0.05). Ruminal fermentation profiles showed increased concentrations of propionate and total volatile fatty acids (TVFA) in the Treat group (P < 0.05). Microbiome analysis revealed that FCHM supplementation selectively modulated the ruminal microbial community, enriching beneficial genera such as Prevotellaceae_UCG-003 and Butyrivibrio, while reducing the abundance of potentially harmful genera like Streptococcus, despite no significant changes in the overall community diversity. Metagenomic sequencing further demonstrated the enrichment of KEGG enzymes and carbohydrate-active enzyme genes involved in carbohydrate metabolism and propionate biosynthesis. Correlation network analyses revealed significant associations among specific microbial taxa, serum antioxidant, immune biomarkers, and growth performance. In conclusion, dietary FCHM supplementation improves growth performance in suckling lambs by optimizing ruminal fermentation patterns, selectively regulating gastrointestinal microbiota, and enhancing systemic antioxidant capacity. These findings support the potential of FCHM as a functional feed additive in lamb production systems.

IMPORTANCE: Enhancing growth performance and ensuring gastrointestinal health during the suckling period are critical for lamb productivity and welfare. In the context of the antibiotic-free mandate in animal feed, we evaluated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth, antioxidant status, immune parameters, and gastrointestinal microbiota in lambs. Our findings demonstrate that FCHM improves average daily gain, enhances systemic and mucosal antioxidant capacity, and modulates ruminal and hindgut microbiota by enriching beneficial taxa and suppressing potentially harmful bacteria. These effects are linked to upregulated microbial functions in carbohydrate metabolism and propionate biosynthesis. This study provides a microbial-based mechanism for FCHM as a natural feed additive to promote lamb growth and gastrointestinal resilience, offering a sustainable strategy to support early-life development in ruminant production systems.},
}

@article {pmid42402285,
year = {2026},
author = {Mendon, MC and Abeysinghe, S and Witherrite, S and Kim, DG and Yu, L and Chen, S},
title = {Engineering robustness in hyperthermophilic acidification reactor through adaptive laboratory evolution of dairy manure microbiome.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135321},
doi = {10.1016/j.biortech.2026.135321},
pmid = {42402285},
issn = {1873-2976},
abstract = {Hyperthermophilic anaerobic acidification (HTA) of dairy manure (DM) enabled volatile fatty acid (VFA) production from lignocellulose-rich substrates, but stable operation at short hydraulic retention time (HRT) requires microbial adaptation under sustained selection pressure. In this study, a 50 L anaerobic acidification reactor (AAR) treating DM was operated at 70 °C, and HRT was progressively reduced from 8 days to 6 days and then to 5 days to evaluate process performance together with microbial community succession. Shortening HRT increased VFA productivity from 0.29 ± 0.07 g/L/d to 1.22 ± 0.19 g/L/d, while stabilized 5-day operation maintained an average total VFA concentration of 20.83 ± 1.50 g/L. Acetic acid became increasingly dominant as operation progressed, indicating a stable carbohydrate fermentation route under intensified conditions. A linear mixed model confirmed a significant HRT effect on total VFA concentration. Improved reactor performance at short HRT coincided with enrichment of thermophilic fermenters associated with polymer breakdown and carbohydrate fermentation, particularly Clostridiaceae and Ruminococcaceae, followed by reestablishment of a resilient hyperthermophilic core dominated by Caldicoprobacteraceae, Thermodesulfobiaceae, and Clostridiaceae. Diversity analyses further supported structured community reassembly during stabilized 5-day operation. These findings showed that stepwise HRT reduction at 70 °C selected a resilient microbiome that sustained stable, high-rate VFA production from dairy manure and established an operational strategy for hyperthermophilic acidification of lignocellulosic manure for downstream bioprocess integration.},
}

@article {pmid42402338,
year = {2026},
author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandón, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR},
title = {Pre-treatment Gut Microbiome Diversity and Function Linked to Cytotoxic and Natural Killer Cell Immune Responses after N-803 Treatment in People with HIV.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciag369},
pmid = {42402338},
issn = {1537-6591},
abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.

METHODS: In this exploratory longitudinal metagenomic study, we analyzed fecal microbiomes from 10 ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.

RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were nominally enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii showed a nominal increase after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8+ and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA+ cells. MaAsLin2 analyses further identified potentially important associations between short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.

CONCLUSIONS: These findings in a limited Phase 1B clinical study suggest that gut microbiome diversity prior to immunotherapy may influence host response. These results provide a basis for further investigation into microbiome-based strategies to improve efforts to cure HIV.},
}

@article {pmid42402597,
year = {2026},
author = {Chen, L and Hua, G and Pu, L and Cai, N and Tang, J and Mu, D and Xu, Y},
title = {Synthetic microbial communities derived from native niches enhance the high-temperature adaptability of Pinus yunnanensis seedlings.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00924-5},
pmid = {42402597},
issn = {2524-6372},
support = {202401AT070297, 202401BD070001-107, 202201AT070023//Applied Basic Research Programs of Science and Technology Department of Yunnan Province/ ; 32360394//National Nature Science Foundation of China/ ; LXXK-2025D02//Yunnan Provincial First-Class Discipline Construction Fund for Forestry at Southwest Forestry University/ ; XDYC-QNRC-2022-0250//Yunnan Revitalization Talent Support Program Young Talent Project/ ; 112113//Southwest Forestry University Research Project/ ; 2023Y0734//Research Innovation Fund for Graduate Students of Yunnan Provincial Department of Education/ ; 2024-61//Yunnan Graduate Tutor Team Building Project/ ; },
abstract = {The microbiome rewilding hypothesis suggests that understanding and reconstructing the microbial communities lost through domestication is vital for enhancing seedling quality and adaptability. Therefore, we investigated the structure and assembly of symbiotic microbial communities associated with Pinus yunnanensis, the most significant conifer species in southwestern China, and its dwarf variant, P. yunnanensis var. pygmaea. Subsequently, the functions of these microbes were characterized by inoculating dominant microbes and constructing synthetic communities, and examined their colonization status post-inoculation using amplicon sequencing. The results indicate that: (a) microbial communities are primarily differentiated by niche (soil, roots, needles), followed by geographical location, while trunk form variation has a minimal impact; (b) fungi are influenced by both chemistry and geographical factors, showing dispersion limitation, while bacteria are mainly affected by chemistry, exhibiting homogeneous diffusion; (c) single endophyte inoculation has a neutral to slightly negative impact on seedling growth but enhances resistance to high temperatures; (d) synthetic microbial communities (SynComs), constructed based on the strains' origin and initial functional screening, enhanced seedling growth and provided better protection against high-temperature stress than single strains. (e) one SynCom (SC5), composed of the dominant root isolates Phialocephala sp. (Fun6) and Paraburkholderia sp. (Bac7), significantly increased total seedling biomass by 62% and improved thermotolerance. These findings enhance our understanding of the symbiotic microbial communities of P. yunnanensis and demonstrate the potential of using specific SynComs, such as SC5, as bio-inoculants to improve seedling quality and stress tolerance in nursery production.},
}

@article {pmid42402624,
year = {2026},
author = {Ling, H and Williamson, J and Gatenby, S and Pruden, S and Neeley, C and Harland, C and Wallace, A and Couldrey, C},
title = {Using sequence-derived microbiome information from bulk tank milk samples to assess the influence of post-milking teat disinfection in New Zealand dairy herds.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42402624},
issn = {2524-4671},
support = {MPICO6878-6680//New Zealand Ministry for Primary Industries/ ; },
abstract = {BACKGROUND: Post-milking teat spraying plays an important role in the control of mastitis within New Zealand dairy herds. We examined the sample-level associations between post-milking teat spraying and bacterial levels in bulk tank milk (BTM) microbiomes, using shotgun DNA sequencing data within a non-experimental framework.

METHODS: A total of 1325 BTM samples were collected from 219 pasture-based commercial herds voluntarily enrolled across New Zealand, over the 2021 and 2022 dairy seasons. Bacterial levels of Staphylococcus and Streptococcus species and Corynebacterium bovis were quantified (cells/ml) and compared along with two post-milking teat spray actives (iodine and chlorhexidine) and two application methods (manual and automatic). Analyses were performed at the BTM sample level using log-transformed abundances and the Wilcoxon rank-sum test; Benjamini-Hochberg FDR was applied per individual species. A univariate PERMANOVA (Euclidean distance, 9,999 permutations) was used as a permutation-based robustness check.

RESULTS: These data show that post-milking teat spraying was associated with lower BTM levels of Corynebacterium bovis and lower levels across Staphylococcus species compared with samples without teat disinfection, across both seasons. At the teat spray active level, Chlorhexidine-based teat disinfectant was associated with lower Corynebacterium bovis, Staphylococcus aureus, and Streptococcus dysgalactiae than the iodine-based teat disinfectant, while no consistent differences were observed for Streptococcus uberis, Streptococcus agalactiae, Streptococcus chromogenes, or Streptococcus epidermidis. For the teat spray application method, patterns varied by species. Findings were consistent across two seasons and directionally consistent between Wilcoxon and PERMANOVA.

CONCLUSIONS: We demonstrate that sequencing-based BTM microbiome profiling can reveal sample-level associations between teat spray practices and mastitis-associated bacteria. While causal inference is constrained by the observational design and uncertain sources contribution within BTM, these findings suggest that BTM sequencing may complement herd-level monitoring of teat spray performance. Further controlled studies incorporating key covariates are warranted.},
}

@article {pmid42402632,
year = {2026},
author = {Wang, G and Liu, W and Chen, Y and Zhang, S},
title = {Microbiota-gut-brain axis in autism spectrum disorder: integrating brain structure, function, and transcriptomics.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04158-4},
pmid = {42402632},
issn = {2158-3188},
support = {ZR2023QH100//Natural Science Foundation of Shandong Province (Shandong Provincial Natural Science Foundation)/ ; },
abstract = {Growing evidence indicates that disruption of the microbiota-gut-brain (MGB) axis is a key factor in autism spectrum disorder (ASD), affecting neurodevelopment, neural circuit function, and behavior. This review synthesizes multidisciplinary data to clarify mechanistic links between the MGB axis and ASD and to evaluate microbiota-targeted therapeutic strategies. We conducted a narrative synthesis of clinical and translational studies, including human cohort and case-control investigations, animal models, multi-omics analyses, immune profiling, multimodal brain assessments (structural/functional MRI and transcriptomics), and interventional trials. Emphasis was placed on evidence of microbiota-brain associations, intervention outcomes, and methodological limitations. Key findings reveal that individuals with ASD commonly exhibit gut microbiome dysbiosis and altered metabolomic signatures that can influence central nervous system function; three core bidirectional signaling routes link gut microbes to brain outcomes-microbial metabolite production (e.g., short-chain fatty acids, tryptophan metabolites), immune-mediated pathways, and neuroendocrine-vagal communication. Accumulating data associate ASD-related microbial profiles with changes in brain structure, functional connectivity, and transcriptomic patterns, supporting a mechanistic role for the MGB axis in ASD phenotypes. Microbiota-targeted interventions show promising effects on gastrointestinal symptoms, metabolic biomarkers, and selected behavioral measures in small studies, but results are heterogeneous and current evidence is insufficient for widespread clinical application. Integrating multimodal neuroimaging with multi-omics and machine learning provides a promising framework to identify reproducible microbial-brain biomarkers for early detection, clinical subtyping, and stratified treatment. Key challenges include methodological heterogeneity, limited causal inference, small and heterogeneous cohorts, and ethical/safety concerns for pediatric interventions. The MGB axis is a plausible pathogenic mechanism and therapeutic target in ASD. Translating mechanistic insights into precision clinical applications requires standardized, multicenter, longitudinal deep-phenotyping studies that combine multimodal imaging, comprehensive multi-omics, rigorous randomized trials, and careful ethical oversight.},
}

@article {pmid42402696,
year = {2026},
author = {Bennett, F and Stroud, E and Kachroo, P and Grant, M},
title = {Systemic acquired resistance: an emerging role for jasmonates in local signal biogenesis, translocation and distal signal decoding.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71405},
pmid = {42402696},
issn = {1469-8137},
support = {MCB-2435880//Division of Molecular and Cellular Biosciences/ ; B/T00746X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X013049/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Plant systemic acquired resistance (SAR) requires generation and movement of mobile signals from local leaves in which plant disease resistance has been activated (effector-triggered immunity, ETI), to distal, uninfected regions, where they prime host defences. Although salicylic acid (SA) and N-hydroxypipecolic acid (NHP) are widely recognised as key regulators of SAR, the requirement for de novo synthesis implies the existence of upstream or parallel inducing signals. Recent studies using whole plant and confocal reporter imaging, electrical signalling, and single-cell transcriptomics have revealed how specific cell types and the temporal-spatial organisation of phytohormone networks contribute to immune signalling. We summarise these findings alongside previous knowledge to highlight the collective importance of jasmonates, calcium, reactive oxygen species, and electrical signals as early initiators, coordinators, and most likely propagators of long-distance signalling during ETI-induced SAR. We draw parallels with induced systemic resistance and highlight the coordinated roles of jasmonates, volatile compounds, and the microbiome in plant-to-plant communication. Furthermore, we also review environmental modulation of defence responses, a research area deriving further attention. Evidence points towards the coordinated activation of multiple signals, including jasmonates, driving systemic immunity across biological scales from the infected cell to entire plant communities.},
}

@article {pmid42402715,
year = {2026},
author = {Bellucci, M and Mostofa, MG and Benucci, GMN and Kabir, AH and Khan, I and Lombardi, M and Locato, V and Bonito, G and Loreto, F and Sharkey, TD},
title = {Isoprene-Emitting Transgenic Tobacco Shapes Root Microbiome and Enhances Growth of Co-Cultivated Non-Emitting Plants.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70698},
pmid = {42402715},
issn = {1365-3040},
support = {IOS-2022495//National Science Foundation (NSF)/ ; DE-FG02-91ER20021//Basic Energy Sciences/ ; FIS00000382//Italian Ministry of University and Research (MUR) Future in Science (FIS) 2021 program/ ; 2022ZYCCJJ//MUR - PRIN 2022/ ; P20229ZW4A//MUR - PRIN 2022/ ; DEVTF2210892//The Company of Biologists/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; },
abstract = {Isoprene is the most abundant biogenic volatile organic compound emitted by terrestrial vegetation. Here we report the impact of isoprene on root-associated microbiomes. Using isoprene-emitting (IE) transgenic tobacco and isogenic non-emitting (NE) controls, we performed co-cultivation experiments in natural soil and analysed plant phenotypes and growth alongside bacterial and fungal communities across root, rhizosphere, and soil niches. NE plants co-cultivated with IE neighbours displayed increased shoot and root biomass, suggesting interactive belowground functions of isoprene. Amplicon sequencing revealed more growth-promoting microbiota in root and rhizosphere of IE plants than NE plants. Both bacterial and fungal growth-promoting microbiota were enriched in IE and NE plants grown in the same pot. However, isoprene-fumigated plant-free soils did not replicate these shifts, indicating that plant-microbe interactions are required for the modulation of the soil microbiome. Our results suggest that isoprene acts as a belowground cue influencing microbiome assembly and indirectly enhancing growth in neighbouring plants. This work uncovers a potential ecological role for isoprene, highlighting how plant-derived isoprene can mediate plant-plant-microbiome interactions and contribute to community-level processes in the rhizosphere.},
}

@article {pmid42400030,
year = {2026},
author = {Venter, C and Beltran, J and Bracchiglione, J and Fernández-Sáenz, FK and Riera, P and Solà, I and Akdis, C and Arasi, S and Canani, RB and Fleischer, D and Eguíluz-Gracia, I and Hourihane, J and Lunjani, N and Meyer, R and Roberts, G and Roth-Walter, F and Santos, AF and Skypala, I and Smith, PK and Sokolowska, M and Torres, MJ and Vassilopoulou, E and Vlieg-Boerstra, B and Walter, J and Alonso-Coello, P and O'Mahony, L},
title = {Immunonutrition in Early Life: The Role of Complementary Feeding, Dietary Patterns, and Nutritional Exposures on the Health of Young Children-An EAACI Scoping Review.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70429},
pmid = {42400030},
issn = {1398-9995},
support = {//European Academy of Allergy and Clinical Immunology/ ; },
abstract = {BACKGROUND: Immunonutrition examines how diet influences immune development. Complementary feeding represents a critical window for long-term health. We aimed to map evidence linking complementary feeding to immune outcomes, allergy, infection, and growth in infants and toddlers (≤ 3 years). We conducted a scoping review and evidence-gap mapping, following PRISMA-ScR. MEDLINE and Epistemonikos were searched from inception to November 2024. Concepts included diet diversity/patterns, feeding practices/models, and timing of allergen introduction, timing of complementary feeding, macronutrients, micronutrients, foods, supplementation, and ultra-processed foods. We included systematic reviews and recent primary studies meeting criteria.

RESULTS: From 13,512 records screened, 108 systematic reviews were included, comprising 99 randomized controlled trials, 41 cohorts, 22 case-control, and 14 cross-sectional studies. Most reviews addressed nutrient intake, supplementation, or timing of allergen introduction, while fewer reviews explored diet diversity, foods, or ultra-processed food intake. Responsive complementary feeding was consistently associated with healthier growth and lower obesity risk, whereas restrictive practices showed adverse effects. Greater diet diversity was linked to reduced asthma and food allergy risk, though eczema findings were inconsistent. Western-style diets high in processed foods, fat, sugar, and meat correlated with higher allergy risk, while home-prepared diets were protective. Micronutrient supplementation (iron, zinc, vitamin D) reduced infection and anemia risk but had mixed effects on allergy. Early allergen introduction reduced food allergy incidence.

CONCLUSIONS: Complementary feeding research now extends beyond calorie counting, macronutrients, and early allergen introduction to dietary patterns and early life nutrition that supports the microbiome. Evidence supports dietary diversity, timely food allergen introduction, and responsive feeding, while discouraging restrictive practices and ultra-processed foods. Future work should harmonize definitions and investigate plant-based diets, advanced glycation end products, and processed food exposures.},
}

@article {pmid42400043,
year = {2026},
author = {Wang, Y and Xue, X and Usyk, M and Sharma, A and Anastos, K and Post, WS and Hodis, HN and Wang, Z and Witt, MD and Rinaldo, CR and Brown, TT and Palella, FJ and Gange, S and Kuniholm, MH and Sha, BE and Caron, P and Gerszten, RE and Clish, CB and Guillemette, C and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB and Peters, BA},
title = {Multi-omics profiles of sex hormone-binding globulin are associated with subclinical atherosclerosis in men with HIV.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01709-8},
pmid = {42400043},
issn = {1756-994X},
support = {R01HL095129/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; R01HL148094/HL/NHLBI NIH HHS/United States ; R01HL140976/HL/NHLBI NIH HHS/United States ; K01HL137557/HL/NHLBI NIH HHS/United States ; K01HL160146/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Sex hormones and HIV infection both influence cardiovascular health. However, the association between sex hormones and subclinical atherosclerosis is not fully understood, especially in the context of HIV.

METHODS: Among 321 men (65% with HIV) from the MACS/WIHS Combined Cohort Study, we measured 14 serum sex hormones and sex hormone-binding globulin (SHBG), assessed carotid artery plaque (IMT > 1.5 mm) using high-resolution B-mode ultrasound, and performed metagenomic sequencing on stool samples. In 312 men, we measured 986 plasma metabolites via liquid chromatography-tandem mass spectrometry and 2883 plasma proteins using the Olink Explore 3072 platform. In stratified analyses of men with (MWH) and without HIV (MWOH) and adjusting for covariates and multiple testing, we (1) examined associations of sex hormones with plaque; (2) characterized multi-omics profiles related to sex hormones; and (3) generated sex hormone-related omics scores via linear combination of related species, metabolites, and proteins, respectively, to explore whether these sex hormone-related multi-omics profiles were associated with plaque.

RESULTS: Median age of participants was 62 years (interquartile range: 58-68), and 31.5% had carotid artery plaque. Sex hormones were differentially associated with plaque in MWH and MWOH. In MWH, an inverse association was observed between SHBG and plaque (OR = 0.60 per 1-SD increase, 95% CI: 0.41, 0.90). Furthermore, higher SHBG levels were associated with overall gut microbial composition, lower abundance of species from genera Prevotella, Fibrobacter and Coprococcus, higher levels of certain metabolites (primarily lipid and carnitine metabolites) and proteins enriched in the cell-cell adhesion pathway. Some SHBG-related species (e.g., Mediterranea massiliensis), metabolites (e.g., phosphatidylcholine-based lipids) and proteins (e.g., enriched in immune response pathway) were also associated with plaque in MWH. All three SHBG-related omics scores were inter-correlated and inversely associated with plaque in MWH. In MWOH, estrone-sulfate was positively associated with plaque (OR = 3.80, 95% CI: 1.41, 10.22) but not with any species, metabolites or proteins.

CONCLUSIONS: Higher SHBG, and related microbial species, circulating metabolites, and proteins, were inversely associated with carotid artery plaque. These findings suggested that SHBG may play a protective role in subclinical atherosclerosis in MWH.},
}

@article {pmid42400095,
year = {2026},
author = {Franić, I and Sherwood, P and Stolarek, K and Eschen, R and Orbach, J and Prospero, S and Cleary, M},
title = {DNA and RNA metabarcoding reveal shared dominant seed-borne fungi.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00923-6},
pmid = {42400095},
issn = {2524-6372},
abstract = {BACKGROUND: Tree seeds harbor diverse fungal communities, including both pathogens and mutualists, that can influence plant health. These communities comprise living, metabolically active organisms as well as dormant or dead cells. Because only active fungi interact with their hosts, distinguishing active from inactive taxa is crucial, especially for environmental and phytosanitary monitoring. Traditional culturing methods capture living fungi but account for only a small fraction of the total fungal diversity. Currently, these methods are increasingly replaced by high-throughput DNA metabarcoding, which detects a broader range of taxa. However, DNA persists after cell death and occurs in dormant cells, preventing distinction between active and inactive fungi. In contrast, RNA metabarcoding may better reflect living fungal communities than the other two methods, though its use in assessing plant-associated fungi remains underexplored. We used culturing, DNA-, and RNA-based metabarcoding to compare fungal communities associated with seeds of three key European tree species (Fagus sylvatica, Abies alba, Pinus sylvestris).

RESULTS: Dominant fungal communities in seeds were strongly shaped by host species identity and were largely shared across DNA and RNA metabarcoding datasets, with roughly half of the most abundant genera detected by both methods. Differences between DNA- and RNA-derived communities were predominantly associated with rare taxa in the RNA dataset, although distinguishing true biological signals from noise introduced by different methodological workflows remains challenging. Several cultured genera, likely both abundant and metabolically active, were consistently detected by both approaches.

CONCLUSIONS: These results highlight the complementary nature of the three methods for characterising seed-associated fungi. Combining culturing, DNA- and RNA-based metabarcoding may provide the most comprehensive assessment of fungal diversity, while RNA metabarcoding alone offers a promising opportunity to identify the active members of fungal communities for improved environmental and phytosanitary monitoring.},
}

@article {pmid42400257,
year = {2026},
author = {Ghosh, S and Vanwinkle, ZM and Sinha Roy, K and Stýblo, M and Banerjee, M and Collins, J and Jala, VR},
title = {Microbial metabolite Urolithin A protects against inorganic arsenic-induced gut barrier dysfunction in humanized AS3MT mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2696618},
doi = {10.1080/19490976.2026.2696618},
pmid = {42400257},
issn = {1949-0984},
mesh = {Animals ; Intestinal Barrier Function/drug effects ; *Coumarins/metabolism/pharmacology/administration & dosage ; *Arsenic/toxicity ; Mice ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Methyltransferases/genetics/metabolism ; Colon/drug effects/pathology ; Intestinal Mucosa/drug effects/metabolism ; Cytokines/metabolism ; Tight Junction Proteins/metabolism ; Mice, Transgenic ; Bacteria/metabolism/classification/genetics/isolation & purification ; *Protective Agents ; },
abstract = {Chronic exposure to inorganic arsenic (iAs) remains a major environmental health concern and is associated with significant gastrointestinal (GI) disorders, including gastroenteritis, diarrhea, and inflammatory bowel disease-like symptoms. Gut microbiota plays a critical role in mitigating arsenic toxicity, as germ-free or antibiotic-treated mice exhibit reduced fecal arsenic excretion and greater tissue accumulation. We previously showed that the microbial metabolite Urolithin A (UroA) protects against iAs-induced cytotoxicity, apoptosis, oxidative stress, and ROS production in vitro. In this study, using humanized AS3MT mice (mouse arsenic methyltransferase gene (As3mt)replaced with human AS3MT, hAS3MT), we evaluated the in vivo effects of iAs and UroA on gut barrier function. Long-term iAs exposure (100 ppb for 28 weeks) significantly reduced expression of tight junction proteins, indicating compromised intestinal barrier integrity. UroA treatment protected hAS3MT mice from iAs-induced gut permeability, inflammation, colon shortening, and elevated colon weight/length ratio. UroA also reduced iAs-induced inflammatory cytokines, myeloperoxidase (MPO) activity and preserved intestinal epithelial cell tight junction protein expression. Further, microbiome and metabolomic analysis suggested that UroA treatment protected from iAs-induced gut microbial dysbiosis, especially restored several beneficial bacterial strains and short chain fatty acids (e.g., acetate and butyrate) and led to gut homeostasis. Together, these findings demonstrate that UroA mitigates iAs-induced gut toxicity and restores microbiota homeostasis.},
}

Animals
Intestinal Barrier Function/drug effects
*Coumarins/metabolism/pharmacology/administration & dosage
*Arsenic/toxicity
Mice
Humans
*Gastrointestinal Microbiome/drug effects
*Methyltransferases/genetics/metabolism
Colon/drug effects/pathology
Intestinal Mucosa/drug effects/metabolism
Cytokines/metabolism
Tight Junction Proteins/metabolism
Mice, Transgenic
Bacteria/metabolism/classification/genetics/isolation & purification
*Protective Agents

@article {pmid42400260,
year = {2026},
author = {Kim, D and Li, M and Nguyen, TH and Choi, YJ and Jang, S and Kim, M and Kim, YK and Shin, MK and de Guzman, ACV and Park, S},
title = {Vitamin B6 produced by gut microbiome regulates host behavioral phenotypes through dopaminergic metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2695485},
doi = {10.1080/19490976.2026.2695485},
pmid = {42400260},
issn = {1949-0984},
mesh = {Animals ; Caenorhabditis elegans/microbiology/metabolism ; Humans ; *Dopamine/metabolism ; *Gastrointestinal Microbiome ; *Vitamin B 6/metabolism/biosynthesis ; *Parkinson Disease/microbiology/metabolism/genetics ; Mice ; Pyridoxal Phosphate/metabolism ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism ; Phenotype ; Escherichia coli/genetics/metabolism ; alpha-Synuclein/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Male ; Mice, Inbred C57BL ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {The gut microbiome modulates host neuropathology, but the mechanisms linking specific microbial genes and metabolites to host phenotypes remain poorly defined. Here, we identify microbiome-derived vitamin B6 (VB6) and its biosynthesis gene as key regulators of host dopaminergic homeostasis. Metagenomic analysis of fecal samples from Parkinson's disease (PD) patients revealed enrichment of biosynthetic pathways for pyridoxal-5'-phosphate (PLP), the active form of VB6, and tyrosine decarboxylase genes. Using E. coli-C. elegans symbiotic models, we demonstrate that the bacterial pdxJ gene, encoding a key enzyme in de novo VB6 synthesis, is essential in regulating host dopaminergic homeostasis. Colonization with pdxJ-deficient bacteria led to reduced host VB6 and dopamine levels, reduced dopaminergic enzyme activity, and altered motor behavior, which were all rescued by VB6 supplementation. In PD-relevant C. elegans models, bacterial PLP biosynthesis modulated α-synuclein aggregation and behavioral deficits associated with human LRRK2 mutations. In mice, colonization with pdxJ-deficient bacteria reduced serum VB6 levels, decreased tyrosine hydroxylase staining in the substantia nigra, and impaired motor coordination, which were rescued by VB6 supplementation. Overall, our results define a bacterial pdxJ-PLP-dopamine axis that links gut microbial metabolism to host dopaminergic phenotypes and suggest bacterial VB6 biosynthesis as a potential modifier of PD risk and a context-dependent therapeutic target.},
}

Animals
Caenorhabditis elegans/microbiology/metabolism
Humans
*Dopamine/metabolism
*Gastrointestinal Microbiome
*Vitamin B 6/metabolism/biosynthesis
*Parkinson Disease/microbiology/metabolism/genetics
Mice
Pyridoxal Phosphate/metabolism
Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism
Phenotype
Escherichia coli/genetics/metabolism
alpha-Synuclein/metabolism
Bacteria/genetics/metabolism/classification/isolation & purification
Male
Mice, Inbred C57BL
Feces/microbiology
Disease Models, Animal

@article {pmid42400283,
year = {2026},
author = {Jiao, S and Tang, H and Jia, N and Dai, Y and Zeng, X},
title = {The Impact of Storage Conditions on the Microbiome Composition and Metabolites of Fecal Samples.},
journal = {Biopreservation and biobanking},
volume = {},
number = {},
pages = {19475535261464819},
doi = {10.1177/19475535261464819},
pmid = {42400283},
issn = {1947-5543},
abstract = {BACKGROUND: To investigate the effects of storage time and temperature on the quality of fecal samples and to provide a reference for clinical laboratories and biobanks in formulating sample storage operation guidelines.

METHODS: Fresh fecal samples were collected from healthy volunteers and immediately aliquoted into aliquots. Different temperature and time gradients were established to simulate common pre-analytical storage processes in clinical practice, with samples snap-frozen in liquid nitrogen immediately after collection as the control group. 16S rRNA gene sequencing and untargeted lipid metabolomics were employed to determine changes in microbial diversity, species abundance, and metabolite concentrations under different storage conditions, and sample quality was evaluated based on these indicators.

RESULTS: Storage at 4°C significantly minimized fluctuations in α-diversity indices, with the most pronounced protective effect observed within 2-4 hours; beyond 4 hours, changes in microbial community structure intensified. β-diversity analysis revealed that 4°C storage delayed the increase in microbial dissimilarity between samples and the liquid nitrogen-frozen control group, among which samples stored for 2-4 hours exhibited the highest similarity to the control. At the phylum level, the abundance of Firmicutes increased significantly after 6 hours of storage at room temperature, while 4°C storage effectively delayed this change. Metabolomic analysis identified more metabolomic differences (including bile acids and amino acids) in samples stored at room temperature, whereas only minor changes in fatty acid metabolites were observed at 4°C. 3β-hydroxy-5-cholenic acid exhibited a continuous upward trend with prolonged storage at both temperatures, suggesting its potential as a biomarker for evaluating sample storage quality.

CONCLUSION: Short-term storage at 4°C (≤4 hours) can effectively delay the quality degradation of fecal microbial communities and metabolites, making it the optimal transitional storage strategy when immediate liquid nitrogen freezing is not feasible in clinical practice. These findings provide critical experimental data for the establishment of standardized fecal sample storage protocols.},
}

@article {pmid42400322,
year = {2026},
author = {Saati-Santamaría, Z and Pérez-Gorjón, S and Abel-Schaad, D and Acedo-Bécares, A and Alba-Sánchez, F and Alves, AL and Babinska-Wensierska, W and Marfetán, JA and Barroetaveña, C and Barry, K and Beitia, F and Biniari, K and Bobadilla-Peñaló, EM and Bonito, G and Boutaris, M and Bueno-González, V and Cabezas, G and Charalambos, P and Copoț, O and de Errasti, A and de Pedro Noriega, L and Delavault, P and Dianez-Martínez, F and Diez-Méndez, D and Ercole, E and Fernández-Ruiz, A and Ferraguti, M and Gallo, AL and García-Fraile, P and Garrido, M and González Del Pozo, D and Greslebin, AG and Grilli, G and Guilcapi-Pacheco, ED and Haelewaters, D and Henkel, TW and Hirigoyen, A and Hosaka, K and Huais, PY and Jalli, M and Justo, A and Keskitalo, M and La Mantia, T and Lambevska, A and Langer, E and Leconte, C and Lojkowska, E and Marcos-Vidal, D and Mendoza-Fernández, AJ and Miralles-Mellado, I and Molina, L and Muzhinji, N and Nguyen, MN and Nieto-Lugilde, D and Nieto-Palenzuela, A and Njouonkou, AL and Norvell, S and Oficialdegui, FJ and Ortega Pérez, R and Palojärvi, A and Paradelo-Pérez, M and Pavone, Z and Peñas de Giles, J and Persiani, AM and Pildain, MB and Pinto-Carrasco, D and Poulin, L and Pouvreau, JB and Quatrini, P and Rodríguez de la Cruz, D and Romano, GM and Rosas-Ramos, N and Ruano, F and Salcedo-Larralde, I and Salmerón-Sánchez, E and Sam, K and Sharp, C and Tiago, PV and Valenzuela, R and Vasco-Palacios, AM and Vasilis, M and Vélez, ML and Vizzini, A and Volobuev, S and Wood, AR and Yli-Hemminki, P and Yorou, NS and Zmitrovich, IV and Bobo-Pinilla, J},
title = {Soil Microbial Diversity and Network Organization Respond to Land Use and Agricultural Inputs Worldwide.},
journal = {Global change biology},
volume = {32},
number = {7},
pages = {e70984},
doi = {10.1111/gcb.70984},
pmid = {42400322},
issn = {1365-2486},
support = {947084//European Union/ ; CLU-2025-2-04//Consejería de Educación de Castilla y León - Escalera de Excelencia - FEDER/ ; //Consejería de Educación de Castilla y León/ ; 101090267//European Commission/ ; RYC2023-045204-I//Agencia Estatal de Investigación (AEI), Spain/ ; PCI2022-132990//MCIN/AEI/ ; },
mesh = {*Soil Microbiology ; *Agriculture/methods ; *Microbiota ; Fertilizers ; *Biodiversity ; Fungi ; Pesticides ; Bacteria/classification ; Ecosystem ; },
abstract = {Soil microbiomes are critical for ecosystem functioning, yet the global influences of climate and agricultural practices on their diversity and structure remain incompletely characterized. Here we analyzed 1921 soil samples from 33 countries worldwide across diverse biomes to assess how climate gradients and agricultural inputs, including pesticides and fertilizers, shape prokaryotic and fungal communities. We found that microbial diversity peaks at intermediate temperatures and differs markedly between natural and agricultural soils, with agriculture increasing microbial diversity while altering community composition and ecological guilds. Pesticide use selectively reduced bacterial diversity and shifted fungal guilds, decreasing ectomycorrhizal fungi while increasing saprotrophs, whereas fertilization reduced microbial network cohesion, with organic and inorganic fertilizers eliciting distinct community responses. These findings reveal that climatic factors and agricultural management jointly influence soil microbial diversity, community structure, and network connectivity, with implications for soil health and ecosystem resilience in managed landscapes. Overall, our results demonstrate that agricultural practices, including the use of pesticides and both organic and inorganic fertilizers, act as strong ecological filters that reshape soil microbiomes worldwide-enhancing apparent diversity but driving a functional shift toward less mutualistic, more fragmented, and potentially less resilient communities.},
}

*Soil Microbiology
*Agriculture/methods
*Microbiota
Fertilizers
*Biodiversity
Fungi
Pesticides
Bacteria/classification
Ecosystem

@article {pmid42400696,
year = {2026},
author = {Yousefi, M and Farahpour, MR and Alizadeh, N and Abedian, A and Baradaran, B},
title = {Tumor-induced immune escape mechanisms and translational immunotherapeutic strategies.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-026-05518-8},
pmid = {42400696},
issn = {2730-6011},
abstract = {Tumor-induced immune evasion is a critical mechanism that promotes resistance to anticancer therapies and facilitates cancer progression. Notwithstanding the emergence of immunotherapies, especially immune checkpoint inhibitors (ICIs) and adoptive cell therapies, several cancers show resistance against such therapeutic interventions by adopting various methods of immune evasion. These include alterations to the tumor microenvironment (TME), infiltration of immunosuppressive cells, overexpression of inhibitory checkpoint molecules, and modified antigen presentation. This study provides a comprehensive assessment of the cellular and molecular principles behind immune evasion, as well as novel and established strategies for its prevention. The mechanisms, clinical implications, and limitations of significant therapeutic modalities, including checkpoint blockade, CAR-T cell therapy, cancer vaccines, and oncolytic virotherapy, are addressed. Particular emphasis is placed on combinatorial approaches, TME reprogramming, and next-generation targets like LAG-3, TIM-3, and TIGIT. The research examines the potential of predictive biomarkers, including PD-L1, Tumor Mutational Burden (TMB), Microsatellite Instability (MSI), and the microbiome, to guide personalized immunotherapy. Overcoming resistance and achieving enduring responses requires the integration of immunological insights with high-throughput molecular profiling and adaptive clinical trial design as the subject develops. The efficacy of immunotherapies across many cancer types may be enhanced by adopting a systems-level perspectives on tumor-immune interactions. Ultimately, restoring effective antitumor immunity with new, customized therapies is a crucial advancement in current oncology.},
}

@article {pmid42400751,
year = {2026},
author = {Dutta, S and Dutta, TK and Nanda, PK and Dhar, P and Das, AK and Bhunia, AK},
title = {Paradigm Shift of Microbiota-gut-brain Axis During Aging: Potential Role of Probiotics to Improve Cognitive Decline.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42400751},
issn = {1867-1314},
support = {1016249//National Institute of Food and Agriculture/ ; },
abstract = {Population aging is a global demographic inevitability, driven by advancements in healthcare, increased life expectancy, and declining fertility rates. Growing evidence implicates gut microbiota dysbiosis in the pathogenesis of cognitive impairments and neurodegenerative disorders commonly associated with aging, primarily through disruptions in immune, metabolic, and neuroendocrine signaling along the gut-brain axis. This review synthesizes current literature on the therapeutic potential of probiotic bacteria, such as Lactobacillus and Bifidobacterium, to enhance glial function, maintain blood-brain barrier integrity, and neurocognitive performance in older adults. However, probiotic efficacy is highly strain-specific and context-dependent, necessitating individualized evaluation of each microbial strain's therapeutic profile. Future research should prioritize precision microbiome-based strategies to elucidate mechanisms of action, optimal strain combinations, and their effectiveness across varying degrees of cognitive decline in the aging population. Furthermore, diet, physical activity, and microbial exposures represent essential, non-pharmacological tools for maintaining microbiota eubiosis and supporting neurocognitive health in aging populations.},
}

@article {pmid42400761,
year = {2026},
author = {Lieberman, OJ and Rojas-Valencia, L and Amorim, E and Ferguson, AR and Hinson, HE},
title = {Gastrointestinal Dysfunction in Critically Ill Patients With Traumatic Brain Injury: Clinical Implications and Putative Mechanisms: a Narrative Review.},
journal = {Current neurology and neuroscience reports},
volume = {26},
number = {1},
pages = {},
pmid = {42400761},
issn = {1534-6293},
mesh = {Humans ; *Brain Injuries, Traumatic/complications/physiopathology ; *Critical Illness ; *Gastrointestinal Diseases/physiopathology/etiology ; Gastrointestinal Microbiome/physiology ; },
abstract = {PURPOSE OF THE REVIEW: Moderate to severe traumatic brain injury (TBI) requiring intensive care is associated with high morbidity, mortality and long-term disability. In addition to neurologic sequelae, TBI causes a systemic disease with associated injury to other organ systems, including the gastrointestinal (GI) tract. Here, we review the evidence that GI tract dysfunction occurs after TBI and discuss the clinical implications of GI tract dysfunction on the clinical care of TBI patients, including inadequate nutritional support, elevated risk of pneumonia, and a hyperactive inflammatory response.

RECENT FINDINGS: We highlight recent findings that highlight putative mechanisms through which GI tract pathology may arise after TBI, including vagal nerve and enteric nervous system dysfunction, gut microbiome dysbiosis, sympathetic hyperactivity and iatrogenic injury. Finally, we highlight future approaches to target the GI tract that could improve outcomes in this critically ill patient population. In summary, we review the evidence supporting a role for GI tract dysfunction in the pathophysiology of critically ill TBI patients and highlight potential mechanisms through which GI tract dysfunction may worsen outcomes in this population.},
}

Humans
*Brain Injuries, Traumatic/complications/physiopathology
*Critical Illness
*Gastrointestinal Diseases/physiopathology/etiology
Gastrointestinal Microbiome/physiology

@article {pmid42401089,
year = {2026},
author = {Li, X and Yan, M and Cao, A and Zhao, C and Sun, Y and Shang, Z and Xue, Y and Lei, Y and Liu, C},
title = {Podophyllotoxin-induced nephrotoxicity via the microbiota-gut-kidney axis in SD rats based on the toxicological evidence chain (TEC) concept.},
journal = {International immunopharmacology},
volume = {186},
number = {},
pages = {117094},
doi = {10.1016/j.intimp.2026.117094},
pmid = {42401089},
issn = {1878-1705},
abstract = {Podophyllotoxin (PPT) exhibits limited clinical utility due to its nephrotoxicity, and its underlying mechanisms remain poorly understood. This study employs the toxicological evidence chain (TEC) framework and integrated multi-omics analyses to investigate the potential involvement of the microbiota-gut-kidney (MGK) axis in PPT-induced nephrotoxicity in SD rats. Toxicity was systematically evaluated through longitudinal monitoring of body weight, general behavior, biochemical markers, intestinal barrier function, and histopathological alterations. In parallel, multi-omics analyses, encompassing microbiome, metabolomics, and transcriptomics, were conducted to delineate the mechanistic underpinnings. The results showed that PPT exposure induced pronounced renal and intestinal damage, manifesting as significant weight loss, diarrhea, elevated renal injury biomarkers, increased lipopolysaccharide (LPS) levels, and diamine oxidase (DAO), along with histopathological lesions and enhanced apoptosis in renal and colonic tissues. PPT exposure perturbed gut microbiota homeostasis, characterized by depletion of beneficial taxa (e.g., Lactobacillus) and enrichment of potentially pathogenic genera (e.g., Bacteroides and Aggregatibacter), concomitant with diminished short-chain fatty acid (SCFA) production and altered metabolite profiles in fecal, serum, and renal samples. Integrated multi-omics analysis further revealed activation of the JAK1/2-STAT3 signaling pathway, upregulation of pro-inflammatory mediators (TNF-α, IL-6, IL-1β, LPS, TMAO), and suppression of anti-inflammatory cytokines (IL-10, IL-4). These in vivo molecular and inflammatory patterns were partially reproduced in HK-2 cells co-cultured with fecal microbiota supernatant from PPT-treated rats. In addition, the JAK1/2 inhibitor ruxolitinib attenuated PPT-induced JAK1/2-STAT3 phosphorylation and inflammatory cytokine secretion in HK-2 cells. Correlation network analysis further identified associations between gut dysbiosis, systemic inflammation, and metabolic perturbations. Collectively, these findings support a mechanistic hypothesis that MGK-axis disruption and JAK1/2-STAT3 signaling may contribute to PPT-associated nephrotoxicity. However, in vivo interventional studies are required to establish definitive causality.},
}

@article {pmid42401153,
year = {2026},
author = {Green, KD and Thomason, GK and Czuba, LC},
title = {Reduction of secondary 3-keto bile acids by aldo-keto reductase 1C1 and 1C4.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {54},
number = {7},
pages = {100340},
doi = {10.1016/j.dmd.2026.100340},
pmid = {42401153},
issn = {1521-009X},
abstract = {Secondary "keto" bile acids (BAs) are produced by the gut microbiome and contain one or more ketones on the steroid core. Plasma concentrations of keto BAs are limited by hepatic reductase activity, leading to hydroxylation of keto BAs. Although the aldo-keto reductase 1 (AKR1) family is implicated, it is not known which enzymes provide this function in the liver. We hypothesized that AKR1C1 and AKR1C4 metabolize 3-keto BAs. Six BAs with 3-keto groups were tested as potential substrates using purified, recombinant His6-tagged AKR1C1-4, and kinetic parameters were determined. AKR1C1 and AKR1C4 were found to exhibit isoform-specific substrate specificity, which may be explained in part by the hydroxylation pattern at carbon 12 of the BA core. This may suggest distinct biological roles in mediating BA homeostasis in humans. Both enzymes produced only α-OH products, as determined by liquid chromatography-mass spectrometry. We further hypothesized that fatty acids would impair reductase activity. AKR1C4 was more susceptible to inhibition compared to AKR1C1, but unsaturated fatty acids, such as linoleic acid, were the most potent inhibitors for both. We observed a 2- to 10-fold difference in the IC50 of fatty acids for AKR1C4 depending on the tested substrate. Further mechanistic and structure-function studies aim to characterize the substrate-specific kinetic and inhibition patterns observed and to evaluate the translational impact of AKR activity on plasma BA concentrations and cellular signaling. SIGNIFICANCE STATEMENT: Keto bile acids are bioactive secondary metabolites that are reduced upon enterohepatic recycling to the liver. Here, the substrate specificity, kinetics, and inhibition potential of 2 aldo-keto reductase enzymes, AKR1C1 and AKR1C4, were evaluated. This study suggests that AKR1C1 and AKR1C4 exhibit disparate substrate specificity patterns, reductase activity, and susceptibility to inhibition by fatty acids, which may have broad implications in understanding changes in bile acid homeostasis in metabolic diseases.},
}

@article {pmid42401355,
year = {2026},
author = {El-Sehrawy, AAMA and Farah, H and Oripov, F and Shakhmurova, G and Hussein, FM and Maharana, L and Singh, R and Tailor, NK},
title = {Estrobolome and the Endocrine-Microbiome Axis in Breast and Endometrial Carcinogenesis.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105471},
doi = {10.1016/j.critrevonc.2026.105471},
pmid = {42401355},
issn = {1879-0461},
abstract = {The estrobolome, the community of gut microbial genes involved in estrogen metabolism, may influence hormone bioavailability and cancer risk, although human evidence remains largely associative. This review summarizes evidence that bacterial β-glucuronidases, sulfatases, and hydroxysteroid dehydrogenases regulate enterohepatic estrogen recycling, while microbial metabolism also shapes receptor signaling, genotoxic estrogen metabolites, inflammation, and immune responses. Observational studies link gut microbial composition and function with breast and endometrial cancer, but causality remains unproven. Early dietary, probiotic, antibiotic, and fecal microbiota transplantation studies show biological effects, yet they are not sufficient for clinical application. We propose a functional framework that prioritizes microbial enzymatic activity over taxonomy and highlight multiparametric biomarkers and selective β-glucuronidase inhibition as promising research directions for prevention and adjunct therapy in hormone-driven cancers.},
}

@article {pmid42401402,
year = {2026},
author = {El-Sehrawy, AAMA and Oriquat, G and Rizaev, J and Yuldasheva, S and Shakhmurova, G and Abdul, NH and Singh, R and Bainsal, N},
title = {The Microbiome-Gut-Gonad Axis: How Microbial Metabolites Orchestrate Reproductive Physiology, Pathology, and Therapy.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {107079},
doi = {10.1016/j.jsbmb.2026.107079},
pmid = {42401402},
issn = {1879-1220},
abstract = {The human microbiome, a dynamic endocrine organ, exerts profound systemic influence through the production of bioactive metabolites. While the microbiome-gut-brain axis is well-established, the direct conduit between the gut microbiota and the reproductive system, the Microbiome-Gut-Gonad Axis, remains an emerging paradigm. This review explored cutting-edge evidence to construct a comprehensive model of the Microbiome-Gut-Gonad axis, focusing on the mechanistic roles of specific microbial metabolites in both physiological reproductive function and the pathogenesis of endocrine disorders. We move beyond mere correlation to elucidate how gut-derived molecules, such as short-chain fatty acids (SCFAs), secondary bile acids, and indole derivatives, directly and indirectly modulate the hypothalamic-pituitary-gonadal (HPG) axis by modulating the production of neuropeptides and hormones (Gonadotropin-releasing hormone (GnRH)) that regulate reproductive functions and also steroidogenesis and gametogenesis. We examine novel mechanisms including: the epigenetic regulation of steroidogenic enzymes by butyrate; the modulation of enterohepatic circulation of estrogens by β-glucuronidase-producing bacteria; and the role of tryptophan metabolites as ligands for aryl hydrocarbon receptor (AhR) in ovarian and testicular function. Furthermore, we critically appraise the disruptive potential of dysbiosis-driven metabolite shifts in PCOS, endometriosis, and male infertility, highlighting microbial metabolite signatures as promising exploratory biomarkers that require standardized, multi-center clinical validation before diagnostic use. At present, these signatures should be considered candidate biomarkers only, because external validation cohorts, assay reproducibility, and clinically meaningful estimates of sensitivity, specificity, predictive values, and clinical utility have not yet been established. Therapeutically, we evaluate innovative interventions, including precision probiotics, postbiotics, and dietary strategies targeting specific bacterial guilds, but these approaches remain investigational because current human evidence is still limited and heterogeneous. Finally, by integrating microbial endocrinology into reproductive medicine, this review establishes a new framework for understanding the etiology of reproductive endocrine disorders and paves the way for microbiome-targeted therapeutic avenues. Importantly, the evidence base is tiered: mechanistic statements in this review are drawn primarily from in vitro and animal studies, human disease links are described separately as observational evidence, and interventional claims are limited to early clinical studies and randomized trial summaries.},
}

@article {pmid42401477,
year = {2026},
author = {Yang, CH and Tang, HY and Fan, CM and Lin, JF and Cheng, ML},
title = {Integrated multi-matrix bile acid metabolic metrics (BAMMs): A methodological framework for functional metabolic phenotyping in human subjects.},
journal = {Analytica chimica acta},
volume = {1416},
number = {},
pages = {345822},
doi = {10.1016/j.aca.2026.345822},
pmid = {42401477},
issn = {1873-4324},
mesh = {Humans ; *Bile Acids and Salts/metabolism/urine/analysis/blood ; *Metabolomics/methods ; Phenotype ; Feces/chemistry ; },
abstract = {Traditional single-matrix bile acid (BA) analysis, which typically relies on a limited set of analytes in plasma or feces, often fails to capture the compartmentalized complexity of the microbiome-gut-liver axis. To address this, we developed a high-coverage, 61-analyte metabolomics platform integrated via a multifaceted Bile Acid Metabolic Metrics (BAMMs) framework across plasma, urine, and feces. In a 12-week clinical intervention study (n = 13), conventional single-matrix concentration profiling exhibited high inter-individual variance and failed to reflect significant metabolic shifts. In contrast, the BAMMs successfully identified multifaceted metabolic shifts-including carbon-position-specific transformations-that remained obscured in concentration-based analyses. Notable findings include significant decreases in fecal C-3 oxidation (dehydroLCA/LCA) and epimerization (isoLCA/LCA) metrics, alongside a significant increase in urinary C-7 oxidation (7-ketoCA/CA). These results demonstrate that standardized functional ratios are superior to concentrations for resolving the physiological "uncoupling" between the gut lumen and the systemic circulation. A key advantage of our approach is its high extensibility; by disclosing our full calculation methodologies and metabolic ratios, we provide a transparent and adaptable template that researchers can tailor for additional metabolites, such as muricholic acids, or diverse research models. This validated "Three-Matrix Workflow" provides a comprehensive lens for dissecting the compartmentalized dynamics of BA metabolism, offering a scalable and robust tool for future clinical and microbiome-based investigations.},
}

Humans
*Bile Acids and Salts/metabolism/urine/analysis/blood
*Metabolomics/methods
Phenotype
Feces/chemistry

@article {pmid42401599,
year = {2026},
author = {Jin, S and Kim, YT and Yang, J and Lee, JH},
title = {Lactiplantibacillus plantarum SLpl116 attenuates OVA-induced food allergy with ecological restoration of the gut microbiota and immune rebalancing.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00978-2},
pmid = {42401599},
issn = {2396-8370},
support = {RS-2022-NR067505//National Research Foundation of Korea/ ; RS-2024-00332462//Ministry of Food and Drug Safety/ ; },
abstract = {Gut dysbiosis is increasingly recognized as a key contributor to food allergy, yet probiotic strains capable of restoring allergic microbiota and rebalancing host immunity remain limited. Here, we identified Lactiplantibacillus plantarum SLpl116 through a multi-criteria screening pipeline integrating anti-allergic activity, safety, and processing stability, and evaluated its efficacy in a prophylactic ovalbumin (OVA)-induced murine food allergy model. SLpl116 significantly attenuated allergic symptoms, including diarrhea and hypothermia, and suppressed serum IgE, IgG1, OVA-specific immunoglobulins, and mucosal mast cell protease-1. It was also associated with suppression of Th2-related responses and enhancement of systemic Th1-associated signaling, indicating restoration of Th1/Th2 immune balance. Microbiome analysis showed that SLpl116 was associated with ecological restoration of the dysbiotic gut community, including suppression of allergy-associated taxa such as Alistipes finegoldii and Bacteroides and enrichment of beneficial commensals, particularly Lachnospiraceae. Correlation analysis supported an association between microbial reconfiguration and immune rebalancing, while PICRUSt2-based functional prediction suggested enriched butyrate-associated metabolic potential in the effective strain groups. Comparative genome-informed analysis further indicated that SLpl116 possessed distinctive phenotype-linked features, providing a plausible molecular rationale for its favorable phenotype. Together, these findings identify SLpl116 as a promising strain-level probiotic candidate associated with direct immune rebalancing and microbiome-associated ecological restoration.},
}

@article {pmid42401621,
year = {2026},
author = {Zhang, B and Zhong, Y and Pascal Muvunyi, B and Xu, T and Liu, J and Xiong, X and Cheng, X},
title = {Multi-omics profiling of high-carotenoid hybrid potato lines reveals coordinated metabolic reprogramming and associates with distinct tuber microbiota.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00842-3},
pmid = {42401621},
issn = {2396-8370},
support = {Grant No. 32401838 and Grant No. U2202206//National Natural Science Foundation of China/ ; Grant No. HekeZY230302//the Central Guiding Local Science and Technology Development Fund/ ; Grant No. 202130301030004//the Guangdong Major Project of Basic Research/ ; },
abstract = {Potato is a critical staple crop, and enhancing its carotenoid content is a promising strategy to improve its nutritional value. However, the synergistic mechanisms underlying carotenoid accumulation, superior nutritional traits, and the role of the endophytic microbiome remain unclear. Using an integrated multi-omics strategy, we systematically analyzed two high-zeaxanthin/lutein hybrids and four commercial cultivars. The hybrids accumulated significantly higher levels of zeaxanthin, lutein, and minerals, while exhibiting superior processing traits (e.g., higher dry matter/starch, lower reducing sugars). Integrated metabolomic and transcriptomic profiling revealed a coordinated upregulation of carotenoid and phenylpropanoid biosynthesis, alongside enrichment of stress-responsive phenolic acids. Notably, the endophytic microbiome in high-carotenoid tubers was distinct, dominated by Firmicutes and Proteobacteria, with genera like Bacillus and Latilactobacillus positively correlating with carotenoid content. Weighted gene co-expression network analysis identified a core regulatory module containing key genes (e.g., CCD4, BCH2) and novel transcription factors. Our findings elucidate a synergistic network linking metabolism, gene regulation, and the endophytic microbiome that collectively is associated with carotenoid accumulation and tuber quality. This provides critical targets for breeding nutritionally enhanced potatoes with desirable agronomic performance, supporting nutritional security and sustainable agriculture.},
}

@article {pmid42401711,
year = {2026},
author = {Huang, L and Lu, C and Hu, Y and Chen, J and Chen, A and Zhong, C and Chen, D and Qin, Z and He, X and Wu, L},
title = {Washed microbiota transplantation is associated with short-term changes in selected spirometric parameters in patients with abnormal spirometry.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60829-8},
pmid = {42401711},
issn = {2045-2322},
support = {2026P-ZD004//Guangzhou Clinical High-Tech Major and Specialized Technology Project/ ; 82505713//the National Natural Science Foundation of China/ ; 2025A1515011113//the Basic and Applied Basic Research Fund of Guangdong Province/ ; 2025KTSCX058//the Characteristic Innovation Project of Regular Colleges and Universities in Guangdong Province/ ; },
abstract = {Gut microbiota may modulate pulmonary inflammation through the gut-lung axis. This study investigated the association between washed microbiota transplantation (WMT) and short-term changes in pulmonary function, inflammatory markers, and gut microbiota in patients with abnormal spirometric patterns. A total of 110 patients who underwent fecal microbiota transplantation, also referred to as WMT, were consecutively screened between March 2023 and January 2025. Of these, 47 patients with paired baseline and post-WMT spirometric data were included in the primary spirometric analysis. According to baseline spirometric patterns, WMT recipients were classified into an abnormal spirometric-pattern group (DG, n = 19) and a normal spirometric-pattern WMT-recipient group (HC, n = 28; HC denotes WMT recipients with normal spirometry rather than healthy community controls). In addition, 43 patients receiving conventional treatment without WMT were included as a non-WMT comparison group (CON). The WMT group underwent multi-course interventions with longitudinal monitoring of pulmonary function parameters, inflammatory markers, breath-holding time (BHT), and 36-Item Short Form Health Survey scores (SF-36). Gut microbiota composition and predicted functional profiles were analyzed using 16S rRNA gene sequencing. After one WMT course, DG patients showed increases in forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV1). Compared with the non-WMT comparison group, the change in FVC was greater in WMT recipients, whereas the between-group difference in FEV1 change was not statistically significant. Other spirometric indices, BHT, inflammatory markers, SF-36 scores, and microbiome-related findings were considered exploratory. Exploratory 16S rRNA gene sequencing identified differences in selected gut microbial taxa between WMT recipients with abnormal and normal spirometric patterns, including differences in Firmicutes, Faecalibacterium, and Alistipes. Predicted functional profiling suggested changes in glycerolipid metabolism-, Nod-like receptor signaling-, and bacterial chemotaxis-related functional potentials. WMT was associated with short-term changes in selected spirometric parameters, particularly FVC and FEV1, in patients with abnormal spirometric patterns. Changes in inflammatory markers, BHT, SF-36 scores, and microbiome-related findings were exploratory and hypothesis-generating. Further randomized, disease-specific studies with standardized pulmonary function testing and mechanistic validation are needed.},
}

@article {pmid42401802,
year = {2026},
author = {Lee, JW and Loo, EXL and Chong, SS and Ban, KHK and Lee, CG},
title = {An AI-augmented review of childhood atopic dermatitis biomarkers across genetic, immune, microbial, and metabolic domains.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {},
number = {},
pages = {},
doi = {10.1186/s10020-026-01533-1},
pmid = {42401802},
issn = {1528-3658},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a prevalent inflammatory skin disease and a major source of disease burden in children. Biomarker studies in childhood AD span genetic, immune, microbial and metabolic domains, but prior reviews have often focused on single molecular layers, specific sample sites or clinical classification. As a result, the field lacks an integrated, systems-level synthesis that compares and contextualizes biomarkers across domains while clearly distinguishing evidence strength. The rapid growth of literature in this field also poses practical challenges for traditional manual review workflows.

MAIN BODY: To address these gaps, we conducted an AI-augmented, multi-domain review of childhood AD biomarkers. ASReview supported title and abstract screening, while ChatGPT assisted structured data extraction with human validation. Across 526 studies, we identified 141 genome, 95 immunome, 57 microbiome and 75 metabolome childhood AD biomarkers. The most frequently reported biomarkers included Filaggrin, IgE, CCL17, Staphylococcus, Bifidobacterium and vitamin D. Using a structured evidence-grading framework, eight biomarkers were categorized as having strong evidence: IgE, CCL17, CCL27, eosinophil cationic protein, eosinophil, IL-18, IL-31 and Escherichia. By synthesizing evidence across biomarker domains, we developed a systems-level, conceptual AD model in which barrier defects, Th2 inflammation, microbial dysbiosis and metabolic imbalance drive a self-perpetuating cycle of inflammation and barrier dysfunction. We also developed a web app for exploration of the biomarker findings: https://leejw.shinyapps.io/eczema_review_526/.

CONCLUSION: This review provides a broad synthesis of childhood AD biomarkers and frames the evidence within an integrated, multi-domain conceptual model. The findings support the rationale for approaches that consider multiple biological nodes, including barrier repair, immune modulation, microbiome-directed strategies and metabolic factors, while underscoring the need for further validation before clinical implementation. Methodologically, the study illustrates how a hybrid human-AI review workflow can support scalable biomedical evidence synthesis without replacing human oversight.},
}

@article {pmid42401969,
year = {2026},
author = {Karami, F and Shabkhiz, F and Aadeli, S and Tamtaji, OR and Aschner, M and Halimi, S and Fahanik Babaei, J and Nabavizadeh, F},
title = {The combined effects of probiotic and high-intensity interval training on memory function in high fat diet-fed rats.},
journal = {Behavioral and brain functions : BBF},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12993-026-00347-9},
pmid = {42401969},
issn = {1744-9081},
abstract = {INTRODUCTION: This study aimed to investigate whether the probiotic Lactobacillus rhamnosus GG (LGG) (alone or combined with high-intensity interval training (HIIT)) could improve cognitive, electrophysiological changes, oxidative stress and metabolic parameters in HFD-fed rats.

METHOD: Rats were randomly divided into four groups (n = 8): HFD group, HFD + LGG group, HFD+ HIIT group, and HFD + LGG+ HIIT group. Rats were fed HFD daily for a period of 16 weeks, during which LGG (1 × 10[10] colony forming unit (CFU)/ rats, orally), and HIIT protocol were administered four times a week on alternating days. At the end of study, assessment of social behavior, memory function, and Long-term potential (LTP) were performed using three-chambered apparatus, Y-maze task, and electrophysiology technique, respectively. Next, oxidative stress, lipid profiles, and liver enzymes were evaluated with routine kits.

RESULTS: Both LGG and HIIT alone or in combination improved working memory, social memory, and LTP in HFD-fed rats. In addition, both LGG and HIIT alone or in combination increased the hippocampal levels of superoxide dismutase, catalase, and increased the serum levels of high-density lipoprotein (HDL), and decreased the serum levels of leptin, triglyceride, cholesterol, low-density lipoprotein (LDL), aspartate transaminase (AST), alanine transaminase (ALT), and alkaline phosphatase (ALP) in HFD-fed rats.

CONCLUSIONS: The combination of LGG and HIIT provides a multi-pathway intervention that improves HFD-induced memory impairments by concurrently targeting oxidative stress, dyslipidemia, and hippocampal synaptic function. This supports the potential of combined lifestyle and microbiome-based therapies for preventing metabolic and cognitive disorders.},
}