@article {pmid42493595,
year = {2026},
author = {Nagao, I and Kim, HJ},
title = {Engineering human Gut-on-a-Chip culturomics for predictive pharmacomicrobiomics of first-pass metabolism.},
journal = {npj biomedical innovations},
volume = {3},
number = {1},
pages = {},
pmid = {42493595},
issn = {3005-1444},
support = {24KJ0651//Japan Society for the Promotion of Science Research Fellowship for Young Scientists/ ; 1R33CA286797//NIH NCI IMAT program/ ; },
abstract = {For orally administered drugs, intestinal first-pass metabolism influences systemic exposure and accounts for inter-individual pharmacokinetic differences. However, the mechanistic roles of gut microbiome-mediated biotransformation and patient-specific intestinal variability remain underrepresented in current regulatory frameworks. This Perspective explores how human-relevant culturomics platforms, including Gut-on-a-Chip microphysiological systems, allow for quantitative analysis of host-microbiome-drug interactions. We also discuss the potential of predictive intestinal ecosystem models for personalized pharmacomicrobiomics and next-generation translational drug development.},
}

@article {pmid42493609,
year = {2026},
author = {Yang, Y and Li, N and Zhou, L and Gong, S and He, Z and Tang, S and Ni, J and Liu, Y and Chan, JWY and Or, BPN and Lam, SP and Zhang, J and Chan, PKS and Chen, Z and Wong, SH and Mok, VCT and Chan, NY and Chau, SWH and Lai, CKC and Scheperjans, F and Wang, J and Huang, B and Wing, YK},
title = {Gut Microbiome in Depression with and without REM Sleep Behavior Disorder.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {42493609},
issn = {1476-5578},
support = {18190221//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 05162876//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; C4044-21G//Research Grants Council, University Grants Committee (RGC, UGC)/ ; },
abstract = {Major depressive disorder (MDD) is a risk factor for neurodegeneration, yet its heterogeneity makes identifying at-risk subtype challenging. Notably, MDD frequently co-occurs with REM sleep behavior disorder (RBD), a specific prodrome of α-synucleinopathy. It remains unclear whether comorbid MDD + RBD reflects a benign antidepressant effect, or higher neurodegenerative risk. Given growing recognition of gut-brain axis in neuropsychiatry, we aimed to delineate microbial signatures of MDD + RBD. We employed a four-group case-control design (N = 420) comprising 124 healthy controls (HC); 80 MDD without RBD features (MDD-only); 82 MDD + RBD; and 134 iRBD without psychiatric disease. All participants underwent clinical evaluation and provided fecal samples for metagenomic sequencing. Random Forest model was used to distinguish MDD + RBD, and further assessed in a validation dataset of 65 participants with MDD + RBD (n = 31) and MDD-only (n = 34). MDD + RBD exhibited prodromal neurodegenerative features, including elevated total likelihood ratio of prodromal Parkinson's Disease, olfactory deficits, and subtle motor signs. The microbial composition in MDD + RBD differed from HC and MDD-only, while resembling iRBD. Taxonomically, MDD + RBD exhibited an iRBD-like dysbiosis (e.g., enriched Akkermansia muciniphila, Ruthenibacterium lactatiformans; depleted Faecalibacterium prausnitzii), alongside depression-associated shifts (e.g., Streptococcus parasanguinis and Actinomyces oris). Functionally, MDD + RBD showed attenuated capacity of B‑vitamin biosynthesis and polysaccharides degradation, mirroring iRBD. The Random Forest machine-learning model distinguished MDD + RBD in older adults from MDD-only with an AUC of 0.73 in cross-validation and 0.79 in the validation dataset. MDD + RBD may represent a biologically distinct depression subtype associated with potential neurodegenerative risk. Gut microbiome provides a candidate approach for potential risk stratification in psychiatric populations.},
}

@article {pmid42493633,
year = {2026},
author = {Rock, R and Zhang, S and Noecker, C and Turnbaugh, PJ},
title = {Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42493633},
issn = {1740-1534},
abstract = {Despite a tremendous body of literature on environmental Actinomycetota, their role in the human gut remains poorly understood. In this Review, we highlight the representative species Eggerthella lenta, which has emerged as a major player in the gut microbiota and is increasingly amenable to mechanistic dissection. We discuss the unique metabolic niche of this asaccharolytic obligate anaerobe, including growth on amino acids and short-chain fatty acids, versatile anaerobic respiratory capacity, and the extensive biotransformation of endogenous, diet-derived and pharmaceutical small molecules. E. lenta is associated with a wide range of chronic diseases in humans and sufficient to exacerbate disease in preclinical models, prompting a renewed consideration of the pathogenic potential of this common member of the gut microbiota. Further mechanistic dissection coupled with the development of microbiome-editing tools is essential to understand E. lenta and its multifaceted contributions to gut microbial ecology and host pathophysiology.},
}

@article {pmid42493753,
year = {2026},
author = {Pielak, RM and Butler, DC},
title = {The Role of Skin Surface pH in Age Associated Pruritus: Mechanistic and Clinical Insights.},
journal = {American journal of clinical dermatology},
volume = {},
number = {},
pages = {},
pmid = {42493753},
issn = {1179-1888},
abstract = {Skin aging is characterized by progressive structural and biochemical changes that impair epidermal barrier function, alter the cutaneous microbiome, and predispose to chronic pruritus. Epidermal thinning, reduced lipid synthesis, and slowed barrier repair increase transepidermal water loss and vulnerability to irritation. Concurrently, age-related disruption of the acid mantle leads to elevation of skin surface pH, impairing acid-dependent lipid-processing enzymes while enhancing serine protease activity. These changes disrupt lamellar organization, weaken stratum corneum cohesion, and further compromise barrier integrity. Elevated pH and barrier dysfunction also reshape the skin microbiome. These changes favor alkalinity-tolerant and proinflammatory species while reducing protective commensals, thereby reinforcing inflammation and sensory irritation. Barrier impairment, dysbiosis, and pH-driven protease activation converge with neuroimmune dysregulation to sensitize peripheral nerves and promote chronic itch. Important contributors include kallikrein-protease-activated receptor-2 (PAR2) signaling and cytokines such as interleukin-31. This review highlights the pH-protease-itch axis as a unifying framework for pruritus in aging skin and discusses restoration of physiological acidity as a rational therapeutic strategy.},
}

@article {pmid42493771,
year = {2026},
author = {Yi, Y and Xie, F and Xia, C and Li, J and Zhao, P and Liu, M and Ma, X and Chen, J},
title = {Hypertension and gut microbial hydrogenases: a comparison of hydrogen metabolism and etiology.},
journal = {Medical gas research},
volume = {16},
number = {4},
pages = {352-358},
doi = {10.4103/mgr.MEDGASRES-D-25-00128},
pmid = {42493771},
issn = {2045-9912},
mesh = {*Hydrogenase/metabolism/genetics ; *Hydrogen/metabolism ; *Hypertension/microbiology/etiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; },
abstract = {JOURNAL/mgres/04.03/01612956-202612000-00006/figure1/v/2026-07-23T200825Z/r/image-tiff Hypertension is a prevalent chronic condition and serves as a significant risk factor for numerous cardiovascular and cerebrovascular disorders. Gut microbiota dysbiosis has been considered to contribute to the pathogenesis of hypertension. It has been reported that a large majority of gut microbiota possess genes encoding hydrogenases. These hydrogenases are involved in the alteration of gut microbiota in non-infectious colitis, suggesting a potential link between microbial hydrogen metabolism and disease onset. This study aims to explore the relationship between hydrogenase expression patterns in the gut microbiome and the incidence of hypertension. In this study, publicly available gut microbiome metagenomic data were used to comprehensively analyze the expression patterns of hydrogenases in the gut microbiota of hypertensive patients. Compared with the control group, a 2.3-fold increase in electron bifurcating [FeFe] group A3 hydrogenases (P = 0.0299), a 55.6% decrease in [NiFe] group 1d hydrogenases (P = 0.0097), increased hydrogen-sensing hydrogenases and decreased hydrogen-uptake hydrogenases in the hypertension group. The main difference between the two groups is reflected in the abundance of [NiFe] hydrogenase subtypes. After eliminating the effects of factors such as age, sex, and lifestyle, significant differences in the abundance of [FeFe] group A3, [NiFe] group 1d, and [NiFe] group 1c were observed between the two groups, suggesting that these three indicators could serve as potential biomarkers for diagnosing the onset of hypertension. Additionally, Mendelian randomization analysis showed a protective effect of hydrogen metabolism against hypertension (odds ratio = 0.72, 95% confidence interval: 0.61-0.85, P < 0.001). Our study advances the understanding of microbiome-mediated mechanisms in hypertension by demonstrating an association between hydrogenase expression dynamics and blood pressure regulation, providing a foundation for future microbiome-based diagnostic and therapeutic strategies.},
}

*Hydrogenase/metabolism/genetics
*Hydrogen/metabolism
*Hypertension/microbiology/etiology/metabolism
Humans
*Gastrointestinal Microbiome

@article {pmid42493800,
year = {2026},
author = {Van Den Bossche, T and Wolf, M and Armengaud, J and Arntzen, MØ and Benndorf, D and Figeys, D and Grenga, L and Hettich, RL and John, NS and Jagtap, P and Jehmlich, N and Kleiner, M and Kunath, BJ and Li, L and Lipton, M and Mesuere, B and Neely, BA and Ning, Z and Pedersen, AL and Perez-Riverol, Y and Rajan, J and Schallert, K and Seifert, J and Uzzau, S and Verschaffelt, P and Wilmes, P and Vizcaíno, JA and Martens, L and Heyer, R},
title = {The need for standardization and improved open (meta)data practices in metaproteomics.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42493800},
issn = {2049-2618},
mesh = {*Proteomics/standards/methods ; Computational Biology/methods ; *Microbiota ; Metadata ; Humans ; Multiomics ; Reproducibility of Results ; },
abstract = {Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.},
}

*Proteomics/standards/methods
Computational Biology/methods
*Microbiota
Metadata
Humans
Multiomics
Reproducibility of Results

@article {pmid42493801,
year = {2026},
author = {Van Den Bossche, T and Grenga, L and Alves, G and Arntzen, MØ and Benndorf, D and Brauer, M and Figeys, D and Henry, C and Hettich, RL and Heyer, R and Jagtap, PD and Jehmlich, N and Kleiner, M and Li, L and Mesuere, B and Pabst, M and Pandhal, J and Pope, PB and Seifert, J and Trautwein-Schult, A and Verschaffelt, P and Wilmes, P and Armengaud, J and Kunath, BJ},
title = {The Metaproteomics Initiative: five years of community-driven progress.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42493801},
issn = {2049-2618},
mesh = {*Proteomics/methods ; *Microbiota ; Humans ; Metagenomics ; },
abstract = {The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative's organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities. Video Abstract.},
}

*Proteomics/methods
*Microbiota
Humans
Metagenomics

@article {pmid42494129,
year = {2026},
author = {Wang, X and Akanyibah, FA and Zhang, P and Zhou, X and Zhang, M and Mao, F},
title = {Geniposide Alleviates Inflammatory Bowel Disease by Regulating Intestinal Flora and Arginine Metabolism and Inhibiting the NF-κB Pathway Through Targeting Anxa5.},
journal = {Mediators of inflammation},
volume = {2026},
number = {1},
pages = {e6231832},
doi = {10.1155/mi/6231832},
pmid = {42494129},
issn = {1466-1861},
support = {SH2024047//Zhenjiang Key Research and Development Plan (Social Development)/ ; SSF202410//Key Research and Development (Social Development) Projects of the Innovation Special Fund of Danyang/ ; 242102310081//Henan Province 2024 science and technology development plan/ ; KFKT23005//Open topic at the university level of Shangqiu Medical College in 2023/ ; K202423//Suqian Natural Science Fund Project/ ; K2024015//Key Project of Health Commission of Jiangsu Province/ ; JSDW202241//Jiangsu Provincial Medical Key Discipline Cultivation Unit/ ; },
mesh = {Animals ; Mice ; *NF-kappa B/metabolism ; *Arginine/metabolism ; Mice, Inbred BALB C ; *Inflammatory Bowel Diseases/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Iridoids/therapeutic use/pharmacology ; RAW 264.7 Cells ; *Annexin A5/metabolism ; Signal Transduction/drug effects ; Male ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including Crohn's and ulcerative colitis (UC), is a chronic gut inflammation thought to be caused by gut microbial causes and immune system dysfunction. Geniposide (GEN) is a natural compound shown to prevent IBD; however, its mechanism of modifying the gut microbiome, regulating arginine metabolism, and inhibiting the nuclear factor kappa B (NF-κB) pathway by targeting Annexin A5 (Anxa5) remains unexplored.

METHODS: This study examined the regulation of intestinal immunity, gut microbiota, metabolites, and associated activities and pathways, as well as the NF-κB pathway by GEN in a BALB/c mouse model of IBD. The mouse macrophage cell line (RAW264.7) was further utilized to investigate the role of GEN on the macrophage-arginine metabolism and the Anxa5 axis. qRT-PCR, Western blotting, hematoxylin and eosin (H&E), immunohistochemistry (IHC), immunofluorescence (IF), fecal 16S rDNA sequencing, and UHPLC/Q-TOF-MS were used to evaluate the treatment effect of GEN. Drug target sequencing and small interfering RNA (siRNA) were used to establish the target molecule of GEN.

RESULTS: GEN therapy improved colon and spleen tissues, decreased the disease activity index, helped mice maintain their weight, elevated anti-inflammatory cytokines and tight junction proteins, and decreased proinflammatory cytokines. GEN modulated the quantity of dysfunctional metabolites and enhanced the structure and diversity of the gut microbial community. GEN restored the underpopulated genera Enterorhabdus, Rikenella, Anaerotruncus, and Alistipes, regulating arginine metabolism mediated by G-guanidinobutyrate in RAW264.7 cells and the gut mucosa to protect the colon. GEN targeted Anxa5, enhancing its expression in both animal models and RAW264.7 cells. Following Anxa5 knockdown, cyclooxygenase-2 (COX-2) expression increased, along with the activation of NF-κB pathway-related proteins in RAW264.7 cells. GEN reduced the levels of NF-κB pathway-related proteins in both RAW264.7 cells and animal models.

CONCLUSION: GEN mitigated colitis by regulating the intestinal microbiota and arginine metabolism and inhibiting the NF-κB pathway via targeting Anxa5.},
}

Animals
Mice
*NF-kappa B/metabolism
*Arginine/metabolism
Mice, Inbred BALB C
*Inflammatory Bowel Diseases/drug therapy/metabolism
*Gastrointestinal Microbiome/drug effects
*Iridoids/therapeutic use/pharmacology
RAW 264.7 Cells
*Annexin A5/metabolism
Signal Transduction/drug effects
Male

@article {pmid42494203,
year = {2026},
author = {Hafez-Ghoran, S and Taktaz, F and Sang, S},
title = {Germination as a Strategy to Enhance the Bioactivity of Whole Grains: Phytochemical Remodeling and Health Implications.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {4},
pages = {e70574},
doi = {10.1111/1541-4337.70574},
pmid = {42494203},
issn = {1541-4337},
support = {//United States Department of Agriculture/ ; 2018-67001-28265//National Institutes of Food and Agriculture/ ; 2021-67017-33337//National Institutes of Food and Agriculture/ ; R01DK143583/NH/NIH HHS/United States ; },
mesh = {*Germination ; *Phytochemicals/analysis/chemistry ; Humans ; *Whole Grains/chemistry ; Nutritive Value ; },
abstract = {Consumption of microgreens, sprouts, and baby leaves is rapidly increasing, driven by consumer demand for nutrient-dense, minimally processed, and functional foods. Germination has emerged as a powerful biological strategy to enhance the nutritional quality and bioactivity of cereals and pseudocereals. The transition from dormancy to sprouting activates endogenous metabolic pathways that promote the accumulation of vitamins and diverse phytochemicals while reducing antinutritional compounds such as phytic acid. These changes are particularly relevant in the context of growing demand for gluten-free and clean-label food systems. This review evaluates recent advances in cereal and pseudocereal germination, with a focus on changes in whole-grain phytochemical composition and their implications for health-related outcomes. We discuss both shared phytochemicals, including γ-aminobutyric acid, phenolics, flavonoids, carotenoids, tocopherols, phytosterols, and policosanols, as well as grain-specific metabolites such as alkylresorcinols, avenanthramides, avenacosides, benzoxazinoids, hordatines, 3-deoxyanthocyanins, and γ-oryzanols. Emerging nonthermal pretreatments before germination and post-germination interventions may modify phytochemical profiles and could influence bioaccessibility or biological activity; however, their health benefits require further validation. Evidence from preclinical and limited human studies indicates that germination enhances grain bioactivity and may support glycemic regulation, lipid metabolism, inflammatory responses, and gut microbiome function. Collectively, these findings position germinated grains as promising ingredients for next-generation functional foods, while underscoring the need for standardized, mechanistic, and translational research to fully realize their potential.},
}

*Germination
*Phytochemicals/analysis/chemistry
Humans
*Whole Grains/chemistry
Nutritive Value

@article {pmid42494246,
year = {2026},
author = {Pang, Z and Yu, P},
title = {From genotype to microbiome function: a gene-metabolite-microbiome pathway shaping plant nutrient acquisition.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71457},
pmid = {42494246},
issn = {1469-8137},
}

@article {pmid42494273,
year = {2026},
author = {Ventura, EF and Corriger, J and Omer, H and Bodinier, M and Haller, D and Hertz, T and Larsen, M and Collado, MC},
title = {Microbiota Signatures in Early Life and Their Association With Food Allergy: A Systematic Review.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70433},
pmid = {42494273},
issn = {1398-9995},
support = {CEX2021-001189-S-20-1//Spanish Ministry of Science and Innovation and the European Social Fund Plus (ESF+)/ ; CEX2021-001189-S//Spanish Government MCIN/AEI to the Center of Excellence Accreditation Severo Ochoa/ ; //European Grant (Physiological and Ecological impact of pre- and probiotic interventions in relation to food allergy in early-life, EcoBIOTIC)/ ; //ERA-HDHL/ ; PCI2021-122059-2A//Programación Conjunta Internacional (PCI)/ ; ANR-17-HDIM-0002//EarlyFOOD/ ; ANR-20-CE15-0032//EcoBIOTIC/ ; FKZ 01EA2207//German Federal Ministry of Research, Technology and Space (BMFTR)/ ; },
abstract = {Food allergy (FA) is increasing worldwide, and early life may be a critical window for immune training. We systematically reviewed observational human studies linking early-life microbiota (infant, maternal, environmental, or extraintestinal) profiled using culture-based and/or culture-independent methods (including sequencing-based approaches) to subsequent FA or food sensitization outcomes in infants, children, and adolescents up to 18 years of age. PubMed, Web of Science Core Collection, Embase, Scopus, and LILACS were searched from database inception to March 2026. Inclusion required microbiota sampling during pregnancy or childhood and clinically ascertained FA/sensitization; non-human studies and studies without sequencing or clinical outcomes were excluded. Risk of bias was assessed using QUIPS. Owing to heterogeneity, we performed narrative synthesis. Forty studies were included (n = 6530 participants; 2077 cases). Across cohorts, cases were associated with lower diversity, early beta-divergence (1-6 months), neonatal enrichment of Proteobacteria (Pseudomonadota)/Enterobacteriaceae and selected taxa (Clostridium, Streptococcus, Sutterella), and depletion within the first year of Bifidobacterium, Blautia, and butyrate producers (Roseburia, Faecalibacterium). Functional profiles often suggested delayed maturation and reduced short-chain fatty acid capacity. Evidence was limited by moderate risk of bias, residual confounding, and heterogeneous outcome definitions. These findings support distinct early-life microbial configurations associated with FA susceptibility versus tolerance, informing mechanism-based prevention. Trial Registration: PROSPERO CRD420251234739.},
}

@article {pmid42494431,
year = {2026},
author = {Voermans, B and Prange, K and Bruin, S and Acherman, Y and Zaura, E and Nieuwdorp, M and Gerdes, V},
title = {Oral-gut strain sharing after Roux-en-Y gastric bypass: A canonical oral microbiome signature in the gut linked to hepatic and glycemic remodeling.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2693432},
pmid = {42494431},
issn = {2993-3935},
abstract = {Roux-en-Y gastric bypass (RYGB) induces durable weight loss and metabolic improvement, but the role of oral microbiota in shaping postsurgical gut ecology and metabolic outcomes is unclear. We examined whether RYGB promotes transfer and expansion of oral strains in the distal gut and how these relate to hepatic and glycemic health. In 25 patients from a longitudinal RYGB cohort, paired oral and fecal samples were collected before and 12 months after surgery. We examined the presence, abundance, and structure of cohort-specific canonical oral strains in the gut, and assessed α/β-diversity, cross-site correlations, and clinical associations using univariate tests and linear models. Machine-learning models evaluated the prognostic value of oral canonical strains for hepatic and glycemic outcomes. Oral taxon richness increased after RYGB, while Shannon diversity and individual signatures remained stable. In the gut, canonical oral strains expanded: shared oral-gut strains and their summed abundance rose significantly, converging into a reproducible post-RYGB niche. Abundance and fold change of oral-canonical strains associated with FIB-4, ASAT and fasting glucose, and predictive models suggested a prognostic signal for fasting glucose, TBF% and HbA1c. RYGB is associated with reproducible, strain-level enrichment of oral microbiota in the gut, with links to hepatic and glycemic outcomes.},
}

@article {pmid42494439,
year = {2026},
author = {Coote, E and Patel, N and Vijayanarayanan, R},
title = {The oral‒gut axis in periodontal disease: a systematic review of the associated human evidence of its mechanisms and implications for patient care.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2705699},
pmid = {42494439},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontal diseases may influence systemic health through the oral-gut axis, with three mechanistic pathways proposed. Periodontitis-associated gut dysbiosis has been repeatedly observed and may plausibly extend to effects on drug metabolism, yet the literature on periodontitis-associated dysbiosis and that on its potential effects on medicine pharmacokinetics have not previsouly been bridged.

OBJECTIVE: To synthesise the available human evidence for each of the three pathways with a distinct focus on the interventional evidence, and to position the evidence to its clinical context alongside downstream outcomes and the implications for patients and clinicians. Our secondary aim was to connect the dysbiosis and pharmacokinetic literatures in a hypothesis-generating section.

DESIGN: This systematic review was registered on PROSPERO. PubMed and Scopus were searched and eligibility restricted to human studies.

RESULTS: A total of 76 studies were included following full-text assessment by two independent reviewers. Across the three pathways, the human evidence was placed in clinical context with its downstream outcomes. Direct evidence that periodontitis modeifies drug response in humans was not identified, however, we were able to provide a hypothesis-generating section that identifies four drug classes for which a periodontitis-mediated modification of drug response would be most clinically relevant.

CONCLUSIONS: The oral-gut axis is a biologically plausible but, currently, under-evidenced route from periodontal disease to systemic and pharmacological outcomes. Future reserach should prioritise prospective comparative pharmacokinetic studies in periodontitis-affected popualtions and field-wide standardisation of methodology across oral-gut microbiome research.},
}

@article {pmid42494618,
year = {2026},
author = {Zhao, M and Huang, B and Chen, J and Li, J and Zhu, Z and Zhu, G and Hu, J and Li, F and Feng, J},
title = {Mechanism of Action and Therapeutic Potential of Sulforaphane in Skeletal Muscle Diseases: Molecular Pathways and Precision Medicine.},
journal = {Food science & nutrition},
volume = {14},
number = {7},
pages = {e72154},
pmid = {42494618},
issn = {2048-7177},
abstract = {Sulforaphane (SFN), a bioactive isothiocyanate abundant in cruciferous vegetables, has attracted growing interest as a potential nutraceutical intervention for skeletal muscle disorders. This narrative review synthesizes preclinical and early clinical evidence on the mechanisms and therapeutic applicability of SFN in ICU-acquired weakness, diabetic myopathy, sarcopenia, and exercise-induced muscle damage. SFN modulates skeletal muscle pathophysiology through four interconnected axes: regulation of protein homeostasis via mTOR-associated signaling and suppression of ubiquitin-proteasome-mediated catabolism; upregulation of oxidative stress defenses through Nrf2-driven antioxidant enzyme induction; attenuation of inflammatory networks via NF-κB inhibition and promotion of M2 macrophage polarization; and metabolic reprogramming through AMPK-mediated mitochondrial biogenesis and enhanced insulin sensitivity. Preclinical data suggest preliminary protective effects on respiratory and locomotor muscle; however, clinical translation remains uncertain. Several randomized controlled trials have failed to demonstrate significant effects on Nrf2 target genes or metabolic stress biomarkers, and bioavailability varies markedly across formulations and individuals. Heterogeneous responses across muscle fiber types, an undefined therapeutic window, and interindividual variability in gut microbiota-mediated conversion further complicate clinical application. To address these challenges, we propose a conceptual "Sulforaphane Precision Medicine Framework" integrating molecular biomarkers, gut microbiome profiling, and dynamic delivery systems to guide personalized intervention. While SFN shows promise as an adjunctive therapy, standardized formulations, refined patient stratification, and rigorous phase III trials are essential before routine clinical adoption can be recommended.},
}

@article {pmid42494654,
year = {2026},
author = {Dicksion, CA and Chao, DN and Rickmeyer, JD and Bess, EN},
title = {A Validated LC-MS/MS Method for Quantifying Phenolic Acids, Lignans, and Enterolignans from Human Fecal Samples.},
journal = {ACS nutrition science},
volume = {1},
number = {4},
pages = {356-366},
pmid = {42494654},
issn = {3067-6037},
abstract = {The human gut is home to numerous small molecules that impact health. Three prominent classes of molecules in this environment are phenolic acids, lignans, and enterolignans, which have been linked to anti-inflammatory and antioxidant effects as well as protection from cancer, cardiovascular disease, and neurodegeneration. The abundance of these molecules in the intestine as well as their biological significance motivated the development and validation of the LC-MS/MS method reported herein, which provides a simple, robust, and high-throughput approach to simultaneously quantify a 22-membered panel of phenolic acids, lignans, and enterolignans in human fecal samples. Facile sample preparation and a short analytical time (5 min per sample, compared to similar methods that range from 7.8-28 min) allow for high throughput. A 16-fold increase in sensitivity allows for quantitation of lignans that are often not detected via existing methods.},
}

@article {pmid42494770,
year = {2026},
author = {Woolsey, B and Sen, K},
title = {Dietary approaches to support cognition in older adults: a systematic review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1869091},
pmid = {42494770},
issn = {2296-861X},
abstract = {BACKGROUND: Older adults, particularly those residing in long-term care, experience disproportionate rates of cognitive decline and Alzheimer's disease (AD). While isolated nutrient supplementation has demonstrated limited clinical efficacy, comprehensive whole-food dietary patterns may offer significant neuroprotective benefits through complex nutrient synergy. This systematic review evaluates the efficacy of the Mediterranean, Nordic, Okinawan, and plant-based dietary approaches in mitigating cognitive decline and reducing dementia risk in older populations.

METHODS: The study protocol was prospectively registered with the International Prospective Register of Systematic Reviews (PROSPERO) under the registration ID CRD420261349593. Conducted in accordance with PRISMA 2020 guidelines, a systematic search of PubMed, Web of Science, CINAHL, and ScienceDirect was performed to identify peer-reviewed articles published between January 2021 and the present. Eligible studies included randomized controlled trials (RCT), prospective cohort studies, and longitudinal studies evaluating the impact of whole-food dietary patterns on cognitive outcomes in adults aged 60 and older.

RESULTS: Out of 622 initial records, 16 articles met all inclusion criteria. The synthesized evidence demonstrates that high adherence to these comprehensive dietary patterns is consistently associated with improved memory, enhanced executive function, and a reduced incidence of AD. These cognitive improvements are driven by interconnected physiological mechanisms, including reduced systemic inflammation, improved vascular integrity, favorable shifts in the gut microbiome, and optimized circulating endocannabinoid profiles. Additionally, the magnitude of these benefits is frequently modulated by individual biological factors, such as sex and APOE genotype.

CONCLUSION: Whole-food dietary patterns provide an effective, evidence-based framework for preserving cognitive resilience compared to single-nutrient interventions. Integrating these nutrient-dense diets into public health initiatives and long-term care settings offers a powerful strategy for neuroprotection, highlighting the need to advance personalized nutrition strategies in future clinical trials.},
}

@article {pmid42494846,
year = {2026},
author = {Mthembu, TP and Hlongwane, NL and Salawu-Rotimi, A and Hadebe, K and Pierneef, R},
title = {Metagenomic analysis of fecal and environmental microbiota in rural mixed livestock farming systems in South Africa.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1828785},
pmid = {42494846},
issn = {2235-2988},
mesh = {Animals ; South Africa ; *Feces/microbiology ; *Metagenomics ; *Livestock/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Environmental Microbiology ; *Microbiota ; Cattle ; Soil Microbiology ; Phylogeny ; Metagenome ; Swine ; Sheep ; Biodiversity ; Water Microbiology ; Rural Population ; },
abstract = {In South African rural areas, farmers often practice mixed extensive livestock farming, facilitating microbial exchange among and between animal species and their environment. The composition and transmission potential of microbiomes between animals and their environments in these smallholder livestock systems remain largely unexplored, creating a gap in understanding how mixed-livestock farming affects gut and environmental microbiomes. Shotgun metagenomics was used to uncover the fecal and environmental microbiota in smallholder mixed livestock systems, aiming to understand microbiome transfer within these systems. A total of 111 samples were collected in KwaZulu-Natal and Eastern Cape provinces of South Africa, including 76 fecal samples from cattle, goats, sheep, pigs, and chickens; 18 soil samples; and 17 water samples. Taxonomic analysis of the sequencing data identified Proteobacteria as the dominant phylum across most hosts, except that pigs were dominated by Firmicutes. Moraxellaceae and Pseudomonadaceae were the differentiating families between monogastrics and ruminants. Although microbial diversity differences were significantly attributed to the host, genera such as Acinetobacter, Chryseobacterium, Flavobacterium, Pedobacter, and Pseudomonas were consistently found across all animal and environmental hosts. Cattle shared more genera with the environment than other animal species. Opportunistic pathogens, including Enterococcus spp., Escherichia coli, and Clostridium spp., were found across all the livestock species, and were highest in chickens. Additionally, some pathogens were detected in water but none in soil, suggesting water as a potential medium for pathogen transmission. The microbial exchange between livestock and their surroundings highlights the permeability of host-environment boundaries in smallholder systems.},
}

Animals
South Africa
*Feces/microbiology
*Metagenomics
*Livestock/microbiology
*Bacteria/classification/genetics/isolation & purification
*Environmental Microbiology
*Microbiota
Cattle
Soil Microbiology
Phylogeny
Metagenome
Swine
Sheep
Biodiversity
Water Microbiology
Rural Population

@article {pmid42494872,
year = {2026},
author = {Quirino-Vela, LM and Mayoral-Chávez, MA and Matías-Cervantes, CA and Pérez-Cervera, Y and García-Montalvo, IA and Alpuche, J},
title = {The unified cardiometabolic disease continuum: mechanistic stages of a single pathophysiological process.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1897556},
pmid = {42494872},
issn = {1664-2392},
mesh = {Humans ; *Cardiovascular Diseases/physiopathology/metabolism ; *Diabetes Mellitus, Type 2/metabolism/physiopathology ; Animals ; Biomarkers/metabolism ; *Metabolic Diseases/physiopathology ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM), atherosclerotic cardiovascular disease (ASCVD), heart failure with preserved ejection fraction (HFpEF), metabolic dysfunction-associated steatotic liver disease (MASLD), hypertension, and chronic kidney disease (CKD) share risk factors and may represent endpoints of a pathophysiological cardiometabolic continuum. We analyzed data suggesting these phenotypes arise along a unified cardiometabolic disease (UCD) continuum with distinct stages, biomarkers, and therapeutic targets.

METHODS: A structured narrative review was conducted using PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar. Searches combined terms for mechanistic drivers (visceral adipose tissue, ceramides, lipotoxicity, NF-κB/NLRP3 signaling, gut microbiota, TMAO, adipokines, endothelial dysfunction, epicardial fat, metabolic flexibility) and clinical endpoints. Priority was given to peer-reviewed translational studies, major outcome trials, and consensus statements published between 2017-2026.

RESULTS: Current evidence supports a mechanistic framework in which visceral adipose tissue dysfunction and ectopic lipid accumulation, progressing through ceramide-mediated lipotoxicity, NF-κB/NLRP3-driven inflammation, gut microbiome-derived endotoxemia and TMAO, adipokine dysregulation, endothelial dysfunction, epicardial fat-mediated cardiac remodeling, impaired metabolic flexibility, and a cardiorenal amplification loop. Stage-specific mediators (e.g., ceramides, NLRP3, TMAO, leptin-adiponectin ratio) serve as biomarkers. The benefits of GLP-1 receptor agonists, SGLT2 inhibitors, and finerenone across T2DM, ASCVD, HFpEF, MASLD, and CKD reflect pharmacologic modulation of this continuum.

DISCUSSION: Data support a UCD model where T2DM, ASCVD, MASLD, HFpEF, hypertension, and CKD are manifestations of a progressive pathophysiological continuum. Framing these conditions as stages of a continuum informs risk stratification, biomarker development, and mechanism-guided therapy, providing a framework for designing trials targeting the continuum rather than individual endpoints.},
}

Humans
*Cardiovascular Diseases/physiopathology/metabolism
*Diabetes Mellitus, Type 2/metabolism/physiopathology
Animals
Biomarkers/metabolism
*Metabolic Diseases/physiopathology
Gastrointestinal Microbiome

@article {pmid42495133,
year = {2026},
author = {Joo, MK and Tak, J and Ha, S and Yoon, KS and Namgoong, JM and Kim, HO},
title = {The gut resistome as a potential determinant of immunotherapy response: antibiotics, immunometabolism, and precision oncology.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1835588},
pmid = {42495133},
issn = {1664-302X},
abstract = {Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet their efficacy can be compromised by systemic antibiotic exposure and the resulting disruption of the gut microbiome. Across several tumor types, antibiotic use near the initiation of ICI therapy has frequently been associated with reduced progression-free and overall survival. Emerging data suggest that, beyond taxonomic shifts, antibiotic exposure is often accompanied by expansion of the gut resistome, the collective pool of antibiotic resistance genes. Antibiotic-associated dysbiosis and resistome enrichment are linked to alterations in short-chain fatty acid production, bile acid signaling, and microbial purine metabolism, pathways known to shape antigen presentation, T-cell differentiation, and immune tone. Accordingly, gut resistome profiling should be considered an emerging candidate biomarker. Potential strategies to restore a favorable gut ecosystem include dietary modulation, microbiome-based therapies such as probiotics or fecal microbiota transplantation, and emerging anti-resistance approaches designed to limit resistome expansion. Together, these findings support a resistome-centered framework for patient stratification and microbiome-targeted interventions in precision immune-oncology.},
}

@article {pmid42495134,
year = {2026},
author = {Qu, J and Wu, Y and Qi, H and Chen, L and Luo, Y and Wang, Y and Zhang, Q},
title = {From assembly inference to co-occurrence organization: conservation contexts are associated with gut bacterial variation in the endangered Gymnocypris przewalskii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1875592},
pmid = {42495134},
issn = {1664-302X},
abstract = {INTRODUCTION: Conservation programs increasingly rely on in-situ and ex-situ interventions to prevent the loss of endangered species; however, it remains unclear whether such interventions preserve host-associated microbial organization. Understanding how conservation contexts influence gut microbiome structure and function is therefore essential for evaluating their ecological effectiveness.

METHODS: We analyzed gut bacterial communities of the endangered high-altitude fish Gymnocypris przewalskii across wild, in-situ conservation, and ex-situ conservation contexts using 16S rRNA gene sequencing. Analyses included host morphometric covariate assessment, alpha- and beta-diversity statistics, co-occurrence network analysis, PICRUSt2-based functional prediction, and null-model-based community assembly inference.

RESULTS: Gut bacterial communities were consistently dominated by Proteobacteria, with Firmicutes, Bacteroidetes, Actinobacteria, and Chloroflexi as secondary taxa. Alpha diversity showed no significant differences among groups, whereas beta diversity revealed modest but significant compositional shifts associated with conservation context, independent of multivariate dispersion and host morphometric traits. Functional predictions indicated shifts in pathways related to carbohydrate, energy, lipid, amino acid, terpenoid, polyketide metabolism, secondary metabolite biosynthesis, and xenobiotic degradation. Co-occurrence networks exhibited context-dependent restructuring: wild communities showed highest connectivity and positive interactions, in-situ networks were most modular and sparsest, and ex-situ communities showed the highest proportion of negative interactions. Null-model analyses indicated dominance of stochastic processes across all groups, with highest drift and stochasticity in in-situ populations, while ex-situ communities showed stronger deterministic influence and homogeneous selection.

DISCUSSION: These results demonstrate that conservation contexts are associated not only with taxonomic turnover but also with functional potential shifts, altered co-occurrence topology, and changes in community assembly processes. Within the constraints of an observational and site-confounded design, our findings suggest that microbiome-informed conservation assessment should move beyond diversity metrics and incorporate compositional, functional, network, and assembly-based perspectives when evaluating conservation outcomes in endangered aquatic hosts.},
}

@article {pmid42495136,
year = {2026},
author = {Gewirtz, MA and Zhang, Y and Vaidy, N and Redekar, NR and Minerva, N and Haddad, JA and Oringher, JL and Afruza, R and Chakraborty, M and Menkart, MG and Gopalakrishna, H and Hercun, J and Lack, J and Kleiner, DE and Lionakis, MS and Koh, C and Heller, T},
title = {Chronic hepatitis D infection is associated with distinguishing microbial and functional features in the gut microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1851892},
pmid = {42495136},
issn = {1664-302X},
abstract = {BACKGROUND: The microbiome of patients with hepatitis D virus (HDV) has yet to be characterized. This study aims to (1) characterize gut microbial composition in HDV, (2) determine its functional profile, (3) identify microbial species that contribute to changes in pathway expression, and (4) correlate the changes in the gut microbiome with clinical markers of disease severity.

METHODS: Cross-sectional analyses of 35 HDV-infected patients and 32 healthy controls (HCs) were performed. DNA and RNA were isolated from stool and sequenced by shotgun-sequencing. Microbial and functional profiles were compared between the HDV-cohort and HCs to identify disease-specific alterations to the gut microbiome. Clinical metadata were used to identify correlations with disease severity.

RESULTS: There were significant changes in the composition of the gut microbiome in HDV-infected patients as compared with HCs, spanning multiple bacterial phyla. Expression of 194 pathways was significantly increased in the HDV group. Pathways that were upregulated in the HDV cohort were related to amino acid and carbohydrate biosynthesis or involved important metabolic cofactors and carriers. Several microbial species, including Bacteroides fragilis, Cateibacterium mitsuokai, and Faecalibacterium prausnitzii, were identified as contributing to the differentially expressed pathways. Four genera correlated with hepatic venous pressure gradient (HVPG).

CONCLUSION: There are significant differences in microbial composition between HDV and HCs, several of which are found to be altered in other liver diseases. Upregulated pathways suggest a broader dysregulation of energy metabolism, even in early disease. These findings provide insight into pathways that may lead to liver disease progression in HDV.},
}

@article {pmid42495138,
year = {2026},
author = {Pang, Y and Chen, Y and Huang, Q and You, F and Fang, R and Geng, M and Ke, X and Tang, J and Ling, J and Cheng, Y and Zhao, C and Deng, X and Guo, J and Miao, C},
title = {Temperature regulation mechanisms of diapause in Coridius chinensis revealed by multi-omics integration: coordinated responses of Brain-Gut-Fat Body.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1810191},
pmid = {42495138},
issn = {1664-302X},
abstract = {Diapause in Coridius chinensis is a complex survival strategy that enables them to survive under prolonged cold stress. To elucidate the mechanisms of temperature regulation during diapause, we conducted multi-omics analyses, including gut metagenomics, brain transcriptomics, and fat body metabolomics, under both normal (25 °C) and diapause conditions (4 °C). Gut microbiome analysis revealed an extreme polarization during diapause, dominated by the endosymbionts Pantoea endophytica (52%) and Rickettsia bellii (47.4%), while functional microbiota such as Pantoea and Dietzia were significantly reduced. This shift suggests a trade-off where microbial metabolic diversity is sacrificed in favor of intracellular symbionts that may regulate host mitochondrial activity and suppress energy consumption. Brain transcriptomic analysis indicated a downregulation of neural signaling pathways related to feeding suppression, stress resistance, and circadian rhythm regulation. Fat body metabolomics identified the coordinated activation of 13 core pathways that link energy storage with stress adaptation, with dynamic changes ranging from rapid stress responses (0-300 AU) to energy storage dominance (300-500 AU), and finally to a state of homeostasis (>500 AU). Notably, dysregulated choline metabolism was significantly correlated with necrotic features (r = 0.78, p < 0.001), while catecholamine biosynthesis derived from tyrosine emerged as a corrective pathway, revealing the mechanistic link between metabolic flexibility and survival. Adults primarily utilize plants within the Cucurbitaceae, Fabaceae, and Solanaceae families as hosts, underpinned by long-standing folk traditions in specific localities regarding their dietary consumption or therapeutic application.},
}

@article {pmid42495144,
year = {2026},
author = {Yoon, SH and Lew, LC and Park, YH and Rather, IA},
title = {Identification and functional characterization of lactic acid bacteria with probiotic potential for alleviating premenstrual syndrome symptoms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1866966},
pmid = {42495144},
issn = {1664-302X},
abstract = {INTRODUCTION: Premenstrual syndrome (PMS) is a relatively widespread disorder associated with cyclical hormonal oscillations and disruptions in microbial homeostasis, particularly involving β-glucuronidase -producing bacteria that facilitate estrogen reabsorption. This study aimed to isolate, identify and functionally characterize probiotic strains from the vaginal microbiota of healthy Korean women in order to evaluate their potential in mitigating PMS-associated pathophysiology.

MATERIALS AND METHODS: A total of 12 isolates, named as KVS strains, were evaluated for their probiotic potential, including antimicrobial, enzyme inhibitory, and anti-adhesive activities associated with PMS. These isolates were further evaluated for adhesion capacity, survival under acidic conditions, auto-aggregation ability, inhibition of β-glucuronidase activity, antimicrobial activity, and suppression of Gardnerella vaginalis adhesion to HeLa cells.

RESULTS AND DISCUSSION: Several KVS strains, such as KVS001, KVS002, KVS004, KVS006, and KVS008 showed strong probiotic potential, adhesion capacity, high auto-aggregation rates, and survival in acidic conditions. In addition, these strains showed high antimicrobial activity and significantly suppressed β-glucuronidase activity, suggesting a mechanism for reducing estrogen recirculation. Moreover, many isolates effectively inhibited G. vaginalis adhesion to HeLa cells, indicating strong potential to counteract dysbiosis-associated PMS triggers. Collectively, the findings identify multiple KVS strains as promising probiotic candidates with multifunctional mechanisms relevant to PMS alleviation, supporting their prospective development as health-functional foods or therapeutic agents targeting microbiome-mediated hormonal modulation.},
}

@article {pmid42495148,
year = {2026},
author = {Cagle, R and Proll, S and Minot, SS and Purcell, H and Zhu, W and Djukovic, D and Liu, C and Fiedler, T and DeMeules, M and Mielcarek, M and Srinivasan, S and Raftery, D and Wu, M and Pergam, SA and Fredricks, DN},
title = {Acute gastrointestinal graft-versus-host disease is associated with reductions of secondary bile acids following allogeneic hematopoietic cell transplantation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818647},
pmid = {42495148},
issn = {1664-302X},
abstract = {INTRODUCTION: Allogeneic hematopoietic cell transplantation (HCT) can cure hematologic malignancies, but 30-70% of recipients experience acute graft-versus-host disease (GvHD). GvHD is associated with perturbations in the gut microbiome. Bile acids are host derived compounds that are transformed by gut bacteria and bind to specific host cell receptors, informing our hypothesis that changes in bile acid-metabolizing gut bacteria alter bile acid levels to affect gut physiology and immunity during GvHD.

METHODS: In a longitudinal case-control study of patients with and without acute gut GvHD, we characterized bile acid concentrations and the gut microbiome in stool.

RESULTS: Primary and conjugated bile acid levels were similar regardless of gut GvHD status, but endogenous secondary bile acid concentrations were associated with gut GvHD (p = 0.009). We observed 4.4-fold lower levels of endogenous secondary bile acids in GvHD, particularly lithocholic acid and derivatives (p = 0.004/padjusted = 0.02, fold change (FC) = 0.23). There was a 100-fold lower median abundance (p = 0.002 and FC < 0.01) and 20-fold lower median diversity of bacterial bile acid 7α-dehydroxylation (bai) genes (p = 0.0007 and FC < 0.05) in patients with GvHD.

DISCUSSION: This provides evidence that acute gut GvHD patients are deficient in microbial bai genes that make secondary bile acids.},
}

@article {pmid42495540,
year = {2026},
author = {Chen, Y and Lai, Y and Liu, Z and Zhang, K and Zheng, J and Lu, S and Huang, Z},
title = {The adaptation of the gut microbiome to social environmental changes in an Asian langur.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116779},
pmid = {42495540},
issn = {2589-0042},
abstract = {Social environments profoundly impact social animals' gut microbiome. Understanding such effects is critical for evaluating population fitness and conservation. Employing 16S rRNA and metagenomic sequencing, we investigated the gut microbiome of the endangered white-headed langur (Trachypithecus leucocephalus) to clarify its potential adaptive strategies to social environmental changes. Distinct differences were observed among social groups: the all-male group was enriched in Bacillota and showed stronger cellulose degradation potential, which might be associated with greater cellulose intake and higher cortisol and T3 levels; mixed-sex group was enriched in Actinomycetota, Pseudomonadota, and non-carbohydrate metabolism genes, possibly due to more young leaves consumption and reproductive needs. Alpha male replacement also shaped gut microbiome: the third alpha male period had highest Bacteroidota and lowest metabolic genes abundance, potentially related to improved food quality during this period. These preliminary findings highlight gut microbial adaptation to social environments in the studied population, providing implications for the conservation of this endangered species.},
}

@article {pmid42495752,
year = {2026},
author = {Anjum, N and Ahmed, Z and Anjum, F and Liaqat, S},
title = {Efficacy of prebiotics, probiotics, and postbiotics on depression: a systematic review and meta-analysis of randomized controlled trials.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/1028415X.2026.2703621},
pmid = {42495752},
issn = {1476-8305},
abstract = {BACKGROUND: Depression is a global health issue linked to gut-microbiota-dysbiosis, which influences brain function through the gut-brain axis. Dietary biotics offer a promising therapeutic avenue.

OBJECTIVE: This systematic review and meta-analysis aimed to evaluate the efficacy of biotic interventions in managing depression.

METHODOLOGY: Five databases were searched for randomized controlled trials (RCTs) from 2016 to 2024. 27 RCTs with a control group and standard depression rating scales were included. Data extraction and risk-of-bias assessment were conducted independently by two reviewers, with certainty-of-evidence appraised using GRADE. Meta-analyses employed standardized mean differences, with subgroup analyses by intervention duration (short: <6 weeks, medium: 6-12 weeks, and long: >12 weeks), respectively.

RESULTS: Probiotic interventions showed no significant effects in short and medium-duration subgroups (6 and 12 studies, respectively), both of which demonstrated substantial heterogeneity. A significant effect was observed in the long-duration subgroup (2 studies) with no observed heterogeneity, although based on limited evidence. Prebiotic interventions showed no significant effects, while postbiotic interventions demonstrated no clear effects across durations, with variable heterogeneity. Sensitivity analyses were generally consistent with the main findings. Overall certainty of evidence was rated as moderate due to inconsistency across studies.

CONCLUSION: Probiotics administered over longer durations may be associated with improvements in depressive symptoms, although this finding is based on limited evidence. Evidence for prebiotic and postbiotic interventions remains inconclusive. Overall, substantial heterogeneity was observed across studies, and findings should be interpreted cautiously. Further well-designed randomized controlled trials are needed to clarify the effects of microbiome-targeted interventions in depression.},
}

@article {pmid42495760,
year = {2026},
author = {Hou, J and Li, Y and Lin, S and Liu, Q and Zheng, H and Liu, W and Wang, Y and Peng, L and Wang, Z},
title = {Gut‑liver‑kidney axis: A systems biology framework for understanding and treating chronic kidney disease (Review).},
journal = {International journal of molecular medicine},
volume = {58},
number = {4},
pages = {},
doi = {10.3892/ijmm.2026.5937},
pmid = {42495760},
issn = {1791-244X},
mesh = {Humans ; *Systems Biology/methods ; *Renal Insufficiency, Chronic/therapy/metabolism/pathology ; *Liver/metabolism/pathology ; *Kidney/metabolism/pathology ; Animals ; *Gastrointestinal Microbiome ; Signal Transduction ; },
abstract = {Chronic kidney disease (CKD) is traditionally studied through an organ‑centric paradigm, despite its frequent coexistence with intestinal dysbiosis and metabolic dysfunction‑associated steatotic liver disease, which confers a 38% increased CKD risk. Multi‑organ crosstalk along the gut‑liver‑kidney axis remains inadequately addressed in current guidelines. The present study aimed to establish the gut‑liver‑kidney axis as an integrated systems biology framework for understanding CKD progression and to translate this framework into diagnostic, therapeutic and clinical trial strategies. The present review aimed to combine mechanistic summaries with systems biology perspectives, including weighted gene co‑expression network analysis, Bayesian causal inference and ordinary differential equation‑based dynamic modeling, to map bidirectional signaling across microbial, metabolic, inflammatory and hemodynamic dimensions, with diabetic kidney disease (DKD) as the principal exemplar. The axis operates through anatomically and molecularly defined positive feedback loops in which gut dysbiosis drives barrier failure and endotoxemia, amplifying hepatic lipotoxicity and bile acid dysregulation, precipitating renal tubular injury and fibrosis. This self‑perpetuating cycle, sustained by uremic toxin signaling, dysregulated peroxisome proliferator‑activated receptor/farnesoid X receptor (FXR)/Takeda G protein‑coupled receptor 5 (TGR5) pathways and trained immunity (a persistent hyperinflammatory state of innate immune cells driven by epigenetic and metabolic reprogramming), is most pronounced in DKD. Microbiome‑targeted interventions and FXR/TGR5 modulators are as the most clinically advanced axis‑directed strategies, though most remain at preclinical or early‑phase stages. Reframing CKD as gut‑liver‑kidney axis dysfunction enables systems‑level mechanistic integration, precision diagnostics through composite microbiome‑metabolomic signatures, and adaptive trial designs targeting upstream pathology, providing a foundation for incorporating axis‑based approaches into future CKD management.},
}

Humans
*Systems Biology/methods
*Renal Insufficiency, Chronic/therapy/metabolism/pathology
*Liver/metabolism/pathology
*Kidney/metabolism/pathology
Animals
*Gastrointestinal Microbiome
Signal Transduction

@article {pmid42496089,
year = {2026},
author = {Schweichhart, J and de Paula, CCP and Kreidlová, V and Vrba, J and Šorf, M and Sirová, D},
title = {Fungi Associated With Freshwater Zooplankton Are Taxon-Specific, Temporally Dynamic and Reflect Allochthonous Inputs.},
journal = {Molecular ecology},
volume = {35},
number = {14},
pages = {e70436},
doi = {10.1111/mec.70436},
pmid = {42496089},
issn = {1365-294X},
support = {23-06429S//Grantová Agentura České Republiky/ ; },
mesh = {Animals ; *Zooplankton/microbiology ; *Fresh Water/microbiology ; *Fungi/classification/genetics ; Sequence Analysis, DNA ; Rotifera/microbiology ; Ecosystem ; DNA, Fungal/genetics ; Copepoda/microbiology ; Phylogeny ; },
abstract = {The associations between microbes and planktonic invertebrates in freshwater ecosystems are considered key ecological interactions. However, our understanding of the structure, taxonomic specificity, and environmental drivers of zooplankton microbiomes remains poor. Here, we present the results of a field study using ITS1-amplicon sequencing that assesses the structure of fungal assemblages associated with three zooplankton groups (Cladocera, Copepoda and Rotifera) inhabiting the same water column during a single growing season. Compared with fungal communities in the surrounding water, zooplankton-associated assemblages showed higher genus richness, particularly in Copepoda and Rotifera, but lower diversity and evenness. We identified 190 fungal genera spanning eight phyla, dominated by fast-growing yeasts that thrive in nutrient-rich environments and are commonly associated with soil, leaf litter and decaying wood. The taxonomic identity of the zooplankton emerged as the main factor shaping fungal assemblages, followed by spore size and precipitation. Fungal sequences in zooplankton samples were largely derived from taxa typically linked to soils and plants, and the community composition shifted after precipitation events, consistent with terrestrial inputs to the lake. No fungal taxa were found exclusively in zooplankton guts, suggesting that these associations are transient and trophic rather than colonising. Taken together, these patterns indicate that zooplankton feed on suspended fungal cells or spores, many of which originate from surrounding terrestrial habitats. This suggests an overlooked pathway connecting land and freshwater ecosystems, highlighting terrestrial fungi as an under-recognised component of freshwater trophic linkages.},
}

Animals
*Zooplankton/microbiology
*Fresh Water/microbiology
*Fungi/classification/genetics
Sequence Analysis, DNA
Rotifera/microbiology
Ecosystem
DNA, Fungal/genetics
Copepoda/microbiology
Phylogeny

@article {pmid42496113,
year = {2026},
author = {Piperni, E and Blanco-Míguez, A and Mengoni, C and Piccinno, G and Punčochář, M and Ren, J and Segata, N and Asnicar, F and Poole, AC},
title = {Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0076326},
doi = {10.1128/spectrum.00763-26},
pmid = {42496113},
issn = {2165-0497},
abstract = {Resistant starch (RS) can confer benefits for the gut microbiome and host cardiometabolic health. However, different types of resistant starch can differentially affect gut microbiome composition and functional capacity, especially given interindividual variability in responses, thus limiting the application of resistant starch in dietary strategies. We used shotgun metagenomics to perform a secondary analysis of samples collected during a previously reported randomized clinical trial to determine the effects of dietary supplementation with two types of resistant starch (RS2 and RS4) and a digestible starch (control) on the gut microbiome. Both resistant starch types induced distinct but transient alterations in the gut microbial community. RS2 enriched the keystone degrader, Ruminococcus bromii, and Blautia glucerasea, whereas RS4 favored Parabacteroides distasonis and known but uncharacterized microbial species such as a Lachnospiraceae bacterium. Moreover, we detected strain-level differences in the response of Bifidobacterium adolescentis to resistant starch. Microbial functional profiling revealed an enhanced capacity for complex carbohydrate utilization following resistant starch intake, including increased abundance of specific α-amylases, glycoside hydrolases, starch utilization systems, and other currently uncharacterized genes. Identifying the bacterial strains and genes that respond to different RS types will help to more accurately predict who will benefit from a given RS type. Our findings demonstrate that RS2 and RS4 differentially shape microbial ecology and metabolic capacity and provide a foundation for microbiome-informed personalization of resistant starch-based dietary interventions.IMPORTANCEDietary intake influences human health by modulating metabolism, partly by shaping the microbiota inhabiting the gut. Resistant starch (RS), a dietary fiber, is associated with metabolic improvements. While previous research has explored how RS alters the gut microbiome, RS comprises five types with differing physical and chemical characteristics, and the distinct impacts of each type on the microbiome and host health have not been fully characterized, particularly using high-resolution approaches such as shotgun metagenomics. In this secondary analysis of samples from a longitudinal crossover intervention study, we link dietary supplementation with RS2 and RS4 with distinct and transient changes in the composition and functional potential of the human gut microbiome. Specifically, we identify species that increase in abundance with each RS type, accompanied by increases in genes and pathways involved in complex carbohydrate utilization. The findings support the development of precision nutrition strategies utilizing RS supplementation to improve metabolic health.This study is registered with ClinicalTrials.gov as NCT05743790.},
}

@article {pmid42496154,
year = {2026},
author = {Zhang, J and Cai, L and Wang, L and Zhang, L and Meng, N and Chen, A and Ma, Q},
title = {Marine antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one disrupts sediment microbiome structure and function: insights from absolute quantification and enzyme activity dynamics.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0081926},
doi = {10.1128/aem.00819-26},
pmid = {42496154},
issn = {1098-5336},
abstract = {The organic booster biocide DCOIT (4,5-dichloro-2-n-octyl-4-isothiazolin-3-one) is widely used in marine antifouling systems, yet its ecological impacts on sediment microbiomes remain poorly understood. Here, we integrated absolute quantitative 16S rRNA gene sequencing, metagenomics, and enzyme activity assays to examine microbial responses to DCOIT exposure (0-50 μg/g sediment) over 30 days. DCOIT induced oxidative stress and bioenergetic impairment, accompanied by reduced microbial activity and inhibition of key enzyme-mediated processes involved in organic matter turnover and nitrogen transformation. Absolute quantification revealed a compensatory increase in total microbial abundance by Day 30, despite persistent diversity loss and community restructuring. Metagenomic analysis showed that DCOIT disturbed functional potentials related to carbon and nitrogen cycling. Kordiimonas, Aliikangiella, and Neptuniibacter emerged as potential contributors to nitrogen transformation, whereas Marinobacter was more closely associated with potential DCOIT transformation. DCOIT exposure also enriched adaptive traits, including chemotaxis, motility, quorum sensing, and biofilm regulation, and was accompanied by increased multidrug efflux systems and heavy metal resistance determinants. Our findings provide novel insights into the ecotoxicological risks of isothiazolinone biocides and highlight the potential for DCOIT to undermine sediment ecosystem functions and microbial habitat health. Given its extensive application, this study emphasizes the need to consider the microbial ecological consequences of DCOIT accumulation in seafloor environments.IMPORTANCEDCOIT is widely used in marine antifouling coatings and can accumulate in benthic sediments, yet its effects on sediment microbiomes remain poorly defined. This study shows that DCOIT disrupts microbial energy status, enzyme activities, community structure, and nitrogen-cycling functions while selecting for adaptive traits and resistance-related determinants. By integrating absolute quantification, metagenomics, and enzyme assays, our work demonstrates that DCOIT poses microbial ecological risks beyond toxicity to macroorganisms and should be considered in assessments of antifouling biocides.},
}

@article {pmid42496155,
year = {2026},
author = {Maldarelli, GA and Marino, J and Lee, JR and Westblade, LF and Hovan, M and Douglass, C and Davidson, E and Longman, RS and Satlin, MJ},
title = {Enteric Microbiome Features that Contribute to Gram-Negative Bloodstream Infections in Hematopoietic Cell Transplant Recipients Colonized with Fluoroquinolone-Resistant Enterobacterales.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag376},
pmid = {42496155},
issn = {1537-6613},
abstract = {BACKGROUND: Hematopoietic cell transplant (HCT) recipients colonized with fluoroquinolone-resistant Enterobacterales (FQRE) frequently develop bloodstream infection (BSI) from their colonizing FQRE strains while receiving fluoroquinolone prophylaxis during neutropenia. However, enteric microbiome features that contribute to this increased BSI risk are unknown.

METHODS: 16S ribosomal RNA gene sequencing and quantitative cultures were performed on stool samples collected before and after the initiation of levofloxacin prophylaxis during a single-center prospective study of patients undergoing HCT. Enteric microbiome features were compared between FQRE-colonized and non-colonized patients and between FQRE-colonized patients who did and did not develop FQRE BSI.

RESULTS: We evaluated samples from 26 participants colonized with FQRE pre-HCT (nine developed FQRE BSI) and 69 not colonized with FQRE (none developed FQRE BSI). FQRE-colonized participants had a higher median baseline relative abundance of Enterobacterales (4.7% vs.0.3%) and Bacteroidales (14.3% vs. 0.5%) than non-colonized participants. After starting levofloxacin prophylaxis, the relative abundance of Enterobacterales declined in all but one HCT recipient without FQRE colonization, but increased in approximately one-third of participants with FQRE, including those who subsequently developed FQRE BSI. Among FQRE-colonized HCT recipients, there were no significant differences in FQRE colonization density or microbial diversity or composition between those who did and did not develop FQRE BSI.

CONCLUSIONS: FQRE-colonized HCT recipients have a distinct microbiome composition compared to HCT recipients without FQRE colonization and frequently have an expansion of Enterobacterales during levofloxacin prophylaxis that precedes FQRE BSI. Additional studies of FQRE-colonized HCT recipients are needed to clarify microbiome risk factors for FQRE BSI.},
}

@article {pmid42496300,
year = {2026},
author = {Ntais, C and Chatziprodromidou, IP},
title = {Antimicrobial Resistance as a Global Public Health Challenge: Epidemiological Burden, Bioethical Dimensions and Emerging Therapeutic Strategies.},
journal = {Infectious disease reports},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/idr18040070},
pmid = {42496300},
issn = {2036-7430},
abstract = {BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a major global public health threat, compromising prevention and treatment of infectious diseases. This narrative review examines AMR as a multifactorial and transnational crisis through epidemiological, One Health, social and bioethical perspectives, and discusses emerging non-antibiotic preventive and therapeutic strategies.

METHODS: PubMed and Scopus were searched using terms related to AMR, epidemiology, public health, surveillance, One Health, bioethics, equity and alternative therapies. Peer-reviewed medical and public health articles were considered, together with selected reports from international organizations and public health agencies.

RESULTS: AMR is driven by inappropriate antibiotic use in human medicine, livestock, aquaculture and agriculture, combined with weaknesses in infection prevention, stewardship, environmental control and surveillance. Epidemiological evidence shows a substantial global burden, marked regional inequalities in resistance patterns, surveillance capacity and policy response, and major consequences, including increased mortality, prolonged hospitalization, rising healthcare costs and disproportionate effects on vulnerable populations. Key bioethical concerns include collective responsibility, equitable access to effective treatment, stewardship, global justice and intergenerational accountability. Emerging non-antibiotic strategies vary in translational maturity: vaccines and selected microbiome-based interventions have preventive or supportive roles in defined settings, bacteriophage therapy is used mainly in compassionate or specialized contexts, and many antimicrobial peptides and nanotechnology-based platforms remain experimental or early translational.

CONCLUSIONS: AMR requires coordinated global action grounded in One Health, strong public health systems, integrated surveillance, responsible antimicrobial use and sustained innovation. Effective containment must also address social inequalities, ethical stewardship, equitable access to diagnostics and treatment, and responsibility toward future generations.},
}

@article {pmid42496597,
year = {2026},
author = {Montanari, S and Hartmann, M and Nesler, A and Giovannini, O and Longa, CMO and Perazzolli, M},
title = {Choline pelargonate treatments decreased downy mildew and powdery mildew symptoms with negligible effects on grapevine phyllosphere microorganisms.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag082},
pmid = {42496597},
issn = {1574-6941},
abstract = {Grapevine is an important crop worldwide, but most cultivars are susceptible to downy mildew and powdery mildew. This study aimed to evaluate the efficacy of choline pelargonate (CP) against grapevine downy mildew and powdery mildew under controlled and field conditions, and to assess its effects on phyllosphere microorganisms. CP decreased the severity of both pathogens under greenhouse and field conditions. In greenhouse trials, 16 mM CP showed efficacy comparable to copper and sulfur applied at label-recommended concentrations as reference fungicides in organic viticulture. CP showed direct inhibitory activity against both pathogens, and slightly induced defense-related grapevine genes (CHIT-3, OSM-2, and PR-1). Field experiments corroborated the efficacy of CP against powdery mildew and downy mildew severity on leaves and bunches. Microbial community analysis revealed that plant compartment, vineyard location, and sampling time were key drivers of microbial community structure, while treatments showed negligible effects on microbial alpha-diversity and beta-diversity of grapevine leaves and bunches. CP treatment partially modified the relative abundances of some bacterial and fungal taxa, while reference fungicides caused broad changes across multiple genera. CP showed promising antifungal activity with minimal effects on phyllosphere microorganisms, supporting its potential as a sustainable disease management approach that preserves indigenous microbial communities.},
}

@article {pmid42496608,
year = {2026},
author = {Küper, K and Kittler, S and Peh, E and Hirnet, J and Hetterich, J and Kopp, JS and Plötz, M and Rohn, K and Müsken, M and Fruth, A and Pees, M},
title = {Salmonella-specific phages from captive bearded dragons (Pogona vitticeps): Temperate traits and temperature-dependent variability in inhibition across isolates.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag188},
pmid = {42496608},
issn = {1365-2672},
abstract = {AIMS: Zoonotic infections with Salmonella spp. transmitted from reptiles to humans are an increasing concern due to the growing number of documented cases and the close contact between humans and reptiles. Reptiles, such as bearded dragons (Pogona vitticeps), frequently carry Salmonella enterica asymptomatically as part of their intestinal microbiota.Given the rise of antibiotic-resistant Salmonella strains in reptiles, bacteriophages (phages) may provide a targeted and sustainable alternative for preventing reptile-to-human transmission.

METHODS AND RESULTS: Seventeen phages were isolated from ten of eighteen faecal samples collected from bearded dragons. Seven of these phages were selected for further analyses. Host range assays on 41 S. enterica and nine non-Salmonella isolates revealed a narrow spectrum: phages infected up to 63.4% of Salmonella isolates and lysed one non-Salmonella strain. Planktonic killing assays at 25 °C and 37 °C showed pronounced bacterial growth reduction, with 8 of 12 significant inhibitions observed at 37 °C. Phage cocktails generally showed stronger inhibition than individual phages. Electron microscopy and whole-genome sequencing identified six Myovirus-like and one Siphovirus-like phage, all temperate with integrase or transposase genes despite lytic activity.

CONCLUSIONS: This study expands knowledge of S. enterica-specific phages from reptiles, detailing host specificity, morphology and genomic features. While in vitro results are promising, in vivo efficacy may be influenced by host physiology, immunity and microbiome interactions. The predominance of temperate phages may limit direct therapeutic use, though low lysogeny rates in related phages and genetic engineering advances may enable future applications.},
}

@article {pmid42496748,
year = {2026},
author = {Manda, T and Hwarari, D and Dzinyela, R},
title = {Phosphorylation networks as regulatory hubs in plant stress signaling: kinase dynamics, crosstalk, and network plasticity.},
journal = {Plant cell reports},
volume = {45},
number = {8},
pages = {},
pmid = {42496748},
issn = {1432-203X},
mesh = {Phosphorylation ; *Signal Transduction ; *Stress, Physiological/physiology ; *Protein Kinases/metabolism ; Protein Processing, Post-Translational ; *Plants/metabolism ; Plant Proteins/metabolism/genetics ; },
abstract = {Agriculture faces significant limitations from climate change, soil degradation, and a wide range of abiotic and biotic stresses that continually threaten global food security. Although transcriptional and hormonal regulatory networks have been extensively studied, post-translational modifications (PTMs), particularly phosphorylation, remain comparatively underexplored despite their central role in rapid stress signaling. In this review, we synthesize recent advances in phosphoproteomics, kinase network mapping, and systems biology to highlight phosphorylation as a key regulatory hub in plant stress responses. Drawing from both model species and crops, we emphasize major kinase families, including MAPKs, CDPKs, RLKs, and SnRK1/TOR, which translate calcium signatures, reactive oxygen species (ROS) waves, and cellular energy status into precise physiological outputs. We also discuss how multi-omics integration, precision breeding, synthetic biology, and microbiome engineering can leverage phosphorylation dynamics to advance climate-smart agriculture. By outlining phosphorylation networks as functional regulators, this work underscores their translational potential for developing resilient crops that can maintain yield under environmental extremes.},
}

Phosphorylation
*Signal Transduction
*Stress, Physiological/physiology
*Protein Kinases/metabolism
Protein Processing, Post-Translational
*Plants/metabolism
Plant Proteins/metabolism/genetics

@article {pmid42496816,
year = {2026},
author = {Kumari, A and Koli, VK and Singh, NA},
title = {Diversity and antibiotic profile of Enterobacterales spp. bacteria from Red-naped ibis.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {42496816},
issn = {1612-9210},
support = {918/(CSIR-UGC NET JUNE 2018//University Grants Commission/ ; },
abstract = {Antibiotic resistance in wildlife is an emerging concern, as birds can serve as reservoirs and vectors for resistant bacteria. In this study, we investigated the diversity of bacteria belonging to the Enterobacterales order and their antibiotic resistance patterns in the unexplored Red-naped ibis (Pseudibis papillosa). It is a resident wading bird species in western India, i.e., Udaipur city, Rajasthan. It inhabits a wide range of environments, including urban areas, wetlands, agricultural fields, and fallow lands. Fecal samples (n = 45) were collected and a total of 60 bacterial isolates were analyzed for bacterial diversity and bacteria were characterized using biochemical, molecular, methods. Interestingly, four novel bacterial taxa from this host species were identified, i.e., Enterobacter mori, Enterobacter soli, Citrobacter freundii, and Leclercia adecarboxylata. Notably, E. mori and E. soli were reported for the first time in this bird species globally. Antibiotic susceptibility testing revealed high levels of multidrug resistance, with 40% of isolates resistant to at least three classes of antibiotics. Notably, resistance to clinically important antimicrobials, including the third-generation cephalosporin cefotaxime and reduced susceptibility to the carbapenem imipenem, was observed, raising concerns for spread of antibiotic resistance bacteria. Resistance to linezolid (100%) and rifampicin (100%) was also observed across isolates, consistent with the intrinsic resistance of Gram-negative bacteria to these agents. Our findings reported the presence of antibiotic-resistant bacteria in wild bird species which may contribute to the spread of antibiotic resistance through their fecal deposits and pose a serious risk to the health of humans and wild animals.},
}

@article {pmid42496932,
year = {2026},
author = {Kumar, A and Dakal, TC and Parveen, K and Bhushan, R and Dhabhai, B and Parveen, A and Yadav, P and Tandon, R},
title = {Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {42496932},
issn = {1573-4927},
support = {BT/RLF/Re-entry/38/2017//Department of Biotechnology, India Department of Biotechnology (DBT), Government of India/ ; },
abstract = {Integrating high-throughput sequencing with phylogenetic analysis now spans everything from single genes to long-read pangenomes and metagenomes, yet practitioners still face fragmented, tool-centric guidance. This review revisits algorithms, tools, and workflows for sequence and phylogenetic analysis in the NGS-based omics era, with a focus on comparative performance and scenario-driven decision-making. We first organise classical approaches to tree reconstruction - distance methods, maximum parsimony, maximum likelihood, and Bayesian inference - around core criteria of consistency, efficiency, robustness, and computational cost. We then examine multiple sequence alignment strategies, contrasting progressive, consistency-based, and structure-aware algorithms (such as MAFFT variants and T-Coffee family tools) with segment-based and incremental approaches (for example DIALIGN, anchored domains, and local updates) and alignment-free representations based on k-mers, absent words, and related statistics. For inference, we compare heuristic engines optimised for ultra-large alignments (FastTree, VeryFastTree, online tree optimisation) with full ML frameworks (IQ-TREE, RAxML-NG) and Bayesian platforms for time-scaled phylogenies and phylodynamics (MrBayes, BEAST family). We explicitly discuss trade-offs in accuracy, memory, scalability, and uncertainty support, and show how GPU-enabled implementations change the feasible design space. Beyond these core components, we address current trends that strongly influence method choice: long-read assemblies and pangenomes; data quality issues, contamination, recombination, and horizontal gene transfer; phylogenetic placement and alignment-free screening in metagenomics; and real-time pathogen surveillance using Nextstrain-style workflows. A dedicated section covers workflow management and containerisation (Snakemake, Nextflow, Docker/Singularity) together with benchmarking datasets and FAIR reporting, positioning reproducible pipelines as a first-class requirement rather than an afterthought. To make the review directly actionable, we provide a methodological checklist, a decision framework figure mapping input data to recommended strategies, and a large comparative table summarising algorithmic principles, best use cases, strengths, limitations, scalability, uncertainty support, and reproducibility notes for widely used tools. Applications in infectious disease genomics, oncology, and microbiome research illustrate how these choices translate into biological and clinical insight in practice.},
}

@article {pmid42497015,
year = {2026},
author = {Ma, D and Uhlemann, AC and Abrams, JA and Freedberg, DE},
title = {Clinical and Culture-Based Predictors of Gut Microbiome Alpha Diversity at the Time of ICU Admission.},
journal = {Critical care explorations},
volume = {8},
number = {7},
pages = {e1455},
doi = {10.1097/CCE.0000000000001455},
pmid = {42497015},
issn = {2639-8028},
mesh = {Humans ; *Intensive Care Units/statistics & numerical data/organization & administration ; Female ; Retrospective Studies ; *Gastrointestinal Microbiome/physiology ; *Sepsis/microbiology/drug therapy ; Male ; Middle Aged ; Aged ; Anti-Bacterial Agents/therapeutic use ; Vancomycin-Resistant Enterococci/isolation & purification ; },
abstract = {OBJECTIVES: Microbiome-based therapies to improve gut colonization resistance are being developed for the ICU, but their efficacy may depend on the baseline gut microbiome at ICU admission. We sought to identify clinical predictors of alpha diversity at ICU admission.

DESIGN: Retrospective reanalysis of a randomized clinical trial (NCT03865706).

SETTING: Single-center ICU.

PATIENTS: ICU patients with sepsis as the primary diagnosis who were receiving broad-spectrum antibiotics and could be enrolled within 24 hours of ICU admission.

INTERVENTIONS: None.

MEASUREMENTS AND MAIN RESULTS: Demographic and clinical characteristics for medical ICU patients with sepsis were recorded during a previously published randomized clinical trial. Deep rectal swabs were collected within 24 hours of ICU admission and sequenced to describe alpha diversity (Shannon index) and cultured for vancomycin-resistant Enterococcus (VRE). Patients were organized into tertiles of Shannon diversity (low, middle, high) with a primary outcome of a lower Shannon tertile at ICU admission. Overall, 90 patients were enrolled. The three variables of location before ICU admission (adjusted odds ratio [aOR], 3.54; 95% CI, 1.21-10.3 for ICU transfer vs. emergency department [ED]; aOR, 6.09; 95% CI, 1.89-19.6 for hospital ward vs. ED), prior culture-proven infection within 1 year (aOR, 2.46; 95% CI, 1.02-5.96), and VRE status on ICU admission (aOR, 4.18; 95% CI, 1.44-12.1 for positive vs. negative swab) were sufficient to describe a quasi-linear trend in alpha diversity at ICU admission.

CONCLUSIONS: Baseline gut microbiome Shannon alpha diversity at ICU admission could be described with three readily ascertained clinical variables. Our model shows promise as a preliminary framework of factors that collectively best predict baseline alpha diversity at ICU admission and warrants validation in larger independent cohorts.},
}

Humans
*Intensive Care Units/statistics & numerical data/organization & administration
Female
Retrospective Studies
*Gastrointestinal Microbiome/physiology
*Sepsis/microbiology/drug therapy
Male
Middle Aged
Aged
Anti-Bacterial Agents/therapeutic use
Vancomycin-Resistant Enterococci/isolation & purification

@article {pmid42497072,
year = {2026},
author = {Wang, C and Bi, L and Wang, Y},
title = {Bidirectional Modulation of the Tumor Immune Microenvironment by Gut Microbiota-Derived Indoles: Mechanisms and Therapeutic Potential.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {14},
pages = {e72048},
doi = {10.1096/fj.202601162R},
pmid = {42497072},
issn = {1530-6860},
support = {82474230//The National Natural Science Foundation of China/ ; Qian Ke He XKBF (2025)027//Special Funds for High-level Creative Talents Cultivation in Guizhou Province/ ; 2021KJ03-12//Shanghai Frontier Research Base of Disease and Syndrome Biology of Inflammatory Cancer Trans-formation/ ; HQL2025OPA016//Open Foundation of Chinese Medicine Guangdong Laboratory/ ; },
mesh = {Humans ; *Indoles/metabolism ; *Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Neoplasms/immunology/therapy ; },
abstract = {The tumor immune microenvironment (TIME) plays a decisive role in cancer progression and therapeutic response. Emerging evidence highlights gut microbiota-derived indole metabolites, produced from dietary tryptophan, as key regulators of tumor immunity. These metabolites function through complex metabolic networks and exert dual immunomodulatory effects: they can enhance antitumor immunity by promoting CD8[+] T cell stemness, increasing tumor immunogenicity, and relieving immunosuppression, while also suppressing immunity by inducing regulatory T cells (Tregs), M2 macrophage polarization, and anti-inflammatory cytokine production. This review systematically summarizes the biosynthetic pathways and microbial sources of major indole compounds, and discusses their context-dependent roles in shaping the TIME via aryl hydrocarbon receptor (AhR)-dependent and -independent mechanisms. Unlike previous reviews that often extrapolate findings from non-tumor inflammation models to cancer without adequate contextualization, we critically evaluate evidence from both tumor and non-tumor models, with explicit distinction between direct tumor-relevant findings and speculative insights for the tumor immune microenvironment (TIME). Special attention is given to the therapeutic potential of indoles as adjuvants to immune checkpoint blockade and their promise in precision immuno-oncology. By integrating microbiology, immunology, and metabolomics, we aim to provide a theoretical foundation for developing indole-based strategies to overcome immunotherapy resistance and improve clinical outcomes.},
}

Humans
*Indoles/metabolism
*Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
Animals
*Neoplasms/immunology/therapy

@article {pmid42497111,
year = {2026},
author = {Dubey, I and Yadav, M and Kushwaha, S},
title = {Irisin-treated microbiota restore blood-testis barrier integrity and spermatogenesis in chronically stressed rats.},
journal = {Tissue barriers},
volume = {},
number = {},
pages = {2700679},
doi = {10.1080/21688370.2026.2700679},
pmid = {42497111},
issn = {2168-8370},
abstract = {Chronic psychological stress impairs male fertility by disrupting spermatogenesis and the blood-testis barrier (BTB), which is essential for testicular function. Irisin, a myokine/adipokine involved in metabolic regulation, protects against testicular dysfunction and may beneficially modulate gut microbiota, highlighting its potential in the gut-testis axis. This study investigated the effect of fecal microbiota transplantation (FMT) from irisin-treated rats in restoring BTB integrity in a chronic unpredictable stress (CUS) rat model. Male Sprague-Dawley rats were randomized into four groups: Control, CUS, CUS + Control-FMT, and CUS + Irisin-FMT. CUS-exposed rats received FMT (5 mL, intra-rectally, on alternate days for 2 weeks) from donors treated with either irisin (100 ng/kg, subcutaneously, 4 weeks) or vehicle. The CUS + Irisin-FMT group showed marked improvements in sperm quality, and hormonal profiles, including testosterone, LH, FSH, and irisin. Irisin-FMT increased crypt length, goblet cells, and histological scores, and improved the testicular histological structure and Johnsen's index. These effects were accompanied by upregulation of BTB proteins, E- and N-cadherin, spermatogonia markers, suppression of inflammatory markers (NF-κB, IL-1β, IL-6), and activation of integrin-FAK/Akt/mTOR signaling. Microbiota analysis revealed an increase in beneficial genera, including Lactobacillus and Blautia, as well as the restoration of key families and phyla. Dysbiosis promotes systemic inflammation by altering butyrate and acetate, impairing BTB integrity and testicular function via immune activation, oxidative stress, and endocrine disruption. Irisin-FMT mitigates stress-induced testicular dysfunction by modulating gut microbiota and activating protective signaling pathways, highlighting a novel microbiome-based strategy for male infertility.},
}

@article {pmid42497250,
year = {2026},
author = {Zhou, Z and Yang, Y and Zhou, F and Liang, K and Gong, T and Zhou, X and Li, J and Luo, J and Li, J and Yang, J},
title = {Energy-assisted CRISPR cleavage and probiotic vesicle signaling platform: Microbiome reprogramming for homeostasis.},
journal = {Science advances},
volume = {12},
number = {30},
pages = {eaef1760},
doi = {10.1126/sciadv.aef1760},
pmid = {42497250},
issn = {2375-2548},
mesh = {*Probiotics ; *Homeostasis ; *Microbiota/genetics ; *Streptococcus mutans/genetics/metabolism ; Adenosine Triphosphate/metabolism ; *CRISPR-Cas Systems ; Quorum Sensing ; *Extracellular Vesicles/metabolism ; Humans ; Signal Transduction ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Animals ; },
abstract = {Pathogenic infections drive microbial dysbiosis and persistent inflammation, posing therapeutic challenges due to difficulties in precise pathogen eradication and microbiome restoration. Although CRISPR-based therapeutics enable pathogen-specific antibacterial targeting, their effectiveness in treating pathogenic infections is constrained by difficulties in navigating complex microbial ecosystems, penetrating pathogenic barriers, sustaining energy-intensive intracellular cleavage, and, critically, restoring microbial balance after pathogen clearance. Here, we engineer a probiotic vesicle-synergized CRISPR platform by encapsulating gtfB-targeting CRISPR plasmids within hybrid extracellular vesicles from probiotics and pathogenic Streptococcus mutans. The pathogen-derived vesicle component enables targeted uptake by S. mutans, facilitating intracellular cleavage of the virulence gene gtfB. Vesicle-carried endogenous adenosine triphosphate (ATP) boosts CRISPR activity, amplifying targeted DNA cleavage for potent and selective pathogen elimination. Probiotic-derived vesicle components further remodel quorum-sensing networks and immunity, restoring microbial homeostasis. This probiotic vesicle-based strategy integrates ATP-enhanced CRISPR cleavage with microbiome and immune modulation, offering a next-generation therapeutic paradigm for microbiome-associated diseases.},
}

*Probiotics
*Homeostasis
*Microbiota/genetics
*Streptococcus mutans/genetics/metabolism
Adenosine Triphosphate/metabolism
*CRISPR-Cas Systems
Quorum Sensing
*Extracellular Vesicles/metabolism
Humans
Signal Transduction
*Clustered Regularly Interspaced Short Palindromic Repeats
Animals

@article {pmid42497358,
year = {2026},
author = {Vibert, J and Stojanov, M and Da Silva, T and Baud, D and Pluchino, N},
title = {Microbiome and chronic pelvic pain in women: a mini-review.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/deag110},
pmid = {42497358},
issn = {1460-2350},
abstract = {Chronic pelvic pain (CPP) is a prevalent, disabling syndrome encompassing overlapping disorders such as endometriosis/adenomyosis, bladder pain syndrome/interstitial cystitis, irritable bowel syndrome, vulvodynia, and myofascial pain syndrome. Despite distinct clinical phenotypes, these conditions converge on shared biological axes-immune dysregulation, endocrine imbalance, and central sensitization-that sustain chronic pain. Increasing evidence implicates the human microbiome as a potential upstream regulator of these pathways. Dysbiosis across the gut, vaginal, urinary, and endometrial microbial ecosystems may promote local and systemic inflammation, compromise epithelial barrier integrity, alter estrogen recirculation through the estrobolome, and engage aberrant neuroimmune signalling along gut-brain and hypothalamic-pituitary-ovarian circuits. Recent multi-site profiling suggests that microbial alterations often co-occur across pelvic compartments but remain anatomically distinct, with shifts in anaerobic taxa and paired cervicovaginal immune signatures supporting microbiome-immune interactions in CPP pathophysiology. This narrative review synthesizes observational, multi-omics, and mechanistic evidence linking microbial dysbiosis to CPP, highlights microbial metabolites as key functional mediators, and evaluates causal data from experimental models. Finally, it discusses translational opportunities and limitations, including microbiome-targeted interventions (dietary modulation, probiotics/psychobiotics, postbiotics, and microbiota transfer approaches) and the need for harmonized, longitudinal and biomarker-embedded trials to enable mechanism-based stratification and rational therapeutic development.},
}

@article {pmid42497521,
year = {2026},
author = {Su, S and Ren, L and Wang, S and Zhang, Z and Yang, K and Zhou, D and Wang, M and Xi, X and Zhong, W},
title = {Targeting cystathionine-β-synthase (CBS)-mediated cell stemness and gut microbiome homeostasis: mechanism and clinical study of combined resveratrol-curcumin treatment for ulcerative colitis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {159},
number = {},
pages = {158625},
doi = {10.1016/j.phymed.2026.158625},
pmid = {42497521},
issn = {1618-095X},
abstract = {BACKGROUND: Durable mucosal healing is the primary therapeutic goal in ulcerative colitis (UC). Intestinal epithelial stemness and microbiota homeostasis drive this healing process. Cystathionine-β-synthase (CBS) is a key enzyme in endogenous sulfur metabolism. Sulfur metabolism is essential for mitochondrial energy production and mucosal integrity. However, the precise role of CBS in UC pathogenesis remains unclear. Single plant-derived polyphenols, such as resveratrol or curcumin, show limited clinical efficacy due to low bioavailability. The combined effect of these botanical agents on CBS-mediated gut homeostasis requires further investigation.

PURPOSE: This study aimed to define the molecular function of CBS in colitis and to evaluate the therapeutic mechanism and clinical translational potential of a combined plant-derived resveratrol-curcumin treatment for UC.

STUDY DESIGN: A comprehensive bench-to-bedside translational approach was employed. The study integrated human clinical sample analysis, in vivo animal experiments using transgenic models, in silico molecular docking, and a pilot clinical trial.

METHODS: CBS expression was quantified in colonic biopsies from UC patients and healthy controls. Dextran sulfate sodium (DSS) was used to induce colitis in wild-type (WT) and CBS knockout (Cbs[-/-]) mice. Clinical phenotypes, mucosal protein expression, microbiota composition, and short-chain fatty acid (SCFA) profiles were systematically assessed. Molecular docking evaluated the binding affinity between the CBS protein and the resveratrol-curcumin combination. The in vivo efficacy of this combination was tested in both WT and Cbs[-/-] mice. Finally, a pilot clinical trial assessed the combination therapy alongside mesalamine in UC patients.

RESULTS: Colonic CBS expression was downregulated in both UC patients and colitis mice. CBS deficiency worsened DSS-induced clinical damage. It disrupted intestinal barrier homeostasis and severely impaired SCFA production. Molecular docking demonstrated strong binding affinity between the resveratrol-curcumin combination and the CBS protein. In vivo, this combined treatment effectively alleviated colitis symptoms. It reduced pro-inflammatory cytokines, upregulated mucosal proteins via CBS activation, and restored microbiota structure. Notably, these mucosal protective effects were completely abolished in Cbs[-/-] mice, confirming CBS as the essential target for this combined protective effect. In the pilot trial, the addition of resveratrol and curcumin to mesalamine improved clinical outcomes in UC patients.

CONCLUSION: CBS acts as a crucial endogenous protector in the colon. It maintains epithelial stemness and microbiota metabolic homeostasis. The plant-derived resveratrol-curcumin combination specifically targets and restores CBS expression, promoting epithelial regeneration and microbiota remodeling. These findings highlight host-microbiome interactions in UC pathogenesis and offer a novel, targeted polyphenol strategy to achieve mucosal healing.},
}

@article {pmid42497625,
year = {2026},
author = {Jamshed, H and Arslan, J and Iqbal, MP and Siddiqi, HS and Gilani, AU},
title = {Beyond the gut-dietary fiber mediated interorgan crosstalk and systemic health: Mechanistic insights and human evidence.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {151},
number = {},
pages = {113345},
doi = {10.1016/j.nut.2026.113345},
pmid = {42497625},
issn = {1873-1244},
abstract = {Dietary fibers (DFs) are increasingly recognized as key modulators of systemic physiology, exerting effects beyond the gastrointestinal tract through coordinated interorgan communication. Advances in nutrition and microbiome research indicate that physicochemical properties of DFs, including structure, viscosity, fermentability, and molecular weight, shape their metabolic and immunological functions. By serving as substrates for microbial fermentation, DFs promote the production of short‑chain fatty acids and other bioactive metabolites that influence epithelial integrity, immune regulation, bile‑acid signaling, and host metabolic pathways across multiple gut-organ axes. Human studies consistently demonstrate that higher fiber intake is associated with reduced cardiovascular risk, improved hepatic lipid metabolism in non‑alcoholic fatty liver disease, lower gut‑derived uremic toxins in chronic kidney disease, enhanced pulmonary outcomes in inflammatory airway diseases, and potential benefits for mood, cognition, and sleep via neuroimmune pathways. Despite these well-established effects, global intake remains below recommended levels (25-38 g/day), contributing to a measurable burden of noncommunicable diseases, including an estimated ∼453,000 deaths attributable to low fiber intake worldwide. This review provides a focused synthesis of DF-mediated interorgan crosstalk by integrating mechanistic insights with human evidence across major gut-organ axes, with particular emphasis on the role of fiber characteristics in shaping clinical outcomes. Collectively, the evidence positions DFs as a low‑risk, scalable, and mechanism‑guided intervention for improving systemic health. Addressing the global "fiber gap" represents a promising strategy for reducing chronic disease risk through precision nutrition approaches. However, the current evidence remains heterogeneous, with several extraintestinal outcomes supported mainly by observational studies and a limited number of long-term randomized trials.},
}

@article {pmid42497724,
year = {2026},
author = {Jiang, G and Yin, Y and Tian, L and Lu, JN and Cai, X and Deng, T and Cao, Y and Wang, S and Tang, YT and Morel, JL and Qiu, R and Ruan, Z and Chao, Y},
title = {Keystone and potentiator taxa in hyperaccumulator rhizospheres: A new perspective for microbiome-assisted phytoremediation.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143053},
doi = {10.1016/j.jhazmat.2026.143053},
pmid = {42497724},
issn = {1873-3336},
abstract = {Soil heavy-metal contamination threatens agroecosystem functioning, and hyperaccumulators, together with their rhizosphere microbiomes, offer promise for the phytoremediation of contaminated soils. Most rhizosphere microbiome studies have emphasized keystone taxa, but abundant and stable non-keystone members may also contribute to community functioning. Here, we examined the rhizosphere microbiome of the Ni hyperaccumulator Odontarrhena chalcidica using a combination of amplicon and metagenomic sequencing. Keystone taxa were identified as taxa supported by multiple ecological inference approaches, whereas potentiator taxa were defined as abundant and stable taxa that were not identified as keystones. We then compared their taxonomic composition, functional potential, and model-predicted metabolic interactions. Keystone and potentiator taxa were taxonomically distinct. Potentiator taxa showed broader functional potential than keystone taxa, suggesting that these stable non-keystone members may contribute functions that are overlooked by keystone-focused analyses alone. Genome-scale metabolic modeling further predicted greater metabolite exchange in mixed keystone-potentiator assemblages than in single-role assemblages, with model-predicted metabolic support directed mainly from potentiator taxa to keystone taxa. These findings indicate that abundant and stable non-keystone taxa can complement keystone taxa in the rhizosphere microbiome of a Ni hyperaccumulator. More broadly, this study provides an analytical strategy for identifying candidate microbial combinations that may support microbiome-assisted phytoremediation of metal-contaminated soils.},
}

@article {pmid40930304,
year = {2026},
author = {Nguyen, L and Feuerstadt, P and Allegretti, JR and Axelrad, J},
title = {Fecal Microbiota-Based Therapies Compared to Fecal Microbiota Transplantation for Preventing Recurrent C difficile Infection.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {24},
number = {8},
pages = {2305-2307},
pmid = {40930304},
issn = {1542-7714},
support = {K23 DK124570/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Clostridium Infections/prevention & control/therapy ; Clostridioides difficile ; Female ; Male ; Anti-Bacterial Agents/therapeutic use ; *Secondary Prevention/methods ; Treatment Outcome ; Feces/microbiology ; Recurrence ; Gastrointestinal Microbiome ; },
abstract = {Fecal microbiota-based therapies are safe and effective in preventing recurrent Clostridioides difficile infection (rCDI) after standard of care (SOC) antibiotic treatment with either vancomycin or fidaxomicin.[1,2] Prior studies of United States Food and Drug Administration (FDA)-unapproved, full-spectrum fecal microbiota transplant (FMT) following SOC antibiotic therapy have been shown to prevent rCDI through restoration of the gut microbiota by infusion of healthy donor stool. In November of 2022 and April of 2023, the FDA approved fecal microbiota, live-jslm (RBL), and fecal microbiota spores, live-brpk (VOS), to prevent rCDI by targeting dysbiosis and restoring the gut microbiome following SOC antibiotic therapy in those at greatest risk for future recurrence.[3,4] The efficacy of these novel microbiota-based live biotherapeutics in a real-world cohort and compared with conventional FMT remains unknown. Thus, we aimed to analyze the efficacy and safety of RBL and VOS in a real-world multicenter patient population and compare this with FDA-unapproved FMT.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Clostridium Infections/prevention & control/therapy
Clostridioides difficile
Female
Male
Anti-Bacterial Agents/therapeutic use
*Secondary Prevention/methods
Treatment Outcome
Feces/microbiology
Recurrence
Gastrointestinal Microbiome

@article {pmid42485357,
year = {2026},
author = {Hu, K and Jin, L and Feng, Z and Yu, Q and Si, X and Ding, L and Han, Y and Zhu, M and Shi, C and Zeng, X and Wang, K and Wei, J and Lv, Y and Kong, D and Qin, L and Yu, L and Wang, L and Zhang, M and Qian, P and Hu, Y and Wang, D and Huang, H},
title = {The Gut Microbiome Drives Endogenous T Cell Activation Following CAR-T Cell Therapy.},
journal = {Cancer immunology research},
volume = {},
number = {},
pages = {},
doi = {10.1158/2326-6066.CIR-25-1230},
pmid = {42485357},
issn = {2326-6074},
abstract = {Chimeric antigen receptor (CAR)-T cell therapy has become a promising clinical approach against hematological malignancies, but patients receiving CAR-T cell therapy still presented inconsistent clinical outcomes and are complicated by incomplete tumor eradication. The gut microbiome has shown strong correlation with the therapeutic outcomes of CAR-T cell therapy. However, the underlying mechanism of how gut microbiota affect CAR-T cell therapeutic potency remained undetermined. In this study, we established a syngeneic CD19+ murine lymphoma model which allows for the evaluation of both endogenous immune cells and gut microbiota following CD19-CD28ζ CAR-T therapy. Using single-cell transcriptomic analyses, we report that CAR-T cell infusion led to the activation of peripheral and gut-infiltrating endogenous CD8+ T cells towards an effector-like phenotype. In parallel, 16S RNA sequencing revealed substantial alterations of gut microbiota post-infusion. The composition of gut bacteria was associated with the activation status of endogenous CD8+ T cells and responsiveness to CAR-T therapy. More specifically, we identified gut bacteria strains Turicibacter and Parvibactor as critical determinants towards effective CAR-T treatment. Supplementation of these species of gut bacteria during CAR-T cell therapy led to superior antitumor efficacy. Furthermore, both strains facilitated CAR-T therapy-induced activation of endogenous CD8+ T cells, enhancing their capability to express activation-associated surface markers as well as tumor-lysis potency. In summary, our results demonstrate that gut microbiome plays an essential role in endogenous immune activation after CAR-T therapy and provide specific targets for therapeutic interventions.},
}

@article {pmid42485436,
year = {2026},
author = {Rouanne, M and Chen, N and Mariuzza, DL and Yang, Z and Li, F and de Los Santos-Alexis, K and Savage, TM and Vincent, RL and Mendelsohn, CL and Danino, T and Arpaia, N},
title = {Tumor-specific antibodies elicited by engineered bacteria promote bladder cancer immunotherapy in preclinical mouse models.},
journal = {Science translational medicine},
volume = {18},
number = {859},
pages = {eadv7600},
doi = {10.1126/scitranslmed.adv7600},
pmid = {42485436},
issn = {1946-6242},
mesh = {Animals ; *Immunotherapy ; *Urinary Bladder Neoplasms/immunology/therapy ; Humans ; Disease Models, Animal ; *Escherichia coli/metabolism/genetics ; Mice ; Cell Line, Tumor ; *Antibodies, Neoplasm/immunology ; Female ; Chemokine CXCL13/metabolism ; Mice, Inbred C57BL ; },
abstract = {The intratumoral microbiome has recently emerged as a potential hallmark of cancer, with implications for response or resistance to therapy. Bacteria can either promote or inhibit cancer growth. However, intratumoral bacteria can also be engineered using synthetic biology to remodel the tumor microenvironment. Here, we engineered the probiotic bacterium Escherichia coli Nissle 1917 (EcN) to express the human chemokine CXCL13 (C-X-C motif chemokine ligand 13), a critical component of germinal center (GC) formation. Antibody affinity maturation and class switching are fundamental aspects of adaptive immune response. Both occur primarily in the GCs of secondary lymphoid organs for defense against pathogens. Immune checkpoint blockade (ICB) efficacy is primarily driven by T cells; however, recent studies in mice and humans have shown that humoral immune responses act as critical partners for ICB-mediated antitumor activity. Using orthotopic models of bladder cancer, intravesically delivered engineered CXCL13-expressing EcN colonized bladder tumors and elicited GC responses in bladder tumor-draining lymph nodes after intravesical delivery. When combined with programmed cell death protein 1 (PD-1) blockade, engineered EcN improved antitumor activity in two aggressive, fast-growing, and immunologically cold orthotopic mouse models of bladder cancer. Mechanistically, this antitumor effect was dependent on the presence of CD8[+] T cells and CD4[+] T follicular helper cells; combination therapy increased tumor-specific antibody responses and promoted long-term survival and protective immunity upon tumor rechallenge. Thus, we demonstrate that synthetically engineered CXCL13-expressing EcN can enhance the efficacy of PD-1 checkpoint blockade immunotherapy by amplifying tumor-specific humoral immunity.},
}

Animals
*Immunotherapy
*Urinary Bladder Neoplasms/immunology/therapy
Humans
Disease Models, Animal
*Escherichia coli/metabolism/genetics
Mice
Cell Line, Tumor
*Antibodies, Neoplasm/immunology
Female
Chemokine CXCL13/metabolism
Mice, Inbred C57BL

@article {pmid42485503,
year = {2026},
author = {Khanamani Falahatipour, S and Soltani, M},
title = {Targeting the Gut-Brain Axis: Pharmacological Modulation of the Microbiome for Neurological and Behavioural Disorders in Companion Animals.},
journal = {Veterinary medicine and science},
volume = {12},
number = {4},
pages = {e71105},
doi = {10.1002/vms3.71105},
pmid = {42485503},
issn = {2053-1095},
mesh = {Animals ; Dogs ; Cats ; *Gastrointestinal Microbiome/drug effects ; *Cat Diseases/microbiology/drug therapy ; *Dog Diseases/microbiology/drug therapy ; *Nervous System Diseases/veterinary/drug therapy/microbiology ; *Mental Disorders/drug therapy/microbiology ; *Pets ; *Brain ; Prebiotics ; },
abstract = {BACKGROUND: The gut-brain axis (GBA) represents a paradigm shift in veterinary neuropharmacology, offering novel approaches for managing neurological and behavioural disorders in companion animals.

OBJECTIVES: This review synthesizes current evidence on the bidirectional communication between the gut microbiome and the central nervous system, examining the neural, endocrine, immune, and metabolic pathways that facilitate this dialogue. We explore the unique aspects of canine and feline microbiomes and their implications for species-specific drug development and critically evaluate emerging pharmacological strategies, including psychobiotics, prebiotics, synbiotics and faecal microbiota transplantation (FMT), highlighting their clinical applications in conditions ranging from anxiety and aggression to cognitive dysfunction and epilepsy.

METHODS: This narrative review followed established guidelines for evidence synthesis in veterinary medicine. A comprehensive literature search was performed using PubMed, Google Scholar and Scopus databases covering publications from January 2011 to March 2026.

RESULTS: While promising results have been demonstrated with specific strains, such as Bifidobacterium longum BL999 and Lactiplantibacillus plantarum PS128, significant challenges remain. These include methodological limitations in microbiome research, the predominance of correlative over causal evidence and the need for standardized diagnostic tools.

CONCLUSIONS: Future directions must prioritize large-scale longitudinal studies, robust clinical trials and advanced multi-omics approaches to establish causal mechanisms and develop personalized, microbiome-targeted therapies. Realizing this potential requires a shift from correlative data to causal mechanisms, from a one-size-fits-all approach to species-specific therapeutics and from rodent models to rigorous trials in dogs and cats.},
}

Animals
Dogs
Cats
*Gastrointestinal Microbiome/drug effects
*Cat Diseases/microbiology/drug therapy
*Dog Diseases/microbiology/drug therapy
*Nervous System Diseases/veterinary/drug therapy/microbiology
*Mental Disorders/drug therapy/microbiology
*Pets
*Brain
Prebiotics

@article {pmid42485555,
year = {2026},
author = {Wang, P and Liu, M and Zhao, C and Lu, Q and Gao, S and Guo, L and Li, Y and Wan, J and Yuan, L and Yi, F and Cai, C and Liu, J and McClung, CR and Zhang, X and Liu, X and Xu, X and Cai, Y and Xie, Q},
title = {Circadian Clock Gates Verticillium dahliae Defence in Cotton by Modulating JAZs Expression.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
pmid = {42485555},
issn = {1467-7652},
support = {2022YFD1200303//National Key Research and Development Program of China/ ; 2021YFA1300402//National Key Research and Development Program of China/ ; 234200510023//Zhongyuan Science and Technology Innovation Leadership Talent Project/ ; 32170259//National Natural Science Foundation of China/ ; 32170275//National Natural Science Foundation of China/ ; U1904202//National Natural Science Foundation of China/ ; 32100250//National Natural Science Foundation of China/ ; 32370084//National Natural Science Foundation of China/ ; 32522005//National Natural Science Foundation of China/ ; U25A20661//National Natural Science Foundation of China/ ; 262300421262//National Science Foundation of Henan Province/ ; },
abstract = {The circadian clock plays critical roles in orchestrating temporal regulation of diverse physiological processes. However, its role in mediating root-associated immunity against soil-borne pathogens in crops remains poorly understood. Here, we show that cotton circadian clock gates nighttime resistance to vascular fungal pathogen Verticillium dahliae by shaping rhizosphere microbiome composition and activating jasmonic acid (JA)-dependent immune signalling. Pathogen infection, in turn, accelerates clock pace and perturbs nighttime microbial community structure. We identify GhLUX, an evening complex component, as a key regulator of this defence program. GhLUX enhances immunity by repressing GhJAZ expression, thereby amplifying JA signalling at night. Overexpression of GhLUX in field trials confers enhanced resistance to V. dahliae while simultaneously improving cotton fibre yield and quality. These findings uncover a mechanistic link between the circadian clock, rhizosphere microbiota and root immunity in cotton and suggest that circadian regulators can be harnessed to optimize both disease resistance and agronomic performance.},
}

@article {pmid42485562,
year = {2026},
author = {Dalal, R and Barot, J and Binsuwaidan, R and Alshammari, N and Adnan, M and Patel, M and Patel, K},
title = {Substrate-Driven Microbiome Assembly in Water Hyacinth Vermicompost: Combined 16S rRNA and Shotgun Metagenomics for Sustainable Agriculture.},
journal = {Journal of basic microbiology},
volume = {66},
number = {7},
pages = {e70185},
pmid = {42485562},
issn = {1521-4028},
support = {PNURSP2026R304//Princess Nourah bint Abdulrahman University/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Eichhornia/microbiology ; Metagenomics ; Biomass ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Animals ; *Soil Microbiology ; Archaea/classification/genetics/isolation & purification/metabolism ; Composting ; Agriculture ; Fungi/classification/genetics/isolation & purification/metabolism ; Shotgun Sequencing ; Phylogeny ; },
abstract = {Substrate composition is a primary determinant of microbial succession and functional dynamics in vermicomposting systems. However, comparative insights into how biomass pre-treatment influences microbial architecture and how different sequencing approaches capture these changes remain limited. In this study, evaluation was carried out on microbial community structure and metabolic potential in vermicompost derived from three forms of Eichhornia crassipes (water hyacinth) biomass, burnt biomass (BB), composted biomass (CB) and dry biomass (DB) using both 16S rRNA gene amplicon sequencing and shotgun metagenomics. All treatments were dominated by bacterial communities (> 97%), with Proteobacteria (Pseudomonadota), Firmicutes (Bacillota), Actinobacteria and Bacteroidota representing core phyla across substrates. However, metagenomics revealed broader domain-level coverage, detecting Archaea and Fungi that were underrepresented in 16S datasets. Substrate-specific signatures were evident such as, composted biomass exhibited enrichment of lignin degradation and carbon cycling pathways; dry biomass showed methanogenesis, fermentation and phosphate solubilization signatures; and burnt biomass was associated with nitrogen fixation and sulphur metabolism. Shannon diversity was highest in composted biomass (H' = 5.21), reflecting enhanced niche diversification during substrate maturation. Comparative analysis demonstrated that 16S rRNA sequencing effectively captured dominant bacterial structure, whereas shotgun metagenomics provided superior taxonomic resolution and direct functional inference, particularly for low-abundance and non-bacterial taxa. Notably, functional differentiation among treatments was more pronounced than broad taxonomic shifts, indicating that biomass pre-treatment exerts stronger influence on ecological function than on core community composition. These findings demonstrate that integrating taxonomic and functional metagenomics enables substrate-specific optimization of vermicompost formulations and provides a framework for designing microbiome-informed strategies for sustainable agriculture and invasive biomass valorization.},
}

RNA, Ribosomal, 16S/genetics
*Eichhornia/microbiology
Metagenomics
Biomass
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
Animals
*Soil Microbiology
Archaea/classification/genetics/isolation & purification/metabolism
Composting
Agriculture
Fungi/classification/genetics/isolation & purification/metabolism
Shotgun Sequencing
Phylogeny

@article {pmid42485614,
year = {2026},
author = {Zhang, J and Xu, W and Xing, J and Sun, Y and Huang, S and Su, X},
title = {CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {4},
pages = {},
pmid = {42485614},
issn = {1477-4054},
support = {2025Z154//Innovation Yongjiang 2035 Key R&D Program/ ; 25-3-1-11-zyyd-jch//Qingdao Natural Science Foundation/ ; 32572519//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; Algorithms ; *Computational Biology/methods ; *Microbial Interactions ; },
abstract = {Microbes exist within complex community contexts, particularly for key functional species whose stable colonization critically depends on specific ecological partners. However, conventional microbial correlation analyses predominantly rely on isolated pairwise metrics (e.g. Spearman, SparCC, and FlashWeave), which ignore community-level dependencies. This limitation leads to spurious associations in large-scale datasets and obscures the true structure of microbial interactions. Here, we introduce CAM-Net, a context-aware framework that identifies a target microbe's optimal consortium, a fully connected network subset that accurately predicts its abundance. By constructing networks via multi-hop information propagation, CAM-Net effectively filters false positives from indirect associations and captures complex, context-dependent patterns that are inaccessible to traditional pairwise approaches. We evaluated CAM-Net on over 25 000 human gut microbiome samples using Akkermansia muciniphila and Lactobacillus acidophilus as representatives of indigenous and transient colonizers. CAM-Net identified a coherent and reproducible consortium for A. muciniphila, but only weak association structures for L. acidophilus, consistent with their ecological behaviors. In contrast, pairwise methods produced spurious associations for both species. Notably, despite substantial geographic heterogeneity, Alistipes shahii consistently emerged as a conserved core member of the A. muciniphila consortium, demonstrating the advantage of context-aware modeling. The source code is available at https://github.com/qdu-bioinfo/CAM-Net.},
}

Humans
*Microbiota
Algorithms
*Computational Biology/methods
*Microbial Interactions

@article {pmid42485917,
year = {2026},
author = {Lyte, JM and Proszkowiec-Weglarz, M},
title = {Importance of methods selected for microbiome studies: State of the science and challenges.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107417},
doi = {10.1016/j.psj.2026.107417},
pmid = {42485917},
issn = {1525-3171},
abstract = {The microbiota has impact on virtually every aspect of poultry production, including performance, health, and food safety. It is therefore not surprising that considerable promise exists for the application of microbiota science in addressing current and future challenges faced across the poultry industry. Yet, methodological variation among poultry microbiota studies has had negative impact on reproducibility of findings, thereby slowing the application of effective microbiota-based solutions in a production setting. The experimental workflow in microbiota research involves many steps, ranging from sample collection to bioinformatic processing. Likewise, at each experimental stage there exists a vast methodological toolbox available to poultry microbiota researchers. As the technical decisions made at each experimental stage have demonstrable impact on each downstream step, outcomes in microbiota research are largely dependent on the methodologies employed. In order to improve translatability and reproducibility between different methodological pipelines, it is essential that a best practice framework be adopted in poultry science regarding microbiota research. The present review seeks to briefly encapsulate our symposium on microbiome methodology in poultry research. This symposium discussed the need for a robust set of evidence-based guidelines that streamline microbiota research in poultry. Attention was given to each major stage of a typical poultry microbiota study, including sample collection, storage, extraction, library preparation, sequencing, bioinformatic and data analyses, as well as data reporting and repositories. The use of positive and negative controls, improved reporting of raw data, and other tangible aspects that improve consistency and reproducibility across poultry microbiota study designs were highlighted. Ultimately, it was the goal of this symposium not to advocate a single methodology, but instead to demonstrate the need for robust practices at each experimental stage that enable cross-study comparisons of findings in poultry microbiota research.},
}

@article {pmid42485926,
year = {2026},
author = {de Bruijn, DGJ and Gusinac, A and Ederveen, THA and Le, ND and Kulkarni, P and Meijer, RI and Janssen, MCH and Zweers, HEE},
title = {Gut microbiota alterations in individuals with mitochondrial disease caused by the m.3243A >G mutation.},
journal = {Molecular genetics and metabolism},
volume = {149},
number = {1-2},
pages = {110208},
doi = {10.1016/j.ymgme.2026.110208},
pmid = {42485926},
issn = {1096-7206},
abstract = {People with mitochondrial disease (MD) associated with the m.3243 A > G mutation often experience gastrointestinal complaints and dysmotility, suggesting dysbiosis of the gut microbiome. A common phenotype of the m.3243 A > G mutation is Maternally Inherited Diabetes and Deafness (MIDD). Previous studies have shown that other forms of diabetes are associated with an altered gut microbiome. Therefore, our study aimed to investigate the gut microbiota of people with MD caused by the m.3243 A > G mutation compared to healthy controls (Lifelines®) and people with type 1 diabetes (T1D). Fecal samples of 30 people with the m.3243 A > G mutation were used for shotgun metagenomic sequencing. The MD group was compared with 60 healthy controls and 60 people with T1D from different datasets, and were matched for age, sex, and BMI. We found that the Bray-Curtis β-diversity of the gut microbiota differed significantly between MD compared to healthy controls and T1D, while there was a non-significant reduction in Shannon α-diversity in the MD group. The gut microbiota of the MD group was characterized by reduced Faecalibacterium prausnitzii, and increased Escherichia coli, Ruminococcus gnavus, and Ruminococcus torques levels compared to healthy controls and T1D. This pattern aligns with microbial signatures reported in inflammatory bowel disease, which is associated with mitochondrial dysfunction in intestinal epithelial cells. Overall, our explorative study suggest that people with the m.3243 A > G mutation exhibit a dysbiotic gut microbiota, which may pave the way for future research aimed at developing new therapies, dietary adjustments and their potentials to improve quality of life.},
}

@article {pmid42485957,
year = {2026},
author = {Zannini, E and Nyhan, L and Gobbetti, M and Di Cagno, R and Arendt, EK},
title = {The food microbiome: an evolutionary architect, a modern healer, and a future shield.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103555},
doi = {10.1016/j.copbio.2026.103555},
pmid = {42485957},
issn = {1879-0429},
abstract = {The food microbiome, comprising microorganisms present in foods and fermentation, links diet, environment, and host physiology. This review examines its evolutionary, contemporary, and future nutritional relevance, including emerging applications of artificial intelligence (AI). In early human diets, fermentation likely improved food safety and nutrient accessibility, although its contribution to encephalization remains unproven. In modern populations, fermented foods and microbial metabolites shape the composition of the gut microbiome and modulate host metabolic, immune, and neuroactive functions. Rising atmospheric CO2 is projected to reduce protein and micronutrient concentrations in staple crops, increasing interest in microbial fermentation as a strategy to enhance nutrient availability. Integration of AI with multi-omics enables functional characterisation of fermentation ecosystems and supports the development of targeted, personalised nutritional strategies, although translational and mechanistic challenges remain unresolved.},
}

@article {pmid42485963,
year = {2026},
author = {Fu, Y and Chen, M and Zhang, X and Yu, G and Jiang, P and Liu, J and You, S},
title = {Multi-omics analysis of the rhizosphere effects and molecular mechanisms of Ageratum conyzoides linn. at different stages of Cd, Pb, and Zn co-stress.},
journal = {Journal of environmental management},
volume = {414},
number = {},
pages = {130461},
doi = {10.1016/j.jenvman.2026.130461},
pmid = {42485963},
issn = {1095-8630},
abstract = {Ageratum conyzoides Linn. is a promising candidate for multi-metal remediation. This study examined the rhizosphere microecology and molecular regulation of A. conyzoides under Cd, Pb, and Zn co-stress after 21 and 50 days of exposure. The ethanol-extracted fraction was found to be the predominant form of Cd, Pb, and Zn in the roots, whereas the NaCl-, HCl-, and HAc-extracted fractions prevailed in the shoots. Heavy metals were mainly distributed in the cell wall and soluble fractions. Metabolome and microbiome analyses revealed dynamic changes in rhizosphere exudate metabolic profiles and bacterial community composition in the rhizosphere soil after 21 and 50 days of exposure to stress. After 21 days of stress, increased exudation of oxalic acid, L-valine, and L-glutamate was correlated with the enrichment of Clostridium_sensu_stricto_12 and norank_p_FCPU426. After 50 days of stress, significantly increased exudation of jasmonic acid, gibberellin A24, and 4-hydroxynonenal was correlated with the enrichment of Bauldia, Candidatus_Udaeobacter, and norank_f_Anaerolineaceae. Transcriptome analysis revealed that prolonged stress upregulated the expression of SEC61A2, Uggt, Ggt7, gss, and PRX1 in A. conyzoides leaves; the differentially expressed genes were found to be significantly enriched in the protein processing in the endoplasmic reticulum pathway and glutathione metabolic pathway. Overall, these findings provide a theoretical foundation for optimizing phytoremediation using A. conyzoides.},
}

@article {pmid42485992,
year = {2026},
author = {Vallini, F and Salvucci, B and Biava, M and Carradori, S and Poce, G and Tammaro, C},
title = {Targeting Fusobacterium nucleatum in cancer therapy: A new frontier in solid tumor treatment.},
journal = {European journal of medicinal chemistry},
volume = {318},
number = {},
pages = {119170},
doi = {10.1016/j.ejmech.2026.119170},
pmid = {42485992},
issn = {1768-3254},
abstract = {Recently, the tumor-infiltrating microbiome (TIM) has gained increasing attention due to its pivotal role in carcinogenesis, tumor progression, resistance to chemotherapy, and immune evasion. Although the composition of these microbial communities is not yet fully elucidated, emerging studies have demonstrated that certain bacteria exert pro-tumoral effects, either through enzymatic activities or by modulating the host immune response. Among them, Fusobacterium nucleatum (Fn) represents one of the most pathogenic residents of several solid tumors, making it a novel and promising target in the fight against cancer. In detail, Fn promotes oncogenic signaling, epithelial-mesenchymal transition, inflammatory responses, and autophagy-mediated drug resistance, thereby contributing to poor clinical outcomes. This review explores different strategies to selectively target Fn, aiming to reduce its pro-tumoral behavior, spanning from drug repurposing, synthetic small molecules, natural products, and antimicrobial peptides to advanced nanoformulations, vaccine-based platforms, and sequence-specific interventions, such as antisense oligomers and microbiota-modulating strategies. A focused section covers stimuli-responsive and biomimetic nanoplatforms potentially capable of eradicating Fn and restoring chemosensitivity, while sparing the commensal gut microbiota. Collectively, these findings support the feasibility of targeting the TIM in combination with canonical anticancer regimens. Although further refinements and additional investigations are needed, targeting Fn represents a novel paradigm shift in the management of bacterially colonized solid tumors.},
}

@article {pmid42486137,
year = {2026},
author = {Davido, B and Loubet, P and Saleh-Mghir, A and Leroux, P and Rottman, M and Corcione, S and , },
title = {mRNA vaccines for multidrug-resistant bacteria: promise, challenges, and microbiome-informed strategies.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101467},
doi = {10.1016/j.lanmic.2026.101467},
pmid = {42486137},
issn = {2666-5247},
abstract = {Antimicrobial resistance (AMR) has made multidrug-resistant organisms (MDROs), particularly ESKAPE-E pathogens (including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp, and Escherichia coli), a major threat to modern medicine. Although novel antibiotics, antimicrobial stewardship, and infection prevention remain essential, such interventions are unlikely to offset projected AMR trends on their own. Vaccines can help to mitigate AMR by preventing infections and reducing antibiotic exposure. WHO estimates that vaccines targeting 23 pathogens (excluding Neisseria gonorrhoea) could reduce global antibiotic need by 22%, equivalent to 2·5 billion defined daily doses annually. In the mRNA era, modular vaccine platforms enable rapid design of protein antigens and multivalent constructs, with emerging preclinical proof of concept against selected bacterial pathogens. In this Personal View, we argue that mRNA vaccines should be considered enabling platforms for selected protein-based MDRO targets rather than universal solutions for antibacterial vaccine development. We propose a microbiome-informed framework that distinguishes systemic protection from mucosal decolonisation and aligns antigen selection, delivery route, and trial endpoints with colonisation dynamics, microbiome resilience, and AMR reduction goals.},
}

@article {pmid42486172,
year = {2026},
author = {Hanifeh, M and Huhtinen, M and Ganz, HH and Heilmann, RM and Huang, W and Spillmann, T and Suchodolski, JS},
title = {Clinical trial reveals limited clinical and microbiome effects following oral fecal microbiota transplantation in dogs with chronic enteropathy responsive to tylosin.},
journal = {Journal of the American Veterinary Medical Association},
volume = {},
number = {},
pages = {1-11},
doi = {10.2460/javma.26.03.0178},
pmid = {42486172},
issn = {1943-569X},
abstract = {OBJECTIVE: To evaluate clinical response and fecal biomarkers in dogs with tylosin-responsive enteropathy (TRE) treated with oral fecal microbiota transplantation (FMT).

METHODS: In this prospective, randomized, double-blind, placebo-controlled trial (conducted between August 1, 2020, and December 31, 2022), 14 client-owned dogs with confirmed tylosin-responsive enteropathy entered the treatment phase. Dogs received oral FMT (n = 7) or placebo (7) for 4 weeks; 1 placebo-treated dog was excluded (pyometra), leaving 7 FMT-treated and 6 placebo-treated dogs for analysis. Canine Chronic Enteropathy Clinical Activity Index, fecal consistency, and fecal biomarkers (dysbiosis index, core bacteria, bile acids, short-chain fatty acids, lactate, and calprotectin) were assessed at pretreatment and posttreatment visits. Intestinal permeability was evaluated with serum iohexol. Analyses were limited to pre- and posttreatment comparisons.

RESULTS: Relapse occurred in 2 of 7 FMT-treated dogs (28.6%) and 3 of 6 placebo-treated dogs (50.0%). The dysbiosis index decreased over time in both groups, with no treatment effect. Faecalibacterium spp increased, with higher posttreatment values in the FMT group, whereas Turicibacter spp increased in both groups. Peptacetobacter hiranonis increased over time without between-group differences. Bile acid conversion was observed in a subset of dogs without group differences. Other biomarkers showed no consistent treatment-specific effects.

CONCLUSIONS: Oral FMT was associated with variable microbiome changes and inconsistent clinical response, with no clear treatment-specific effects compared with placebo. These findings support further evaluation of optimized microbiome-based therapies in larger studies.

CLINICAL RELEVANCE: Oral FMT may serve as an adjunctive strategy for microbiome modulation in dogs with chronic enteropathy; however, clinical benefits were inconsistent and optimized protocols may be required.},
}

@article {pmid42486297,
year = {2026},
author = {Gomes, BPFA and Arruda-Vasconcelos, R and Louzada, LM and Lopes, ABS and Passini, MRZ and Bronzato, JD and Lopes, EM and Chen, T and Paster, BJ},
title = {Infected Dentin and Symptomatic Irreversible Pulpitis Share a Core Microbiome.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.07.012},
pmid = {42486297},
issn = {1878-3554},
abstract = {INTRODUCTION: The objective of this clinical study was to identify and compare the bacterial taxa in teeth with infected dentin (ID) and its associated root canals with symptomatic irreversible pulpitis (SIP) using high-throughput next-generation sequencing.

METHODS: Teeth diagnosed with symptomatic irreversible pulpitis were included, with samples collected from infected dentin adjacent to the pulp and from the root canal. A total of 20 samples were analyzed, comprising 10 from each site. The microbiomes were examined using 16S rRNA gene amplicon sequencing.

RESULTS: At the phylum level, Firmicutes predominated in ID and SIP, followed by Proteobacteria, with all samples showing consistent detection of these phyla. Actinobacteria and Bacteroidetes were also frequently detected. At the genus level, both microbial communities were dominated by Lactobacillus, followed by Streptococcus and Olsenella. At the species level, however, the shared core microbiome was represented by individual taxa belonging to several predominant genera, including Lactobacillus ultunensis, Veillonella dispar, Streptococcus salivarius, Campylobacter rectus, Streptococcus parasanguinis clade 411, Oribacterium sp. HMT-078, and Fretibacterium fastidiosum. Notably, ID samples displayed a predominance of Gram-positive bacteria, accounting for 78.9% of the oral microbiota, whereas SIP samples showed a relative enrichment of Gram-negative anaerobes, which represented 31.5% of the community.

CONCLUSION: In conclusion, infected dentin and symptomatic irreversible pulpitis samples shared a substantial core microbiome, supporting ecological continuity along the dentin-pulp infection pathway.},
}

@article {pmid42486317,
year = {2026},
author = {Uchitel, Y and Roggenbuck, D and Leibovitzh, H and Cohen, NA and Izhar, R and Lobel, L and Maharshak, N and Werner, L},
title = {Reduced fecal GP2 levels in ulcerative colitis associate with inflammatory activity and microbial composition.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121241},
doi = {10.1016/j.cca.2026.121241},
pmid = {42486317},
issn = {1873-3492},
abstract = {BACKGROUND AND AIM: Loss of tolerance to GP2, an antimicrobial immune-modulating component of intestinal cells and receptor on microfold cells, is associated with disease severity in Crohn's disease (CD). However, the role of GP2 in inflammatory bowel diseases remains poorly understood. This study aimed to evaluate fecal GP2 levels in patients with ulcerative colitis (UC) and CD and to examine associations with disease activity, response to biologic therapy, and microbial features.

METHODS: We conducted a retrospective study of adults with UC, CD, and healthy controls recruited at a tertiary IBD clinic. Fecal GP2 levels and serum anti-GP2 antibodies were measured using ELISA and correlated with disease activity, inflammatory biomarkers (CRP, fecal calprotectin and elastase activity), and microbiome assessed by 16S rRNA amplicon sequencing.

RESULTS: The study included 87 patients with CD, 58 with UC, and 31 healthy controls. Fecal GP2 levels were significantly lower in UC, particularly in active UC, compared with CD or controls (P ≤ 0.05). In CD, fecal GP2 levels did not differ significantly from controls across activity strata but correlated with elastase activity. Further, fecal GP2 levels increased following induction therapy among clinical responders and were associated with gut microbial diversity. No correlation was observed between serum anti-GP2 and fecal GP2 levels, or serum anti-GP2 and responsiveness to induction therapy.

CONCLUSIONS: Fecal GP2 concentrations are reduced in UC, particularly during active disease, but are preserved in CD. This suggests a disease-specific pattern in UC, potentially reflecting altered microbial interactions or increased luminal protein degradation.},
}

@article {pmid42486390,
year = {2026},
author = {Hong, JS and Shamim, A and Atta, H and Merl, S and Park, H and Eliby, D and Tillman, A and Tekal, M and Patwardhan, S and Chauhan, I and Jordache, P and Chen, B and Almesallmy, A and Gunes, ME and Manell, E and Shen, B and Dionigi, B and Kiran, RP and Wells, SB and Farber, DL and Fu, J and Kato, T and Martinez, M and Cheung, YK and Uhlemann, AC and Weiner, J},
title = {Trending ileal microbiome dysbiosis over time as an early assessment of intestinal transplant rejection risk.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2026.07.007},
pmid = {42486390},
issn = {1600-6143},
abstract = {Rejection is a barrier to intestinal transplantation (ITx). ITx rejection may be associated with changes in the ileal microbiome. We sought to analyze whether shifts in the microbiome were associated with intestinal transplant rejection. Ileal effluent samples were collected from ITx patients (n = 8) with multiple samples taken from each patient at times of no (n = 83), mild (n = 39), or moderate (n = 3) rejection, Crohn's disease (n = 20), and noninflamed control patients (n = 25). Ileal microbiota were quantified using 16S rRNA gene sequencing. Compared to nontransplant samples (noninflamed control, Crohn's disease), ITx samples had lower alpha diversity (Shannon and Chao1, P < .001) and different beta diversity (Bray-Curtis, P < .005). Beta diversity differed between samples with and without rejection (P = .002). Differential abundance analyses showed enrichment of pathogenic taxa and depletion of commensals in ITx rejection samples. ITx rejection is associated with ileal microbiome dysbiosis, which is a potential target for diagnostic and therapeutic interventions.},
}

@article {pmid42486470,
year = {2026},
author = {Delebecque, CJ and La Monica, MB and Keller, D and Shannon, W and Ziegenfuss, TN and Zimmerman, NP},
title = {The effects of a postbiotic supplement on biomarkers of microbiome, gastrointestinal, cardiometabolic, and immunometabolic health.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-14},
doi = {10.1163/18762891-bja00129},
pmid = {42486470},
issn = {1876-2891},
abstract = {The gut microbiome is increasingly recognised as a modifiable contributor to metabolic, immune, and stress-related physiology, yet many nutritional interventions produce broad microbial shifts that may be poorly tolerated. We investigated the effects of a fermented and pasteurised oat-based preparation (Keystone) on microbiome composition and selected biomarkers in a 4-week randomised, double-blind, placebo-controlled trial in generally healthy adults. Seventy-six participants completed the intervention (38 placebo, 38 Keystone). Stool samples collected at baseline and week 4 underwent shotgun metagenomic sequencing, and serum butyrate, IL-8, morning cortisol, albumin/globulin ratio, routine clinical chemistries, DASS-21, and SF-36 were assessed. The intervention did not affect alpha or beta diversity. In contrast, species-level analysis showed a distinct compositional signature, with enrichment of taxa including Akkermansia spp., Bacteroides intestinalis, Bifidobacterium pseudocatenulatum, and Anaerostipes caccae in the Keystone group, alongside lower abundance of several Haemophilus, Megasphaera, and Prevotella taxa relative to placebo (FDR < 0.001). Nominally significant baseline-by-treatment interactions were observed for morning cortisol (P = 0.03), IL-8 (P = 0.04), and albumin/globulin ratio (P = 0.03), while serum butyrate showed a near-significant trend (P = 0.053). SF-36 emotional well-being improved within the Keystone group. No adverse events were reported. These results indicate that Keystone was safe and well tolerated and selectively modulates the gut microbiome, with exploratory associations for host stress and inflammatory markers that offer key insights for future follow-up studies. Trial registration: The trial was IRB approved and registered with ClinicalTrials.gov NCT07527286.},
}

@article {pmid42486573,
year = {2026},
author = {James, S and Wodeyar, AM and Chaurasia, A},
title = {Modulating the head & neck microbiome for cancer- prevention.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {127-140},
doi = {10.1016/bs.ai.2026.03.006},
pmid = {42486573},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/prevention & control/microbiology/immunology ; *Dysbiosis/immunology/microbiology ; *Microbiota/immunology ; Fecal Microbiota Transplantation ; Probiotics ; Animals ; Prebiotics ; *Gastrointestinal Microbiome/immunology ; },
abstract = {The head and neck microbiome plays a critical role in maintaining epithelial homeostasis, regulating immune surveillance, and shaping inflammatory responses that influence carcinogenesis. Increasing evidence suggests that microbial dysbiosis within the oral and gut ecosystems contributes to the initiation and progression of head and neck cancers, particularly oral squamous cell carcinoma. Given that the microbiome is a modifiable risk factor, targeted modulation has emerged as a promising preventive and supportive strategy in HNC. This chapter highlights current knowledge on microbiome-based interventions, including dietary modification, probiotics, prebiotics, postbiotics, synbiotics, fecal microbiota transplantation, and lifestyle changes, with emphasis on their immunomodulatory and anti-inflammatory effects. These approaches aim to restore microbial balance, enhance barrier integrity, reduce chronic inflammation, and strengthen anticancer immune responses. The chapter also discusses mechanistic links between microbial metabolites and immune pathways, the relevance of the oral-gut axis, and emerging evidence connecting microbiome composition with treatment response and toxicity. Finally, key challenges such as inter-individual variability, site-specific microbial niches, safety considerations, and the need for longitudinal and mechanistic studies are addressed. Overall, microbiome modulation represents a promising, precision-oriented avenue for cancer prevention, risk reduction, and survivorship in head and neck oncology, although robust clinical validation is still required.},
}

Humans
*Head and Neck Neoplasms/prevention & control/microbiology/immunology
*Dysbiosis/immunology/microbiology
*Microbiota/immunology
Fecal Microbiota Transplantation
Probiotics
Animals
Prebiotics
*Gastrointestinal Microbiome/immunology

@article {pmid42486574,
year = {2026},
author = {Choudhury, M and Tavassoli, M},
title = {Microbiome-targeted therapeutics in head & neck cancer.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {141-161},
doi = {10.1016/bs.ai.2026.03.012},
pmid = {42486574},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/therapy/microbiology/immunology ; *Microbiota/immunology ; Probiotics/therapeutic use ; Animals ; *Dysbiosis/immunology/therapy/microbiology ; Fecal Microbiota Transplantation ; Prebiotics ; },
abstract = {The oral microbiome is increasingly recognized as a critical factor in the development, progression, and response to therapy of head and neck cancer. Microbial dysbiosis has been associated with chronic inflammation, immune modulation, altered cellular proliferation and apoptosis, and the production of carcinogenic metabolites which collectively shape the tumor microenvironment. Various bacterial species, including Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus mutans, and Treponema denticola, as well as fungal species such as Candida albicans and non-albicans Candida, have been implicated in oral carcinogenesis. These microorganisms promote tumorigenic processes through the generation of carcinogens such as nitrosamines and acetaldehyde, which activate innate immune pathways such as nuclear factor kappa B and Wnt/β-catenin. Conversely, several commensal species, including Neisseriaceae, Kingella, Corynebacterium, Prevotella nanceiensis, Capnocytophaga leadbetteri, and Selenomonas sputigena, have been associated with a reduced prevalence of head and neck cancer, suggesting a potential association between microbial homeostasis and reduced cancer risk. Advances in microbiome research have led to the exploration of microbiome-targeted therapeutic strategies as adjuncts to conventional head and neck cancer treatment. Approaches including probiotics, prebiotics, postbiotics, dietary modulation, and fecal microbiota transplantation aim to restore microbial balance, enhance antitumor immune responses, mitigate therapy-induced toxicities, and improve treatment efficacy. Probiotic formulations containing Lactobacillus and Bifidobacterium species have shown promise in reducing adverse effects and improving patient quality of life and treatment adherence. This chapter summarizes current evidence on microbiome dysbiosis in head and neck cancer and reviews emerging microbiome-targeted interventions with potential clinical relevance.},
}

Humans
*Head and Neck Neoplasms/therapy/microbiology/immunology
*Microbiota/immunology
Probiotics/therapeutic use
Animals
*Dysbiosis/immunology/therapy/microbiology
Fecal Microbiota Transplantation
Prebiotics

@article {pmid42486575,
year = {2026},
author = {Kurt, B and Babalola, AE and Chaurasia, A},
title = {Artificial intelligence in microbiome data analysis: Applications in head and neck cancer.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {163-187},
doi = {10.1016/bs.ai.2026.03.008},
pmid = {42486575},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/diagnosis/therapy ; *Microbiota ; *Artificial Intelligence ; Multiomics ; Machine Learning ; Biomarkers, Tumor ; Precision Medicine ; },
abstract = {This chapter reviews AI-driven approaches, including machine learning and deep learning, for analyzing microbiome data in head and neck cancer (HNC). It highlights the role of artificial intelligence in identifying microbial biomarkers, predicting treatment outcomes, and supporting early diagnosis through the integration of multi-omics and clinical data. The chapter also discusses key challenges, including data heterogeneity, model interpretability, and clinical applicability, and outlines future directions for precision oncology. Recent advances in artificial intelligence have enabled novel analytical strategies for microbiome-based research in HNC, offering new opportunities for biomarker discovery and data-driven clinical decision-making. By combining high-dimensional microbiome profiles with clinical and multi-omics information, AI-based methods provide a promising framework for improving disease characterization and advancing precision oncology.},
}

Humans
*Head and Neck Neoplasms/microbiology/diagnosis/therapy
*Microbiota
*Artificial Intelligence
Multiomics
Machine Learning
Biomarkers, Tumor
Precision Medicine

@article {pmid42486576,
year = {2026},
author = {Venugopal, DC and Srinivas, KS},
title = {Challenges and future directions in head and neck microbiome research.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {189-227},
doi = {10.1016/bs.ai.2026.03.010},
pmid = {42486576},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/therapy/immunology ; *Microbiota/immunology ; Animals ; *Dysbiosis/microbiology/immunology/therapy ; Fecal Microbiota Transplantation ; Metabolomics ; Metagenomics ; Probiotics/therapeutic use ; },
abstract = {The microbial imbalance in head and neck cancer (HNC) is a promising area of research for developing targeted therapies. Maintenance of microbial diversity and balance through prebiotics, probiotics and faecal microbial transplantation (FMT) holds a potential approach in reestablishing the gut health. Preclinical studies and early clinical trials have shown positive results in restoring the favourable microbial environment, thereby minimizing the inflammation and maximizing the positive immune response. However, the link between microbial flora associated with oral dysbiosis, the associated biomarkers and HNC tumorigenesis needs to be further explored. Future research focusses on developing standardised strategies for maintaining the microbial environment, to serve as an adjunct to the standard treatment protocols for HNC. Biomarkers predicting immune response, synthetic genetically engineered beneficial bacteria, integration of metagenomics, metabolomics and meta transcriptomics for intra-tumoral microbial evaluation are the focus areas of emerging research.},
}

Humans
*Head and Neck Neoplasms/microbiology/therapy/immunology
*Microbiota/immunology
Animals
*Dysbiosis/microbiology/immunology/therapy
Fecal Microbiota Transplantation
Metabolomics
Metagenomics
Probiotics/therapeutic use

@article {pmid42486578,
year = {2026},
author = {Tavassoli, M and Antoniou, A and Tatsis, D},
title = {The role of the oral microbiome in oral cancer (OSCC).},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {35-74},
doi = {10.1016/bs.ai.2026.03.011},
pmid = {42486578},
issn = {1557-8445},
mesh = {Humans ; *Mouth Neoplasms/microbiology/immunology/etiology ; *Microbiota/immunology ; *Carcinoma, Squamous Cell/microbiology/immunology ; *Dysbiosis/immunology/microbiology ; *Mouth/microbiology ; Animals ; },
abstract = {This chapter explores the significant role of oral microbiome dysbiosis in oral squamous cell carcinoma (OSCC) pathogenesis, highlighting mechanisms such as chronic inflammation via NF-κB activation by Porphyromonas gingivalis and Fusobacterium nucleatum, production of oncogenic metabolites (for example, acetaldehyde, N-nitrosamines), immune evasion through PD-L1 upregulation and T-cell suppression, and direct carcinogenic effects including epithelial-mesenchymal transition and apoptosis inhibition. In this comprehensive overview, microbes with key role in OSCC pathogenesis, including F. nucleatum (invasion promotion, hypoxia mimicry), P. gingivalis (EMT induction), Capnocytophaga gingivalis (diagnostic potential), and Candida albicans (acetaldehyde synthesis), are examined, alongside interactions with established risk factors. Diagnostic advancements could potentially include salivary biomarkers (IL-6, miRNAs, bacterial panels) and AI-driven models achieving AUC >0.9, with microbial diversity shifts aiding early detection and prognosis. Recent research investigate findings in mycobiome and HPV influences, therapy modulation (e.g., radiotherapy-induced dysbiosis), epigenetic effects, and hypoxia pathways. Challenges include establishing causality, study inconsistencies, and the need for multiomics approaches, with future directions emphasizing longitudinal research, standardized protocols, and microbiome-targeted therapies to enhance OSCC prevention, diagnosis, and management.},
}

Humans
*Mouth Neoplasms/microbiology/immunology/etiology
*Microbiota/immunology
*Carcinoma, Squamous Cell/microbiology/immunology
*Dysbiosis/immunology/microbiology
*Mouth/microbiology
Animals

@article {pmid42486579,
year = {2026},
author = {James, S and Ponangi, K},
title = {Microbiome as prognostic indicator in oral cancer.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {75-90},
doi = {10.1016/bs.ai.2026.03.007},
pmid = {42486579},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; Prognosis ; *Mouth Neoplasms/microbiology/immunology/diagnosis/therapy ; Dysbiosis/immunology/microbiology ; Animals ; Neoplasm Recurrence, Local ; },
abstract = {OSCC affects over 377,000 patients annually with poor prognosis. While conventional prognostic indicators like TNM staging provide structural information, they inadequately explain clinical outcome variability. The oral microbiome has emerged as a dynamic prognostic factor offering functional insights through non-invasive sampling and longitudinal monitoring. Specific microbial signatures strongly associate with clinical outcomes. Pathogens including Fusobacterium nucleatum, Porphyromonas gingivalis, Eubacterium, and Lactobacillus correlate with increased recurrence and reduced survival, while commensals like Veillonella, Streptococcus, and Staphylococcus predict favorable outcomes. Microbiome-based models outperform traditional parameters in recurrence stratification, with beta diversity distinguishing recurrent from non-recurrent cases. Functional pathways involving PI3K/AKT/mTOR signaling and immunomodulation demonstrate prognostic relevance. High-risk patterns promote immune evasion through CD8+ T-cell depletion, while favorable patterns maintain anti-tumor immunity. The microbiome influences treatment response, with dysbiosis reducing therapy effectiveness and increasing mucositis. Probiotic interventions show promise in restoring diversity and improving outcomes. Despite standardization challenges, the oral microbiome represents a promising non-invasive prognostic indicator for refining risk stratification and personalizing OSCC management.},
}

Humans
*Microbiota/immunology
Prognosis
*Mouth Neoplasms/microbiology/immunology/diagnosis/therapy
Dysbiosis/immunology/microbiology
Animals
Neoplasm Recurrence, Local

@article {pmid42486580,
year = {2026},
author = {Perera, ML and Perera, IR},
title = {Microbiome based diagnostic approaches.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {93-125},
doi = {10.1016/bs.ai.2026.03.004},
pmid = {42486580},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; *Head and Neck Neoplasms/diagnosis/microbiology ; Dysbiosis ; Animals ; Early Detection of Cancer ; },
abstract = {Cancers of the Head and Neck (HNC) ranks seventh most abundant cancer category according to global incidence. thus posing a pertinent health hallenge. Shift in the homeostatic relationship of head and neck microbiome, causes microbial metabolic dysbiosis. Consequently, there is an increase in the pathobiome and pathogenic functions potentiating initiation and progression of carcinogenesis. Infection, inflammation and immune mediation trigger the pathogenic mechanisms. Accordingly, periodontitis perpetrated by unsatisfactory oral hygiene is connected to initiation and progression of HNC supported by substantial evidence. Further, mechanistic evidence is emerging on pathogenesis of bacteria-mediated carcinogenesis via toxins, carcinogenic metabolites and inflammatory cytokines with a view to possible treatments to halt progression of cancers. Advancements in surgical management techniques and adjuvant radiotherapy treatment, chemotherapy and emerging therapies such as immunotherapy, have not significantly increased overall disease free survival rates of most of HNCs. Early detection of cancers therefore, facilitates favorable outcomes such as better survival rates. Nevertheless, traditional invasive diagnostic approaches such as tissue biopsy gives rise to pain and discomfort to the patient In contrast, microbiome based diagnostic approaches, underpinned by salivary and mouth rinse microbiome analyses offers promising non-invasive, screening tools for early detection of HNC. This is augmented by advances in next generation sequencing, third generation sequencing, bioinformatics and machine learning technologies. Current developments in metagenomics, transcriptomics along with metabolomics enhanced harnessing the immense potential saliva possesses as a valuable screening and diagnostic tool, not only for cancer detection but for a range of diseases such as gastrointestinal diseases, autoimmune and metabolic disorders. Microbiome signatures in risk assessment of HNC is emerging as a new dimension in personalized risk assessment, risk stratification and care based pathways. Salivary microbiome analyses provides a promising approach for risk stratification, early stratification, through to assessment of prognosis, treatment success and survival of HNC patients suggested by accumulating evidence. Against this backdrop, we aim to provide an overview of microbiome based diagnostic approaches exploring new dimensions of detection and identification of HNC specific microbial biomarkers, microbial signatures, screening tools, primary diagnostic biomarkers, prognostic markers and interpersonal microbiome in the arena of personalized medicine.},
}

Humans
*Microbiota/immunology
*Head and Neck Neoplasms/diagnosis/microbiology
Dysbiosis
Animals
Early Detection of Cancer

@article {pmid42486598,
year = {2026},
author = {Hussain, N and Trivedi, PJ},
title = {Primary Sclerosing Cholangitis.},
journal = {Clinics in liver disease},
volume = {30},
number = {3},
pages = {715-750},
doi = {10.1016/j.cld.2026.04.013},
pmid = {42486598},
issn = {1557-8224},
mesh = {Humans ; *Cholangitis, Sclerosing/epidemiology/therapy/diagnosis ; Cholagogues and Choleretics/therapeutic use ; Inflammatory Bowel Diseases ; Liver Transplantation ; },
abstract = {Sclerosing cholangitis encompasses a spectrum of disorders, characterised by multi-level biliary stricturing. The prefix 'primary' refers to the commonest form, PSC. Although rare, incidence and prevalence are rising, which when coupled with the absence of life-prolonging therapy has resulted in PSC being one of the lead indications for liver transplantation. Herein, we present a clinically focussed overview of PSC epidemiology, natural history, and nuances surrounding monitoring and surveillance. We go on to discuss how gut inflammation may affect the clinical course that patients experience, whilst giving way to bile acid therapies, molecularly targeted antifibrotics, and a bevy of microbiome-based interventions.},
}

Humans
*Cholangitis, Sclerosing/epidemiology/therapy/diagnosis
Cholagogues and Choleretics/therapeutic use
Inflammatory Bowel Diseases
Liver Transplantation

@article {pmid42486733,
year = {2026},
author = {Nieto Estrada, VH and Reyes Zambrano, V and Molano Franco, D and Tavella, M},
title = {Prognosis of the critically ill cancer patient in the era of precision oncology.},
journal = {Medicina intensiva},
volume = {},
number = {},
pages = {502526},
doi = {10.1016/j.medine.2026.502526},
pmid = {42486733},
issn = {2173-5727},
abstract = {The prognosis of critically ill cancer patients has improved significantly in the era of precision oncology. Advances in organ support, timely ICU admission, and the availability of targeted therapies and immunotherapy have improved survival rates in many settings, enabling an increasing number of patients to resume their oncological treatment. However, predicting individual outcomes remains challenging, as traditional models do not capture the biological complexity or clinical heterogeneity of cancer. Important prognostic determinants have emerged, including functional status, reversibility of the acute event, presence of organ failure, and the molecular characteristics of the tumor. Additionally, the microbiome is recognized as a critical modulator of immune responses that influences susceptibility to infections and contributes to carcinogenesis. Integrating these elements is essential to advance toward more accurate prognostication in critically ill cancer patients.},
}

@article {pmid42486816,
year = {2026},
author = {Zhong, H and Zhao, Y and Fu, H and Dong, J and Ding, G and Chen, Y and Guo, W},
title = {Causal association between oral microbiota and hepatocellular carcinoma in East Asian populations: a Mendelian randomization study.},
journal = {Nan fang yi ke da xue xue bao = Journal of Southern Medical University},
volume = {46},
number = {7},
pages = {1467-1473},
doi = {10.12122/j.issn.1673-4254.2026.07.01},
pmid = {42486816},
issn = {1673-4254},
support = {82371792//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Liver Neoplasms/microbiology ; *Carcinoma, Hepatocellular/microbiology/epidemiology ; Mendelian Randomization Analysis ; *Microbiota ; Polymorphism, Single Nucleotide ; *Mouth/microbiology ; Genome-Wide Association Study ; Asian People ; },
abstract = {OBJECTIVES: Emerging evidence highlights the crucial role of the oral microbiota in various malignancies, but its causal relationship with hepatocellular carcinoma (HCC) remains largely unexplored. This study aimed to investigate the causal association between oral microbiota composition and HCC risk in East Asian populations using Mendelian randomization (MR) analysis.

METHODS: We performed a two-sample Mendelian randomization to investigate the causal association of 309 tongue dorsum microbiomes and 285 salivary microbiomes with liver cancer progression using the latest pooled data from genome-wide association study (GWAS) of oral microbiomes in East Asian populations. We selected single nucleotide polymorphism (SNP) independent of confounders as the instrumental variable (IV) for causal inference analysis using various Mendelian randomization statistical techniques. The heterogeneity and pleiotropy of the IV was evaluated to ensure the reliability of the results.

RESULTS: Our analysis revealed a complex association between specific bacterial genera in the oral microbiome and liver cancer. Streptococcus showed a mixed association with hepatocellular carcinoma, while Oribacterium and Centipeda showed a positive correlation with HCC occurrence. Gemella genus was negatively correlated with HCC. Heterogeneity or pleiotropy of the IV was not detected in the sensitivity analysis.

CONCLUSIONS: This study provides the first Mendelian randomization evidence linking oral microbiota to HCC susceptibility in East Asian populations. Our findings suggest causal roles of specific oral bacterial taxa in hepatocarcinogenesis, and offer new insights into the mechanisms of the oral-liver axis and potential microbial targets for HCC prevention and treatment.},
}

Humans
*Liver Neoplasms/microbiology
*Carcinoma, Hepatocellular/microbiology/epidemiology
Mendelian Randomization Analysis
*Microbiota
Polymorphism, Single Nucleotide
*Mouth/microbiology
Genome-Wide Association Study
Asian People

@article {pmid42486971,
year = {2026},
author = {Robbins, S and Terzin, M and Dougan, K and Zaugg, J and Bell, SC and Laffy, PW and Engelberts, JP and Lê Cao, KA and Gruber, RK and Webster, NS and Bourne, DG and Hugenholtz, P and Yeoh, YK},
title = {The planktonic microbiome of the Great Barrier Reef.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42486971},
issn = {1476-4687},
abstract = {Large genome databases have markedly improved our understanding of marine microorganisms[1-5]. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pelagibacter and Prochlorococcus, are conspicuously underrepresented. Here we present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), comprising 5,283 prokaryotic genomes obtained from Great Barrier Reef seawater samples using Nanopore and Illumina sequencing, including a collection of high-quality genomes of underrepresented groups. We show that standard short-read assemblies miss these populations owing to a combination of strain heterogeneity and low-GC-percentage sequencing bias. The GBR-MGD also comprises 20 chromosome-level picoeukaryote and 808,585 viral genomes, including a newly described clade of marine Crassvirales. We demonstrate the utility of the GBR-MGD to identify indicator taxa that can reliably predict the effects of reef management practices, such as the establishment of marine protected zones.},
}

@article {pmid42487293,
year = {2026},
author = {Teng, ZP and Han, QQ and Shen, XF},
title = {Haemophilus abundance is associated with response to sublingual immunotherapy in children with allergic rhinitis.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {37},
number = {7},
pages = {e70437},
doi = {10.1111/pai.70437},
pmid = {42487293},
issn = {1399-3038},
support = {YKK24167//General Science and Technology Health Development Project of Nanjing City/ ; },
mesh = {Humans ; Female ; Male ; Child ; *Sublingual Immunotherapy/methods ; *Rhinitis, Allergic/therapy/immunology/microbiology ; Prospective Studies ; *Microbiota ; *Haemophilus/isolation & purification/immunology ; Child, Preschool ; Biomarkers ; Animals ; Allergens/immunology ; Treatment Outcome ; Pyroglyphidae/immunology ; Severity of Illness Index ; },
abstract = {BACKGROUND: The nasal microbiome's role in predicting sublingual immunotherapy (SLIT) efficacy in children with allergic rhinitis (AR) remains unclear. Haemophilus, a Proteobacteria genus linked to respiratory inflammation, is a promising candidate biomarker.

OBJECTIVE: To evaluate Haemophilus dynamics as a potential predictor of SLIT response in children with moderate-severe AR.

METHODS: In this prospective cohort, 63 children with AR and 40 healthy controls (CG) were enrolled. AR patients were stratified by disease severity (mild [MAR] vs. moderate-severe [MSAR]), with MSAR patients receiving 1-year standardized house dust mite SLIT. Based on >20% reduction in Total Nasal Symptom Score (TNSS), patients were classified as responders (RG, n = 25) or non-responders (NRG, n = 15). Nasal microbiome was profiled via 16S rDNA sequencing.

RESULTS: Compared to CG, AR children showed increased alpha diversity (Chao1, p < .05; Shannon, p < .01) and enrichment of Staphylococcus. MSAR patients had significantly higher Proteobacteria abundance, particularly Haemophilus, compared to MAR (LDA score >4, p < .001). After SLIT, RG patients showed normalized microbial evenness (Pielou E index) to CG levels, driven by marked Haemophilus depletion (p < .001). In contrast, NRG patients maintained high Haemophilus abundance. Haemophilus and Moraxella showed strong positive correlation (r = .68, p < .001), with both decreasing in RG post-SLIT.

CONCLUSION: Elevated nasal Haemophilus is associated with AR severity, and its depletion correlates with SLIT efficacy. Haemophilus may serve as a clinically actionable microbial biomarker for monitoring SLIT response in pediatric AR, offering a novel precision medicine approach to allergen immunotherapy.},
}

Humans
Female
Male
Child
*Sublingual Immunotherapy/methods
*Rhinitis, Allergic/therapy/immunology/microbiology
Prospective Studies
*Microbiota
*Haemophilus/isolation & purification/immunology
Child, Preschool
Biomarkers
Animals
Allergens/immunology
Treatment Outcome
Pyroglyphidae/immunology
Severity of Illness Index

@article {pmid42487409,
year = {2026},
author = {Kim, S and Seo, H and Kim, TR and Rahim, MA and Tajdozian, H and Yoon, Y and Jo, S and Shuvo, MSH and Barman, I and Park, C and Lee, S and Lee, S and Cho, MH and Ha, J and Hong, H and An, S and Chu, S and Sohn, M and Ahn, YK and So, YJ and Rheem, S and Han, SH and Song, HY},
title = {Microbiome-Modulating Effects of Heat-Treated Lactiplantibacillus plantarum LM1004 and Its Enhancement of NK Cell Activity: Evidence from a Clinical Trial and a Simulated Human Intestinal Microbiome Ecosystem.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604046},
doi = {10.4014/jmb.2604.04046},
pmid = {42487409},
issn = {1738-8872},
mesh = {Humans ; *Killer Cells, Natural/immunology ; *Probiotics/administration & dosage ; *Lactiplantibacillus plantarum/physiology ; Hot Temperature ; *Gastrointestinal Microbiome/drug effects ; Adult ; Male ; Female ; Colon/microbiology ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; },
abstract = {Probiotics are increasingly recognized for their capacity to modulate gut microbiota, regulate microbial metabolic activity, and influence host immune responses, thereby contributing to the maintenance of immune homeostasis and overall health. In this study, we assessed the efficacy and safety of heat-treated Lactiplantibacillus plantarum LM1004 (HT-LM1004) in a randomized, placebo-controlled clinical trial and explored its mechanisms of action in a simulated human intestinal microbiome ecosystem. After 8 weeks of supplementation, we observed significantly enhanced natural killer (NK) cell activity with a concurrent improvement in white blood cell (WBC) counts relative to the placebo group, suggesting an overall enhancement of the host's primary immune defense baseline within the normal physiological range. Mechanistic investigations within the simulated human intestinal microbiome ecosystem demonstrated that HT-LM1004 increased microbial species diversity in the ascending colon (AC), followed by elevated richness in the transverse colon (TC) and descending colon (DC) at the End and Post time points, suggesting selective enrichment of low-abundance beneficial bacterial taxa. Metabolomics analyses indicated compartment-specific changes, especially within bile acid metabolism pathways, while non-bile acid metabolites were predominantly enriched in the DC. Short-chain fatty acid (SCFA) profiling also revealed distinct, time-dependent changes across the different gut compartments. Collectively, these results indicate that L. plantarum LM1004 boosts NK cell activity in humans by enriching low-abundance beneficial bacteria and modulating their metabolic products, underscoring its promise as a microbiome-based functional food and preventative option to support immune health.},
}

Humans
*Killer Cells, Natural/immunology
*Probiotics/administration & dosage
*Lactiplantibacillus plantarum/physiology
Hot Temperature
*Gastrointestinal Microbiome/drug effects
Adult
Male
Female
Colon/microbiology
Fatty Acids, Volatile/metabolism
Bile Acids and Salts/metabolism

@article {pmid42487487,
year = {2026},
author = {Llaja, JC and Oyola, JE and Carrion, JV and Chuquizuta, F and Calderon, MS and Bustamante, DE},
title = {Hidden Microbiota Inhabiting in Pollen Reserves of Honey Bee (Apis mellifera) From Amazonas Region Revealed by DNA Metabarcoding.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70392},
doi = {10.1111/1758-2229.70392},
pmid = {42487487},
issn = {1758-2229},
support = {PE501083491-2023-PROCIENCIA//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; PE501079652-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; CUI N° 2315092//Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas/ ; VRIN//Vicerrectorado de Investigación de la Universidad Nacional Toribio Rodriguez de Mendoza/ ; },
mesh = {Bees/microbiology ; Animals ; *Pollen/microbiology ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Ecosystem ; Peru ; Biodiversity ; Pollination ; },
abstract = {Pollen functions as a dynamic microbial habitat and the microbes living in pollen reserves play vital roles in pollinator health and nutrition. However, the microbiota composition of honeybee pollen reserves in biodiverse Neotropical regions remains largely unknown. This study provides the first comprehensive analysis of bacterial and fungal communities in honeybee pollen reserves across six ecosystems in the Amazonas region of Peru using high-throughput metabarcoding of the 16S rRNA gene and ITS2 markers. We found that ecosystem type is a primary driver of community structure, with bacteria and fungi responding differently to environmental changes. Despite high taxonomic heterogeneity and a limited number of shared core microbes, the main functions of these microbes were maintained, featuring enrichment of bacterial pathways involved in nutrient metabolism and saprotrophic fungal guilds. Lactobacillus and an unclassified Tremellomycetes fungus were dominant, yet their abundance varied with respect to floral resource diversity. The simplified Palm Swamp ecosystem showed significantly reduced microbial diversity, underscoring the vulnerability of these communities to habitat homogenization. Our results demonstrate that the pollen reserve microbiome is assembled through environmental filtering and pollinator-mediated selection, resulting in taxonomically flexible but functionally stable communities essential for hive processes. This work provides a foundation for understanding the microbial ecology of pollen in the Amazonas region.},
}

Bees/microbiology
Animals
*Pollen/microbiology
DNA Barcoding, Taxonomic
RNA, Ribosomal, 16S/genetics
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
Ecosystem
Peru
Biodiversity
Pollination

@article {pmid42487516,
year = {2026},
author = {Damianos, JA and Matar, A and Carlson, P and Busciglio, I and Jencks, KJ and Johnson, S and Mars, RA and Kashyap, PC and Harmsen, WS and Camilleri, M},
title = {Clinical Trial: Multi-Strain Probiotic Improves Bile Acid Profile, Microbiome, and Metabolomic Parameters in Patients With History of Bile Acid Malabsorption-A Randomized, Controlled Trial.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70876},
pmid = {42487516},
issn = {1365-2036},
support = {//ExeGi Pharma/ ; },
abstract = {BACKGROUND: Bile acid (BA) malabsorption (BAM) is a common cause of chronic diarrhoea and may occur in some patients due to abnormalities of the gut microbiota. Effects of probiotics on faecal secretory BAs, particularly the primary BA, chenodeoxycholic acid, are unclear.

AIM/METHODS: We conducted a randomized, double-blind, placebo-controlled trial of the De Simone formulation 8-strain probiotic in 24 patients previously diagnosed with BAM. Patients were randomized to 3 weeks of the probiotic (900 billion bacteria) or placebo (maltose), both administered three times daily. Symptoms, serum 7αC4, faecal primary BAs, intestinal permeability by [13]C-mannitol-lactulose test (0.1 and 1 g of the sugars respectively) over 24 h, faecal short chain fatty acids (SCFA), microbiome, and metabolome were assessed at baseline and post-intervention.

RESULTS: Data from 22 patients were included. Probiotic supplementation was associated with a significant decrease in % faecal primary BAs (chenodeoxycholic acid and cholic acid) with median change from baseline -5.7 [IQR -10.3, 0.9]% compared to 9.8 [IQR 0.2, 20.6]% on placebo (p = 0.012). The faecal microbiome was significantly different in the probiotic group after intervention, driven by probiotic-specific species. There were no significant differences in symptoms, intestinal permeability, or SCFA. However, there was a numerical difference in the changes from baseline in 0-2 h [13]C-mannitol excretion -1.9 [-13.9, 4.2] mg for the probiotic and 1.0 (-0.5, 12.7) mg for placebo (p = 0.084).

CONCLUSIONS: The De Simone formulation probiotic induced significant microbiome and metabolome changes in patients with BAM, ultimately leading to a decrease in % faecal primary BAs and possible reduction in intestinal permeability.

CLINICAL TRIALS: gov registration NCT #06609148, January 2, 2025.},
}

@article {pmid42487569,
year = {2026},
author = {Allen, XJ and Cowger, C and Brown-Guedira, G and Hawkes, CV},
title = {Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum.},
journal = {Molecular ecology},
volume = {35},
number = {14},
pages = {e70485},
pmid = {42487569},
issn = {1365-294X},
support = {NNF19SA0059348//Novo Nordisk Fonden/ ; 7005451//U.S. Department of Agriculture (HATCH Project)/ ; },
mesh = {*Triticum/microbiology/genetics ; *Ascomycota/pathogenicity/genetics ; *Plant Diseases/microbiology/genetics ; *Mycobiome/genetics ; Host-Pathogen Interactions/genetics ; North Carolina ; Plant Leaves/microbiology ; Metagenomics ; },
abstract = {Plant mycobiomes are essential to plant health, yet their assembly under biotic stressors such as pathogen infection remains poorly understood. Plant pathogens can influence microbial community composition through direct antagonism and suppression of host immune responses, potentially altering mycobiome composition in ways that could affect plant performance. We investigated how the wheat (Triticum aestivum L.) foliar mycobiome was associated with inoculation with the fungal pathogen Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crous, which can cause substantial loss of yield and grain density throughout its range. To address this, we studied inoculation effects in four wheat cultivars planted in a randomized block design at two North Carolina field sites. We used ITS amplicon metagenomics to characterize wheat mycobiome richness, composition, and structure. We found that P. nodorum inoculation reduced fungal richness by up to 38.5%. We also found simplified foliar fungal networks for plants inoculated with P. nodorum, with up to 13.1% fewer taxa present and up to 41.2% fewer associations among those taxa. As part of these changes, increasing P. nodorum absolute abundance was correlated with increasing proportional representation of pathogens in wheat leaves due to loss of non-pathogenic taxa. Fewer fungal taxa and reduced network connectivity were particularly evident in reportedly susceptible cultivars and at one of the two sites where conditions favoured pathogen success. Based on these results, we suggest that pathogen infection plays a significant role in mycobiome assembly and has implications for disease management and mycobiome-based interventions in agricultural systems.},
}

*Triticum/microbiology/genetics
*Ascomycota/pathogenicity/genetics
*Plant Diseases/microbiology/genetics
*Mycobiome/genetics
Host-Pathogen Interactions/genetics
North Carolina
Plant Leaves/microbiology
Metagenomics

@article {pmid42487710,
year = {2026},
author = {Zhili, G and Jie, L and Yuyue, X and Fang, Y and Dianqun, R and Qin, Z and Xiaojun, L},
title = {Fecal metagenomic profiling in patients with colorectal adenomas to characterize gut microbial composition and functional potential.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1842365},
pmid = {42487710},
issn = {1664-302X},
abstract = {OBJECTIVE: To investigate differences in gut microbiota between patients with colorectal adenoma (CRA) and healthy individuals using metagenomic sequencing, and to analyze the correlation between microbial abundance and polyp diameter and number.

METHODS: Metagenomic sequencing was performed on fecal samples from 60 patients with CRA and 30 healthy controls. Species-level and functional analyses of the gut microbiome were conducted.

RESULTS: Metagenomic profiling revealed a distinct microbial signature in CRA. Statistical analysis identified significant differences in taxonomic composition between the two groups. Overall, 487 genes showed significant abundance differences. Among these, approximately 55.37% were significantly enriched in the adenoma group, suggesting specificity for CRA, while 175 genes were significantly reduced. Alpha diversity analysis indicated similar microbial richness and evenness between the groups, whereas beta diversity confirmed significant structural differences in the microbial community. KEGG enrichment analysis of the top 20 differentially abundant species showed that these microbes were primarily associated with metabolic pathways. The greater number of increased versus decreased genes implied a more pronounced expansion of pathogenic bacteria relative to the loss of beneficial bacteria. Linear discriminant analysis effect size (LEfSe) analysis indicated that Fusobacterium nucleatum, Alistipes, and Bacteroides fragilis could serve as diagnostic microbial biomarkers for CRA. LEfSe further identified 38 differentially abundant bacterial clades, with genera such as Bacteroides, Peptostreptococcus, and Parabacteroides enriched in patients. Finally, correlation analysis linked the abundance of specific microbial taxa with polyp number and diameter.

CONCLUSION: This study confirms distinct gut microbiota profiles in patients with CRA compared with healthy individuals, highlights significant microbiome alterations associated with CRA, and reveals novel correlations between specific microorganisms and polyp characteristics, suggesting that microbial changes may contribute to adenoma development.},
}

@article {pmid42487713,
year = {2026},
author = {Chen, M and Zhang, S and Lu, M and Zhu, D and Xiao, M and Liao, Y and Li, Y and Zhou, T and Wang, M and Song, Q},
title = {Age-associated gut microbiome succession, colonization resistance, and relative resistome patterns in an antibiotic-restricted infant cohort.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1862116},
pmid = {42487713},
issn = {1664-302X},
abstract = {BACKGROUND: Early infancy is critical for gut microbiome assembly and the establishment of colonization resistance against pathobionts. Whether age-associated microbiome maturation is accompanied by changes in colonization-resistance proxies and relative antimicrobial resistance gene profiles under low infant antibiotic exposure remains unclear.

METHODS: We analyzed shotgun metagenomes from 82 fecal samples collected from 54 healthy infants (54 at 1 month and 28 at 6 months). Taxonomic and functional profiles were generated using MetaPhlAn 4 and HUMAnN3, and AMR genes were annotated using RGI/CARD. Age-associated taxa were screened by LEfSe and tested using MaAsLin2 with adjustment for key perinatal covariates.

RESULTS: Age group was associated with modest but statistically significant differences in community structure (Bray-Curtis PERMANOVA R [2] = 0.03, p = 0.005) and higher species richness at 6 months (p < 0.001), with no statistically significant difference in Shannon or Simpson indices. In adjusted models, skin-associated pioneer taxa, including Staphylococcus epidermidis, were lower at 6 months, whereas several anaerobic or oral-associated taxa were higher, including Flavonifractor plautii. Enterobacteriaceae relative abundance was lower at 6 months than at 1 month (median 16.64 vs. 1.86%, p < 0.001), and Bifidobacterium-Enterobacteriaceae antagonism indices were higher. However, Escherichia coli and Klebsiella spp. did not show significant genus-level reductions. Copies per million (CPM)-normalized β-lactamase (bla) relative abundance showed no statistically significant timepoint difference and was positively correlated with selected Bifidobacterium species.

CONCLUSIONS: In this infant antibiotic-restricted cohort, microbiome profiles at 6 months were associated with lower relative abundance of potential pathobionts and higher colonization-resistance proxy indices. CPM-normalized bla relative abundance showed no statistically significant timepoint difference. These observational findings do not establish the genomic host or mobility of bla genes. Quantitative and host-resolved studies are needed to distinguish compositional shifts from absolute resistome trajectories.},
}

@article {pmid42487715,
year = {2026},
author = {Zlatnar, M and Alves, RP and Toledo, GV and Wicaksono, WA and Berg, G},
title = {Metagenomic analysis reveals functional potential and storage-driven dynamics of the Kalamata olive microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1890405},
pmid = {42487715},
issn = {1664-302X},
abstract = {BACKGROUND: Fermented olives are a staple of the Mediterranean diet due to their nutritional value. Despite advances in olive microbiome research, published research on the functional contributions of fermented food-associated microbiota and the impact of storage on these microbial communities remains limited.

METHODS: We studied the bacterial communities of ready-to-eat Kalamata olives, stored in glass jars or vacuum-sealed bags at various temperatures (4°C, 8°C and 15°C) for 55-day period. The bacterial abundance, taxonomical composition and functional potential were analyzed by quantitative PCR and amplicon sequencing of 16 rRNA gene, and metagenome sequencing.

RESULTS: The microbiota was dominated by Lactobacillaceae (94.6%), a family of lactic acid bacteria (LAB), with dominant genera such as Pediococcus, Lactiplantibacillus and Secundilactobacillus. At the functional level, bacterial genes involved in the biosynthesis of vitamins B1, B2, B5, B7, B9, B12, and vitamin K, as well as short-chain fatty acid metabolism, were observed. Importantly, those functions were not restricted to LAB, underscoring the potential functional contribution of non-LAB taxa to the olive microbiome. Despite conservation, post-fermentation storage, especially the incubation time, temperature, and packaging, influenced the bacterial communities. Lactic acid bacteria were enriched in olives stored at 15°C, whereas non-LAB taxa proliferated more at lower temperatures.

CONCLUSION: Our study showed that Kalamata olives contain a highly abundant and diverse microbiota that responds to storage practices and carries genes encoding functions that may contribute to the characteristics and quality of the fermented product.},
}

@article {pmid42487817,
year = {2026},
author = {van den Bosch, M and Paciência, I and Al-Delaimy, WK and Jaakkola, JJK},
title = {Editorial: Interconnected impacts: climate change, biodiversity loss, and health.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1912102},
pmid = {42487817},
issn = {2296-2565},
}

@article {pmid42487857,
year = {2026},
author = {Farooq, U and Sadiqa, A and Arshad Jarral, S},
title = {Pathophysiological and Therapeutic Association between Brain-Gut Axis and Irritable Bowel Syndrome: A Systematic Review.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {7},
pages = {1869-1876},
pmid = {42487857},
issn = {1682-024X},
abstract = {OBJECTIVE: To identify the association among the gut, brain, and related microbiota, to reach the best-suited personalized management plan for Irritable Bowel Syndrome (IBS).

METHODOLOGY: A systematic review was conducted by reviewing studies across multiple Databases, i.e., Scopus, MEDLINE, PubMed, Web of Science, ScienceDirect (Elsevier), Cochrane Library, Embase, and Google Scholar. The timeframe of selected publications was from 2007 to 2025. The results were extracted from 49 selected manuscripts using PRISMA guidelines. The review discussed the pertinent link between the brain-gut axis and IBS, in relation to etiology, clinical features, and underlying pathophysiological mechanisms, and an optimal management plan that aligns with the new concept of personalized health care, alongside evidence-based medicine.

RESULTS: IBS is a multidimensional ailment concerning gut hypersensitivity, hyper-immunity, imbalanced gut flora, and excessive anxiety or derailed psychology, each presented with a particular feature and associated with related etiology. Conventional therapeutic management benefits from reducing fermentation through a suitable diet plan, antibiotics to regulate gut flora, and neuroregulators that augment signaling pathways between visceral (gut-related) and central (brain) nervous systems. Stress-reducing interventions helped to decline the nociception and symptomatic-anxiety bursts. Upcoming advanced techniques such as Fecal microbiota transplantation (FMT), psychedelic-assisted therapy, traditional Chinese medicine, and the use of neuromodulator devices express possibilities to cure.

CONCLUSION: IBS is a multisystem pathology triggered by gut dysbiosis, hyper-immune responses, visceral hypersensitivity, and stress-axis dysregulation. Thus, it is evident that a multimodal personalized management approach, including dietary, microbiome-targeted, pharmacological, and psychological therapies, is recommended for IBS, based on symptomology and etiology.},
}

@article {pmid42487965,
year = {2026},
author = {Donmez, E and Sener Okur, D and Ozsoy, AU and Senol, H and Yuksel, S},
title = {Composition of and changes in faecal microbiota in children diagnosed with oligoarticular juvenile idiopathic arthritis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1877706},
pmid = {42487965},
issn = {2296-858X},
abstract = {BACKGROUND: In genetically predisposed individuals, changes in the balance of pro- and anti-inflammatory bacteria in the intestinal microbiota may affect the mucosal immune system and contribute to the development of Juvenile Idiopathic Arthritis (JIA). In this study, we aimed to compare the bacterial composition of the faecal microbiota between children with newly diagnosed, untreated oligoarticular JIA and healthy children, in Türkiye.

MATERIALS AND METHODS: This study included 25 healthy children and 25 treatment-naive patients diagnosed with oligoarticular JIA. Targeted sequencing of the bacterial 16S ribosomal RNA (rRNA) gene was performed on the genetic material obtained from stool samples.

RESULTS: Diversity analyses revealed that the dominant bacteria were present in similar proportions, and their distributions were similar. The number of rare species differed, and their distributions were heterogeneous. The patient group was found to have a higher abundance of Bacteroidetes and a lower Firmicutes/Bacteroidetes ratio. The relative abundance of Dialister was reduced, while Oscillibacter and Alistipes were increased in the patient group. In the patient group, we noted an increase in the Akkermansiaceae family and in the Catenibacterium, Howardella, Holdemanella, Megasphaera and Akkermansia genera, a decrease in the Clostridiaceae and Lactobacillaceae families and Lactobacillus genera.

CONCLUSION: To the best of our knowledge, our study is the first of its kind conducted on this subject in Türkiye. Given that microbiota composition is influenced by geographical characteristics, our study also contributes to the literature regarding the faecal composition of JIA patients in our country. Funding Scientific Research Projects Unit of Pamukkale University.},
}

@article {pmid42488410,
year = {2026},
author = {Li, J and Hu, X and Liu, Y and Ma, J and Ren, L and Guo, J and Zhang, X and Meng, Y and Liu, J and Zhao, J and Zan, L and Guan, X and Bai, W},
title = {Tumor tissue-associated Phascolarctobacterium is associated with lymph node metastasis, prognosis, and immune-contexture features in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1784151},
pmid = {42488410},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/pathology/microbiology/immunology ; *Lymphatic Metastasis ; Prognosis ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Middle Aged ; Aged ; },
abstract = {BACKGROUND: Lymph node metastasis (LNM) critically influences prognosis in colorectal cancer (CRC), yet the mechanisms driving this process, particularly the contribution of the intratumoral microbiota, remain insufficiently defined.

METHODS: We performed 16S rRNA sequencing on tumor tissue from a discovery cohort of 122 CRC patients, followed by validation in one internal and one external validation cohort. Immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and transcriptomic deconvolution were used to explore tumor immune-contexture features and tissue-associated Phascolarctobacterium-like signals. Bulk RNA-seq data were analyzed using Weighted Gene Co-expression Network Analysis (WGCNA) and pathway enrichment to explore host transcriptomic modules and molecular pathways associated with microbial abundance.

RESULTS: Higher tumor tissue-associated Phascolarctobacterium abundance showed a modest positive association with lymph node metastasis and was associated with worse overall survival in the discovery cohort (HR = 3.892, 95% CI = 1.441-10.513, P = 0.007). These tumors showed exploratory immune-contexture differences, including lower CD8+ T-cell-related signals and higher macrophage/M2 macrophage-related signals. WGCNA identified exploratory abundance-associated modules enriched in keratinocyte differentiation, epithelial development, and MAPK signaling, whereas low-abundance-associated modules were linked to lipid metabolism and redox regulation.

CONCLUSIONS: Tumor tissue-associated Phascolarctobacterium abundance showed exploratory associations with lymph node metastasis, poorer overall survival in the discovery cohort, and immune-contexture features in CRC. These findings are exploratory and require validation in larger independent cohorts and functional studies.},
}

Humans
*Colorectal Neoplasms/pathology/microbiology/immunology
*Lymphatic Metastasis
Prognosis
RNA, Ribosomal, 16S/genetics
Female
Male
Middle Aged
Aged

@article {pmid42488412,
year = {2026},
author = {Xiang, X and Pei, Y and Wang, Q},
title = {Probiotic preparations in mitigating chemotherapy-induced oral mucositis: therapeutic efficacy, mechanisms, and clinical translation potential.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1870000},
pmid = {42488412},
issn = {2235-2988},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Stomatitis/chemically induced/therapy ; *Antineoplastic Agents/adverse effects/therapeutic use ; Microbiota/drug effects ; Animals ; Mouth Mucosa/microbiology/pathology/drug effects ; Neoplasms/drug therapy ; Treatment Outcome ; Immunomodulation ; },
abstract = {Chemotherapy-induced oral mucositis (CIOM) is a prevalent toxic side effect of cancer treatment, severely compromising patients' quality of life, nutritional intake, and treatment adherence. Its pathogenesis has evolved from the traditional model of simple epithelial damage to a complex pathological process involving the interplay of chemotherapy toxicity, host immunity, and oral microbiota. Research indicates that chemotherapy can disrupt the oral microbiota, promoting the proliferation of pathogenic bacteria and exacerbating damage to the mucosal barrier and local inflammatory responses. Current clinical interventions, such as mouth rinses and cryotherapy, have limited efficacy and lack standardized protocols. In recent years, modulating the oral microbiota has emerged as a promising therapeutic strategy. Probiotic preparations have demonstrated potential in clinical studies to alleviate CIOM severity through mechanisms including competitive colonization, metabolic regulation, and immunomodulation. This review systematically summarizes the clinical manifestations, epidemiological characteristics, pathogenesis, and existing treatment strategies of CIOM. It highlights the critical role of the oral microbiota in CIOM pathogenesis and further outlines the promising application prospects of microbiome-targeted interventions, particularly probiotic preparations, aiming to provide novel insights for CIOM prevention and treatment.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Stomatitis/chemically induced/therapy
*Antineoplastic Agents/adverse effects/therapeutic use
Microbiota/drug effects
Animals
Mouth Mucosa/microbiology/pathology/drug effects
Neoplasms/drug therapy
Treatment Outcome
Immunomodulation

@article {pmid42488426,
year = {2026},
author = {Bautista, J and Carrión-Ruiz, R and Bourne-Cabezas, A and Robles, LA and Velez-Navarrete, AM and López-Cortés, A},
title = {Host-microbiome interactions in leukemia: mechanisms, treatment response, and clinical implications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1842279},
pmid = {42488426},
issn = {2235-2988},
mesh = {Humans ; *Leukemia/microbiology/therapy/immunology ; *Host Microbial Interactions ; *Gastrointestinal Microbiome ; Animals ; *Microbiota ; Intestinal Barrier Function ; Homeostasis ; Hematopoietic Stem Cell Transplantation ; },
abstract = {Host-microbiome interactions regulate immune function, epithelial barrier integrity, and hematopoietic homeostasis. Intestinal microbial communities show consistent disruption in leukemia, particularly during intensive chemotherapy and hematopoietic stem cell transplantation. Reduced microbial diversity, depletion of short-chain fatty acid (SCFA)-producing commensals, and expansion of opportunistic taxa are recurrent findings across cohorts. Such patterns correlate with inflammatory signaling, impaired barrier function, and shifts in immune responses affecting treatment tolerance and hematopoietic recovery. Clinical associations show greater consistency for treatment-related outcomes, including infection risk, mucosal injury, and delayed immune reconstitution, than for leukemogenesis. Evidence supporting a direct causal role of specific microbial taxa in disease initiation remains limited. This review examines microbiome composition, microbial taxa, and mechanistic pathways in leukemia, with emphasis on how microbiome alterations may influence leukemia biology, disease progression, treatment response, and clinical outcomes, while acknowledging that most human evidence remains associative.},
}

Humans
*Leukemia/microbiology/therapy/immunology
*Host Microbial Interactions
*Gastrointestinal Microbiome
Animals
*Microbiota
Intestinal Barrier Function
Homeostasis
Hematopoietic Stem Cell Transplantation

@article {pmid42488442,
year = {2026},
author = {Wang, J and Li, J and Fan, X and Niu, X and Deng, X and Nian, F and Wang, H and Han, N and Yang, S and Dong, J and Tang, L and Shi, Q and Liu, Y and Liu, D},
title = {Effects of AMF on tobacco growth in continuous cropping soils: impacts on soil chemical properties and rhizosphere microbial diversity.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1827990},
pmid = {42488442},
issn = {1664-462X},
abstract = {INTRODUCTION: Continuous tobacco cropping leads to reduced nutrient bioavailability, severe autotoxicity, and disrupts the rhizosphere microbial balance, ultimately reducing leaf yield and quality. Inoculation with arbuscular mycorrhizal fungi (AMF) can promote plant growth by enhancing nutrient uptake and modulating soil microbial communities.

METHODS: This study investigated the mechanisms underlying growth inhibition in consecutively cropped soils and evaluated the potential of AMF to alleviate such cropping stress through a pot experiment.

RESULTS: Compared with non-inoculated plants, AMF inoculation significantly improved photosynthetic parameters, agronomic traits, and biomass during the vigorous growth stage. It also increased antioxidant enzyme activities in both leaves and roots, elevated soil enzyme activities (catalase, sucrase, polyphenol oxidase), and enhanced soil nitrogen, phosphorus, and potassium content. Furthermore, AMF inoculation enriched soil microbial diversity, particularly increasing the abundance of Lysobacter, and exerted stronger effects on the fungal community than bacteria. AMF inoculation also reduced concentrations of allelopathic compounds in soil, including hydroxybenzoic acid, vanillic acid, p-coumaric acid, ferulic acid, and myristic acid. In contrast, tobacco grown in consecutively cropped soils exhibited decreased photosynthetic performance, root growth, biomass, and reduced enzyme activities, including CAT, PAL and SOD in leaves and SOD, CAT, PAL and POD in roots.

DISCUSSION: Overall, continuous cropping negatively affects tobacco growth and soil homeostasis, whereas AMF inoculation promotes plant growth, mitigates allelopathic stressors associated with continuous cropping, and significantly improves soil chemical properties and microbial abundance and functionality.},
}

@article {pmid42488451,
year = {2026},
author = {Sharma, A},
title = {YoMiCom framework for guild-based design of resilient microbial consortia in multi-stress agricultural systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1854447},
pmid = {42488451},
issn = {1664-462X},
abstract = {Microbial consortia show promise for sustainable agriculture, yet their field performance often remains inconsistent due to ecological imbalance and instability in complex soil environments. The Yogic Microbiome (YoMiCom) framework addresses this challenge by presenting a systems-based approach to microbial consortium design, where plant-beneficial functions are organized into coordinated functional guilds that support ecological balance, compatibility, and resilience. By combining guild-based assembly with quantitative design metrics, such as the Functional Guild Index for strain prioritization and the Guild Balance Coefficient for functional distribution, within an iterative Design-Build-Test-Learn framework, YoMiCom shifts the focus from empirical assembly to structured, context-driven design. This framework is presented as a testable conceptual design approach that can be evaluated and refined across diverse agroecological contexts, thereby supporting the development of ecologically compatible and functionally balanced solutions for sustainable agriculture.},
}

@article {pmid42488457,
year = {2026},
author = {Wang, Y and Wang, F and Li, Y and Han, S},
title = {Multi-omics analysis reveals associations among endophytic microbiome shifts, host transcriptional responses, and metabolic variation across variegated leaf sectors of Aspidistra elatior.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1860906},
pmid = {42488457},
issn = {1664-462X},
abstract = {Leaf variegation in Aspidistra elatior provides a useful system for exploring localized plant-microbiome associations, yet the biological factors linked to sector-specific chlorosis remain unclear. To investigate potential relationships among endophytic microbial communities, host transcriptomic responses, and metabolic variation, we integrated 16S/ITS amplicon sequencing, transcriptomics, and widely targeted LC-MS/MS-based metabolomics across normal green (GG), adjacent green (SG), and chlorotic spot (SS) sectors. SS sectors showed sector-associated bacterial community patterns characterized by lower Shannon diversity relative to SG, enrichment of unclassified Rickettsiales, Stenotrophomonas, and Salinivibrio, and reduced abundance of several Actinobacteriota-associated taxa. By contrast, fungal community structure remained comparatively stable across sectors. Transcriptomic analysis identified sector-associated expression differences involving stress- and defense-related genes, including heat shock protein 70 (HSP70) and the F-box regulator SKIP23. Metabolomic profiling identified 52 core differentially accumulated metabolites (DEMs) between SS and SG, of which 37 showed higher abundance in SS. These metabolites included alkaloids, flavonoids, phenolic acids, and amino acids and derivatives. Integrated multi-omics correlation analyses linked host gene-expression modules to metabolite classes and revealed a significant correspondence between bacterial community dissimilarity and metabolic variation across sectors. Together, these findings identify SS sectors as spatially distinct leaf microenvironments in which bacterial community structure, host transcriptional state, and metabolite accumulation vary in parallel, placing localized variegation in a broader microbiome-host-metabolite context.},
}

@article {pmid42488460,
year = {2026},
author = {Gangwar, P and Xu, Q and Seangmany, J and Katte, P and Turakhia, Y},
title = {metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag080},
pmid = {42488460},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Phylogeny ; *Haplotypes ; Humans ; *Software ; Biological Specimen Banks ; },
abstract = {Metagenomic sequencing is transforming diverse areas of health and biological sciences, including pathogen surveillance, clinical diagnostics, and microbiome research. However, the inherent complexity of metagenomic data limits most computational tools to species-level classification and abundance estimation, overlooking within-species genetic diversity that drives key phenotypes. We present metaWEPP, a novel computational pipeline that achieves near-haplotype resolution in metagenomic analysis for species with adequate representation in reference genome biobanks and having sufficient sequencing depth and genome coverage. Specifically, metaWEPP assigns sequencing reads to species using standard taxonomic classifiers, phylogenetically places them onto species-specific mutation-annotated trees of publicly available sequences, and selects the haplotypes that best explain the sample. It also reports unaccounted alleles indicative of novel variants and provides an interactive dashboard for read-level visualization. Applied to diverse metagenomic and mixed-genome samples from prior studies, metaWEPP produced concordant species-level results, while revealing finer lineage- and haplotype-level insights not captured by existing tools. On various clinical samples, metaWEPP identified infecting pathogens and additionally provided credible lineage- and haplotype-level information that can support clinical decision-making. On wastewater samples, metaWEPP uncovered previously undetected haplotype clusters of epidemiological relevance. These findings demonstrate metaWEPP's ability to advance various clinical, epidemiological, and research applications with deeper, actionable insights.},
}

*Metagenomics/methods
*Phylogeny
*Haplotypes
Humans
*Software
Biological Specimen Banks

@article {pmid42488615,
year = {2026},
author = {Ogwu, MC and Izah, SC and Alum, EU and Aliu, OO and Raimi, MO and Kari, A},
title = {Redefining feed efficiency through the livestock gut microbiome.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1852759},
pmid = {42488615},
issn = {1664-042X},
abstract = {Feed efficiency remains a central goal in livestock production because it determines both economic viability and environmental performance. Yet conventional measures such as feed conversion ratio and residual feed intake often treat efficiency as a host-level outcome and do not fully capture the biological processes that govern nutrient transformation and use. This perspective argues that the gastrointestinal microbiome is a critical, and still underappreciated, mediator of feed efficiency across livestock systems. In ruminants, rumen microbial communities drive the conversion of fibrous feeds into volatile fatty acids and microbial protein, thereby shaping host energy supply, nitrogen utilization, and methane loss. In monogastrics, intestinal microbiota influence nutrient salvage, short-chain fatty acid production, barrier integrity, immune tone, and metabolic signaling, with direct consequences for growth and productive performance. We contend that feed efficiency should be reframed as an emergent property of diet-microbiome-host interactions rather than as a simple input-output trait. From this viewpoint, microbial mediation helps explain between-animal variation in nutrient bioavailability, digestive stability, inflammatory burden, and resilience under commercial production conditions. We further highlight how microbiome-informed feeding strategies, including dietary bioactives, probiotics, prebiotics, enzymes, and precision nutrition approaches, could improve nutrient conversion while reducing methane emissions and reliance on antibiotics. Recognizing the microbiome as a functional regulator of feed efficiency offers a more mechanistic and sustainability-oriented framework for livestock nutrition research and practice, with important implications for breeding, management, and future multi-omics innovation.},
}

@article {pmid42488628,
year = {2026},
author = {Tian, X and Qu, Z and Cao, Y and Wang, Y and Zhang, B},
title = {Gut microbiota and osteoarthritis: mechanisms and translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1873110},
pmid = {42488628},
issn = {1664-3224},
mesh = {Humans ; *Osteoarthritis/microbiology/immunology/metabolism/etiology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Dysbiosis/immunology/microbiology ; },
abstract = {Osteoarthritis (OA) is increasingly recognised as a whole-joint disease driven by biomechanical stress, metabolic dysfunction, low-grade inflammation and immune dysregulation, yet effective disease-modifying treatments remain unavailable. Growing evidence suggests that gut microbiota dysbiosis may contribute to OA pathogenesis, giving rise to the concept of a functional and potentially targetable gut-joint axis. In this narrative review, we synthesise current evidence linking gut microbial alterations to OA and highlight the immunological mechanisms through which intestinal dysbiosis may influence joint degeneration. Human studies have identified OA-associated changes in gut microbial composition and microbial metabolites, whereas preclinical models, germ-free experiments and faecal microbiota transplantation studies provide mechanistic support for a contributory role of dysbiosis in cartilage damage, synovitis and subchondral bone remodelling. Gut dysbiosis can impair intestinal barrier integrity, facilitate systemic exposure to microbial products such as lipopolysaccharide, disturb short-chain fatty acid, bile acid and tryptophan-derived metabolite profiles, and alter enteroendocrine and immune signalling. These processes may activate Toll-like receptor, NF-κB, NLRP3 inflammasome, aryl hydrocarbon receptor and JAK/STAT pathways, thereby reshaping macrophage polarisation, Th17/Treg balance, mucosal IgA responses, innate lymphoid cell and γδT-cell activity, immunosenescence and low-grade systemic inflammation. Through these interconnected immune-metabolic pathways, the gut microbiota may influence cartilage catabolism, synovial inflammation, subchondral bone remodelling and inflammation-related pain. Microbiome-derived taxa, metabolites and host-microbe immune signatures might support risk assessment, endotype stratification and therapeutic monitoring; however, causality in humans remains incompletely established, and current findings are limited by heterogeneity in OA phenotypes, microbiome methods, host metabolic status and clinical endpoints. Microbiota-targeted strategies remain promising adjuncts rather than established disease-modifying treatments. Future studies should integrate standardised microbiome profiling, immune phenotyping, multi-omics approaches, longitudinal cohorts and rigorously designed clinical trials to translate gut-joint axis biology into microbiome-informed precision care for OA.},
}

Humans
*Osteoarthritis/microbiology/immunology/metabolism/etiology
*Gastrointestinal Microbiome/immunology
Animals
*Dysbiosis/immunology/microbiology

@article {pmid42488629,
year = {2026},
author = {Sun, M and Xu, Y and Song, G and Zhang, B and Peng, M and Yu, S and Zhang, G},
title = {Precision identification and targeted therapy for neutrophilic asthma: from molecular mechanisms to clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1878339},
pmid = {42488629},
issn = {1664-3224},
mesh = {Humans ; *Asthma/immunology/drug therapy/etiology/diagnosis/metabolism/therapy ; *Neutrophils/immunology/metabolism/drug effects ; *Precision Medicine/methods ; Extracellular Traps/immunology/metabolism ; Animals ; Molecular Targeted Therapy ; Th17 Cells/immunology ; Inflammasomes/metabolism/immunology ; Interleukin-17/metabolism ; Translational Research, Biomedical ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Biomarkers ; },
abstract = {Neutrophilic asthma represents a distinct inflammatory phenotype characterized by sputum neutrophilia (≥61% neutrophils), glucocorticoid resistance, and more severe disease course compared to eosinophilic asthma. This review comprehensively examines the molecular mechanisms underlying neutrophilic asthma pathogenesis, focusing on the Th17/IL-17 axis, neutrophil extracellular traps (NETs), and NLRP3 inflammasome activation. We present a precision identification framework integrating molecular endotypes with clinical phenotypes and biomarker profiles to guide therapeutic decisions. Unlike eosinophilic asthma, neutrophilic asthma demonstrates intrinsic resistance to glucocorticoids due to impaired neutrophil apoptosis and persistent activation of pro-inflammatory pathways. Emerging therapeutic approaches targeting IL-17, NET formation, and inflammasome components show promise, with several agents in clinical development. The microbiome-neutrophil axis represents a novel therapeutic target, with evidence suggesting that airway dysbiosis perpetuates neutrophilic inflammation through pattern recognition receptor activation. This review provides a comprehensive framework for understanding neutrophilic asthma pathogenesis and outlines precision medicine approaches for this difficult-to-treat asthma phenotype.},
}

Humans
*Asthma/immunology/drug therapy/etiology/diagnosis/metabolism/therapy
*Neutrophils/immunology/metabolism/drug effects
*Precision Medicine/methods
Extracellular Traps/immunology/metabolism
Animals
Molecular Targeted Therapy
Th17 Cells/immunology
Inflammasomes/metabolism/immunology
Interleukin-17/metabolism
Translational Research, Biomedical
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
Biomarkers

@article {pmid42488935,
year = {2026},
author = {Whelan, FJ},
title = {How the social lives of bacteria affect their pangenome.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250039},
pmid = {42488935},
issn = {1744-1358},
support = {MR/Y016343/1//UK Research and Innovation (UKRI)/ ; SBF009\1062//Academy of Medical Sciences (The Academy of Medical Sciences)/ ; },
abstract = {Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.},
}

@article {pmid42489221,
year = {2026},
author = {Ishizaka, A and Koga, M and Hayashi, T and Ishii, KJ and Yamamoto, H and Yotsuyanagi, H and Mizutani, T},
title = {Gut Microbiota-Derived Bacterial Extracellular Vesicles in COVID-19: Their Signature and Immunological Impact.},
journal = {Journal of extracellular vesicles},
volume = {15},
number = {7},
pages = {e70341},
doi = {10.1002/jev2.70341},
pmid = {42489221},
issn = {2001-3078},
support = {JP25fk0410076//Japan Agency for Medical Research and Development (AMED)/ ; JP25gm4010025//Japan Agency for Medical Research and Development (AMED)/ ; JP223fa627001//Japan Agency for Medical Research and Development (AMED)/ ; JP223fa727001//Japan Agency for Medical Research and Development (AMED)/ ; JP223fa727002//Japan Agency for Medical Research and Development (AMED)/ ; JP24K11630//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; JP25K15924//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; //Taiju Life Social Welfare Foundation/ ; //Takeda Science Foundation/ ; //Mochida Memorial Foundation for Medical and Pharmaceutical Research/ ; //OTC Self-Medication Promotion Foundation/ ; //Yamaguchi memorial/ ; },
mesh = {Humans ; *Extracellular Vesicles/immunology/microbiology/metabolism ; *COVID-19/immunology/microbiology ; SARS-CoV-2 ; Female ; *Gastrointestinal Microbiome/immunology ; Cytokines/metabolism/immunology ; Male ; Feces/microbiology ; Middle Aged ; Dysbiosis/immunology/microbiology ; Adult ; Monocytes/immunology ; U937 Cells ; *Bacteria/immunology/genetics ; RNA, Ribosomal, 16S/genetics ; Aged ; },
abstract = {Gut microbial dysbiosis has been observed in several diseases. Although causal links and direct effects on host cells remain unclear, bacteria-derived extracellular vesicles (BEVs) from the gut microbiota may regulate the host immune response. We examined the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the gut microbiome and BEVs release, and the effects of released BEVs on cytokine responses in monocyte-derived cell lines. Fecal samples from 17 patients with coronavirus disease 2019 (COVID-19) and 20 healthy individuals were collected to isolate bacterial and BEV fractions. Parental BEV-releasing bacteria were identified from vesicle-encapsulated bacterial DNA by 16S rRNA gene sequencing. Patients with COVID-19 exhibited altered gut microbiota composition and the profile of bacterial DNA-containing BEVs (dcBEVs) release compared to healthy controls. BEVs from patients, but not from healthy individuals, significantly changed cytokine levels in U937 monocyte cells. Following COVID-19 recovery, dcBEV profiles diverged into two distinct groups: those that retained the capacity to induce cytokines in monocytes and those that lost this functionality. BEVs from single bacterial cultures within families altered after COVID-19 onset affected the expression of genes in monocytes, primarily immune-response genes, notably chemokine ligands and G protein-coupled receptors. SARS-CoV-2-induced dysbiosis alters the profile of dcBEVs release, thereby modulating the host immune response and potentially contributing to COVID-19 pathogenesis.},
}

Humans
*Extracellular Vesicles/immunology/microbiology/metabolism
*COVID-19/immunology/microbiology
SARS-CoV-2
Female
*Gastrointestinal Microbiome/immunology
Cytokines/metabolism/immunology
Male
Feces/microbiology
Middle Aged
Dysbiosis/immunology/microbiology
Adult
Monocytes/immunology
U937 Cells
*Bacteria/immunology/genetics
RNA, Ribosomal, 16S/genetics
Aged

@article {pmid42489235,
year = {2026},
author = {Li, M and Cheng, K and Lou, M and Wang, P and Xu, W},
title = {Entropy-Guided Sample-Specific Feature Selection for Robust Incomplete Multi-Omics Learning in Gut Microbiome Disease Prediction and Biomarker Discovery.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261472595},
doi = {10.1177/15578100261472595},
pmid = {42489235},
issn = {1557-8100},
abstract = {The rapid advancement of multi-omics integration facilitates deep insights into complex diseases. However, incomplete modalities, heterogeneity, and high dimensionality hinder robust analysis. To address these limitations, we propose entropy-guided sample-specific feature selection for robust incomplete multi-omics learning (ESSFS-IMO), a novel framework for accurate disease prediction and interpretable biomarker discovery under missing-data conditions. It combines instance-wise feature selection, entropy-adaptive optimization, and variational representation learning. Specifically, a Gumbel-Softmax-based selector performs per-sample differentiable feature selection, guided by an entropy-based annealing strategy that dynamically adjusts selection sharpness. Selected features are integrated via an information-bottlenecked variational backbone with variance-weighted fusion, enabling robust classification despite missing modalities. Experiments on inflammatory bowel disease datasets demonstrate that ESSFS-IMO outperforms state-of-the-art baselines in accuracy, F1-score, and area under the receiver operating characteristic curve. The model maintains high performance across missing patterns and yields biologically coherent biomarkers, effectively linking microbial, transcriptional, and metabolic profiles to immune regulation. In conclusion, ESSFS-IMO provides a robust, interpretable solution for incomplete multi-omics learning. By integrating entropy-guided selection and variational information bottlenecks, it achieves superior predictive power and resilience while identifying meaningful signatures associated with intestinal inflammation, holding promise for broader biomedical applications.},
}

@article {pmid42489317,
year = {2026},
author = {Chen, YY and Shi, YF and Zhang, XY and Zhang, JY and Zhang, SM and Zhao, HX and Liu, DL},
title = {The mediating role of genes in the influence of intestinal flora on type 2 diabetes and the screening of diagnostic markers.},
journal = {Journal of diabetes investigation},
volume = {},
number = {},
pages = {},
pmid = {42489317},
issn = {2040-1124},
support = {SZZYSM202411016//Shenzhen "Three Famous Project" for Medical and Health Development (grant number: SZZYSM202411016)/ ; },
abstract = {INTRODUCTION: The composition of intestinal flora affects the occurrence and development of type 2 diabetes to some extent, with dysregulation of the microbiome being a clinical manifestation of the disease.

METHODS: The key intestinal flora with causal relationship to type 2 diabetes was obtained by mendelian randomization (MR) analysis. Meanwhile, differentially expressed genes (DEGs) were analyzed in the GSE76894 dataset and overlapped with causal genes. The differentially expressed causal genes were screened by machine learning, and diagnostic markers of type 2 diabetes were identified. We also analyzed the expression of diagnostic markers for different cell types using the single-cell data to provide a more reliable basis for disease diagnosis.

RESULTS: The study identified 10 key intestinal flora that were causally linked to type 2 diabetes through MR analysis. Transcriptome-wide association study (TWAS) and cis-expression quantitative trait loci.(eQTL) MR analysis of type 2 diabetes identified 228 genes that were causally linked to type 2 diabetes (|Z score| > 1, P < 0.05). About 20 causal genes were selected by MR analysis of 228 genes and intestinal flora causally related to type 2 diabetes. The diagnostic markers screened by machine learning were verified by the area under the curve (AUC), the results were all >0.7, indicating good diagnostic efficiency. Single-cell analysis suggested that BEND7 was specifically high expression in the control group, and C1orf85 was specifically high expression in samples with type 2 diabetes.

CONCLUSIONS: The study provided a solid theoretical basis for further understanding of the underlying mechanisms of type 2 diabetes pathogenesis and progression.},
}

@article {pmid42489455,
year = {2026},
author = {Aguilar-Rangel, EJ and Lüneberg, K and Medina, DA and Siebe, C and Alcántara-Hernández, RJ and Servín-Garcidueñas, LE},
title = {Metagenomes from untreated wastewater and the soil irrigated with it for 50 years in the Mezquital Valley, Mexico.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0129925},
doi = {10.1128/mra.01299-25},
pmid = {42489455},
issn = {2576-098X},
abstract = {The Mezquital Valley is a unique site for studying the gradual effects of wastewater irrigation on agricultural soils. We report metagenomes from soils irrigated for 50 years and their corresponding irrigation water. Potentially pathogenic bacteria dominated the wastewater, while the soil harbored a diverse community mainly involved in biogeochemical cycling.},
}