@article {pmid42700869,
year = {2026},
author = {Dipa, P and Neha, and Mandal, S and Aran, KR},
title = {Postbiotics as a Therapeutic Target in Cognitive Impairment: Exploring into Molecular Pathways and Neuroprotective Effects.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103353},
doi = {10.1016/j.arr.2026.103353},
pmid = {42700869},
issn = {1872-9649},
abstract = {Cognitive impairment (CI) refers to impairment of cognitive domains that comprise memory, attention, language, and processing speed that exceed normal age-related changes and interfere with daily functions. Its pathophysiology includes neuronal dysfunction of synaptic activity, cerebral hypoperfusion, microglial inflammatory response, oxidative stress, mitochondrial dysregulation, impairment of the blood-brain barrier (BBB), and lipopolysaccharide (LPS). These interconnected mechanisms promote neuroinflammatory responses, impair neuronal connectivity, and gut-brain axis (GBA) balance, thereby contributing to the development and progression of CI. Postbiotics are non-viable microbial cells or structural components with therapeutic potential without live colonisation. They promote synaptic plasticity, reduce oxidative stress and neuroinflammation, enhance BBB integrity, improve mitochondrial activity, and regulate neurotransmitter levels, including serotonin, dopamine, and γ-aminobutyric acid (GABA). Postbiotics can be utilised in CI for their ability to generate bioactive metabolites that enhance gut-brain axis communication, immune modulation, and neuronal and BBB activity. Emerging preclinical evidence indicates that postbiotics modulate key pathological processes, including synaptic plasticity, oxidative stress, neuroinflammation, and BBB integrity; however, the majority of these findings are derived from in vitro and animal models, with limited clinical validation. This review aims to provide a systematic evaluation of the role of postbiotics in the prevention and management of CI across different neurological and metabolic disorders, and to summarise the available preclinical findings with potential therapeutic implications and future directions.},
}

@article {pmid42701161,
year = {2026},
author = {Rocha, GM and Amaral, RS and Bhandari, V},
title = {Epigenetic programming in bronchopulmonary dysplasia: a framework linking early-life exposures to persistent lung disease-a narrative review.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42701161},
issn = {1530-0447},
abstract = {Bronchopulmonary dysplasia (BPD) is the most common chronic pulmonary complication of extreme prematurity in infants, now understood as a disorder of disrupted lung development rather than acute injury alone. Conventional clinical and functional criteria fail to capture the full heterogeneity of outcomes or the persistence of pulmonary morbidity into adulthood. Epigenetic mechanisms-including DNA methylation, histone modifications, and non-coding RNAs-provide a unifying biological framework linking perinatal exposures to long-term lung dysfunction. In the preterm lung, hyperoxia, inflammation, infection, pharmacologic interventions, and microbiome alterations durably influence gene expression without changing the DNA sequence, contributing to impaired alveolarization, pulmonary vascular growth, antioxidant defenses, immune regulation, and cellular senescence. Hyperoxia, specifically, has been associated with lasting epigenetic changes in redox-sensitive pathways, angiogenic signaling, and cell cycle control, while inflammatory stimuli may establish epigenetic "memory" that is consistent with the persistence of chronic inflammation and defective repair. Collectively, these processes support a model in which epigenetically programmed lung phenotypes may emerge, characterized by reduced pulmonary reserve, accelerated lung aging, and heightened vulnerability to respiratory disease across the lifespan. Although evidence for transgenerational inheritance in humans is limited, inherited susceptibility remains plausible, but unproven. Framing BPD as a disorder of biological memory emphasizes the need for epigenetic biomarkers, longitudinal cohort studies, and targeted preventive or therapeutic strategies to improve lifelong outcomes in survivors. IMPACT: This review reframes Bronchopulmonary Dysplasia as a disorder of developmental programming and biological memory, integrating hyperoxia, inflammation, and pharmacologic exposures within a DOHaD-based epigenetic framework to explain long-term pulmonary and systemic heterogeneity. It synthesizes experimental, translational, and clinical evidence-including redox epigenetics, trained immunity, sex-specific responses, and lung-brain-immune interactions-supporting a model in which early-life exposures shape lifelong respiratory and extra-pulmonary outcomes, while acknowledging that some mechanisms remain unproven. It identifies key translational priorities, including validation of epigenetic biomarkers, longitudinal multi-omics studies, and cautious development of epigenetic therapies, while emphasizing current methodological limitations and remaining evidence gaps.},
}

@article {pmid42701266,
year = {2026},
author = {Dollar, AN and Kelley, DW and Webb, IK},
title = {Proteoform-Resolved Cross-Linking Reveals Environment-Dependent Structural Effects of α-Synuclein S129 Phosphorylation.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {34},
pages = {37102-37109},
doi = {10.1021/jacs.6c10987},
pmid = {42701266},
issn = {1520-5126},
support = {R35GM151251/GM/NIGMS NIH HHS/United States ; },
mesh = {*alpha-Synuclein/chemistry/metabolism ; Phosphorylation ; Humans ; *Cross-Linking Reagents/chemistry ; Methylamines/chemistry ; Protein Conformation ; },
abstract = {Intrinsically disordered proteins (IDPs) drive many neurodegenerative disorders, but their structures remain difficult to define because they populate dynamic ensembles that change with the chemical environment. This problem is central for α-synuclein (aSyn), a Parkinson's disease-linked IDP in which S129 phosphorylation is highly enriched in disease-associated aggregates. Although S129 phosphorylation stabilizes a more compact aSyn ensemble in dilute solution, whether this structural effect persists across other biochemical environments has remained unknown. Here, we developed a quantitative cross-linking mass spectrometry framework to determine how WT and pS129 aSyn respond to chemically distinct environments. We compared dilute buffer with two perturbations relevant to aSyn biology: trimethylamine N-oxide (TMAO), a gut-microbiome-derived metabolite associated with Parkinson's disease that can also act as a compacting osmolyte at high concentration, and octyl glucoside (OG) micelles, which provide a membrane-mimetic surface. TMAO rewired the phosphorylation-dependent structural response in a concentration-dependent manner: 1.8 M TMAO shifted WT aSyn toward the dilute pS129 contact pattern by increasing long-range contacts between the N-terminal and C-terminal regions, whereas 3.4 M TMAO collapsed both proteoforms and reduced their structural differences. In OG micelles, the proteoforms diverged. WT favored an extended-helix-like contact pattern with stronger contacts between the C-terminal tail and micelle-bound N-terminal region, whereas pS129 favored contacts between the N-terminal and NAC regions and fewer contacts to the C-terminal tail, consistent with a broken-helix-like topology. By integrating regional contact counts, normalized cross-link intensities, and geometric compatibility analysis, this workflow distinguishes broad contact accessibility from the residue-level contacts that dominate each condition. These results establish a proteoform-by-environment model for IDP structure, in which phosphorylation effects are not fixed but are rewritten by the surrounding chemical environment.},
}

*alpha-Synuclein/chemistry/metabolism
Phosphorylation
Humans
*Cross-Linking Reagents/chemistry
Methylamines/chemistry
Protein Conformation

@article {pmid42701321,
year = {2026},
author = {Harahap, IA and Weber, D and Grune, T},
title = {Non-hormonal strategies for menopausal health: the role of phytoestrogens.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/10408398.2026.2728287},
pmid = {42701321},
issn = {1549-7852},
abstract = {Menopause is characterized by hormonal decline, increasing susceptibility to osteoporosis, cardiovascular disease, cognitive impairment, and metabolic dysfunction. Phytoestrogens, plant-derived bioactive compounds with estrogenic and anti-inflammatory properties, have emerged as potential alternatives to hormone therapy for mitigating these risks. This review critically examines their molecular mechanisms, bioavailability challenges, and clinical applications. Their impact on bone mineral density, cardiovascular function, neuroprotection, and metabolic regulation is evaluated, alongside safety considerations. However, inconsistencies in clinical outcomes underscore the need for standardized dosing strategies and precision-based approaches informed by genetic and microbiome profiling. Beyond clinical utility, their role in sustainable nutrition and global health equity is also considered. By integrating molecular insights with translational applications, phytoestrogens represent a promising, non-hormonal strategy for improving menopausal health.},
}

@article {pmid42701680,
year = {2026},
author = {Jain, A and Saxena, R and Omhare, A and Fatima, A and Saxena, R and Hashmi, SZA and Singh, K and Paul, R},
title = {Microbiological and Histopathological Features of Gynecologic Cancers: A Systematic Review of Current Evidence and Future Directions.},
journal = {Cureus},
volume = {18},
number = {8},
pages = {e114047},
pmid = {42701680},
issn = {2168-8184},
abstract = {Gynecologic cancers are a diverse group of malignancies with distinct microbiological, histopathological, and molecular characteristics. This systematic review examined the available evidence on these features in gynecologic cancers and premalignant lesions. A total of 46 studies involving 18,742 patients or samples were included. Because the studies differed considerably in design, sampling methods, laboratory techniques, histopathological classification, and reported outcomes, the findings were synthesized narratively. The strongest and most consistent evidence was found for persistent high-risk human papillomavirus (HPV) infection, particularly HPV-16 and HPV-18, in cervical cancer and other lower genital tract neoplasms. Cervicovaginal dysbiosis, marked by reduced Lactobacillus dominance, increased microbial diversity, and anaerobic bacterial overgrowth, was frequently associated with HPV persistence and higher-grade cervical lesions. However, current evidence suggests that dysbiosis acts as a contributing factor rather than an independent cause of malignancy. Histopathology remained central to tumour diagnosis, classification, and risk assessment. Squamous cell carcinoma was the predominant histological type in cervical, vulvar, and vaginal cancers. Endometrioid adenocarcinoma was commonly reported in endometrial cancer, while high-grade serous carcinoma was the main ovarian cancer subtype. Evidence regarding uterine, endometrial, and ovarian tumour-associated microbiota was limited and exploratory because of low microbial biomass, methodological variation, and the risk of contamination. Combining microbiological findings with histopathological and molecular classification may improve understanding of gynecologic carcinogenesis and support future risk-stratification approaches. Standardized sampling, strict contamination control, and well-designed longitudinal studies are needed before microbiome-based markers can be introduced into routine clinical practice.},
}

@article {pmid42701704,
year = {2026},
author = {Maleha, M},
title = {Linking oral microbiome with mental health: A review.},
journal = {Bioinformation},
volume = {22},
number = {6},
pages = {3667-3672},
pmid = {42701704},
issn = {0973-2063},
abstract = {The gut microbiome shapes depression and anxiety, yet the oral microbiome that seeds it daily remains overlooked. Therefore, it is of interest to review on the oral microbiome's role in the gut-brain axis. A reproducible signature emerges: enriched Prevotella with depleted Haemophilus and Rothia. Four pathways connect a dysbiotic mouth to the brain inflammation, bacterial translocation, neurotransmitter signalling and HPA-axis dysregulation. As adults see hygienists more than any other clinician, dental visits could screen, prevent and refer along this axis.},
}

@article {pmid42701924,
year = {2026},
author = {Zhao, B and Li, M and Liu, D and Liu, C and Jiang, J and Han, X and Song, C and Liu, Y},
title = {Polyglutamic acid-functionalized carbon dots enhance cadmium tolerance in Houttuynia cordata through coordinated regulation of physiological responses, gene expression and the rhizosphere microbiome.},
journal = {Plant cell reports},
volume = {45},
number = {10},
pages = {},
pmid = {42701924},
issn = {1432-203X},
support = {32102420//National Natural Science Foundation of China/ ; 2021M700739//the China Postdoctoral Science Foundation/ ; YQ2021C014//the Natural Science Foundation of Heilongjiang Province/ ; rc372307//Talent Introduction Project of Anhui Agricultural University/ ; },
mesh = {*Cadmium/toxicity/metabolism ; Carbon Quantum Dots/chemistry ; Rhizosphere ; *Polyglutamic Acid/chemistry/pharmacology ; *Houttuynia/drug effects/physiology/genetics/microbiology/metabolism ; Gene Expression Regulation, Plant/drug effects ; *Microbiota/drug effects ; Photosynthesis/drug effects ; Reactive Oxygen Species/metabolism ; },
abstract = {polyglutamic acid-functionalized carbon dots improve Cadmium tolerance in Houttuynia cordata by reducing Cadmium accumulation, restoring physiological functions, and reshaping rhizosphere microbial communities. Cadmium (Cd) pollution significantly inhibits the growth and development of H. cordata and poses a serious threat to the safe production of this medicinal plant. In this study, polyglutamic acid-functionalized carbon dots (PGA-CDs) were synthesized by the hydrothermal method, and the mechanism of their role in alleviating Cd stress in H. cordata was systematically investigated. The results showed that compared with the Cd group, the biomass of H. cordata in the Cd+PGA-CDs group significantly increased, and the Cd[2+] concentration in the plant decreased. At the same time, PGA-CDs effectively removed reactive oxygen species and regulated the activity of related antioxidant enzymes to alleviate oxidative damage. Moreover, PGA-CDs significantly alleviated the damage to the ultrastructure of chloroplasts caused by Cd stress and enhanced the photosynthetic capacity of the plants. Transcriptome analysis indicated that PGA-CDs treatment significantly changed the expression patterns of genes related to photosynthesis, secondary metabolism, lipid metabolism, and signal response, and regulated the expression of multiple transcription factors and genes related to metal ion homeostasis and transport. Additionally, PGA-CDs increased the α diversity of the rhizosphere microbial community and promoted the enrichment of microbial groups related to plant symbiosis or environmental adaptation, such as the Pseudomonadota, Bacteroidota and Verrucomicrobiota. Through integrated analysis, it further revealed the potential synergistic relationship between gene expression changes, rhizosphere microbial composition, and plant physiological indicators. This study provides new insights into the use of nanomaterials to enhance the adaptability of plants to heavy metals stress.},
}

*Cadmium/toxicity/metabolism
Carbon Quantum Dots/chemistry
Rhizosphere
*Polyglutamic Acid/chemistry/pharmacology
*Houttuynia/drug effects/physiology/genetics/microbiology/metabolism
Gene Expression Regulation, Plant/drug effects
*Microbiota/drug effects
Photosynthesis/drug effects
Reactive Oxygen Species/metabolism

@article {pmid42702090,
year = {2026},
author = {Zayen, A and Sayadi, S and Tedetti, M and Taba, H and Sammari, C and Mhiri, N and Fauvelle, V and Sempéré, R and Karray, F},
title = {Time-driven plastisphere: Temporal dynamics shape the marine microplastic microbiome under natural field conditions.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108390},
doi = {10.1016/j.marenvres.2026.108390},
pmid = {42702090},
issn = {1879-0291},
abstract = {Microplastics (MPs) are well-recognized as vectors for microbial colonization, forming complex biofilms known as the plastisphere. In this study, we investigated the colonization of four common plastic polymers, namely Linear Low Density Polyethylene (LLDPE), Polyethylene Terephthalate (PET), Polystyrene (PS), and Polyvinyl Chloride (PVC) with an average size range of 3.2-4.1 mm by marine microorganisms under natural shallow coastal water column conditions (∼2 m depth) near the fishing port of Gabès, in southeastern Tunisia (Gulf of Gabès, southern Mediterranean Sea). Biofilms were monitored over 7, 30, and 90 days using 16S rRNA gene amplicon sequencing to assess the simultaneous effect of exposure time and polymer type. Temporal succession emerged as the dominant driver of plastisphere composition, with PERMANOVA revealing that exposure time explained 58% of the total community variance (p = 0.001), while polymer type accounted for 15% (p = 0.001). Distance-based redundancy analysis (db-RDA) further demonstrated that this successional trajectory was closely associated with seasonal environmental shifts. Proteobacteria, Campylobacterota, Bacteroidota, and Actinobacteriota dominated the plastisphere, with Rhodobacteraceae, Saprospiraceae, and Flavobacteriaceae consistently established throughout. Putative hydrocarbonoclastic and plastic-associated taxa were detected at different stages of biofilm development, alongside organisms promoting biofilm cohesion. PET supported the most diverse biofilm, harboring approximately 2400 ASVs, including nearly 900 unique ASVs, after three months of exposure, whereas PVC hosted the most distinct microbial communities.},
}

@article {pmid42702184,
year = {2026},
author = {Bilal, M and Abideen, ZU and Murtaza, N and Abbas, B and Rasheed, H and Yar, MS and Ramadan, MF and Ghazali, MH},
title = {Pigmented cereals as functional food systems: Linking phytochemistry, processing, and health.},
journal = {Food chemistry},
volume = {528},
number = {},
pages = {151014},
doi = {10.1016/j.foodchem.2026.151014},
pmid = {42702184},
issn = {1873-7072},
abstract = {This review combines the chemistry, processing and health-related aspects of anthocyanins in a single structure-processing function paradigm, limited to wheat, rice and maize, and evaluates the in vitro to human evidence in a logical framework. These compounds exhibit cereal-specific structural signatures: cyanidin-3-glucoside predominates across cereals like wheat, while maize displays the most complex glycosylation and acylation patterns. Preclinical and limited human evidence link pigmented cereal consumption to improved glycemic modulation (via inhibition of carbohydrate-digesting enzymes), enhanced insulin sensitivity, attenuation of NF-κB-mediated inflammation, and activation of Nrf2 antioxidant pathways; neuroprotective associations are so far supported almost exclusively by cell and animal models. However, the inherent instability of anthocyanins during milling, thermal processing, and cooking substantially compromises bioactivity. Emerging strategies, including encapsulation, superheated steam treatment, and fermentation, offer promising routes to enhance pigment stability and bioaccessibility. Addressing critical gaps in methodological standardization, human intervention studies, and microbiome-mediated metabolism is essential to advance pigmented cereals as functional food ingredients. Future research should prioritize integrated multi-omics approaches and personalized nutrition strategies to fully elucidate the health potential of these cereals across diverse populations.},
}

@article {pmid42702245,
year = {2026},
author = {Dremuk, IA and Smolensky, IV},
title = {Biological mechanisms underlying avoidant/restrictive food intake disorder (ARFID).},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.09.002},
pmid = {42702245},
issn = {1873-7544},
abstract = {Avoidant/restrictive food intake disorder (ARFID) is a complex eating disorder characterized by persistent avoidance or restriction of food intake that is not driven by concerns about body weight or shape. ARFID is characterized by an extremely low food intake and may be driven by sensory aversions to certain foods, a low interest in food, and/or traumatic experiences related to food intake, leading to avoidance. Although ARFID has a number of specific criteria and symptoms, many aspects of its diagnosis, development, and treatment remain unclear. In this narrative review, we summarize the available evidence on molecular, cellular, and neurobiological mechanisms potentially underlying the core manifestations of ARFID, including food avoidance and restriction, sensory-based food aversion, and fear of aversive consequences. The potential mechanisms discussed include altered sensory processing, dysregulation of hunger and satiety signals, conditioned taste aversion and other forms of associative learning, alterations in the microbiome-gut-brain axis, immune mechanisms, and genetic factors. Because direct evidence from ARFID populations remains limited, we also consider findings from related but diagnostically distinct conditions and phenotypes, including picky or selective eating, food neophobia, and sensory food aversion. Such findings may provide insights into mechanisms relevant to ARFID but cannot be assumed to be specific to the disorder. By integrating evidence across these biological domains, this review aims to identify potential mechanisms underlying the heterogeneous manifestations of ARFID and highlight priorities for future research.},
}

@article {pmid42702307,
year = {2026},
author = {Vázquez de Aldana, BR and Arellano, JB and Morcuende, R and Vicente, R and Vega, C and González, G and Sotomayor-Alge, A and Lanati, M and Zabalgogeazcoa, I},
title = {Context-dependent responses of Festuca rubra subsp. pruinosa to salinity, nutrient availability, and Epichloë festucae.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {113433},
doi = {10.1016/j.plantsci.2026.113433},
pmid = {42702307},
issn = {1873-2259},
abstract = {Festuca rubra subsp. pruinosa is a maritime grass native to sea cliffs, a habitat characterized by high salinity and low nutrient availability. This species forms symbiotic associations with Epichloë festucae, a vertically transmitted endophytic fungus that colonizes aerial tissues. Two experiments evaluated whether E. festucae influences the salinity tolerance of its host. In Experiment 1, symbiotic and non-symbiotic plants were irrigated with saline solution or tap water, whereas Experiment 2 additionally included fertilization. In both experiments, unfertilized symbiotic plants exhibited the highest leaf biomass under saline conditions, whereas in the absence of salinity they showed the lowest biomass. Fertilized symbiotic plants produced less biomass than non-symbiotic ones. Spectral vegetation indices further suggested that symbiosis effects on plant performance under salinity depended strongly on nutrient availability and that its occurrence enhanced fertilized plants resilience to salinity. Overall, these results indicate that the symbiosis between Festuca rubra subsp. pruinosa and Epichloë festucae is context-dependent, conferring benefits under saline and nutrient-poor conditions characteristic of its natural habitat. Regardless of endophyte presence, plant growth was either enhanced or unaffected by salinity, demonstrating the high salt tolerance of Festuca rubra subsp. pruinosa. Salinity increased foliar concentrations of Na, photosynthetic pigments, proline, glycine betaine, glucose, fructose, and sucrose. Additionally, salinity increased the leaf concentration of the fungal alkaloid ergovaline, which was also detected in roots. Anatomical observations revealed a nearly tubular leaf morphology with a thick epicuticular wax layer and stomata confined to the inner adaxial surface, traits likely associated with osmotic stress tolerance.},
}

@article {pmid42702387,
year = {2026},
author = {Yu, L and Wu, M and Zheng, X},
title = {[Gut microbiota and allergic diseases].},
journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences},
volume = {51},
number = {6},
pages = {1272-1279},
doi = {10.11817/j.issn.1672-7347.2026.260103},
pmid = {42702387},
issn = {1672-7347},
mesh = {Humans ; *Hypersensitivity/microbiology/immunology ; *Gastrointestinal Microbiome/immunology/physiology ; Dysbiosis/immunology ; Immune Tolerance ; Dermatitis, Atopic/microbiology ; Asthma/microbiology/immunology ; Animals ; Th2 Cells/immunology ; },
abstract = {Incidence of allergic diseases continues to increase, particularly among children, and has become an important public health concern. As a key link connecting environmental exposure, immune development, and susceptibility to allergic diseases, the gut microbiota has emerged as an important focus of related research. The gut microbiota plays a crucial role in immune system maturation during early life, establishment of immune tolerance, and maintenance of mucosal barrier integrity. Gut dysbiosis may contribute to the occurrence and progression of allergic diseases through multiple mechanisms, including reduced metabolite production, promotion of Th2-type immune skewing, impaired T-cell induction, and disruption of epithelial barrier function. Furthermore, the gut microbiota participates in allergic disease development through the "gut-skin axis" "gut-nose axis", and "gut-lung axis". Although different allergic phenotypes exhibit distinct clinical manifestations, they share certain common characteristics, including reduced microbial diversity, depletion of key commensal bacteria, and insufficient immune tolerance. Investigation of gut microbiota and metabolic characteristics in patients with allergic diseases, as well as their roles and clinical implications in disease pathogenesis, may provide a theoretical basis for early prevention, risk identification, and precision microbiome-based interventions for allergic diseases.},
}

Humans
*Hypersensitivity/microbiology/immunology
*Gastrointestinal Microbiome/immunology/physiology
Dysbiosis/immunology
Immune Tolerance
Dermatitis, Atopic/microbiology
Asthma/microbiology/immunology
Animals
Th2 Cells/immunology

@article {pmid42702405,
year = {2026},
author = {Šulčius, S and Kuznecova, J and Kasperovičienė, J and Alzbutas, G and Šimoliūnas, E and Voss, M and Jürgens, K and Dziga, D},
title = {Cyanophage lysis reshapes nitrogen cycling and microbiome composition in diazotrophic cyanobacterium Aphanizomenon flos-aquae.},
journal = {Harmful algae},
volume = {159},
number = {},
pages = {103186},
doi = {10.1016/j.hal.2026.103186},
pmid = {42702405},
issn = {1878-1470},
mesh = {*Aphanizomenon/virology/metabolism/physiology/genetics ; *Bacteriophages/physiology ; *Microbiota ; Nitrogen Fixation ; *Nitrogen Cycle ; Nitrogen/metabolism ; },
abstract = {Although it is presumed that viruses play a significant role in nutrient cycling and bacterial community dynamics, this has only rarely been addressed in studies of diazotrophic cyanobacteria. In this study, we therefore examined how cyanophage infection affects the expression of nitrogen (N) cycling genes, N2 fixation rates, and population structure in the diazotrophic cyanobacterium Aphanizomenon flos-aquae, a prevalent bloom-forming species in temperate brackish and freshwater ecosystems. We also assessed the influence of A. flos-aquae lysis on co-occurring bacterial assemblages throughout an incubation experiment. We found that nitrogen fixation, its release, and the relative availability of different nitrogen forms (e.g. ammonium versus nitrate/nitrite) varied substantially during cyanophage infection, population lysis, and recovery phases. Interestingly, resistant A. flos-aquae subpopulation emerged during viral infection, showed increased expression of N fixation (e.g. nitrogenase (nifH) and heterocyst differentiation regulator (hetR)) and assimilation (e.g. glutamine (glnA) and glutamate (gltB) synthase) genes, as well as higher cell-specific N2 fixation rates. These changes were accompanied by a fast recovery of A. flos-aquae population structure (e.g. filament length and heterocyte-to-vegetative cell ratio) to pre-infection level, indicating A. flos-aquae ability to quickly compensate for short-term population decline. Lysis of the cyanobacterial host significantly altered the successional trajectory and increased diversification of the co-occurring bacterial community. The compositional changes corresponded well with the prevalent inorganic nitrogen form, implying a substantial, nitrogen-driven reorganization of the microbial network and its interactions within the A. flos-aquae microbiome. This study improves our understanding of nitrogen cycling and microbial dynamics within cyanobacteria-driven communities disturbed by viral infections and lysis.},
}

*Aphanizomenon/virology/metabolism/physiology/genetics
*Bacteriophages/physiology
*Microbiota
Nitrogen Fixation
*Nitrogen Cycle
Nitrogen/metabolism

@article {pmid42702416,
year = {2026},
author = {Glibert, PM and Heil, CA and Hall, ER and Fei, C and Amin, SA},
title = {Red tides, blue holes, and the importance of groundwater and terrestrial sources of nutrients fueling blooms of Karenia brevis.},
journal = {Harmful algae},
volume = {159},
number = {},
pages = {103208},
doi = {10.1016/j.hal.2026.103208},
pmid = {42702416},
issn = {1878-1470},
mesh = {*Groundwater/chemistry ; Gulf of America ; Florida ; *Dinoflagellida/physiology ; *Harmful Algal Bloom ; Denitrification ; Nitrogen Isotopes/analysis ; Microbiota ; Nutrients ; },
abstract = {Blooms of Karenia brevis occur almost annually in the eastern Gulf of Mexico (Gulf of America). Submarine ground water discharges (SGD) have been previously suggested as a potential nutrient source in sustaining blooms. The West Florida Shelf is dotted with blue holes, or underwater sinkholes, which may be a route by which SGD seeps into offshore waters. Previously reported measurements within the holes demonstrated potentially high rates of denitrification, and dissimilatory nitrate reduction to ammonia (DNRA). Here, multiple water column stations were monitored monthly for four years near to-and away from-these sinkholes to assess the nitrogen (N) isotopic signatures of the particulate material. One offshore site, but not others, had mean δ[15]N values of 13.28 in surface samples and 12.58 in bottom samples, with the highest value reaching 38.86, reflecting highly processed N. Other sites had much lower δ[15]N values. Higher δ[15]N values were associated with lower river flows, as N would have a longer time to undergo processing. The microbiome of the free-living (>0.22 μm) planktonic communities of this site, examined via 16S rRNA amplicon sequencing, confirmed the presence of putative denitrifying bacteria. Following Hurricane Ian, a K. brevis bloom formed with low δ[15]N (<5), but as the bloom was sustained, the δ[15]N of the particulate material increased significantly, reflecting greater reliance on recycled N. Historical reports of Karenia within 10 km of known blue holes show that K. brevis can concentrate in these locations, which may be hot spots for a diversity of Karenia species.},
}

*Groundwater/chemistry
Gulf of America
Florida
*Dinoflagellida/physiology
*Harmful Algal Bloom
Denitrification
Nitrogen Isotopes/analysis
Microbiota
Nutrients

@article {pmid42702754,
year = {2026},
author = {Sengupta, S and Ghorai, S and Bose, S and Hazra, S and Mukhopadhyay, A and Majumdar, A and Roychowdhury, T},
title = {Integrating Plant Physiology and Microbiome Engineering for Climate-Resilient Crops: Bridging Knowledge Gaps in Multi-Stress Tolerance.},
journal = {Physiologia plantarum},
volume = {178},
number = {5},
pages = {e71088},
doi = {10.1111/ppl.71088},
pmid = {42702754},
issn = {1399-3054},
mesh = {*Crops, Agricultural/physiology/microbiology ; *Stress, Physiological/physiology ; *Microbiota/physiology ; Climate Change ; *Plant Physiological Phenomena ; },
abstract = {Climate change is intensifying the frequency and co-occurrence of abiotic and biotic stresses, posing significant challenges to global crop productivity and stability. Conventional approaches based on single-stress responses are increasingly insufficient for addressing complex field environments where plants experience multiple simultaneous stresses. This review synthesizes current knowledge on plant physiological responses, microbiome interactions, and emerging technological interventions to develop an integrative framework for climate-resilient agriculture. It highlights how stress perception, hormonal regulation, metabolic adjustments, and epigenetic mechanisms collectively shape plant adaptation under multi-stress conditions. The review further examines the role of plant-associated microbiomes in enhancing nutrient acquisition, regulating stress signaling, and improving resilience through mechanisms such as phytohormone modulation, antioxidant activity, and induced systemic resistance. Advances in microbiome engineering, including synthetic microbial communities and computational prediction frameworks, are discussed as promising strategies for improving stress tolerance. In addition, emerging tools such as nanotechnology-assisted delivery systems and biosensing platforms are considered for precision management of plant-microbe systems. By identifying critical knowledge gaps in multi-stress physiology, microbiome assembly, and field-level predictability, this review proposes an interdisciplinary approach that integrates plant physiology, microbial ecology, and technological innovations to support sustainable crop production under changing climatic conditions.},
}

*Crops, Agricultural/physiology/microbiology
*Stress, Physiological/physiology
*Microbiota/physiology
Climate Change
*Plant Physiological Phenomena

@article {pmid42702815,
year = {2026},
author = {Qiao, Y and Wang, T and Zhang, H and Xu, Q and Ruan, Y and Shen, Q and Ling, N},
title = {Decoding microbial metabolic complementarity from individual traits to community structuring.},
journal = {Ecology},
volume = {107},
number = {9},
pages = {e70474},
doi = {10.1002/ecy.70474},
pmid = {42702815},
issn = {1939-9170},
support = {32302670//National Nature Science Foundation of China/ ; },
mesh = {*Bacteria/metabolism/genetics/classification ; Models, Biological ; *Microbiota/physiology ; Citrullus/microbiology ; },
abstract = {A fundamental challenge in microbiome research lies in elucidating the functional capacity of microbial communities through community membership and genomic data. As community structuring and emergent functional traits are determined by bacterial community metabolic networks, it is important to gain insights into the principles that govern bacteria-bacteria interactions. Here, we applied an integrative framework linking individual strain-level traits to community structuring in a simplified synthetic bacterial community (SSC8) that promotes the growth of ungrafted watermelon. By combining mono- and coculture assays with genome-scale metabolic modeling and metabolomic profiling of spent media, we characterized directional interactions and resource dependencies among community members. Our findings show that positive interactions dominated the community network, accounting for 55% of all pairwise combinations, indicating a high prevalence of growth-promoting effects among strains. Genome-scale metabolic modeling showed that functional divergence among strains enhanced the potential for metabolic complementarity as phylogenetic distance increased. Integrating metabolic modeling with metabolomics further suggested that Pseudomonas azotifigens Q6 not only benefited from all other community members, but also exhibited mutualistic interactions with the other three strains, with metabolite exchange involving compounds such as L-lysine and L-cysteine. Pseudomonas azotifigens Q6 acted as an important driver of community composition by affecting the abundance of several other consortium members in vitro. These findings highlight the role of metabolic complementarity in driving community structuring by promoting selective persistence of specific strains. Our work provides mechanistic insights into microbial interaction networks in vitro and offers a conceptual foundation for the rational design of functionally robust and plant-beneficial microbiomes.},
}

*Bacteria/metabolism/genetics/classification
Models, Biological
*Microbiota/physiology
Citrullus/microbiology

@article {pmid42702821,
year = {2026},
author = {Zaidan, N and Jaber, K and Ho, M and Zhou, B and Pei, Z and Bui, ML and Cardozo, L and Merritts, K and Mishra, R and Xiong, X and Kim, Y and Wu, M and Knight, J and Fargue, S and Li, H and Nazzal, L},
title = {Determinants of enteric hyperoxaluria in the SAMP1/YitFc mouse model of spontaneous ileitis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725367},
doi = {10.1080/19490976.2026.2725367},
pmid = {42702821},
issn = {1949-0984},
mesh = {Animals ; *Hyperoxaluria/metabolism/microbiology/physiopathology ; Mice ; Disease Models, Animal ; *Ileitis/microbiology/metabolism ; Gastrointestinal Microbiome ; Oxalates/metabolism/urine ; Permeability ; Intestinal Barrier Function ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Mice, Inbred AKR ; Feces/chemistry ; Ileum ; Diet, High-Fat/adverse effects ; Kidney/pathology ; },
abstract = {Enteric hyperoxaluria (EH) results from increased oxalate bioavailability in the gastrointestinal (GI) tract, often affecting patients with inflammatory bowel disease (IBD). We investigated the pathophysiology of EH in an ileitis mouse model, hypothesizing that fat malabsorption, increased gut permeability, and microbial shifts collectively contribute to the hyperoxaluric phenotype in the setting of GI tract inflammation. SAMP1/YitFc (SAMP1) mice and their parental AKR controls were fed one of three diets varying in fat content (10%, 45%, or 60% kcal), each supplemented with 1% oxalate, for 6 weeks. Plasma (P), urine (U), oxalate (Ox), and creatinine (Cr) levels were measured, while stool lipid species were analyzed using mass spectrometry. Intestinal permeability was assessed using sucralose and [13]C2 oxalate gastric gavage in SAMP1 and AKR mice. Histology, qPCR, and Western blotting were performed on kidney, liver, and GI tissues. Microbial DNA was analyzed at the community, genus, and functional levels. Changes in bacterial metabolic pathways were investigated in the mice fed the highest fat content. The oxalobiome of SAMP1 and AKR mice was characterized using our bioinformatics pipeline. On high-fat diets, SAMP1 mice had higher UOx, POx, and PCr levels than AKR mice. Increased levels of diacylglycerols and free fatty acids in SAMP1 stool samples suggested fat malabsorption. A decrease in ZO1 and occludin intestinal expression, coupled with significantly increased urinary sucralose and oxalate levels, indicated increased intestinal permeability. Microbiome analysis revealed the enrichment of Lactobacilli and Bacteroides in SAMP1 mice, with bacterial pathways favoring lipid synthesis and glyoxylate metabolism. Ileal SLC26A6 protein expression was significantly reduced in SAMP1 mice. SAMP1 mice also developed progressive kidney injury with interstitial inflammation. These findings highlight fat malabsorption as a central pathophysiologic disturbance in EH that reduces luminal calcium availability for oxalate binding, is associated with enhanced intestinal permeability, and accompanies microbiome and enzymatic pathway alterations.},
}

Animals
*Hyperoxaluria/metabolism/microbiology/physiopathology
Mice
Disease Models, Animal
*Ileitis/microbiology/metabolism
Gastrointestinal Microbiome
Oxalates/metabolism/urine
Permeability
Intestinal Barrier Function
Male
Bacteria/classification/genetics/isolation & purification/metabolism
Mice, Inbred AKR
Feces/chemistry
Ileum
Diet, High-Fat/adverse effects
Kidney/pathology

@article {pmid42702911,
year = {2026},
author = {Sievert, EDC and Eitze, S and Betsch, C},
title = {Do individual or societal consequences matter more? Reducing antibiotic expectations for uncomplicated urinary tract infections in females.},
journal = {British journal of health psychology},
volume = {31},
number = {3},
pages = {e70109},
doi = {10.1111/bjhp.70109},
pmid = {42702911},
issn = {2044-8287},
support = {BE 3970/8-2//Deutsche Forschungsgemeinschaft/ ; Leibniz Best Minds Program 106/2020//Leibniz-Gemeinschaft/ ; },
mesh = {Humans ; Female ; *Urinary Tract Infections/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Adult ; Trust ; Decision Making ; *Physician-Patient Relations ; United Kingdom ; Middle Aged ; Young Adult ; },
abstract = {OBJECTIVES: Antimicrobial resistance (AMR) is an urgent public health threat. Antibiotic prescriptions in primary care, such as for uncomplicated urinary tract infections (UTIs) in females, contribute substantially to antibiotic overuse. We examined whether consequence-based risk communication emphasizing either individual (gut microbiome disruption) or societal (AMR) consequences can reduce expectations to receive antibiotics and improve decision-related outcomes.

DESIGN AND METHODS: Across three online experiments (N = 3057), women in the United Kingdom were exposed to a hypothetical physician consultation for an uncomplicated UTI. Depending on the experimental condition, the physician explained individual consequences of antibiotic use, societal consequences or no such consequences. Outcomes included expectations to receive antibiotics, trust in the physician and decisional conflict.

RESULTS: An internal meta-analysis showed that both societal and individual consequence messages significantly reduced patients' expectations to receive antibiotics. Neither message type undermined trust in the physician (in Studies 1 and 2), and both communication messages significantly reduced decisional conflict (in Study 3).

CONCLUSIONS: These findings indicate that brief, targeted communication regarding consequences of antibiotic use can lower antibiotic expectations and support decision-making without eroding physician trust. Such messages represent a useful tool that can be adapted to different clinical contexts for patient-centred antibiotic stewardship in primary care.},
}

Humans
Female
*Urinary Tract Infections/drug therapy
*Anti-Bacterial Agents/therapeutic use
Adult
Trust
Decision Making
*Physician-Patient Relations
United Kingdom
Middle Aged
Young Adult

@article {pmid42702945,
year = {2026},
author = {Szelest, M and Zaleska, J and Kiełbus, M and Paziewska, M and Masternak, M and Wawrzyniak, E and Kotkowska, A and Siemieniuk-Ryś, M and Morawska, M and Kalicińska, E and Jabłonowska-Babij, P and Wróbel, T and Wolska-Washer, A and Błoński, JZ and Robak, T and Giannopoulos, K},
title = {Predicted microbiome-associated metabolic pathways are linked to immune checkpoint modulation in chronic lymphocytic leukaemia.},
journal = {British journal of haematology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bjh.70797},
pmid = {42702945},
issn = {1365-2141},
support = {2018/29/B/NZ5/02706//Narodowe Centrum Nauki/ ; PBsd250//Uniwersytet Medyczny w Lublinie/ ; },
abstract = {Microbial metabolites are key regulators of host immunity, yet their functional impact in chronic lymphocytic leukaemia (CLL) remains unclear. Following up on our earlier observations of microbiome dysbiosis in CLL, we performed predictive metabolic profiling based on 16S ribosomal RNA (rRNA) sequencing of oral and stool samples collected from 81 newly diagnosed CLL patients and 21 healthy volunteers (HVs). Comparative analysis revealed a broad reduction in predicted microbial functional potential in advanced disease, affecting pathways related to short-chain fatty acids (SCFAs) production, carbohydrate and carboxylate degradation and fatty acid biosynthesis. Similar SCFA-associated alterations were observed in oral samples, which additionally exhibited broader suppression of nucleotide and cofactor biosynthesis pathways. To explore the functional consequences of the predicted reduction in SCFA-related pathways, peripheral blood mononuclear cells from 18 CLL patients were treated ex vivo with sodium butyrate (SB). SB treatment modulated immune checkpoint expression, increasing CD8+ T-cell proportions and programmed cell death protein 1 (PD-1) levels while significantly reducing T cell immunoreceptor with Ig and ITIM domains (TIGIT) expression across CD8+, CD4+ and total CD3+ T cells. SB also decreased TIGIT levels in leukaemic CD5+CD19+ B cells. Overall, these findings demonstrate consistent alterations in predicted microbiome-derived metabolic pathways across oral and gut niches in CLL and suggest a potential functional association between microbial metabolic activity and immune regulation.},
}

@article {pmid42702966,
year = {2026},
author = {Broadribb, M and Thomas, T and Rogers, A and Bell, JJ},
title = {Induced Dysbiosis Modifies Physiological Responses to Warming in a Temperate Sponge.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70402},
doi = {10.1111/1462-2920.70402},
pmid = {42702966},
issn = {1462-2920},
support = {//Victoria University of Wellington/ ; //George Mason Charitable Trust/ ; },
mesh = {Animals ; *Porifera/microbiology/physiology ; *Microbiota/drug effects ; Symbiosis ; Hot Temperature ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification/drug effects ; *Dysbiosis ; Climate Change ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; },
abstract = {Marine sponges host complex and specific microbiomes, yet the role of these microbial symbionts in sponge responses to acute environmental stress is not fully understood. We investigated how altering the microbiome influences physiological responses to temperature in the temperate calcareous sponge Rowella lancifera under simulated marine heatwave (MHW) conditions. Sponges were treated with broad-spectrum antibiotics to disrupt their microbiome and then exposed to sub-lethal MHW temperatures. Microbial community composition was analysed using 16S rRNA gene sequencing, including assessing diversity and differential abundance, while sponge physiological response to temperature was quantified via respiration rates. Antibiotic treatment significantly altered microbial community structure but did not independently induce a physiological response. Heat exposure increased respiration rates, with a stronger response observed in microbiome-altered sponges. Multivariate analyses revealed a relationship between microbial community structure and respiration rate, suggesting an association between microbiome composition and host physiological responses. Overall, these findings indicate that sponge-microbe symbioses may play a role in modulating physiological responses to increased temperatures. As MHWs become more frequent and severe under climate change, understanding sponge-microbe partnerships will be important for predicting responses of sponges and the stability of benthic ecosystems.},
}

Animals
*Porifera/microbiology/physiology
*Microbiota/drug effects
Symbiosis
Hot Temperature
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification/drug effects
*Dysbiosis
Climate Change
Anti-Bacterial Agents/pharmacology
Ecosystem

@article {pmid42702999,
year = {2026},
author = {P K, AK and C, VN and Sunkar, S},
title = {Unveiling the Molecular Secrets of Seaweeds: A Comprehensive Review of Bioinformatics Applications in Algal Research.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261484211},
doi = {10.1177/15578100261484211},
pmid = {42702999},
issn = {1557-8100},
abstract = {Recent advances in high-throughput sequencing, bioinformatics, and multi-omics technologies have transformed seaweed research by overcoming long-standing challenges associated with complex genomes, diverse life cycles, and limited genomic resources. This review provides a comprehensive overview of bioinformatics approaches used to investigate seaweed genomics, transcriptomics, proteomics, metabolomics, microbiomes, and functional genomics, with emphasis on the computational tools and databases that support these analyses. Applications of bioinformatics in phylogenetics, drug discovery, microbiome characterization, and the development of biofuels, nutraceuticals, pharmaceuticals, and sustainable agriculture are also discussed. Particular attention is given to emerging strategies involving multi-omics integration, genome editing, artificial intelligence, machine learning, and synthetic biology that are reshaping seaweed research. The review further examines current challenges, including incomplete genomic resources, data standardization, and the need for experimental validation of computational predictions. Collectively, these advances highlight the growing role of bioinformatics in enabling systems-level understanding of seaweed biology and accelerating their translation into sustainable biotechnological and marine bioeconomy applications.},
}

@article {pmid42703211,
year = {2026},
author = {Yoo, JY and Ravi, K and Sarkar, A and Lau, C and Osborn, C and Groer, M},
title = {Adverse Childhood Experiences: Biological Signatures of Stress.},
journal = {Journal of child & adolescent trauma},
volume = {19},
number = {3},
pages = {1545-1557},
pmid = {42703211},
issn = {1936-1521},
abstract = {Adverse Childhood Experiences (ACEs) are strongly associated with an increased risk of major chronic diseases in adulthood. Early exposure to adversity imposes a toxic stress load that disrupts stress physiology, immune responses, brain development, and behavior. These alterations accumulate across the lifespan, contributing to elevated risks of chronic disease, mental illness, and premature mortality. Although many studies have examined associations between ACEs and biological markers using diverse methods, the evidence remains fragmented, and potential pathways to later outcomes are not well integrated. This gap limits our ability to delineate shared risk processes and to design coordinated preventive and therapeutic interventions. This narrative review paper focuses on a potential stress mechanism and biomarkers associated with ACEs, particularly those associated with the HPA axis, gene methylation, and the gut microbiome, which has emerged as a cross-cutting biomarker across multiple disease domains. A core innovation of this review is the proposed integrated cross-system model of development and interactions among the hypothalamic-pituitary axis, epigenetic alterations, and the gut microbiome.},
}

@article {pmid42703380,
year = {2026},
author = {Inoue, D},
title = {Unexplained Recurrent Pregnancy Loss and Emerging Endometrial Biology: A Clinically Oriented Narrative Review.},
journal = {Cureus},
volume = {18},
number = {8},
pages = {e114105},
pmid = {42703380},
issn = {2168-8184},
abstract = {A substantial proportion of couples who experience recurrent pregnancy loss (RPL) complete a full guideline-based evaluation without an identifiable cause and are given a diagnosis of unexplained RPL. This category should be interpreted as the current limitation of clinically validated biological explanation rather than as the absence of underlying pathology, and it is within this diagnostic gap that interest in emerging endometrial biology has grown. Recent advances in endometrial biology have generated substantial interest in three closely related investigational domains: the endometrial microbiome, chronic endometritis (CE), and the endometrial immune milieu. Each domain has independently been associated with reproductive failure in observational research, and growing evidence suggests potential biological interactions among them. However, significant methodological heterogeneity, absence of standardized diagnostic criteria, and insufficient prospective validation currently preclude routine clinical implementation. This narrative review synthesizes current evidence in each of these domains and weighs their relevance to how unexplained RPL is managed. The review concludes that abnormalities involving endometrial microbial composition, chronic endometrial inflammation, and local immune dysregulation represent biologically plausible contributors to unexplained pregnancy loss in selected women, but that the principal barriers to clinical adoption are reproducibility, methodological standardization, and demonstrated clinical utility rather than biological plausibility alone. Major professional guidelines currently advise against routine use of these tests outside a research context. Emerging endometrial biology should therefore be interpreted as a framework for ongoing scientific inquiry, not as a basis for expanded clinical testing. Incorporation into routine practice will require standardized methodology, independent multicenter validation, and prospective demonstration that diagnosis and treatment improve clinically meaningful reproductive outcomes.},
}

@article {pmid42703491,
year = {2026},
author = {Bonner-Reid, FT},
title = {Gastrointestinal Microbiota Imbalance and Sensory Processing Dysregulation in Autism Spectrum Disorder: A Systematic Review.},
journal = {Cureus},
volume = {18},
number = {8},
pages = {e114142},
pmid = {42703491},
issn = {2168-8184},
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by challenges with social communication and repetitive behaviors. Many people with ASD also experience gastrointestinal symptoms and sensory processing dysfunction. New research has identified a potential role for microbial dysbiosis (imbalance of gut microbiota) in these comorbidities. This systematic review aimed to explore the links between gut microbiota composition, gastrointestinal symptoms, sensory processing differences, and dietary patterns in individuals with ASD, as well as the potential for a bidirectional relationship and dietary-based interventions targeting the microbiota. PubMed, Scopus, Web of Science, and Google Scholar were used to retrieve publications from 2011 to 2026, and a systematic review was conducted. Studies were chosen that examined gut microbiota, gastrointestinal symptoms, and sensory processing in people with ASD. Only intervention and observational studies were included. Many people with ASD reported gastrointestinal symptoms, sensory processing differences, restricted dietary patterns, and gut microbiota composition. However, the majority of studies included were cross-sectional, which does not allow for an inference of temporal direction or causality. The evidence indicates there may be a bidirectional relationship between gastrointestinal and sensory symptoms and microbial differences, and the sensory symptoms, food selectivity, food restriction, stool consistency, use of medication, and clinical characteristics may also affect the composition of the microbiota. Initial microbiome interventions had some potential for improvement in selected outcomes, but with limited confidence due to small sample sizes, heterogeneity in methods used, and potential for bias. The current evidence suggests that changes in the gut microbiota composition are associated with gastrointestinal symptoms, sensory dysregulation, and dietary patterns in ASD, but does not provide evidence to indicate that microbial dysbiosis is a primary mechanism. The possibility of reverse causation exists, as the food environment could be influenced by sensory sensitivity and/or eating habits, and, in turn, these factors could affect the composition of the microbiota. To better understand directionality and the efficacy of microbiome-targeted interventions, longitudinal studies and sufficiently powered randomized controlled trials are warranted.},
}

@article {pmid42703634,
year = {2026},
author = {Tomás, I and Suárez-Rodríguez, B and Blanco-Pintos, T and Sánchez-Barco, A and Alonso-Sampedro, M and Carreira, MJ and Regueira-Iglesias, A and Balsa-Castro, C},
title = {Comparative Diagnostic Performance of Oral Microbial Habitats for Periodontitis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345261473819},
doi = {10.1177/00220345261473819},
pmid = {42703634},
issn = {1544-0591},
abstract = {Periodontitis affects more than 1 billion people worldwide but remains largely underdiagnosed. The oral microbiota offers a noninvasive diagnostic window, but studies based on 16S rRNA data have reported heterogeneous and often suboptimal performance. It remains unclear which oral habitat and modeling strategy best support clinical decision making. We analyzed 2,303 adult samples from 33 publicly available 16S rRNA V3-V4 Illumina projects encompassing saliva, supragingival, and subgingival habitats. Amplicon sequence variants (ASVs) were identified against the expanded Human Oral Microbiome Database. Compact microbial signatures were identified through multivariate techniques (sparse partial least squares discriminant analysis and a customized genetic algorithm). Five machine-learning algorithms were benchmarked under repeated cross-validation and test-set evaluation. Diagnostic performance was assessed using the area under the receiver-operating characteristic curve (AUC), and clinical net benefit was assessed using decision curve analysis (DCA). Generalized additive models (GAMs) provided the best discrimination with compact panels of 6 to 12 ASVs. Saliva and supragingival achieved the best discrimination (AUC = 0.928 and 0.903; sensitivity = 92.4% and 87.6%; specificity = 85.3% and 81.7%), significantly outperforming subgingival plaque (0.803, 78.2% and 75.1%, respectively; adjusted P ≤ 0.001). DCA further demonstrated the highest and most stable net clinical benefit in saliva (AUC-DCA = 0.437), followed by supragingival (0.419) and subgingival (0.331). Forty-eight taxonomically annotated ASVs emerged as predictors, underscoring the models' biological interpretability. In subgingival sites, the most prevalent features were health-associated commensals, such as Streptococcus oralis subsp. dentisani. Supragingival plaque and saliva predominantly revealed periodontitis-associated taxa, including Porphyromonas gingivalis and Filifactor alocis. Thus, saliva and supragingival plaque better capture the microbial fingerprint of periodontitis-associated dysbiosis. Oral microbiome-based models across habitats showed consistent diagnostic performance for periodontitis. The GAM algorithm with compact, interpretable microbial signatures achieved strong discrimination and superior net benefit in saliva and supragingival samples, highlighting its potential for translation into scalable, noninvasive diagnostic tools for precision periodontics.},
}

@article {pmid42699515,
year = {2026},
author = {Hou, Z and Cheng, Z and Xue, B},
title = {Plant polyphenols as context-dependent modulators of cellular signalling networks.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1885983},
pmid = {42699515},
issn = {2296-861X},
abstract = {Plant-derived polyphenols have attracted considerable attention because of their antioxidant, anti-inflammatory, and metabolic regulatory activities. However, despite extensive research, their biological actions are still frequently interpreted through simplified one-compound-one-pathway models, which inadequately explain their pleiotropic and context-dependent effects. Furthermore, existing studies and reviews often examine signalling pathways, structural characteristics, metabolism, and exposure biology separately, limiting a comprehensive understanding of how polyphenols regulate cellular networks. Therefore, this review aims to re-evaluate the mechanisms of representative polyphenols, including curcumin, quercetin, epigallocatechin-3-gallate (EGCG), and resveratrol, from a systems-level perspective and to examine how structural features influence signalling behaviour across different biological contexts. By integrating evidence from molecular studies, omics technologies, biotransformation research, microbiome-related metabolism, and translational investigations, we highlight that polyphenols function not as pathway-specific regulators but as context-dependent modulators of interconnected networks governing redox homeostasis, inflammation, autophagy, and energy metabolism. We further demonstrate that structural motifs such as electrophilic centres, catechol groups, gallate esters, and stilbene scaffolds influence signalling tendencies by affecting chemical reactivity, target accessibility, and metabolic fate without conferring pathway exclusivity. Based on these observations, we propose a conceptual framework of conditional signalling bias, in which polyphenol activity emerges from the dynamic interplay among chemical structure, metabolic transformation, target exposure, and network state. This framework provides a more realistic and mechanistically grounded interpretation of polyphenol action and offers a valuable foundation for future biomarker-guided, exposure-informed, and precision-oriented translational research in cardiometabolic, neurological, inflammatory, and oncological diseases.},
}

@article {pmid42699605,
year = {2026},
author = {Yue, Y and Wei, W and Wu, C and Suo, N and Zhang, Z and Liu, W and Su, Q and Wang, M and Zhang, Y and Xie, B},
title = {Four-domain gut metagenomics reveals archaeal-centered cross-kingdom remodeling across coronary artery disease and acute myocardial infarction.},
journal = {iScience},
volume = {29},
number = {9},
pages = {117227},
pmid = {42699605},
issn = {2589-0042},
abstract = {Cardiovascular microbiome research has focused mainly on bacterial taxa and pathways. We profiled stool archaea, bacteria, fungi, and viruses in patients with acute myocardial infarction (AMI) and healthy controls. Paired plasma metabolomics was examined in a subset. An independent angiography-defined cohort included angiographically normal controls, severe coronary artery disease (CAD), and AMI. No archaeal genus remained differentially abundant after multiple-testing correction. In the discovery cohort, archaeal-bacterial correlations were predominantly positive in healthy controls and negative in AMI, while archaeal-fungal rewiring was prominent. The extension cohort identified sign-flip archaeal-virome edges between severe CAD and AMI, while severe CAD showed the lowest archaeal-bacterial connectivity. Plasma metabolomics captured a broad AMI-associated systemic shift. These findings show that gut archaeal signals are expressed through multi-kingdom ecological organization across coronary disease states.},
}

@article {pmid42699672,
year = {2026},
author = {Wu, D and Dong, T and Chen, X and Lin, Z and Pan, Q and Wei, J and Liang, J and Wei, J},
title = {Insights into microbiome and ARGs diversity in patients with upper and lower respiratory tract infections by targeted next-generation sequencing.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21615},
pmid = {42699672},
issn = {2167-8359},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Male ; Middle Aged ; Adult ; *Bacteria/genetics/drug effects/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Drug Resistance, Bacterial/genetics ; Coinfection/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Respiratory tract infections (RTIs) cause substantial global morbidity and mortality, with antimicrobial resistance presenting an increasing challenge to the effective management. Characterizing the differences in microbiome composition and antimicrobial resistance genes (ARGs) between upper respiratory tract infections (URTIs) and lower respiratory tract infections (LRTIs) may inform site-specific diagnostic and therapeutic strategies. We retrospectively analyzed 1,340 URTIs samples (nasopharyngeal swab) and 699 LRTIs samples (bronchoalveolar lavage fluid) admitted to a single medical center to characterize the epidemiology of the respiratory microbes and ARGs using targeted next-generation sequencing (tNGS). Microbiome diversity, ARGs profiles, and coinfection patterns were compared between LRTIs and URTIs groups. Random forest machine learning was employed to identify discriminating species. LRTIs patients exhibited significantly higher microbiome abundance and ARGs diversity than URTIs patients (P < 0.001. Beta-lactam, multidrug, phenicol, and fluoroquinolone resistance genes were significantly more abundant in LRTIs (P < 0.01). Bacteria-virus coinfections predominated in both LRTIs (39.3%) and URTIs (54.6%). Thirty species were identified as potential discriminators between LRTIs and URTIs, with an Area Under Curve (AUC) of 0.852 in the training set. These findings reveal distinct microbial and ARGs profiles between URTIs and LRTIs patients, and provide a foundation for understanding site-specific microbial ecology in RTIs for clinical diagnosis and antimicrobial stewardship.},
}

Humans
*Respiratory Tract Infections/microbiology
*Microbiota/genetics
Female
High-Throughput Nucleotide Sequencing
Retrospective Studies
Male
Middle Aged
Adult
*Bacteria/genetics/drug effects/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Drug Resistance, Bacterial/genetics
Coinfection/microbiology
Anti-Bacterial Agents/pharmacology

@article {pmid42699828,
year = {2026},
author = {Akcan, A},
title = {A Narrative Review of Airway and Gut Microbiota in Chronic Obstructive Pulmonary Disease: Clinical Associations, Methodological Heterogeneity, and Translational Priorities.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e115698},
pmid = {42699828},
issn = {2168-8184},
abstract = {Chronic obstructive pulmonary disease (COPD) is a heterogeneous disorder in which exacerbation susceptibility, persistent inflammation, disease progression, and treatment response are not fully explained by spirometry. Culture-independent studies have associated airway and gut microbial features with clinically relevant COPD phenotypes, but findings are highly sensitive to sampling site, low biomass, contamination control, sequencing depth and platform, bioinformatic workflow, microbial-load quantification, medication exposure, disease state, and host or environmental confounding. Methodological and clinical heterogeneity is therefore a central explanation for inconsistent results. This narrative review, a non-systematic synthesis using a prespecified focused PubMed/MEDLINE search (1 August 2021-1 August 2026), English-language eligibility, single-reviewer selection, structured data charting, and thematic appraisal without formal study-level risk-of-bias grading, evaluates recent human evidence on the airway bacteriome and mycobiome, gut microbiota and metabolites, host-microbe relationships, and the ecological effects of antibiotics and inhaled corticosteroids. Across cohorts, lower airway diversity, states dominated by potential pathobionts (normally resident organisms that may contribute to disease under altered host or ecological conditions), and altered microbial networks are recurrent but not universal associations; no disease-specific taxonomic signature has been validated. Gut microbial and metabolic differences may represent causes, consequences, treatment effects, shared determinants, or combinations of these mechanisms. Relative abundance is difficult to interpret without absolute microbial-load measurement. No microbiota-based diagnostic test, prognostic classifier, or intervention is ready for routine COPD care. Progress requires standardized longitudinal sampling, rigorous controls, absolute quantification, paired airway-gut multi-omics, diverse external validation, and randomized trials with prespecified patient-centered outcomes.},
}

@article {pmid42700052,
year = {2026},
author = {Liu, X and Shen, K and Zhu, F and Cheng, C and Yu, H},
title = {Exploring the role of gut microbiota in coronary atherosclerosis through lipoprotein-mediated cholesterol transport and distribution: A Mendelian randomization analysis.},
journal = {Medicine},
volume = {105},
number = {36},
pages = {e50447},
doi = {10.1097/MD.0000000000050447},
pmid = {42700052},
issn = {1536-5964},
mesh = {Mendelian Randomization Analysis ; Humans ; *Coronary Artery Disease/genetics/metabolism/microbiology ; *Cholesterol/metabolism ; Genome-Wide Association Study ; *Lipoproteins/metabolism ; *Gastrointestinal Microbiome/genetics/physiology ; Biological Transport ; },
abstract = {We employed Mendelian randomization (MR) to explore causal relationships between gut microbiota (GM), coronary atherosclerotic heart disease (CAHD), and potential metabolic mediators. We utilized summary statistics from genome-wide association studies (GWAS), encompassing data on 473 GM traits from comprehensive microbiome GWAS, 61 lipoprotein-mediated cholesterol transport and distribution data from large-scale metabolic biomarker studies, and coronary atherosclerosis (CA) data from the GWAS catalog (study accession GCST90043957) involving 456,348 European participants. Bidirectional MR analyses were conducted to investigate the causal relationships between GM and CA. Two-sample Mendelian randomization analyses were performed to identify potential mediating metabolites and quantify the mediation proportion. Ultimately, the GM GCA-900066755, identified through MR as having a potential causal relationship, was selected to investigate its potential effects on CA by influencing cholesterol transport and distribution. Our results indicated that GCA-900066755 was positively associated with an increased risk of CA (odds ratio = 1.156). CA did not significantly affect the levels of GCA-900066755 (odds ratio = 1.009). GCA-900066755 was negatively correlated with total cholesterol levels in medium high-density lipoprotein, which reduced CA risk, and was positively correlated with total cholesterol levels in low-density lipoprotein (LDL), large LDL, medium LDL, and small LDL, which were positively associated with CA. Mediation analysis showed 7 data points mediating the association between GCA-900066755 and CA. Our MR study supports a causal relationship between specific GM groups and the risk of CAHD, highlighting that cholesterol traits are not merely outcomes associated with the relationship between GM and CAHD, but are important mediating factors. Understanding the biological mechanisms of these traits can provide a concrete foundation for future targeted interventions.},
}

Mendelian Randomization Analysis
Humans
*Coronary Artery Disease/genetics/metabolism/microbiology
*Cholesterol/metabolism
Genome-Wide Association Study
*Lipoproteins/metabolism
*Gastrointestinal Microbiome/genetics/physiology
Biological Transport

@article {pmid42700124,
year = {2026},
author = {Dardouri, A and Chahbouni, M and Meftah Elkhair, M and Lazar, S and Amine, A},
title = {Tumor-linked microbiota in the breast: a systematic review and meta-analysis.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/17460913.2026.2728819},
pmid = {42700124},
issn = {1746-0921},
abstract = {AIMS: Breast cancer is the most common cancer among women worldwide. Recent research suggests that the microbiota may contribute to tumorigenesis via immune, inflammatory, or metabolic mechanisms. This meta-analysis aimed to compare the relative abundance of bacteria among cancerous(C), adjacent normal (NAT) and non-cancerous(N) breast tissues to identify microbial profiles associated with cancer.

MATERIALS AND METHODS: A systematic search was conducted in PubMed and Scopus according to PRISMA guidelines. We have included twenty-nine studies published between 2014 and 2024, using 16S rRNA sequencing. Data were extracted from graphs using ImageJ and subsequently analyzed in Python using log-transformed ratios and statistical models adapted to the degree of heterogeneity (I[2]).

RESULTS: At the phylum level, Proteobacteria and Firmicutes predominated in tumor tissues without significant differences (p > 0.05). However, significant increases were observed at lower taxonomic levels. Pseudomonadaceae, Corynebacteriaceae, and Staphylococcaceae were enriched in cancerous tissues. The genera Pseudomonas and Lactobacillus were also significantly enriched in the pooled analysis (p < 0.05).

CONCLUSION: Although methodological heterogeneity was observed among studies, the findings suggest recurrent microbial patterns potentially associated with breast cancer. These observations should be considered exploratory and hypothesis-generating. Future research should prioritize standardized protocols, multi-omic integration, and geographically diverse cohorts to better elucidate causal relationships and clinical implications.},
}

@article {pmid42700191,
year = {2026},
author = {Olawale, F and Alake, SE and Chandrashekar, R and Kim, Y and Chowanadisai, W and McCullagh, EA and Smith, BJ and Lucas, EA},
title = {Biotics in Menopausal Health: A Two-Decade Bibliometric Analysis and Narrative Review.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {},
pmid = {42700191},
issn = {2161-3311},
support = {1R15AT011962-01/AT/NCCIH NIH HHS/United States ; },
mesh = {Humans ; *Menopause/physiology ; Female ; *Prebiotics/administration & dosage ; *Probiotics/administration & dosage ; Bibliometrics ; *Gastrointestinal Microbiome/physiology ; Synbiotics/administration & dosage ; },
abstract = {PURPOSE OF REVIEW: Menopause, defined as amenorrhea due to loss of ovarian function, is associated with osteoporosis, metabolic syndrome, vasomotor disturbances, and cardiovascular disease. While menopause hormone therapy (MHT) remains the gold standard for high-potency symptom management, biotic interventions offer a safe, alternative approach for those who cannot or choose not to use MHT. This review examines biotic interventions (probiotics, prebiotics, synbiotics, postbiotics) and their influence on the gut-menopause axis.

RECENT FINDINGS: Declining estrogen during menopause alters gastrointestinal physiology, including shifts in gut microbiota composition and impaired gut barrier function. Bibliometric analysis of the past two decades shows a sharp rise in publications after 2017, peaking in 2024. The intellectual landscape centers on "probiotics," "menopause," and "osteoporosis," highlighting bone health as a key focus. Evidence indicates that biotic interventions, particularly Lactobacillus and Bifidobacterium species and selected fibers, can restore microbial balance, enhance short-chain fatty acid production, improve gut barrier integrity, modulate the estrobolome, reduce systemic inflammation, and support bone, metabolic, cardiovascular, and vasomotor health. Biotic strategies represent a multi-targeted, non-hormonal approach to managing menopausal health, addressing underlying physiological changes. These findings highlight emerging research trends while underscoring the need for long-term clinical trials, and support further exploration of personalized, microbiome-targeted interventions in menopause.},
}

Humans
*Menopause/physiology
Female
*Prebiotics/administration & dosage
*Probiotics/administration & dosage
Bibliometrics
*Gastrointestinal Microbiome/physiology
Synbiotics/administration & dosage

@article {pmid42700252,
year = {2026},
author = {Wang, J and Tian, ZX and Chen, S and Chen, GY and Wang, YP and Wang, P},
title = {Depleting luminal cysteine with engineered bacteroides vulgatus alleviates experimental colitis by suppressing Th17 differentiation through an ATF6-dependent mechanism.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {75},
number = {1},
pages = {},
pmid = {42700252},
issn = {1420-908X},
support = {2024CX21//National High Level Hospital Clinical Research Funding/ ; 32020103002//ational Natural Science Foundation of China/ ; 7262129//Beijing Natural Science Foundation/ ; 32370837,32571072//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Th17 Cells/immunology/cytology ; Cell Differentiation ; Dextran Sulfate ; Mice, Inbred C57BL ; *Cysteine/metabolism/deficiency ; *Bacteroides/genetics ; *Colitis/immunology/chemically induced/therapy ; Mice ; Cytokines/immunology ; *Colitis, Ulcerative/immunology ; *Probiotics/therapeutic use ; Colon/pathology ; Intestinal Barrier Function ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease driven by dysregulated immune responses, particularly the aberrant activation of T helper 17 (Th17) cells. While microbiome-based therapies show promise, wild-type probiotics often lack specific mechanisms to target the metabolic and immunological drivers of inflammation.

METHODS: In this study, we engineered a cysteine-auxotrophic strain of Bacteroides vulgatus (BV1608) by chromosomally integrating the E. coli cyuP gene to enhance cysteine uptake. We evaluated its colonization capability, safety, and therapeutic efficacy in dextran sulfate sodium (DSS)-induced acute and chronic colitis murine models.

RESULTS: BV1608 exhibited superior colonization and cysteine assimilation compared to the wild-type strain. Oral administration of BV1608 significantly alleviated colitis symptoms, reduced pro-inflammatory cytokines, and restored intestinal barrier integrity. Mechanistically, BV1608 created a localized cysteine-restricted microenvironment in the gut and suppressed pathogenic Th17 differentiation. Under cystine-restricted conditions, ATF6 was activated in CD4⁺ T cells, and its inhibition partially restored IL-17A⁺ CD4⁺ T cell differentiation, indicating a functional role for ATF6. Meanwhile, cystine restriction was associated with increased BATF2 expression and enhanced ATF6 binding at the BATF2 promoter, suggesting BATF2 as a potential downstream node.

CONCLUSION: Our findings demonstrate that metabolically engineered B. vulgatus BV1608 ameliorates colitis by coupling microbial cysteine sequestration with host immune modulation via the ATF6-dependent suppression of Th17 differentiation, while implicating BATF2-associated transcriptional regulation as a potential downstream mechanism. This study provides a novel synbiotic strategy for treating UC by targeting the immunometabolic interface.},
}

Animals
*Th17 Cells/immunology/cytology
Cell Differentiation
Dextran Sulfate
Mice, Inbred C57BL
*Cysteine/metabolism/deficiency
*Bacteroides/genetics
*Colitis/immunology/chemically induced/therapy
Mice
Cytokines/immunology
*Colitis, Ulcerative/immunology
*Probiotics/therapeutic use
Colon/pathology
Intestinal Barrier Function

@article {pmid42700342,
year = {2026},
author = {Swamikkannu, DM and Dasarapu, S and Mohan, KD and Shanmugam, A},
title = {Decoding dysbiosis: the role of gut microbiota in MASLD progression and emerging therapeutic interventions.},
journal = {Journal of physiology and biochemistry},
volume = {82},
number = {1},
pages = {},
pmid = {42700342},
issn = {1877-8755},
mesh = {Humans ; *Dysbiosis/therapy/microbiology ; Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; Animals ; Prebiotics ; Disease Progression ; Liver/metabolism/microbiology/pathology ; *Fatty Liver/therapy/microbiology ; Mesenchymal Stem Cell Transplantation ; Synbiotics ; Bile Acids and Salts/metabolism ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD), affects a substantial proportion of the global population and is closely associated with metabolic disorders. The gut microbiota, comprising a diverse community of microorganisms within the gastrointestinal tract, plays a crucial role in maintaining host health. Dysbiosis, defined as an imbalance in this microbial ecosystem, has been increasingly implicated in the development and progression of liver diseases, including MASLD. This review examines the role of the gut microbiota in MASLD pathogenesis and highlights its potential as a therapeutic target. The gut-liver axis facilitates bidirectional communication between the intestine and the liver, thereby influencing metabolic regulation. In MASLD, dysbiosis characterized by reduced microbial diversity and an increased abundance of Gram-negative bacteria leads to altered bile acid metabolism, increased intestinal permeability, enhanced endotoxin translocation, and hepatic inflammation. Additionally, it disrupts short-chain fatty acid production and interferes with the endocannabinoid system and choline metabolism, collectively driving disease progression. Emerging non-invasive diagnostic approaches, including gut microbiome profiling, show promise for early detection. Although specific pharmacological treatments remain limited, microbiota-targeted strategies such as probiotics, prebiotics, and synbiotics aim to restore microbial balance. Furthermore, emerging modalities within microbiome-based therapies, including mesenchymal stromal cell therapy and bacteriophage therapy, offer potential for targeted modulation of the gut microbiota and liver repair. The gut microbiota-liver axis plays a central role in the pathogenesis of MASLD. Growing insights into this relationship have driven the development of microbiome-based diagnostic and therapeutic approaches. Non-invasive diagnostic tools, particularly gut microbiome profiling, show promise for early detection. Therapeutically, microbiota-targeted strategies including probiotics, prebiotics, synbiotics, and emerging modalities such as cellular and bacteriophage-based therapies offer potential to restore microbial balance and improve liver function. Nevertheless, robust clinical studies are essential to validate their efficacy, safety, and applicability in personalized MASLD management.},
}

Humans
*Dysbiosis/therapy/microbiology
Probiotics/therapeutic use
*Gastrointestinal Microbiome
Animals
Prebiotics
Disease Progression
Liver/metabolism/microbiology/pathology
*Fatty Liver/therapy/microbiology
Mesenchymal Stem Cell Transplantation
Synbiotics
Bile Acids and Salts/metabolism

@article {pmid42700384,
year = {2026},
author = {Braverman, D and Batushansky, A and Sal-Man, N},
title = {Milk-derived peptone reduces EHEC virulence by inhibiting the type III secretion system.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2721084},
doi = {10.1080/21505594.2026.2721084},
pmid = {42700384},
issn = {2150-5608},
mesh = {*Peptones/pharmacology/metabolism ; Virulence/drug effects ; Animals ; Humans ; *Milk/chemistry ; *Enterohemorrhagic Escherichia coli/pathogenicity/drug effects ; Bacterial Adhesion/drug effects ; Escherichia coli Proteins/metabolism ; },
abstract = {The link between diet and overall human health is well established, with certain diets known to promote better health and be associated with a reduced risk of developing chronic diseases. Previous research has also demonstrated the direct effects of diet on microbiome composition, diversity, and fitness, which can, in turn, alter colonization resistance and the immune response against enteric pathogens. However, much less is known regarding the direct effect of diet on the virulence of pathogenic bacteria. To examine the effect of diet on bacterial virulence while maintaining constant macronutrient composition, we used peptones from different sources (plant- and animal-based) to simulate various dietary protein sources. The peptones were examined for their effect on the virulence of enterohemorrhagic Escherichia coli (EHEC). We found that bacteria grown with peptone derived from casein - the main protein component of milk - exhibit a significant reduction in their type III secretion system (T3SS) activity. This effect manifested as a significant reduction in bacterial adherence to host cells and limited translocation activity of the T3SS effector Tir. We additionally found evidence suggesting that milk-derived peptone causes a shift in bacterial behavior from hyper-virulent, adherent bacteria to a more motile state. Finally, we observed that the inhibitory effects of milk-derived peptone extend beyond EHEC to other T3SS-possessing pathogens. While the specific inhibitory components in casein remain to be identified, our findings provide a foundation for developing casein-based, non-antibiotic therapies against bacterial diarrheagenic pathogens.},
}

*Peptones/pharmacology/metabolism
Virulence/drug effects
Animals
Humans
*Milk/chemistry
*Enterohemorrhagic Escherichia coli/pathogenicity/drug effects
Bacterial Adhesion/drug effects
Escherichia coli Proteins/metabolism

@article {pmid42700527,
year = {2026},
author = {Yin, Z and Ping, H and Li, C},
title = {Antimony species-dependent enrichment and transcriptional activity of antibiotic and metal resistance genes in the gut microbiome of male mice.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130867},
doi = {10.1016/j.jenvman.2026.130867},
pmid = {42700527},
issn = {1095-8630},
abstract = {The gut microbiome is a reservoir for antibiotic resistance genes (ARGs) and is sensitive to environmental pollutants. ARGs in environmental and host-associated microbiomes can be enriched by metal(loid)s through co-selection with metal resistance genes (MRGs). However, as a ubiquitous toxic metalloid, antimony (Sb) induced alterations of ARGs in the gut microbiome and the underlying mechanisms remain unclear. Here, by integrating genome-resolved metagenomics and metatranscriptomics, we characterized the genomic potential and transcriptional activity of ARGs and MRGs in the gut microbiome of mice exposed to Sb(III)- and Sb(V)-contaminated drinking water. We found that both Sb(III) and Sb(V) significantly increased ARGs abundance, whereas only Sb(III) enhanced ARGs transcription (288.40 ± 41.67 TPM, P < 0.05). Co-selection of ARGs and MRGs was observed through metagenome-assembled genomes (MAGs) analysis, and key taxa driving this process were identified (e.g., Eubacterium_J and Lachnospiraceae_COE1). Sb(III), but not Sb(V), induced co-regulation of macrolide-lincosamide-streptogramin resistance genes and arsRABC operon. A potentially higher risk of ARG dissemination under Sb(III) stress was suggested by the increased abundance and transcription of mobile genetic elements (MGEs). This study advances our understanding of the interactions between Sb and ARGs in the gut microbiome and highlights the potential chemical species-dependent enrichment and transcriptional activation of ARGs.},
}

@article {pmid42700718,
year = {2026},
author = {Maglione, A and Rosso, R and Tortarolo, D and Pantini, F and Pernice, S and Contaldo, SG and Lanzillo, R and Spiezia, AL and Cordioli, C and Virgilio, E and Masuzzo, F and Matta, M and Malucchi, S and Cavalla, P and Cocolin, L and Sirovich, R and Beccuti, M and Ferrocino, I and Cordero, F and Clerico, M and Rolla, S},
title = {Gut microbiome profiling at multiple sclerosis onset as a potential early prognostic marker of disease course: evidence from an observational cohort study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106470},
doi = {10.1016/j.ebiom.2026.106470},
pmid = {42700718},
issn = {2352-3964},
abstract = {BACKGROUND: Alterations in gut microbiome composition have been associated with multiple sclerosis (MS), but their impact on disease severity and early progression remains poorly understood. In this study we investigated whether gut microbiome profiling at diagnosis could identify microbial signatures associated with clinical and radiological features of early MS and provide prognostic information.

METHODS: We analysed the gut microbiome of 53 treatment-naïve patients with MS (pwMS) and 55 healthy donors (HD) using shotgun metagenomic sequencing, combined with clinical features collected over 1 year from diagnosis. To clarify whether gut microbiome composition at MS onset could have prognostic relevance, pwMS were stratified according to lesion burden, lesion localisation, and magnetic resonance imaging (MRI) activity.

FINDINGS: Overall beta diversity in Bacteria, Archaea, and Eukarya differed significantly between pwMS and HD (p-value <0.001, <0.02, <0.03, respectively). Within the MS group, glucocorticoid treatment at disease onset was the clinical factor most strongly associated with gut microbiota diversity. Stratification according to lesion burden, lesion localisation, and MRI activity identified two clinically distinct MS subgroups with different baseline clinical characteristics at onset (p-value <0.03) and different risk of early disease progression. The cluster associated with an unfavourable prognosis showed greater progression within 12 months and was enriched for motor symptoms and spinal cord lesions at diagnosis.

INTERPRETATION: Our findings suggest that gut microbiome alterations are detectable at the earliest stages of MS and are associated with clinical and radiological features linked to short-term disease evolution. Gut microbial profiling may therefore represent a promising early prognostic biomarker and may help to identify candidate targets for early intervention and therapeutic development in MS, although further validation in larger longitudinal cohorts is needed.

FUNDING: This study was supported by grants from the Italian Multiple Sclerosis Foundation, the Cassa di Risparmio di Torino Foundation, and the Italian Ministry of University and Research.},
}

@article {pmid42700824,
year = {2026},
author = {Meng, Y and Dun, M and Liu, X and Chen, W and Zhang, Z and Lu, S and Zhang, G and Ling, J},
title = {Gut microbiome-targeted bile acid metabolomics integration reveals dietary cordycepin alleviates NAFLD in diabetic mice by enriching Clostridia and affecting the PXR/Sult2a1/CA7S.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110500},
doi = {10.1016/j.jnutbio.2026.110500},
pmid = {42700824},
issn = {1873-4847},
abstract = {Non-alcoholic fatty liver disease (NAFLD) frequently coexists with type 2 diabetes mellitus (T2DM), posing a significant metabolic disorder with limited dietary intervention options. Cordycepin, a food‑derived nucleoside from the edible fungus Cordyceps militaris, exhibits hypoglycemic and hypolipidemic effects, but its role in T2DM combined with NAFLD remains unknown. Here, we established a mouse model of T2DM combined with NAFLD in male KM mice using high-fructose and high‑fat diet, and streptozotocin. Both cordycepin (COR) and Cordyceps militaris water extract (CWE) attenuated glucose intolerance, dyslipidemia, hepatic steatosis, liver injury, inflammatory response and oxidative stress, with cordycepin showing superior efficacy. Multi‑omics analysis revealed that cordycepin uniquely reshaped the gut microbiota by significantly enriching the c__Clostridia, including g__Acetatifactor, g__Anaerovorax, g__Monoglobus, s__Acutalibacter_muris, and further affected liver metabolism, which was characterized by enrichment of bile acid metabolism-related pathways. Targeted bile acid metabolomics demonstrated that cordycepin specifically promoted the production of cholic acid‑7‑sulfate (CA7S), a gut‑restricted secondary bile acid, through activation of the hepatic PXR/Sult2a1 pathway. Notably, integrated correlation analysis revealed a significant positive association between CA7S and c__Clostridia (e.g., g__Monoglobus, g__Lachnoclostridium, and g__Anaerovorax), suggesting that cordycepin enhances CA7S production by enriching these Clostridia members. And CA7S activated TGR5 to stimulate glucagon‑like peptide‑1 (GLP‑1) secretion, thereby improving glucose and lipid homeostasis. Therefore, these findings demonstrate that dietary cordycepin improves T2DM combined with NAFLD by modulating gut microbiota, particularly Clostridia, and affecting the PXR/Sult2a1/CA7S/GLP‑1 pathway, thereby exerting beneficial effects on glucose and lipid homeostasis.},
}

@article {pmid42697072,
year = {2026},
author = {Wu, Q and Li, L and Lei, Y and Zhou, T and Tang, H and Zhang, B and Lu, Y and Salvatore, M and Zhang, D and Tong, J and Wang, T and Chen, S and Li, H and Xu, Z and Huang, Y and Hu, Y and Hong, N and Zhou, Y and Lin, F and O'Brien, KS and Chen, Y and Li, R and Xu, H and Wang, F and Bian, J and Wolk, DA and Chen, Y},
title = {Discovering repurposable drugs for Alzheimer's disease and related dementias: target trial emulation using decentralised real-world data.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106466},
doi = {10.1016/j.ebiom.2026.106466},
pmid = {42697072},
issn = {2352-3964},
abstract = {BACKGROUND: Alzheimer's disease and related dementias (ADRD) affect nearly 6.9 million Americans, with the number expected to triple by 2050, while disease-modifying therapies remain unavailable. Drug repurposing, which identifies new indications for already approved medications, offers a more efficient and cost-effective pathway to accelerate development of effective therapies for ADRD. The aim of this study is to identify potential drug repurposing signals by systematically screening routinely prescribed drugs for associations with progression from mild cognitive impairment (MCI) to ADRD.

METHODS: We conducted a multi-site target trial emulation using electronic health record (EHR) data from four decentralised databases: INSIGHT Clinical Research Network, OneFlorida + Clinical Research Consortium, the University of Pennsylvania Health System, and Yale New Haven Health System. We performed an independent validation using EHR data from the TriNetX Research Network and a genetic risk-stratified sensitivity analysis in the Penn Medicine BioBank (PMBB) database. Eligible participants were adults aged 50 years or older at the time of MCI diagnosis, with no prior diagnosis of ADRD and no prior use of the trial drugs. Initiation of each of 181 routinely prescribed drugs was compared with two active control groups defined by initiation of supplements or cardiovascular medications. Risk ratios (RRs) and 95% CIs were estimated using a federated target trial emulation framework (LATTE) with stabilised inverse probability of treatment weighting and Poisson regression.

FINDINGS: A total of 122,972 eligible patients were identified from the four decentralised databases, 335,506 patients identified from the TriNetX network for validation and 898 from PMBB database. Federated, multi-site target trial emulation identified 20 drug repurposing hypotheses with statistically significant protective effects, including anti-inflammatory and pain-modulating agents (celecoxib: RR 0.43; 95% CI: 0.23-0.81; dexamethasone RR 0.46; 95% CI: 0.29-0.73; gabapentin: RR 0.55; 95% CI: 0.36-0.83; ketorolac: RR 0.50; 95% CI: 0.31-0.80; methylprednisolone: RR 0.43; 95% CI: 0.24-0.76; prednisone: RR 0.48; 95% CI: 0.28-0.83; pregabalin: RR 0.53; 95% CI: 0.35-0.79), antimicrobial and microbiome-associated agents (cefazolin: RR 0.62; 95% CI: 0.45-0.84; clavulanate: RR 0.56; 95% CI: 0.44-0.71; fluconazole: RR 0.36; 95% CI: 0.23-0.58), neuromodulators and adrenergic agents (epinephrine: RR 0.42; 95% CI: 0.31-0.56; propranolol: RR 0.56; 95% CI: 0.37-0.85; salmeterol: RR 0.49; 95% CI: 0.32-0.74; tizanidine: RR 0.29; 95% CI: 0.14-0.57), vascular, metabolic, and hormonal modulators (empagliflozin: RR 0.29; 95% CI: 0.17-0.50; oestradiol: RR 0.47; 95% CI: 0.28-0.81; ezetimibe: RR 0.69; 95% CI: 0.52-0.91; sodium bicarbonate: RR 0.49; 95% CI: 0.29-0.84; spironolactone: RR 0.43; 95% CI: 0.31-0.60), and histamine-related and gastrointestinal agents (famotidine: RR 0.64; 95% CI: 0.55-0.74). Results were consistent in the independent validation using TriNetX network and sensitivity analysis in PMBB database.

INTERPRETATION: 20 widely used medications may be associated with reduced progression from MCI to ADRD and represent promising candidates for clinical evaluation as repurposed therapies for dementia.

FUNDING: National Institutes of Health.},
}

@article {pmid42697200,
year = {2026},
author = {Tueux, G and Pouilly, N and Bernigaud Samatan, J and Blanchet, N and Boniface, MC and Catrice, O and Carrère, S and Gouzy, J and Jacquemot, MP and Lauber, E and Legendre, A and Moreau, S and Moroldo, M and Roldan, A and Carlier, A and Langlade, NB},
title = {A loss-of-function allele fixed during domestication reshapes nectar chemistry, microbial diversity, and pollinator visits.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.08.022},
pmid = {42697200},
issn = {1879-0445},
abstract = {Nectar is a hub for plant-pollinator interactions, yet gene-level causal links between plant genetic variation, pollinator foraging, and nectar microbial assembly remain poorly resolved. Using near-isogenic lines, innovative field time-lapse monitoring of pollinator visits, and long-read amplicon sequencing of nectar microbiota, we show that a natural single-nucleotide variant at a cell-wall invertase gene (HaCWINV2) controls sunflower nectar chemistry and influences both pollinators and microbes. Plants homozygous for a loss-of-function HaCWINV2 allele produce sucrose-rich nectar, resulting in fewer bee visits under field conditions. In pollinator-excluded flowers, invertase-deficient plants harbored greater fungal diversity and compositionally distinct communities, indicating that nectar sugar profiles act as ecological filters shaping the nectar microbiome. This loss-of-function allele is rare in wild sunflowers, but fixed in 35% of cultivated lines, indicating positive selection during domestication. Our findings establish a causal link between a single gene and nectar chemistry, with cascading ecological effects in a plant-pollinator system, thus illustrating how subtle genetic changes scale up to alter nectar traits, microbial assembly, and pollinator foraging behavior.},
}

@article {pmid42697201,
year = {2026},
author = {Jiao, Y and Cheng, CH and Gao, X and Li, W and Ji, F and Liang, C and Huang, P and Ko, LH and Ye, L and Kam, ICH and Cheung, AH and Kang, W and Yu, J and Wong, CC},
title = {Bacteroides acidifaciens enriched by KRAS mutation promotes colorectal tumorigenesis.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.08.010},
pmid = {42697201},
issn = {1934-6069},
abstract = {Colorectal cancer (CRC) is a multifactorial disease impacted by the tumor microbiome and host genetics, notably mutations that activate KRAS to stimulate a RAF-MEK-extracellular signal-regulated kinase (ERK) proliferative cascade. However, whether host genetics interplays with the tumor microbiome remains unclear. Here, we profiled intratumoral microbiomes from KRAS-mutant CRC patients and intestine-specific oncogenic KRAS[G12D] mice, revealing that KRAS reshapes the microbial community, enriching Bacteroides acidifaciens that predicts poor prognosis in KRAS-mutant CRC patients. Employing isogenic CRC cells and mice with or without mutant KRAS, we demonstrate that B. acidifaciens promotes malignant phenotypes in KRAS-mutant CRC cells and intestine-specific KRAS[G12D] mice but not in wild-type counterparts. B. acidifaciens SusF binds and stabilizes ARHGEF2, which promotes active KRAS and RAF-MEK-ERK signaling. SusF ablation or ARHGEF2 knockout in KRAS-mutant CRC cells abrogates the pro-tumorigenic effects of B. acidifaciens. These observations offer strategies for targeting mutant KRAS-driven B. acidifaciens to mitigate feedforward signaling leading to tumorigenesis.},
}

@article {pmid42697284,
year = {2026},
author = {Yan, H and Qin, Q and Li, Y and Yang, L and Jiang, M and Xin, Y and Li, Y and Li, X and Lu, J},
title = {Multiomics analyses identify diet-derived creatine and α-linolenic acid linking with metastatic thyroid cancer.},
journal = {Molecular and cellular probes},
volume = {},
number = {},
pages = {102086},
doi = {10.1016/j.mcp.2026.102086},
pmid = {42697284},
issn = {1096-1194},
abstract = {BACKGROUND: Thyroid cancer (TC) has traditionally been regarded as an indolent malignancy. However, it retains the potential for metastasis and lethality, underscoring its status as a malignant tumor. To explore the interplay between serum metabolite profiles, gut microbial communities, and TC metastasis, we conducted a comprehensive study.

METHODS: Serum metabolites were analyzed using untargeted metabolomics methods to characterize the metabolic changes. Two diet-derived metabolites, creatine (Cr) and α-linolenic acid (ALA), were selected for in vitro validation. Finally, 16S rRNA gene sequencing was used to characterize the intestinal microbial composition and analyze the correlation between differential metabolites and differential intestinal microbiota.

RESULTS: LC-MS analysis of serum metabolites identified Arginine and proline metabolism and Arginine biosynthesis as the primary metabolic pathways altered in TC metastasis. Both Cr and ALA effectively inhibited EMT, migration, and invasion of TC cell lines, TPC1 and FTC-133. The analysis of gut microbiota composition revealed that Cr and ALA showed significant correlations with the bacteria genera, Porphyromonas and Papillibacter.

CONCLUSIONS: This study highlights that TC metastasis is associated with significant alterations in the serum metabolite profiles of patients, and Cr and ALA play a role in inhibiting TC development. Furthermore, Cr and ALA were correlated with Porphyromonas and Papillibacter, implying their potential link with food-borne components and their connected impact on TC metastasis. The findings provide new insights into the role of metabolites and gut microbiota in TC progression, suggesting novel avenues for dietary intervention in cancer treatment.},
}

@article {pmid42697449,
year = {2026},
author = {Botolin, P and Helbing, J and Khanuja, HS and Patel, NK and Goldman, AH},
title = {Impact of Gastrointestinal Bleeding History on Postoperative Outcomes in Total Hip and Knee Arthroplasty: A Retrospective Analysis.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2026.08.057},
pmid = {42697449},
issn = {1532-8406},
abstract = {INTRODUCTION: Gastrointestinal (GI) bleeding is common in older adults and contributes to immune dysregulation, yet its impact on total hip (THA) and total knee (TKA) arthroplasty outcomes is poorly understood. We evaluated the association between GI bleeding history with risk of periprosthetic joint infection (PJI) and other complications up to two years following THA and TKA.

METHODS: A retrospective review identified patients who had a history of GI bleeding within two years prior to THA or TKA. Patients were matched to a control cohort who had no GI bleeding history. The THA cohort included 6,420 GI bleed and 6,420 control patients. The TKA cohort included 9,688 GI bleed and 9,688 control patients. Odds ratios were calculated for 90-day and 2-year outcomes.

RESULTS: In the THA cohort, GI bleed within two years prior to surgery was not associated with PJI (odds ratio (OR): 1.1 [0.8 to 1.4]; P = 0.544) at two years; however, it was associated with increased odds of mechanical loosening (OR: 1.6 [1.01 to 2.5]; P = 0.044) and revision surgery (OR: 1.4 [1.1 to 1.8]; P = 0.002). In the TKA cohort, GI bleed history was associated with greater 2-year odds of PJI (OR: 1.3 [1.1 to 1.7]; P = 0.012) and revision surgery (OR: 1.4 [1.2 to 1.7]; P < 0.001). The GI bleed patients in both cohorts demonstrated greater 90-day medical complication odds, including urinary tract infection (P < 0.05).

CONCLUSION: A GI bleeding history was associated with increased 90-day medical and 2-year surgical complications following THA and TKA. Patients undergoing THA had higher odds of mechanical loosening, whereas TKA patients demonstrated higher odds of PJI. While the complication rate was low, these findings should be interpreted cautiously and viewed as hypothesis-generating. Further prospective studies are needed to better characterize postoperative risk factors in this population.},
}

@article {pmid42697479,
year = {2026},
author = {Luo, Y and Jiang, Y and Tingting, Z},
title = {Targeting Nrf2 in oxidative liver injury: expanding the role of gut microbiota and metabolites.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.09.006},
pmid = {42697479},
issn = {2090-1224},
abstract = {BACKGROUND: Liver diseases are a major cause of illness and death worldwide. Oxidative stress is a pivotal driver in the pathogenesis of a spectrum of liver diseases, including alcoholic liver disease (ALD), metabolic dysfunction-associated fatty liver disease (MAFLD), drug-induced liver injury (DILI), and hepatocellular carcinoma (HCC). The transcription factor Nrf2, a master regulator of cellular antioxidant responses, plays a central yet context-dependent role in modulating this injury. Additionally, the gut-liver axis is a critical regulator of hepatic homeostasis.

AIM OF REVIEW: This review presents recent advances to propose a refined gut-microbiota-Nrf2 axis as a key mechanistic link in the treatment of liver injury. We detail how specific gut-derived microbial metabolites, such as short-chain fatty acids (SCFAs), tryptophan derivatives, and urolithins, directly or indirectly activate the hepatic Keap1/Nrf2 signaling pathway. This activation orchestrates a cytoprotective program that enhances the redox balance, promotes detoxification, and induces selective autophagy, thereby protecting against oxidative liver injury. Conversely, we examine the dual role of Nrf2, highlighting how its dysregulated and constitutive activation in established HCC can paradoxically promote tumor progression and ferroptosis resistance. Finally, we evaluate the therapeutic potential of targeting this axis using microbiome-modulating strategies, including probiotic and prebiotic supplementation, fecal microbiota transplantation (FMT), dietary intervention, and synergy with Nrf2-targeting drugs.

This review provides an integrated framework that connects gut microbial ecology with host redox signaling, offering novel mechanistic insights and translational perspectives for the prevention and treatment of oxidative liver diseases.},
}

@article {pmid42697520,
year = {2026},
author = {Sharma, A and Jatana, N},
title = {Microbiota-derived metabolite-GPCR signalling in neurodegeneration.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.09.001},
pmid = {42697520},
issn = {1873-7544},
abstract = {The gut microbiome acts as a primary regulator of host homeostasis, influencing the entire body through bidirectional communication along the gut-brain axis (GBA). Dysbiosis, which is defined as a state of microbial imbalance involving alterations in community composition and function, can disrupt the synthesis of important microbiota-derived metabolites, such as short-chain fatty acids (SCFAs), bile acids and neurotransmitter precursors. This can lead to impaired essential host signalling pathways. There is growing evidence that metabolic alterations associated with dysbiosis contribute to the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS). In this context, G protein-coupled receptors (GPCRs) act as essential molecular transducers that link microbial metabolites to intracellular signalling networks. Aberrant GPCR activation, driven by altered metabolite profiles, modulates key downstream pathways including cAMP, MAPK, PI3K/Akt, NF-κB and Ca2 + signalling. This promotes neuroinflammation, oxidative stress, mitochondrial dysfunction and pathological protein aggregation - hallmark processes underlying neurodegeneration. By identifying convergent and disease-specific signalling pathways, the review highlights mechanistic nodes of therapeutic relevance and discusses GPCR-centric emerging and other microbiome-targeted strategies aimed at restoring metabolic and signalling homeostasis in neurodegenerative disorders.},
}

@article {pmid42697639,
year = {2026},
author = {Gao, Y and Chen, J and Zhang, Y and Duan, J and Qiu, T and Wu, J and Wang, X and Li, J and Cao, W and Gao, H},
title = {Pseudomonas chlororaphis YL21 synergistically controls Fusarium crown rot of wheat by reshaping rhizosphere microbiota and reprogramming host defense metabolism.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107261},
doi = {10.1016/j.pestbp.2026.107261},
pmid = {42697639},
issn = {1095-9939},
mesh = {*Triticum/microbiology/metabolism ; *Fusarium ; *Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; *Pseudomonas chlororaphis/physiology ; *Microbiota ; Soil Microbiology ; },
abstract = {Fusarium crown rot (FCR) poses a major threat to wheat (Triticum aestivum L.) production worldwide, with severe outbreaks occurring in the Xinjiang Uygur Autonomous Region, China. As a soil-borne disease caused by Fusarium species, FCR is considered difficult to detect and manage, which often leads to poor control efficacy. Therefore, developing novel green biocontrol agents represents an urgent scientific challenge. Here, we report a rhizosphere bacterium, Pseudomonas chlororaphis YL21, which exhibits strong antagonistic activity against Fusarium spp. Inoculation with P. chlororaphis YL21 significantly reduced FCR severity and promoted plant growth. This strain produces proteases that inhibit pathogens, as well as plant growth-promoting factors including nitrogen fixation, siderophores, hydrogen cyanide (HCN), indole-3-acetic acid (IAA), and ammonia. ITS and 16S rRNA sequencing revealed that strain YL21 substantially reshaped the rhizosphere microbiota structure and promoted the enrichment of other beneficial microorganisms. RNA-Seq showed upregulation of plant hormone signal transduction and vitamin B6 metabolism pathways, as well as defense-related genes including PR1 and RPM1. Untargeted metabolomics revealed substantial metabolic changes in the wheat stem base following YL21 inoculation, with metabolites such as xanthoxylol, dihydrochelerythrine, and zeanic acid being significantly upregulated. Plants reprogrammed key metabolic pathways, including glucosinolate biosynthesis, ABC transporters, and the biosynthesis of various plant secondary metabolites, collectively indicating activated defense responses. This work elucidates the biocontrol mechanisms of P. chlororaphis against Fusarium by integrating metabolomics, transcriptomics, and microbiome analyses. Our findings lay a solid foundation for developing sustainable approaches to manage FCR in wheat.},
}

*Triticum/microbiology/metabolism
*Fusarium
*Rhizosphere
*Plant Diseases/microbiology/prevention & control
*Pseudomonas chlororaphis/physiology
*Microbiota
Soil Microbiology

@article {pmid42697647,
year = {2026},
author = {Huang, C and Dai, X and Chen, Y and Ge, H and Zhang, L and Yu, Y and Fang, H},
title = {Chitosan mitigates the dissemination of antibiotic resistance genes caused by metalaxyl in the soil-earthworm system.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107278},
doi = {10.1016/j.pestbp.2026.107278},
pmid = {42697647},
issn = {1095-9939},
mesh = {Animals ; *Chitosan/pharmacology ; *Oligochaeta/drug effects ; Soil Microbiology ; *Alanine/analogs & derivatives/toxicity/pharmacology ; *Fungicides, Industrial/toxicity/pharmacology ; *Drug Resistance, Microbial/genetics ; *Soil Pollutants/toxicity ; Soil/chemistry ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal/drug effects ; },
abstract = {The widespread use of agricultural fungicides can lead to residual contamination and accelerate the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in soil ecosystems. Developing green remediation strategies that simultaneously reduce fungicide residues and mitigate antibiotic resistance risks is therefore beneficial for soil pollutant control. Here, we investigated the effects of chitosan (CHI) on the dissipation of metalaxyl (MET) enantiomers and their influence on the soil-earthworm resistome and microbiome through pot experiments and metagenomics analysis. The results showed that CHI significantly accelerated MET dissipation in soil and reduced its bioaccumulation in earthworms. MET enantiomers, particularly S-MET, promoted the dissemination of ARGs, including high-risk ARGs, in the soil-earthworm system, whereas CHI suppressed these effects, likely by limiting the potential for mobile genetic element (MGE)-mediated horizontal gene transfer (HGT). Compared with the corresponding treatments without CHI amendment, CHI amendment reduced the total relative abundance of ARGs by 16.8%-24.7% in soil and by 34.1%-58.3% in earthworm guts. Furthermore, CHI reshaped microbial community structure in both soil and earthworm gut samples by driving ecological niche differentiation of Actinomycetota and Pseudomonadota and reduced ARG host abundance. These findings offer practical insights for controlling contamination by fungicides and ARGs in agricultural soils.},
}

Animals
*Chitosan/pharmacology
*Oligochaeta/drug effects
Soil Microbiology
*Alanine/analogs & derivatives/toxicity/pharmacology
*Fungicides, Industrial/toxicity/pharmacology
*Drug Resistance, Microbial/genetics
*Soil Pollutants/toxicity
Soil/chemistry
Bacteria/genetics/drug effects
Gene Transfer, Horizontal/drug effects

@article {pmid42697668,
year = {2026},
author = {Zhu, S and Liu, X and Yang, X and Wu, W and Ahmed, T and Jiang, H and Ding, T},
title = {Amplicon and metagenomic sequencing reveal thifluzamide drive rhizosphere microbial structural shifts and functional adaption.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107299},
doi = {10.1016/j.pestbp.2026.107299},
pmid = {42697668},
issn = {1095-9939},
mesh = {*Rhizosphere ; Fungi/drug effects/genetics ; Oryza/microbiology ; Bacteria/drug effects/genetics ; Metagenomics ; *Fungicides, Industrial/pharmacology ; Soil Microbiology ; *Microbiota/drug effects ; Metagenome ; },
abstract = {Thifluzamide (TF) is a widely used phenyl urea fungicide in rice production; however, its impacts on the structural composition and functional dynamics of the rhizosphere microbiome remain poorly understood. Here, we systematically investigated the effects of TF on the structure, interactions, and functional potential of the rice (Oryza sativa L.) rhizosphere microbiome using integrated amplicon sequencing and metagenomic approaches. TF application significantly altered both bacterial and fungal community composition, bacterial diversity was markedly reduced, whereas fungal diversity increased. With bacterial diversity markedly reduced while fungal diversity increased. Beta-diversity analyses revealed strong treatment-driven community separation, indicating pronounced TF-induced microbial restructuring. Co-occurrence network analysis demonstrated reduced complexity and connectivity in bacterial networks but increased negative co-occurrence patterns within fungal communities, suggesting contrasting stability responses between microbial kingdoms. Metagenomic profiling further revealed substantial functional shifts, including the differential enrichment of KEGG and COG pathways associated with xenobiotic metabolism. Notably, while total ARG abundance remained stable, TF exposure altered the resistome profile by selectively enriching specific classes of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Strong positive correlations between MGEs and ARGs highlighted an elevated potential for horizontal gene transfer. Metagenome-assembled genome (MAG) analysis identified specific TF-enriched bacterial taxa, including Methylophilus, Sulfurospirillum, and Azospirillum, which harbored genes involved in pesticide degradation and xenobiotic transformation. Collectively, these findings demonstrate that TF profoundly reshapes the rice rhizosphere microbiome by altering microbial diversity, interaction networks, resistance gene profiles, and functional capacities. This study provides genomic insights into fungicide-microbiome interactions, underscoring the potential ecological implications associated with TF application, while identifying candidate microbial taxa that may contribute to pesticide degradation and rhizosphere microecology resilience.},
}

*Rhizosphere
Fungi/drug effects/genetics
Oryza/microbiology
Bacteria/drug effects/genetics
Metagenomics
*Fungicides, Industrial/pharmacology
Soil Microbiology
*Microbiota/drug effects
Metagenome

@article {pmid42697683,
year = {2026},
author = {Nie, F and He, Z and Zhang, L and Zhang, Y and Gong, L and Li, L and Wang, X and Zhou, B and Gao, Z and Wei, G and Tian, X and Huang, L},
title = {Kojic acid and ε-poly-L-lysine suppress potato common scab and remodel the tuber-associated microbiome.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107314},
doi = {10.1016/j.pestbp.2026.107314},
pmid = {42697683},
issn = {1095-9939},
mesh = {*Polylysine/pharmacology ; *Streptomyces/drug effects ; *Pyrones/pharmacology ; *Solanum tuberosum/microbiology ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention & control ; *Anti-Bacterial Agents/pharmacology ; *Plant Tubers/microbiology ; Soil Microbiology ; },
abstract = {Potato common scab (PCS) is an economically important soil-borne disease whose occurrence is governed not only by pathogen virulence but also by the disease-associated microbiome and soil environment. However, studies on natural bioactive compounds have primarily focused on direct pathogen inhibition, whereas their roles in microbiome remodeling remain largely unexplored. Here, we investigated the antibacterial activity of kojic acid (KA) and ε-poly-L-lysine (ε-PL) against Streptomyces scabies and evaluated their effects on PCS severity and the tuber-associated microbiome. Both KA and ε-PL significantly inhibited the growth of Streptomyces scabies G9, with ε-PL exhibiting stronger in vitro antibacterial activity. Both treatments disrupted hyphal ultrastructure, increased membrane permeability, and triggered extensive transcriptional reprogramming involving cell envelope organization, central metabolism, membrane transport, and genetic information processing. Net-house and field trials showed that both compounds substantially reduced disease severity; significant yield increases were observed in the net-house trial, whereas no significant yield differences were detected among treatments in the field trial. Microbiome analyses revealed that both compounds improved the physicochemical properties and enzyme activities of tuber-associated soil, reshaped the composition and predicted functional profiles of the tuber-associated bacterial community, and reduced the relative abundance of pathogen-associated Streptomyces taxa. Correlation analyses revealed significant associations among soil environmental factors, pathogen-associated Streptomyces taxa, and disease occurrence. Collectively, these findings indicate that KA and ε-PL suppress PCS in association with direct antibacterial activity and remodeling of the tuber-associated bacterial community. This study provides insights into the potential roles of natural bioactive compounds in pathogen suppression and microbiome modulation.},
}

*Polylysine/pharmacology
*Streptomyces/drug effects
*Pyrones/pharmacology
*Solanum tuberosum/microbiology
*Microbiota/drug effects
*Plant Diseases/microbiology/prevention & control
*Anti-Bacterial Agents/pharmacology
*Plant Tubers/microbiology
Soil Microbiology

@article {pmid42697760,
year = {2026},
author = {Armengaud, C and Protto, V and Poitout, A and Krouk, G and Ruffel, S},
title = {Decoupling developmental and physiological adaptations: a strategy to unleash nutrient use efficiency in plants?.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.08.003},
pmid = {42697760},
issn = {1878-4372},
abstract = {Plants respond to spatially and temporally variable soil nutrients through root architectural plasticity, regulation of uptake and assimilation per root unit, and plant-soil-microbiome interactions. Although often viewed as complementary, these responses can also behave as compensatory strategies. Under non-optimal nutrient distributions, plants may invest either in greater root proliferation or in higher uptake capacity per root unit. We propose that this development-transport relationship should be understood as an optimization problem, rather than an additive response. Comparable morphology-physiology trade-offs occur in other resource-acquiring organs, including the gut and the lungs. Tuning or partially uncoupling these constraints could redefine crop ideotypes as dynamic combinations of root architecture, physiological elasticity, and controlled rhizosphere outsourcing, opening new routes to improve nutritional efficiencies.},
}

@article {pmid42697798,
year = {2026},
author = {Ho, PM and Nazeer, RR and Askenasy, I and Quinn, RA and Welch, M},
title = {Microbial content versus microbial interaction: the impact of medications on CF airway microbial ecosystems.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.08.011},
pmid = {42697798},
issn = {1873-5010},
abstract = {BACKGROUND: The airways of people with cystic fibrosis (pwCF) are often colonized by a variety of different microbes. Although much effort has been put into cataloguing the impact of medication on the identities and abundances of these microbes, far less has been directed towards examining this from an ecological perspective, i.e., examining how medications affect the network and types of interactions between microbes.

METHODS: In the current work, we generated an ecological model of the CF airway microbiome and examined how medications affect interactions between co-habiting airway microbiota in six pwCF. Ecological interactions were inferred from a generalized Lotka-Volterra model, and the impact of medications was determined by principal component(s) regression analysis.

RESULTS: For the majority of the subjects studied, antimicrobial interventions had relatively little impact on the CF airway microbial ecology, and even appeared to stabilize ecological interactions between the microbiota. However, the microbial ecosystem in some individuals was more sensitive to external perturbations. More surprisingly, we found that some non-antimicrobial medications, and also certain carriers and excipients affect the ecosystem.

CONCLUSIONS: Medications affect the ecology of the CF airway microbiota. These impacts appear to be very patient-specific. We also note that some nominally non-bioactive ingredients in medications can also potentially impact the CF airway ecosystem. Our data highlight the importance of collecting patient-specific data and in employing suitable computational frameworks for disentangling medication-microbiota interactions in vivo.},
}

@article {pmid42697801,
year = {2026},
author = {Htut, M and Lee, K and Nathwani, N and Rosenzweig, M and Janakiram, M and Goldsmith, S and Sanchez, JF and Scott, M and Keats, J and Krishnan, A and Rosen, ST and Wang, SS},
title = {Gut Microbiome Composition Is Associated With Response to CD38 Antibody (Daratumumab) Treatment Among Relapsed Multiple Myeloma Patients.},
journal = {Clinical lymphoma, myeloma & leukemia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clml.2026.08.004},
pmid = {42697801},
issn = {2152-2669},
abstract = {INTRODUCTION: Growing data support interactions between host-gut microbes and treatment responses in multiple myeloma (MM), where a higher abundance of Eubacterium hallii in stool samples has been found among MM patients with negative minimal residual disease after induction therapy. Here, we evaluated changes in the gut microbiome associated with daratumumab (dara) based therapy in 40 MM patients, before and after therapy.

PATIENTS AND METHODS: Patients with relapsed MM and prior autologous transplantation who had received 1 to 4 prior lines of therapy were eligible. Two stool samples were collected, one within 1 week prior to dara (predara) and one immediately after 4 doses of dara (postdara). Metagenomics sequencing was conducted. Microbiome taxonomic analyses were performed using MetaPhlAn4, and microbial functional pathway analyses were conducted using HUMAnN3.6. QIIME2 was used for compositional and statistical analyses.

RESULTS: Of 40 participants enrolled, there were 5 nonresponders; 35 patients achieved partial response (PR) or better (responders). Among responders, 10 patients achieved complete remission (CR), and 25 patients achieved either very good partial response (VGPR) or PR. There were no statistically significant differences between overall pre and postdara gut microbiomes. Differential abundance analysis (ANCOM-BC) showed statistically significant (q ≤ 0.05) overgrowth of Alistipes finegoldii and Acidaminococcus intestini species in responders and Ruminococcus torques, Sellimonas intestinalis and Clostridium symbiosum in nonresponders. Compared to non-CR, CR samples showed enrichment of Faecalibacterium prausnitzii; non-CR samples were enriched in Segatella copri and Faecalimonas umbilicata.

DISCUSSION/CONCLUSION: Our results suggest differences in species between clinical responders and nonresponders, but larger prospective studies are needed to confirm these results.},
}

@article {pmid42697887,
year = {2026},
author = {Galal, A and Moustafa, A and Salama, M},
title = {Proteo-metabolomic integration identifies stage-specific candidate biomarkers for Parkinson's disease.},
journal = {NPJ Parkinson's disease},
volume = {12},
number = {1},
pages = {},
pmid = {42697887},
issn = {2373-8057},
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder with a prolonged prodromal phase and complex motor symptoms. Despite improved clinical criteria, early diagnosis and longitudinal monitoring remain challenging. While cerebrospinal fluid (CSF) and plasma metabolites and proteins show biomarker potential, their utility in predictive models is insufficiently characterized. We employed a secondary computational approach to integrate proteometabolomic profiles from CSF and plasma samples of >1100 Parkinson's Progression Markers Initiative (PPMI) participants. Using multi-omics machine learning, we identified biofluid-specific signatures and evaluated predictive performance. Twenty-one biomarker candidates were validated across three models (SVM, GLMNET, RF); SVM and GLMNET achieved the highest recall (83-86%) and AUCs of 0.84-0.89. Longitudinal mixed-effects modeling revealed eight candidates associated with progression across diagnostic stages. We identified a three-part molecular framework characterizing neurodegeneration: a diagnostic subpanel reflecting early microbiome dysregulation (secretory granins and metabolites) and synaptic breakdown; a second subpanel monitoring phenoconversion via neurogenesis precursors and extracellular matrix proteins; and a third subpanel tracking progression through chronic neuroinflammation and immune activation. This integrated multi-omics approach provides a robust framework for stage-specific PD monitoring and potential clinical deployment.},
}

@article {pmid42698059,
year = {2026},
author = {Tang, W and Nordmann-Gomes, A and Khalili, L and Rosas, G and Montgomery, E and Zhang, L and Suh, S and Clancy, R and Askanase, AD},
title = {Updates on the Evaluation of Lupus Arthritis.},
journal = {Rheumatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42698059},
issn = {2198-6576},
support = {W81XWH-21-1-0468//U.S. Department of Defense/ ; },
abstract = {Lupus arthritis is the most common manifestation of systemic lupus erythematosus (SLE), affecting up to 95% of patients. Clinical presentations range from inflammatory arthralgia and non-deforming non-erosive (NDNE) synovitis to Jaccoud arthropathy and erosive arthritis, reflecting substantial clinical heterogeneity. Despite its high prevalence, widely used outcome measures lack the granularity to distinguish between these phenotypes or accurately quantify disease severity. This narrative review integrates clinical phenotypes, serologic biomarkers, imaging advances, and emerging therapies to provide a framework for evaluating lupus arthritis. Besides distinct clinical phenotypes, we propose a conceptual hypothesis-generating model describing the evolution of lupus arthritis. In an early, preclinical stage, genetically predisposed individuals may develop pathogenic autoantibodies and alterations in the gut microbiome that can lead to increased inflammation within the synovium. The intermediate stage is characterized by progressive leukocyte accumulation within the joint space, leading to clinical symptoms and early abnormalities on imaging including joint effusions, synovitis, and tenosynovitis. In the late stage, persistent inflammation results in clinically evident joint damage, including synovial hypertrophy, joint capsular swelling, and bone erosions. Biomarkers such as anti-citrullinated protein antibodies (ACPAs), anti-carbamylated protein (anti-carP) antibodies, interleukin (IL)-6, IL-17, and metalloproteinases may help identify patients at risk for erosive or deforming disease and those prone to rapid progression. Advances in imaging technologies including musculoskeletal ultrasound (MSK-US), MRI, and optical tomography may enable earlier detection before clinical manifestations or physical exam findings, creating opportunities for earlier intervention. Therapeutically, hydroxychloroquine (HCQ) remains the foundation of treatment. Belimumab and anifrolumab are US Food and Drug Administration (FDA)-approved biologics now recommended as standard of care for persistent disease, alongside conventional immunosuppressants such as methotrexate, mycophenolate, or azathioprine when indicated. Additional targeted therapies including obinutuzumab and Janus kinase (JAK) inhibitors are closely following behind. Chimeric antigen receptor T cell (CAR-T) represents a promising approach that may transform the future management of SLE.},
}

@article {pmid42698096,
year = {2026},
author = {Li, M and Cui, J and Qu, R and Liu, R and Sun, Y and Li, P and Liu, J and Low, A and Huang, X and Gan, F and Xu, ZZ},
title = {Correction: Porphyromonas gingivalis induces intestinal inflammation through gingipain-dependent gut microbiome dysbiosis.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42698096},
issn = {2049-2618},
}

@article {pmid42698111,
year = {2026},
author = {Turon, M and Díez-Vives, C and Carrier, TJ and de la Cruz-Castillejo, L and Conejero, M and Steiner, L and Jung, S and Pita, L and Koutsouveli, V and Franzenburg, S and Hentschel, U and Riesgo, A},
title = {Phagocytosis of microbial symbionts supports embryonic nutrition in the sponge Halichondria panicea.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42698111},
issn = {2049-2618},
mesh = {Animals ; *Symbiosis ; *Phagocytosis ; RNA, Ribosomal, 16S/genetics ; *Porifera/microbiology/embryology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Embryonic Development ; },
abstract = {BACKGROUND: Animal development is frequently supported by microbial symbionts that contribute to host nutrition, metabolism, and physiology. While the functional importance of microbiomes in adult hosts is increasingly recognized, the role of symbiotic microbes during gametogenesis and embryogenesis remains poorly understood, particularly in early-diverging metazoans. Sponges represent an ideal system to investigate these processes due to their dense and diverse microbial communities. Here, we examined host-symbiont dynamics across the reproductive cycle of the marine sponge Halichondria panicea to assess how microbial communities contribute to reproduction and early development.

RESULTS: Specimens were collected monthly from February to July and classified by reproductive stage using histological analyses. We combined ultrastructural imaging, dual RNA sequencing of host and symbionts, 16S rRNA gene amplicon sequencing, and quantitative PCR to characterize microbial and transcriptional dynamics throughout reproduction. Pronounced shifts in both host gene expression and microbial community composition occurred during early embryogenesis, particularly in May. Transmission electron microscopy revealed nurse cells phagocytosing bacterial aggregates in close proximity to late oocytes, presumably converting them into yolk precursors. This coincided with a significant decline in the abundance of the dominant obligate symbiont, Candidatus Halichondribacter symbioticus. Host transcriptomic analyses showed upregulation of immune and phagocytic pathways, including pattern recognition receptors, lectins, and vesicle trafficking components, specifically in females undergoing embryogenesis in May. Concurrently, symbiont gene expression profiles indicated responses to acidic conditions, consistent with exposure to phagosomal environments.

CONCLUSIONS: Our results are consistent with intracellular digestion of microbial symbionts during early embryogenesis, potentially to supplement the nutritional requirements of embryogenesis. These findings reveal symbiont phagocytosis as a previously underappreciated nutritional strategy during animal development and highlight the dynamic functional integration of microbiomes into reproductive physiology in basal metazoans. Video Abstract.},
}

Animals
*Symbiosis
*Phagocytosis
RNA, Ribosomal, 16S/genetics
*Porifera/microbiology/embryology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Embryonic Development

@article {pmid42698286,
year = {2026},
author = {Ríos-Barbero, J and Martínez, M and Ambrosio, N and García-Bueno, B and Fraguas, D and Leza, JC and Sanz, M and Figuero, E},
title = {Periodontitis and Neuropsychiatric Disorders: Epidemiological and Mechanistic Evidence.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70172},
pmid = {42698286},
issn = {1600-0765},
support = {PD2019-109033RB-100//MINECO-FEDER/ ; PID2021-127256OB-I00//MINECO-FEDER/ ; },
abstract = {This review aims to critically analyze the epidemiological evidence and mechanistic insights linking periodontitis with the onset, progression, or severity of neuropsychiatric disorders. From an epidemiological perspective, eligible evidence was identified regarding disorders related to trauma, stress, anxiety, depressive, and bipolar disorders, whereas no studies meeting the predefined inclusion criteria were found for the remaining considered disorders. The strongest epidemiological evidence was observed for depressive disorders and anxiety- and stress-related conditions. However, the predominance of cross-sectional studies, together with substantial methodological heterogeneity, limits conclusions regarding temporality and causality. From a mechanistic perspective, the available evidence regarding the association between periodontitis and neuropsychiatric disorders predominantly supports as mechanisms (1) microbial pathways (microbial translocation and functional dysregulation of the oral microbiome), (2) inflammatory and immune pathways (systemic (meta)inflammation and trafficking of immune players systemic), and (3) shared underlying vulnerabilities (behavioral factors, medication-related effects, lifestyle and systemic health factors, and genetic mechanisms). Periodontitis may promote a persistent low-grade systemic inflammatory state through the release of bacterial products and inflammatory mediators into the circulation, thereby influencing immune, neuroendocrine, and vascular pathways relevant to neuropsychiatric vulnerability. Moreover, the hematogenous dissemination or swallowing of periodontal bacteria and their virulence factors may contribute to microbial remodeling at distant sites, including the gut, supporting the concept of an oral-gut-brain axis. Overall, the evidence analyzed supports periodontitis as a potential modifiable contributor within a broader biopsychosocial network linking oral and mental health, while highlighting the need for longitudinal studies and interventional trials to clarify causality and clinical relevance.},
}

@article {pmid42698579,
year = {2026},
author = {Murugesan, M and Thankappan, S and Mageshwaran, V and Ramasamy, R and Singaram, A},
title = {Decoding the functional diversity of plant growth-promoting bacterial communities in the soils of Western Ghats, Tamil Nadu, India.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1865342},
doi = {10.3389/fmicb.2026.1865342},
pmid = {42698579},
issn = {1664-302X},
abstract = {Western ghats in India, one of the world's biodiversity hot spots is the reservoirs of microbial resources having agricultural and industrial significance. However, the diversity of plant growth-promoting microbial communities associated with the plants and soil in the Western Ghats is untapped vault. The current emphasis on natural farming is more depending on the indigenous microbial communities and their metabolic functions towards sustainable one -health. With this background, the present study examines the bacterial diversity of soils from the Western Ghats of Nilgiris, Coimbatore and Dindigul regions. Among the 10 soil samples collected (S1 to S10), three soil samples (S2, S4 and S6) representing respective three regions were subjected for metagenomic studies based on their distinct soil chemical and biological properties. The computational analysis of the metagenome revealed the core genus Bradhyrhizobium in all soil samples, while Trebonia, Arthrobacter, Streptomyces, and Pseudomonas are the next most abundant genera, which varied substantially. The results collectively demonstrate that soil sample from Dindigul harbours the richest and most diverse microbial community among the three regions. In culturable studies, a total of 101 bacterial isolates were obtained from 10 soil samples (S1 to S10). Among them four Gram-negative bacterial isolates showed potential plant growth-promoting attributes, such as Ammonia, Indole Acetic Acid, Hydrogen cyanide and siderophore production, phosphorus, potassium, and zinc solubilization. The 16S rDNA analysis revealed that the bacterial isolates were Pseudomonas glycinae S6B1, Pseudomonas tolaasii S2B3, Pseudomonas azotoformans S9H10, and Pseudomonas poae S10B2. The isolate, S10B2, exhibited the maximum inhibition, with 81.25%, 70.1%, and 35% against plant pathogenic fungi, Rhizoctonia solani, Sclerotium rolfsii, and Fusarium oxysporum, respectively, indicating strong biocontrol potential. The effect of bacterial inoculants on chick pea (Cicer arietinum var. JG 62), showed that P. glycinae S6B1 significantly promoted plant growth such as root length, shoot length, and fresh/dry biomass. These findings unlock the core microbiome of soils of Western Ghats, which can be utilized to develop a synthetic microbial consortium to boost agricultural productivity.},
}

@article {pmid42698632,
year = {2026},
author = {Park, J and Cheon, S and Choi, YS and Kim, J and Ahn, SJ and Chung, JE},
title = {Anaerobic antibiotic exposure and risk of maculopathy: a nationwide dual design study.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1840229},
doi = {10.3389/fphar.2026.1840229},
pmid = {42698632},
issn = {1663-9812},
abstract = {The pathogenesis of maculopathy remains incompletely understood, and emerging evidence implicates the gut-eye axis in retinal and macular diseases. Given that antibiotics with anti-anaerobic activity may disrupt gut microbial ecology, this study investigated their association with the risk of incident maculopathy. We conducted a nationwide population-based study using the National Health Insurance Service-National Sample Cohort of South Korea. A retrospective cohort study was used to assess cumulative systemic anaerobic antibiotic exposure during a 5-year baseline period and subsequent incident maculopathy from 2007 to 2019. After 1:1 propensity score matching, hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards regression. A nested case-control study was also conducted using risk-set sampling and 1:10 propensity score matching. Anaerobic antibiotic exposure during the 365 days before the index date was assessed, and odds ratios (ORs) and 95% CIs were estimated using conditional logistic regression. Duration-response relationships were evaluated using formal trend analyses. Sensitivity analyses included age restriction, Fine-Gray competing risk models, extended exposure assessment windows, lag-time analyses, and a negative control comparator analysis using first-generation cephalosporins. In the retrospective cohort study, 326,436 anaerobic antibiotic users were matched to 326,436 non-users. Anaerobic antibiotic use was associated with an increased risk of incident maculopathy in the fully adjusted model (HR, 1.07; 95% CI, 1.03-1.12), with a significant duration-response trend and the highest risk observed for ≥57 days of cumulative use (HR, 1.24; 95% CI, 1.09-1.42). In the nested case-control study, 55,776 cases were matched to 557,760 controls. Anaerobic antibiotic use within 365 days before the index date was associated with increased odds of maculopathy (OR, 1.04; 95% CI, 1.02-1.07), also showing a significant duration-response trend. Sensitivity analyses and first-generation cephalosporin comparator analyses, generally supported the robustness of the findings. Systemic exposure to antibiotics with anti-anaerobic activity was associated with an increased risk of incident maculopathy, with a duration-response pattern across cumulative exposure categories. These findings suggest further investigation into gut microbiome disruption and the gut-eye axis as potential pathways involved in maculopathy.},
}

@article {pmid42698733,
year = {2026},
author = {Elhennawy, F and Naji, B and Butler, AE},
title = {The gut microbiome in polycystic ovary syndrome: mechanistic pathways and therapeutic potential of microbiota-targeted interventions.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1900535},
doi = {10.3389/fendo.2026.1900535},
pmid = {42698733},
issn = {1664-2392},
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Probiotics/therapeutic use/administration & dosage ; Prebiotics/administration & dosage ; Insulin Resistance ; Animals ; *Fecal Microbiota Transplantation ; },
abstract = {Polycystic Ovary Syndrome (PCOS) is one of the most common endocrine disorders worldwide, affecting 6-13% of reproductive-aged women and exerting a profound metabolic, reproductive and psychological toll. Emerging evidence suggests that the gut microbiome may be a potentially critical, yet under-recognized, contributor to the pathophysiology of PCOS. Alterations in microbial composition and function appear to influence hormonal imbalance, metabolic dysfunction and inflammatory processes that characterize the condition. However, much of the current evidence remains associative or derived from preclinical models, and the causal nature of these relationships is only beginning to be established through approaches such as Mendelian randomization. This literature review examines the evolving relationship between the gut microbiome and PCOS through a mechanism-guided, evidence-stratified framework, with particular focus on how microbiota-targeted interventions - including prebiotics, probiotics, synbiotics, dietary modifications and fecal microbiota transplantation, may modulate gut health and mitigate symptom severity. Across the reviewed studies, microbiome-targeted supplementation was associated with improvements in insulin sensitivity, reductions in systemic inflammation and favorable hormonal changes, although the strength of evidence varies across outcomes and intervention types. Importantly, PCOS heterogeneity, including differences in body mass index (BMI), insulin resistance status and phenotype, may influence both gut microbiota composition and therapeutic response, underscoring the need for phenotype-stratified research. These findings suggest that targeting the gut microbiome may serve as a promising adjunct to conventional PCOS management. Though further rigorous, long-term clinical trials are needed to advance both understanding and clinical translation.},
}

Humans
Female
*Polycystic Ovary Syndrome/microbiology/therapy
*Gastrointestinal Microbiome/physiology
Probiotics/therapeutic use/administration & dosage
Prebiotics/administration & dosage
Insulin Resistance
Animals
*Fecal Microbiota Transplantation

@article {pmid42698734,
year = {2026},
author = {Saud Gany, SL and Mohd Sahardi, NFN and Rusli, N and Mohd Zaffarin, AS and Razak, AM and Makpol, S},
title = {Natural products as modulators of age-associated gut microbiota dysbiosis: a systematic review of animal models.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1809547},
doi = {10.3389/fphar.2026.1809547},
pmid = {42698734},
issn = {1663-9812},
abstract = {UNLABELLED: Ageing is increasingly recognised as a microbiota-driven process, with dysbiosis contributing to oxidative stress, chronic inflammation, and cognitive and functional decline. Natural products, long valued in traditional medicine, are emerging as targeted modulators of the gut ecosystem. This systematic review synthesised current evidence on natural product interventions in ageing animal models. Searches of four databases (2000-2024) yielded 762 records, of which 17 studies met eligibility criteria, encompassing naturally aged rodents, D-galactose-induced, genetically accelerated (SAMP8, ob/ob), and diet-induced models. Interventions spanned plant-derived compounds, probiotics, prebiotics, marine microalgae, and animal-derived products. Across models, natural products frequently normalized microbial communities, lowering the Firmicutes/Bacteroidetes ratio, suppressing pro-inflammatory taxa (Helicobacter, Desulfovibrio), and enriching beneficial genera (Lactobacillus, Bifidobacterium, Akkermansia). These shifts are linked to improved systemic outcomes, including enhanced antioxidant defences (SOD, GSH-Px, CAT), reduced levels of inflammatory mediators (IL-6, TNF-α, COX-2), and gains in memory, learning, and motor performance. Taken together, these findings demonstrate that natural products exert multi-targeted benefits in ageing by restoring microbial balance and attenuating hallmarks of decline. Yet, wide heterogeneity in animal models, intervention types, and outcome measures limits comparability. Standardised, long-term, and multi-omics approaches are urgently needed to establish mechanistic pathways and accelerate translation into human ageing interventions.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420250602174.},
}

@article {pmid42698879,
year = {2026},
author = {Cioletti, G and Kenney, S and Hovingh, E and Springer, H and Haley, BJ and Ganda, E},
title = {Nasopharyngeal microbiome and resistome profiles in dairy calves fed milk replacer with low-level β-lactams.},
journal = {JDS communications},
volume = {7},
number = {5},
pages = {670-677},
doi = {10.3168/jdsc.2025-0994},
pmid = {42698879},
issn = {2666-9102},
abstract = {Feeding waste milk (WM) to preweaning dairy calves is a common management practice that offers economic benefits but may influence the microbiome and antimicrobial resistance (AMR) due to the presence of antibiotic residues. The objective of this study was to describe longitudinal patterns in the nasopharyngeal microbiome and AMR gene profiles of dairy calves fed either nonsupplemented milk replacer or milk replacer supplemented with low-level β-lactam antibiotics to simulate WM exposure during the preweaning period. Using shotgun metagenomic sequencing, we profiled the nasopharyngeal microbiome and resistome of 11 Holstein bull calves fed milk replacer with (MR+A; n = 6) or without (MR; n = 5) low levels of β-lactam antibiotics. Antibiotic concentrations were selected to reflect residue levels reported in WM. Deep nasopharyngeal swabs were collected every 2 wk from 1 to 15 wk of age; samples from wk 3 and 15 were excluded due to elevated contaminant burden, resulting in 6 retained time points. No significant differences in microbial α-diversity, β-diversity, or community structure were detected by dietary treatment or sampling age. Tetracycline, macrolide-lincosamide-streptogramin, aminoglycoside, metal, acid, and biocide resistance classes were among the most prominent, with descriptive differences in z-score patterns between groups but no significant differences detected. Larger-scale studies are needed to evaluate the long-term effects of WM feeding on respiratory health and AMR dynamics in dairy calves.},
}

@article {pmid42699222,
year = {2026},
author = {Kumar, M and Almohannadi, N and Al Khodor, S},
title = {Decoding the power of the microbiome in human health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1877371},
doi = {10.3389/fcimb.2026.1877371},
pmid = {42699222},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/microbiology ; *Microbiota/physiology ; Homeostasis ; *Host Microbial Interactions ; Skin Microbiome ; Gastrointestinal Microbiome ; Vitamins/biosynthesis ; Inflammatory Bowel Diseases/microbiology ; },
abstract = {The human microbiota plays a vital role in maintaining physiological homeostasis and overall health. Microbial communities colonize distinct anatomical sites, including the gut, oral cavity, respiratory tract, and skin, where they engage in symbiotic interactions with the host. These site-specific microbial communities contribute to essential functions such as nutrient metabolism, vitamin and short-chain fatty acid (SCFA) synthesis, immune regulation, and epithelial barrier integrity. Disruption of this balance, known as dysbiosis, is increasingly linked to a wide range of diseases, including inflammatory bowel disease (IBD), obesity, diabetes, and cancer. In this review, we summarize the current understanding of the human microbiota, highlighting its role in vitamin biosynthesis, the gut-brain axis, and immune modulation. We further the role of microbiome alterations in disease pathogenesis and outline emerging microbiome-based therapeutic strategies aimed at restoring microbial homeostasis.},
}

Humans
*Dysbiosis/microbiology
*Microbiota/physiology
Homeostasis
*Host Microbial Interactions
Skin Microbiome
Gastrointestinal Microbiome
Vitamins/biosynthesis
Inflammatory Bowel Diseases/microbiology

@article {pmid42699236,
year = {2026},
author = {Zhang, S and Si, Z and Yang, N and Chen, X},
title = {Exposure-aware multi-omics and artificial intelligence for biomarker discovery and precision prevention in diffuse glioma.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1874861},
doi = {10.3389/fimmu.2026.1874861},
pmid = {42699236},
issn = {1664-3224},
mesh = {Humans ; *Glioma/etiology/prevention & control/diagnosis/genetics/metabolism ; Multiomics ; *Biomarkers, Tumor ; *Brain Neoplasms/prevention & control/etiology/diagnosis/genetics ; *Artificial Intelligence ; Precision Medicine/methods ; *Environmental Exposure/adverse effects ; Animals ; Metabolomics ; },
abstract = {Diffuse gliomas are now diagnosed and studied through integrated molecular classification, radiomics, single-cell biology, spatial profiling, proteogenomics, metabolomics, and artificial intelligence. Yet many precision-medicine models still begin at diagnosis and emphasize tumor-intrinsic molecular features, leaving environmental, occupational, lifestyle, microbiome, metabolic, immune, and treatment-related exposures at the margins. This review develops an exposome-informed view of diffuse glioma biomarker discovery. Biomarker discovery is separated from clinical prevention: current evidence does not justify population-level glioma screening based on environmental exposures, but it does support systematic integration of external exposures and internal exposure-related molecular states with tumor and host biology. The synthesis focuses on five linked dimensions: the limits of current artificial intelligence and multi-omics models when exposure biology is excluded; glioma-relevant exposure domains stratified by evidence strength and measurability; genotoxic, epigenetic, vascular, neuroimmune, and immunometabolic conduits through which exposures may shape tumor ecology; computational strategies for temporally anchored integration of geospatial, occupational, clinical, liquid-biopsy, imaging, tumor-omic, single-cell, spatial, microbiome, and metabolomic data; and clinically realistic applications in high-risk surveillance, recurrence-aware monitoring, treatment-toxicity reduction, and biomarker-guided trial stratification. By aligning exposome science with systems neuro-oncology, the review outlines a translational agenda for exposure-aware glioma biomarkers while maintaining a conservative boundary between established evidence, mechanistic hypotheses, and future clinical implementation.},
}

Humans
*Glioma/etiology/prevention & control/diagnosis/genetics/metabolism
Multiomics
*Biomarkers, Tumor
*Brain Neoplasms/prevention & control/etiology/diagnosis/genetics
*Artificial Intelligence
Precision Medicine/methods
*Environmental Exposure/adverse effects
Animals
Metabolomics

@article {pmid42699280,
year = {2026},
author = {Jin, H and Sun, H and Yang, J},
title = {Microbiome-based diagnostic biomarkers in pancreatic ductal adenocarcinoma: Current evidence and translational challenges (Review).},
journal = {Oncology letters},
volume = {32},
number = {4},
pages = {478},
doi = {10.3892/ol.2026.15833},
pmid = {42699280},
issn = {1792-1082},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, as the majority of patients are diagnosed at an advanced disease stage. CA19-9, the biomarker most commonly used in clinical practice, lacks adequate sensitivity and specificity for early PDAC detection. Increasing evidence indicates that alterations in gut, oral and tumor-associated microbiota are associated with PDAC development and progression, supporting the potential diagnostic value of microbiome-based biomarkers in this disease. Multiple diagnostic models have been developed for PDAC using fecal, salivary or tissue-derived microbial profiles, and the combination of microbial signatures with CA19-9 or metabolomic markers has improved diagnostic performance in a number of cohorts. Despite these advancements, the clinical translation of microbiome-based models remains limited by methodological heterogeneity, patient-related variability, low levels of microbial biomass in pancreatic tissue and a lack of large-scale prospective validation. In addition, the majority of available evidence for microbiota-based alterations in PDAC is derived from retrospective case-control studies, and the reported diagnostic performance should therefore be interpreted cautiously. The present review summarizes current evidence on PDAC-associated microbial alterations and microbiome-based diagnostic models, and discusses the methodological, biological and regulatory challenges that must be addressed before microbiota-based approaches can be integrated into routine clinical practice.},
}

@article {pmid42699313,
year = {2026},
author = {Prachansuwan, A and Sukkha, P and Thiyajai, P and Chamtim, P and Kitdumrongthum, S and Sridonpai, P and Dee-Uam, A and Tongdonpo, K and Trachootham, D and Srichamnong, W and Thaipisuttikul, I and Raethong, N},
title = {Gut microbiome and metabolic responses to cricket powder supplementation in Thai subjects with high or borderline-high LDL cholesterol: an exploratory, randomized, crossover controlled trial.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101536},
doi = {10.1016/j.crfs.2026.101536},
pmid = {42699313},
issn = {2665-9271},
abstract = {Edible insects are emerging as sustainable functional foods, yet human evidence for microbiome-mediated effects remains limited, particularly in Asian populations. Therefore, this study investigated whether cricket powder supplementation modulates gut microbiome composition and metabolic outputs in Thai subjects with high or borderline-high LDL cholesterol. In a randomized, crossover controlled trial, 17 subjects received cricket powder or control products for 21 days, separated by a 4-week washout. Gut microbiome composition was profiled using full-length 16S rRNA gene sequencing, and fecal short-chain fatty acids (SCFAs) were quantified by gas chromatography-mass spectrometry. Blood lipids and gastrointestinal tolerance were also assessed. As a result, cricket powder did not alter overall microbial diversity or community structure but induced targeted species-level shifts, including enrichment of Blautia faecis and Mediterraneibacter glycyrrhizinilyticus. Despite these compositional changes, fecal SCFAs remained unchanged. Notably, branched-chain SCFAs were not increased, indicating no shift toward proteolytic fermentation and preservation of microbial metabolic balance. Gastrointestinal tolerance was maintained without adverse effects. Blood lipid parameters were unchanged, with a modest trend toward increased high-density lipoprotein cholesterol (HDL-C). Collectively, cricket powder induces selective microbiome remodeling without disrupting metabolic homeostasis, supporting its potential as a sustainable, microbiome-targeted functional food.},
}

@article {pmid42692206,
year = {2026},
author = {Browning, BD and Kirkland, AE and Meredith, LR and Perica, MI and Engevik, MA and Barb, JJ and Ferguson, PL and Tomko, RL and Squeglia, LM},
title = {Within- and Between-Visit Variability and Reproducibility of the Oral Microbiome in Young Adults with Alcohol Use Disorder.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2026.09.001},
pmid = {42692206},
issn = {1873-6823},
abstract = {BACKGROUND: The oral microbiome has emerged as a potential biomarker and pharmacological target in alcohol use disorder (AUD) due to its associations with alcohol use and related biological processes. However, its temporal variability and reproducibility remain poorly understood, limiting its utility.

METHODS: Saliva samples were obtained from participants enrolled in a randomized controlled trial of young adults with AUD. Temporal variability and reproducibility were evaluated using within-visit samples (∼4 hours apart; before and after sesame oil placebo and standardized snack) and between visits (∼25 days; pre-treatment). Alpha diversity, beta diversity, differential abundance, and intraclass correlation coefficients (ICCs) were calculated at the genus and species levels.

RESULTS: Significant within-visit differences were observed in alpha diversity, beta diversity, and the abundance of several genera and species. Snack type and time since last alcohol use explained comparable or greater variance in microbial composition than within-visit timepoint (4-6%). Although reproducibility of alpha diversity within-visit was generally low, most genera (70.3%) and species (74.6%) demonstrated at least moderate reproducibility. In contrast, no detectable systematic between-visit differences were observed in diversity or taxon abundance, and reproducibility was generally moderate for alpha diversity measures and most genera (67.6%) and species (72.2%).

CONCLUSIONS: Despite group-level microbial shifts within-visit, individual-level microbial features were generally reproducible both within (∼4 hours) and between (∼25 days) visits. No systematic group-level differences were detected between-visits.These findings support the use of the oral microbiome in AUD research while emphasizing the importance of longitudinal designs and accounting for recent exposures.},
}

@article {pmid42692250,
year = {2026},
author = {Wang, L and Zhang, Y and Li, W and Zhang, X and Li, C and Liu, Y and Su, Z and Wang, Y and Sun, C and Huang, L},
title = {Mulberry-derived endophytic Bacillus velezensis suppresses gray mold and promotes mulberry growth via reshaping the root metabolism and microbiome.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.09.002},
pmid = {42692250},
issn = {2090-1224},
abstract = {INTRODUCTION: Gray mold is an important fungal disease caused by Botrytis cinerea which threatens global agriculture. As chemical control faces limitations, biological control using Bacillus has gained attention for its environmental friendliness and growth promotion. However, their ecological basis and application potential in mulberry gray mold control remain insufficiently understood.

OBJECTIVE: This study aimed to evaluate the biocontrol efficacy of the mulberry derived endophytic strain Bacillus velezensis ZJU_268 and to investigate its associated effects on plant growth, root-associated microbiomes, and metabolic profiles.

METHODS: Greenhouse assays were combined with genomic and comparative genomic analyses, amplicon sequencing, non-targeted metabolomics, and functional validation of isolated microbes and metabolites to assess the effects of ZJU_268 and its cell free supernatant (CFS) on mulberry seedlings.

RESULTS: This study isolated a mulberry derived endophytic bacterium, B. velezensis ZJU_268, which exhibits strong antifungal activity and reduces the incidence of gray mold in mulberry seedlings. Whole-genome sequencing and comparative genomic analyses revealed strain-specific regions and genes associated with root colonization, stress adaptation, and antimicrobial biosynthesis. Both live cells and CFS significantly promoted seed germination, seedling growth, and biomass accumulation in a dose dependent manner. Amplicon sequencing showed that ZJU_268 and its supernatant reshaped the mulberry root microbiome, enriching beneficial bacterial and fungal taxa while reducing potentially pathogenic members. Cultivable members of the enriched microbiota displayed strong antifungal activity against B. cinerea and promoted mulberry growth. Metabolomic profiling further showed that ZJU_268 and its supernatant were associated with marked metabolic shifts in mulberry roots, accompanied by the accumulation of selected metabolites that supported the growth of representative enriched isolates.

CONCLUSIONS: This study demonstrates that ZJU_268 suppresses gray mold and promotes mulberry growth in association with direct antagonistic activity, microbiome restructuring, and holobiont-level metabolic shifts, providing a promising biological strategy for sustainable mulberry disease management.},
}

@article {pmid42692351,
year = {2026},
author = {Liu, P and Li, J and Zhu, C and Mao, S and Xie, F and Jin, W},
title = {Dietary supplementation of resveratrol alters rumen microbiome and reduces urinary trimethylamine/trimethylamine N-oxide excretion in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28661},
pmid = {42692351},
issn = {1525-3198},
abstract = {Trimethylamine (TMA) is a major product of ruminal choline metabolism. Understanding the microbial pathways associated with TMA formation may provide opportunities to improve rumen fermentation efficiency and animal productivity; however, effective strategies to regulate rumen TMA production remain poorly understood. In this study, in vitro and in vivo experiments were combined to investigate the effects of resveratrol on rumen TMA production and urinary excretion in dairy cows. In vitro rumen fermentation was conducted with 4 resveratrol doses (0, 0.5, 5, and 50 mmol/L). Concentrations of TMA were significantly lower in the 5 and 50 mmol/L resveratrol treatments compared with the control (0 mmol/L). The in vivo experiment was conducted using 36 mid-lactation Holstein cows with an average days in milk (DIM) of 171 ± 7 d and an average parity of 3.2 ± 0.4. The experiment lasted for 5 weeks, consisting of a 1-week adaptation period followed by a 4-week experimental period. Cows were blocked according to parity, milk yield, and days in milk and then randomly assigned to CON (basal diet), RES2.4 (basal diet + 2.4 g resveratrol/cow/day), and RES4.8 (basal diet + 4.8 g resveratrol/cow/day). The total concentrations of TMA and trimethylamine N-oxide (TMAO) in plasma and urine were reduced in cows in the RES4.8 group. Resveratrol did not affect dry matter intake, apparent nutrient digestibility, and milk performance, but it altered rumen fermentation parameters. Resveratrol also increased serum globulin and glutathione peroxidase levels and reduced serum IL-6, malondialdehyde, and superoxide dismutase. Metagenomic analysis showed that resveratrol shifted the structure of bacterial and archaeal communities but did not affect those of protozoa and fungi. The relative abundance of Prevotella was significantly lower in the RES4.8 group, whereas Eubacterium_S and the archaeal orders Methanobacteriales, Methanomicrobiales, and Methanococcales were higher. Functional profiling showed that resveratrol did not affect the overall composition of carbohydrate-active enzymes but decreased the abundance of pathways related to oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, terpenoid backbone biosynthesis, lipopolysaccharide synthesis, and phenylpropanoid biosynthesis. Collectively, these findings provide new insights into the mechanisms underlying resveratrol-mediated regulation of rumen function and host TMA/TMAO metabolism.},
}

@article {pmid42692433,
year = {2026},
author = {Ahamba, IS and Goswami, N and Kinkpe, L and Han, H and Ikele, CM and Duan, Q and Kadurumba, O and Dong, X and Ren, Z},
title = {Host genetic and gut microbiota interactions regulating intramuscular fat deposition in livestock: mechanistic insights and implications for meat quality.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.260478},
pmid = {42692433},
issn = {2765-0189},
abstract = {Intramuscular fat (IMF) is a major determinant of meat quality, influencing tenderness, juiciness, flavor, oxidative stability, and nutritional value in livestock products. Increasing evidence indicates that IMF deposition is regulated by complex interactions between host genetics and gut microbial metabolism. This review summarizes current advances in the molecular and metabolic mechanisms linking host genetics and gut microbiota to IMF accumulation and meat quality traits. At the host level, IMF deposition is regulated by coordinated adipogenic networks involving PPARγ-C/EBPα signaling, lipogenic regulators, nutrient-sensitive pathways, and epigenetic modifications that control adipocyte differentiation and lipid storage. In parallel, the gut microbiota acts as an important metabolic regulator by producing bioactive metabolites, including short-chain fatty acids and secondary bile acids, which influence adipogenesis, inflammation, nutrient partitioning, and metabolic flexibility. Emerging evidence further demonstrates that microbial metabolites can modulate host transcriptional and epigenetic programs, thereby linking microbial activity with tissue-specific lipid metabolism. Integrative multi-omics approaches are increasingly revealing the mechanistic basis of host-microbiome interactions underlying variation in carcass composition and meat quality across livestock species. This review further highlights the translational potential of precision nutrition, microbiome modulation, and microbiome-informed breeding strategies for sustainable meat production.},
}

@article {pmid42692679,
year = {2026},
author = {Feng, G and Bayinbate, B and Huang, D and Badar, IH and Xu, B and Hu, Y and Zhang, L},
title = {Unraveling the mechanisms of flavor improvement in salt-reduced dry fermented sausages: Insights from yeast-modulated microbial interactions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120265},
doi = {10.1016/j.foodres.2026.120265},
pmid = {42692679},
issn = {1873-7145},
mesh = {*Meat Products/microbiology/analysis ; Fermentation ; *Food Microbiology ; *Taste ; *Sodium Chloride ; *Microbial Interactions ; Candida/metabolism ; *Debaryomyces/metabolism ; Animals ; Lactobacillales/metabolism ; *Fermented Foods/microbiology ; Odorants/analysis ; Microbiota ; Hydrogen-Ion Concentration ; Yeasts ; },
abstract = {The present study investigated the modulatory effects of Candida zeylanoides AKS6 and Debaryomyces hansenii AKS44 on the quality profile attributes of reduced-NaCl fermented sausages. Results indicated that yeast inoculation decreased pH, moisture content and water activity of reduced-NaCl fermented sausages, establishing a foundation for enhanced microbial safety. Microbiome analysis revealed that the inoculated strains dominated the fungal community, exerting competitive exclusion against endogenous undesirable fungi (e.g., Trichosporon), while synergistically promoting beneficial lactic acid bacteria such as Latilactobacillus and Weissella. Volatile profiling demonstrated that NaCl reduction induced severe flavor defects. Yeast inoculation reduced formic acid content and mitigated lipid oxidation. Furthermore, driven by enhanced microbial esterification, the synthesis of fruity esters was promoted. This microbial restructuring drove the flavor improvement: suppression of off-flavor fungi combined with lactic acid bacteria-mediated ester biosynthesis enriching the fruity ester profile. Specifically, the odor activity value of methyl hexanoate significantly increased, becoming the dominant aroma contributor. These findings highlight the remarkable potential of C. zeylanoides AKS6 and D. hansenii AKS44 as starter cultures to reconstruct the microbial metabolic network and rescue the flavor quality of low-sodium fermented meat products.},
}

*Meat Products/microbiology/analysis
Fermentation
*Food Microbiology
*Taste
*Sodium Chloride
*Microbial Interactions
Candida/metabolism
*Debaryomyces/metabolism
Animals
Lactobacillales/metabolism
*Fermented Foods/microbiology
Odorants/analysis
Microbiota
Hydrogen-Ion Concentration
Yeasts

@article {pmid42692700,
year = {2026},
author = {Li, Z and Guo, Y and Zhang, X and Xie, N and Zhang, F and Zhen, Z},
title = {Integrated microbiome and metabolome analysis reveals microbial and metabolic dynamics associated with goose foie gras spoilage during refrigerated storage.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120303},
doi = {10.1016/j.foodres.2026.120303},
pmid = {42692700},
issn = {1873-7145},
mesh = {Animals ; *Metabolome ; *Food Storage/methods ; *Refrigeration ; *Microbiota ; *Geese/microbiology ; Thiobarbituric Acid Reactive Substances/analysis ; *Food Microbiology ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Colony Count, Microbial ; Bacteria ; Chromatography, High Pressure Liquid ; },
abstract = {Goose foie gras spoils rapidly under refrigeration, yet its microbial and metabolite dynamics during storage are poorly described. Samples from a single Landes production batch were stored at 4 °C in air-sealed polyethylene pouches and analysed on days 0, 2, 4, 6, 8, 10 and 12. Three biological replicates per time point were processed for total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substances (TBARS), 16S ribosomal RNA (rRNA) amplicon sequencing, and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based untargeted metabolomics. TVC increased from 3.85 to 6.16 log CFU/g, TVB-N from 8.99 to 27.77 mg/100 g and TBARS from 0.18 to 0.72 mg MDA/kg between day 0 and day 12, with the steepest changes appearing after day 6. The maximum TVC reached 6.16 log CFU g[-1] on day 12, below the 7 log CFU g[-1] level cited for some meat products; no sensory evaluation was performed. The late storage period is therefore described as a phase of concurrent rises in TVC, TVB-N and TBARS rather than as a confirmed spoilage endpoint. The 14 most abundant genera were retained for multivariate analysis. Seven genera, including Brochothrix, Pseudomonas, Lactobacillus and Lactococcus, met the operational definition of candidate spoilage-associated taxa. Forty candidate metabolites were screened by random forest. Five (tyramine, 4-hydroxyphenylacetaldehyde, adenosine monophosphate, oxidized glutathione and γ-glutamylcysteine) were prioritized on the joint basis of random forest importance, Benjamini-Hochberg-adjusted Kruskal-Wallis p < 0.05, ROC AUC ≥ 0.85 and KEGG pathway interpretability. Microbe-metabolite co-variation was quantified through Benjamini-Hochberg-adjusted Spearman correlation, yielding 108 microbe-metabolite pairs at BH-adjusted P < 0.05 (|ρ| ≥ 0.6), and canonical correlation analysis explained 73.39% of the joint cross-covariance in the first two variates. This study establishes a quantitative microbial-metabolic deterioration signature for refrigerated goose foie gras under air-sealed storage, provides a set of biomarker candidates with defined ROC performance, and identifies shifts in specific tyrosine, glutathione, purine and phospholipid pathways. The concordance between microbial succession and these pathway changes is hypothesis-generating and requires metagenomic confirmation, and these findings are presented as preliminary biochemical anchors for future targeted validation and preservation research.},
}

Animals
*Metabolome
*Food Storage/methods
*Refrigeration
*Microbiota
*Geese/microbiology
Thiobarbituric Acid Reactive Substances/analysis
*Food Microbiology
Metabolomics
RNA, Ribosomal, 16S/genetics
Colony Count, Microbial
Bacteria
Chromatography, High Pressure Liquid

@article {pmid42692712,
year = {2026},
author = {Fu, C and Ye, K and Qiu, Z and Hu, X and Wang, X and Xiao, H},
title = {Agaricus bisporus polysaccharides alleviate high-fat diet-induced cognitive impairment via microbiota-gut-brain axis modulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120317},
doi = {10.1016/j.foodres.2026.120317},
pmid = {42692712},
issn = {1873-7145},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Agaricus/chemistry ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; *Cognitive Dysfunction/drug therapy/etiology/prevention & control ; *Brain/drug effects/metabolism ; *Polysaccharides/pharmacology ; Hippocampus/drug effects/metabolism ; *Brain-Gut Axis/drug effects ; Neuronal Plasticity/drug effects ; Microglia/drug effects ; *Fungal Polysaccharides/pharmacology ; Fatty Acids, Volatile/metabolism ; },
abstract = {This study aimed to explore the protective effect of Agaricus bisporus polysaccharide (ABP) against high-fat diet (HFD) induced cognitive impairment (CI), with a particular focus on gut-brain communication. ABP supplementation alleviated anxiety-like behavior and cognitive deficits in HFD-fed mice. These effects were associated with enhanced hippocampal synaptic plasticity and attenuated inflammatory responses, which were accompanied by the elevation of Bdnf levels and the upregulated expression of plasticity-related genes (e.g., Gria2, Grin2b, Tdp2, and Fxr1). Crucially, ABP supplementation was associated with alleviated HFD-induced morphological changes in microglia and reduced inflammatory factor mRNA levels (Tnf, Il1b). Meanwhile, ABP remodeled the gut microbiome, significantly enriching beneficial taxa including Akkermansia and Bacteroides and enhancing the production of short-chain fatty acids (SCFAs), mainly acetate and propionate. These findings suggest that ABP may serve as a promising nutritional component for alleviating diet-related CI with effect associated with modulation of the microbiota-gut-brain axis.},
}

Animals
*Diet, High-Fat/adverse effects
*Agaricus/chemistry
*Gastrointestinal Microbiome/drug effects
Male
Mice
Mice, Inbred C57BL
*Cognitive Dysfunction/drug therapy/etiology/prevention & control
*Brain/drug effects/metabolism
*Polysaccharides/pharmacology
Hippocampus/drug effects/metabolism
*Brain-Gut Axis/drug effects
Neuronal Plasticity/drug effects
Microglia/drug effects
*Fungal Polysaccharides/pharmacology
Fatty Acids, Volatile/metabolism

@article {pmid42692846,
year = {2026},
author = {Vykypělová, M and Khrapova, V and Adamovský, O},
title = {Microplastic in human body - a critical insight into current microplastic research.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {58-62},
doi = {10.48095/ccko2026S58},
pmid = {42692846},
issn = {1802-5307},
mesh = {Humans ; *Microplastics/analysis ; *Environmental Exposure/adverse effects/analysis ; Particle Size ; *Environmental Pollutants/analysis ; },
abstract = {BACKGROUND: Microplastics and nanoplastics are ubiquitous environmental contaminants, and human exposure via ingestion and inhalation is increasingly recognized. Numerous studies report microplastics in human tissues and biological fluids, yet the biological relevance and robustness of these findings remain uncertain. This critical work evaluates current evidence on microplastics in the human body, focusing on exposure pathways, particle size relevance, and analytical limitations. Mechanistic data indicate that translocation across intestinal and pulmonary barriers is likely restricted to small microplastics (< 10 µm) and nanoplastics, raising questions about reports of larger particles in human tissues. Key challenges include secondary contamination, size-dependent detection limits, and methodological artifacts associated with common analytical techniques. Experimental evidence for biological effects, including inflammation, microbiome disruption, and cancer-related pathways, is discussed in the context of physiological relevance.

AIM: Overall, our work highlights the need for standardized analytical methods, rigorous quality control, and mechanistic studies using realistic exposure scenarios to support sound microplastics related human health research.},
}

Humans
*Microplastics/analysis
*Environmental Exposure/adverse effects/analysis
Particle Size
*Environmental Pollutants/analysis

@article {pmid42692847,
year = {2026},
author = {Budinská, E},
title = {Microbiome in early cancer detection - biomarker potential and limitations.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {63-66},
doi = {10.48095/ccko2026S63},
pmid = {42692847},
issn = {1802-5307},
mesh = {Humans ; *Early Detection of Cancer/methods ; *Neoplasms/diagnosis/microbiology ; *Microbiota ; *Biomarkers, Tumor ; },
abstract = {BACKGROUND: Microbiome analysis in cancer research has experienced a surge in interest comparable to the introduction of microarrays for tumor gene expression profiling 25 years ago. Associative studies investigating the composition of the microbiome in stool, tumor tissue swabs and tumor biopsies of oncology patients have been conducted across most cancer types, and their number continues to grow. Screening approaches based on non-invasive or minimally invasive sampling, including the analysis of stool, saliva, urine, and buccal and rectal swabs, are from a clinical perspective among the most promising, owing in part to simpler logistics and the possibility of repeated sampling. These types of specimens are commonly used in microbiome studies, making the microbiome an attractive target for both screening and diagnostic applications.

AIM: This review aims to summarize current knowledge regarding the potential of the microbiome in the early detection of cancer, emphasizing its clinical applicability and limitations in the context of population-based prevention.},
}

Humans
*Early Detection of Cancer/methods
*Neoplasms/diagnosis/microbiology
*Microbiota
*Biomarkers, Tumor

@article {pmid42692848,
year = {2026},
author = {Bořilová Linhartová, P and Száraz, D},
title = {Probiotics, postbiotics, and synbiotics in the prevention of oncological diseases.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {67-71},
doi = {10.48095/ccko2026S67},
pmid = {42692848},
issn = {1802-5307},
mesh = {Humans ; *Probiotics/therapeutic use ; *Synbiotics/administration & dosage ; *Neoplasms/prevention & control/microbiology ; Animals ; Prebiotics ; Microbiota ; },
abstract = {BACKGROUND: In the context of oncological diseases of (not only) the gastrointestinal tract and the oral cavity, the role of microorganisms is being increasingly discussed and investigated. A growing body of evidence supports the significance of specific microbial strains and their products both in the etiopathogenesis of certain cancers and in their prevention and therapy.

AIM: This review summarizes recent findings on the targeted modulation of the human microbiota using probiotics (including Bifidobacteria, Lactobacilli, etc.), their products (postbiotics, e. g. butyrate), and formulations combining probiotics with prebiotics (synbiotics), in the context of cancer prevention and progression, adverse effects of anticancer therapy, and associated complications related to the disease and surgical treatment. The results of clinical studies demonstrate the benefits of these preparations, particularly in preventing and alleviating gastrointestinal symptoms and postoperative infectious complications, as well as inflammatory mucosal damage (including oral mucositis) in oncology patients, with multi-strain probiotic formulations demonstrating greater efficacy. Research is even underway in animal models to explore the use of probiotics in immunotherapy. Despite the promising results obtained from modulating the human microbiota to improve the quality of life of cancer patients, as well as for cancer prevention and potentially even therapy, broader clinical implementation is limited by interindividual variability of the microbiome, safety concerns in immunocompromised patients, and the insufficiently documented quality of some available products. Nevertheless, given the undeniable mechanistic and translational potential of probiotic, postbiotic, and synbiotic supplementation, continued clinical research in this field is highly warranted.},
}

Humans
*Probiotics/therapeutic use
*Synbiotics/administration & dosage
*Neoplasms/prevention & control/microbiology
Animals
Prebiotics
Microbiota

@article {pmid42692861,
year = {2026},
author = {Subrahmanian, A and Patel, A and Veerus, L and Dominguez-Bello, MG and Blaser, MJ},
title = {Methanogens: vital but threatened members of the human microbiome?.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.08.008},
pmid = {42692861},
issn = {1878-4380},
abstract = {Methanogens are an ancestral group of archaea that occupy a unique niche within the human gut microbiome by virtue of their methane production. In this process, they serve as hydrogen sinks, allowing continued bacterial fermentation and influencing short-chain fatty acid production. Available evidence suggests that methanogen abundance may be declining in parallel with the broader reduction in gut microbial diversity accompanying industrialization. We describe the evolution of methanogens, their ecological roles in the human microbiome, and evidence for their apparent decline. If confirmed, reductions in methanogen prevalence and abundance may have substantial metabolic consequences, reframing these archaea as keystone species in need of scientific attention and conservation efforts.},
}

@article {pmid42692903,
year = {2026},
author = {Hejndorf, S and Gulay, A and Zheng, C and Nielsen, RV and Rasmussen, SB and Grønlykke, L and Nørgaard, JC and Rasmussen, KK and Rafiq, S and Català-Moll, F and Ravn, HB and Lundgren, J and Murray, DD and Ilett, E},
title = {The Relationship Between the Preoperative Gut Microbiome and Systemic Inflammatory Response Syndrome After Cardiac Surgery: A Prospective Cohort Study.},
journal = {Journal of cardiothoracic and vascular anesthesia},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.jvca.2026.08.119},
pmid = {42692903},
issn = {1532-8422},
abstract = {OBJECTIVES: To determine whether preoperative intestinal microbiome characteristics are associated with the development of systemic inflammatory response syndrome (SIRS) after cardiac surgery.

DESIGN: Single-center prospective observational cohort study.

SETTING: Tertiary university hospital.

PARTICIPANTS: A total of 196 adults undergoing elective cardiac surgery with extracorporeal circulation between 2018 and 2019.

INTERVENTIONS: No microbiome-targeted intervention was performed.

MEASUREMENTS AND MAIN RESULTS: Shotgun metagenomic sequencing was used to assess microbial diversity (inverse Simpson index, gene richness, dominance), taxonomic composition, and functional potential. The primary outcome was development of SIRS within 24 hours postoperatively. Associations were evaluated using Wilcoxon rank-sum tests, χ[2] tests, and logistic regression adjusted for age and sex. Forty-four patients (22%) developed SIRS. Microbiome diversity did not differ significantly between patients with and without SIRS (median inverse Simpson index 20.4 v 19.3, p = 0.12; gene richness, p = 0.30; dominance, p = 0.61). In adjusted analyses, diversity was not associated with SIRS risk (odds ratio, 1.04; 95% confidence interval, 0.99-1.07). Descriptive analyses of taxonomic composition and functional potential similarly revealed no significant differences between SIRS and non-SIRS groups.

CONCLUSIONS: In this cohort of elective cardiac surgery patients, preoperative gut microbiome diversity, composition, and functional potential were not associated with the development of postoperative SIRS. These findings do not support a strong causal or predictive role of the presurgical gut microbiome in postoperative inflammatory responses after cardiac surgery.},
}

@article {pmid42692915,
year = {2026},
author = {Pushpakumara, BLDU and Coffey, MJ and Hudson, J and Halim, J and Chuang, S and Prentice, B and Jaffe, A and Edwards, R and Day, AS and Oliver, M and Ranganathan, S and Wainwright, C and Selvadurai, H and van Dorst, J and Ooi, CY},
title = {The cystic fibrosis gut microbial dysbiosis index (CF-GMDI): a quantitative measure of gut microbial imbalance in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.08.007},
pmid = {42692915},
issn = {1873-5010},
abstract = {BACKGROUND: Gut dysbiosis is a hallmark of cystic fibrosis (CF), typically characterised using non-specific diversity metrics and study-specific taxonomic lists, limiting comparability across studies. We aimed to develop a metagenomic, species-level CF Gut Microbial Dysbiosis Index (CF-GMDI) to standardise measurement of gut microbial imbalance in children with CF (cwCF) METHODS: CF-GMDI was derived using stool metagenomic data from the PEARL-CF study (70 cwCF; 67 healthy controls (HC); 0-6 years). Differentially abundant taxa were identified between cwCF and HC using MaAsLin2. The index was calculated as the log10 ratio of the summed relative abundances of taxa enriched in CF vs HC to those depleted in CF vs HC. Reproducibility was assessed in the independent EARTH cohort (56 cwCF; 56 HC; 0-18 years). Responsiveness to therapy was evaluated using publicly available metagenomic data from an Elexacaftor/Tezacaftor/Ivacaftor (ETI) study (39 cwCF; 6-18 years).

RESULTS: CF-GMDI was significantly higher in cwCF than HC (p < 0.001), inversely correlated with species richness (ρ = -0.74, p < 0.001), and higher in pancreatic-insufficient vs pancreatic-sufficient cwCF in the PEARL-CF cohort (p = 0.01). Key ecological and clinical associations were replicated in the EARTH cohort. In the ETI study, CF-GMDI decreased significantly at 6 and 12 months post-treatment, whereas alpha diversity remained unchanged.

CONCLUSIONS: CF-GMDI is a CF-associated metric that captures clinically relevant gut microbiome restructuring not detected by standard diversity measures in cwCF (0-18 years). It differentiates disease and pancreatic status and tracks therapeutic modulation, supporting its use as a novel endpoint in CF intervention studies.},
}

@article {pmid42693012,
year = {2026},
author = {Nan, YQ and Wei, LW and Chen, RN and Zheng, XX and Chai, S and You, M and Zhang, H and Qin, N},
title = {[Role of bidirectional interaction between TCM and gut microbiota in treatment of osteoporosis].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {16},
pages = {4581-4593},
doi = {10.19540/j.cnki.cjcmm.20260504.801},
pmid = {42693012},
issn = {1001-5302},
mesh = {Humans ; *Osteoporosis/drug therapy/microbiology/metabolism ; Animals ; *Drugs, Chinese Herbal/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Medicine, Chinese Traditional ; },
abstract = {With the progressive aging of the population in China, the incidence of osteoporosis(OP) is rising annually. This condition not only severely impacts patients' quality of life but also imposes a substantial economic burden on both families and the society. Although modern western medicine has achieved progress in inhibiting OP progression and alleviating associated clinical symptoms, its overall therapeutic efficacy remains suboptimal due to issues such as adverse drug reactions and patient tolerance. Consequently, developing efficient, safe, and cost-effective prevention and treatment strategies has become an urgent priority in current OP-related clinical and scientific research. In recent years, growing insights into the microbiome have revealed that the gut microbiota can regulate bone quantity and quality through multiple mechanisms, including immune modulation, calcium and phosphorus absorption, and the production of short-chain fatty acids, thereby improving the bone microenvironment. As an important component of traditional medicine, TCM is characterized by multi-component and multi-target effects, with therapeutic advantages in holistic regulation. Studies have shown that TCM can effectively improve bone mineral density, inhibit bone resorption, and promote bone formation, with a low incidence of adverse reactions and mild pharmacological effects, demonstrating its unique clinical value in the prevention and treatment of OP. Simultaneously, complex interactions exist between TCM and the gut microbiota. On the one hand, the active components of TCM can modulate the composition and structure of the gut microbiota, reduce systemic inflammation, and ultimately improve bone metabolism. On the other hand, the gut microbiota can metabolize and transform the active components of TCM, enhancing their bioavailability and promoting therapeutic efficacy. This article systematically reviews the roles of gut microbiota and TCM in OP, as well as the bidirectional interaction between TCM and gut microbiota in the prevention and treatment of OP, aiming to provide new insights and evidence for the clinical management of OP.},
}

Humans
*Osteoporosis/drug therapy/microbiology/metabolism
Animals
*Drugs, Chinese Herbal/administration & dosage
*Gastrointestinal Microbiome/drug effects
Medicine, Chinese Traditional

@article {pmid42693341,
year = {2026},
author = {Berto, LP and Ding, J and Sakae, LO and Niemeyer, SH and Wierichs, RJ and Ricomini-Filho, AP and Meyer-Lueckel, H and Baumann, T and Carvalho, TS},
title = {Effect of a sodium fluoride rinse on the composition of early oral biofilms formed in situ on enamel and dentine.},
journal = {Clinical oral investigations},
volume = {30},
number = {9},
pages = {},
pmid = {42693341},
issn = {1436-3771},
mesh = {Humans ; *Biofilms/drug effects ; *Sodium Fluoride/pharmacology ; Double-Blind Method ; *Dental Enamel/microbiology ; Cross-Over Studies ; *Dentin/microbiology ; *Mouthwashes/pharmacology ; Adult ; Male ; Female ; Fluoride Treatment ; *Cariostatic Agents/pharmacology ; },
abstract = {OBJECTIVES: Dental caries results from dysbiotic shifts in the microbial community, so modulating biofilm composition represents a valid preventive strategy. The aim of this double-blind randomized crossover in situ study was to investigate how a fluoride rinse can modify the composition of the early oral biofilm formed on enamel and dentine.

MATERIALS AND METHODS: Twelve volunteers wore mandibular appliances containing 3 enamel and 3 dentine specimens for 1 min, to allow basal pellicle formation, then rinsed (1 min) with a NaF solution (500 ppm F⁻) or deionized water (DW) and kept the appliance overnight (8 h). The composition of the biofilms was analysed using full-length 16 S rRNA gene sequencing.

RESULTS: Alpha and beta diversity did not differ between groups. Dominant genera were Streptococcus (61-71%), Haemophilus (15-24%), Gemella (4-6%), Veillonella (1-3%), and Rothia (1-2%), with no significant group differences. On both enamel and dentine, NaF rinse significantly increased the relative abundance of several Streptococcus spp., including S. salivarius and S. toyakuensis, while decreasing species of Streptococcus, Neisseria, and Prevotella. On enamel, NaF reduced S. gordonii and increased S. oralis and S. parasanguinis; on dentine, it increased species of Rothia and Haemophilus.

CONCLUSIONS: NaF rinse induces subtle species-level changes in early biofilms formed on enamel and dentine, while overall community diversity and dominant genera remain stable.

CLINICAL RELEVANCE: This exploratory study suggests that a 500 ppm NaF rinse is associated with subtle species-level shifts in early oral biofilms. Further studies are needed to determine whether these changes translate into functional benefits or improved oral health outcomes.

CLINICAL TRIAL REGISTRATION: The study protocol was registered at ClinicalTrials.gov (NCT04033263).},
}

Humans
*Biofilms/drug effects
*Sodium Fluoride/pharmacology
Double-Blind Method
*Dental Enamel/microbiology
Cross-Over Studies
*Dentin/microbiology
*Mouthwashes/pharmacology
Adult
Male
Female
Fluoride Treatment
*Cariostatic Agents/pharmacology

@article {pmid42693392,
year = {2026},
author = {Zhao, Q and Hu, X and Zeng, X and Zhang, D and Xiao, X and Wei, Y and Cao, X and Zhang, L and Xi, H and Zhao, S},
title = {Effects of Continuous Cropping on Chili Root Rot: Insights from Rhizosphere Microbial Communities and Synthetic Community Applications.},
journal = {Plant disease},
volume = {},
number = {},
pages = {PDIS06251298RE},
doi = {10.1094/PDIS-06-25-1298-RE},
pmid = {42693392},
issn = {0191-2917},
abstract = {Continuous cropping often results in stunted plant growth and a higher incidence of soil-borne diseases. Soil microbial communities play a crucial role in promoting plant growth, maintaining plant health, and enhancing plant resistance to various diseases. This study examines the impact of continuous cropping on chili root rot and explores the contribution of soil microbial communities to alleviating this issue. The results revealed that prolonged continuous cropping significantly altered the composition of the rhizosphere bacterial community. High-throughput sequencing analysis indicated a marked increase in the abundance of Fusarium pathogens, accompanied by a significant decline in antagonistic bacteria from the genera Bacillus and Pseudomonas. LEfSe analysis showed that Bacillus and Pseudomonas were the core bacterial biomarkers in chili continuous cropping soil, which were successfully isolated and demonstrated significant antagonistic effects against Fusarium solani. Utilizing these antagonistic bacteria, nine different synthetic communities (SynComs) were constructed. Among them, the T7 SynCom exhibited excellent biocontrol efficacy. It effectively suppressed the pathogen, reduced the incidence of root rot, and enhanced systemic induced resistance by activating the plant immune-associated pathways, including the MAPK signaling pathway, ethylene signaling pathway, and pathways mediated by jasmonic acid and salicylic acid. These findings offer new insights into using functional SynComs as a sustainable agricultural solution and open new avenues for overcoming the challenges posed by continuous cropping.[Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}

@article {pmid42693537,
year = {2026},
author = {Liu, C and Wang, J and Liaw, A and Ning, Y and Lai, A and Salomon, C and Seneviratne, CJ and Ivanovski, S and Han, P},
title = {Salivary Extracellular Vesicles from Host, Bacteria and Fungus as Nanomessengers Reflecting Host-Microbiome Interaction in Periodontal Inflammation.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.6c09503},
pmid = {42693537},
issn = {1944-8252},
support = {1195451//National Health and Medical Research Council/ ; 2034591//National Health and Medical Research Council/ ; PJ-0000042//Australian Dental Research Foundation/ ; },
abstract = {Extracellular vesicles (EVs) secreted by the host and polymicrobial oral community are natural endogenous biological nanoparticles that mediate host-microbe interactions. Given their abundance in biofluids, host, fungal and bacterial EVs circulating in saliva may reflect periodontitis-associated microbial dysbiosis and inflammation. In this study, salivary EVs from 20 healthy controls and 57 stages III/IV periodontitis were isolated using a dual strategy: immunoaffinity to isolate host EVs for cytokine profiling, followed by size-exclusion chromatography (SEC) to enrich non-host (microbial) EVs for 16S rRNA and fungal ITS sequencing. In periodontitis, we observed a significant increase in CD49e+ and CD105+ host EV subpopulations and elevated host EV-associated cytokines of tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and granulocyte-macrophage colony-stimulating factor (GM-CSF), indicating an enhanced inflammatory host-EV profile. 16s rRNA sequencing of non-host microbial EV-DNA profiling revealed enrichment of bacterial EVs (BEVs), including genera Porphyromonas, Treponema, Filifactor, and Tannerella, with species of Porphyromonas gingivalis, Filifactor alocis, Tannerella forsythia, Treponema denticola, and Treponema socranskii. In contrast, commensal genera BEVs (Neisseria, Haemophilus) and fungal EVs from Malassezia globosa were enriched in health. Fungal EVs from Candida albicans and M. arunalokeiwere also elevated in disease. Combined host-EVs-IL-9 and T. forsythia-BEVs achieved an AUC of 0.989, increasing to 0.992 with the addition of F. alocis-BEVs, outperforming individual markers (AUC = 0.85-0.91). Pooled periodontitis microbial EVs (10 µg/mL) induced a proinflammatory response in the oral keratinocytes (OKFs) after 24 h, with increased IL-6 and IL-8 cytokines, and upregulated mRNA expression of C-C motif chemokine ligand 2 (CCL2), IL-1β, and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) compared with the no-EV control. Our findings demonstrated that salivary host-, bacterial-, and fungal-derived salivary EVs act as natural nanomessengers reflecting host-microbiome interactions and represent promising non-invasive candidate biomarkers of periodontitis.},
}

@article {pmid42693757,
year = {2026},
author = {Lorefice, L and Fenu, G and Fantola, G and Zoledziewska, M},
title = {Ultra-processed foods and multiple sclerosis: Evidence, pitfalls and perspectives.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585261481479},
doi = {10.1177/13524585261481479},
pmid = {42693757},
issn = {1477-0970},
abstract = {Ultra-processed foods are increasingly recognised as drivers of adverse health outcomes, yet their implications for multiple sclerosis remain underexamined. Emerging evidence suggests that ultra-processed food-rich dietary patterns are associated with greater central adiposity, pro-inflammatory metabolic signatures, microbiota disruption and adverse neuroimmune profiles relevant to multiple sclerosis. Major conceptual pitfalls, including the heterogeneity of ultra-processed foods and the scarcity of longitudinal or interventional studies addressing neuroimmune outcomes, continue to limit interpretation. Ultra-processed food-driven comorbidities, such as obesity, hypertension, dyslipidaemia, insulin resistance and depression, may further accelerate disability accumulation and reduce treatment efficacy in multiple sclerosis, underscoring the need for integrated dietary-immune models. This review integrates evidence from epidemiology, mechanistic studies, microbiome research and exposome science to provide a coherent framework for interpreting ultra-processed food-multiple sclerosis interactions. Recognising ultra-processed food exposure as a potentially modifiable contributor to multiple sclerosis activity may inform future preventive and therapeutic strategies.},
}

@article {pmid42694203,
year = {2026},
author = {Sun, W and Wang, Y and Zhang, X and Yue, Y and Sun, X and Miao, J and Han, S and Zhou, Z and Wang, X and Zhu, W},
title = {Dietary tryptophan ameliorates metalaxyl-induced colitis by restoring microbial tryptophan metabolism and aryl hydrocarbon receptor activation.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1930000},
pmid = {42694203},
issn = {2296-861X},
abstract = {INTRODUCTION: The extensive production of environmental pollutants has heightened susceptibility to intestinal disorders, potentially through alterations in the gut microbiota. However, the precise role of the gut microbiota in environmental pollutant-induced inflammation remains incompletely understood.

METHODS: In this study, wild-type and IL-10[-/-] mice were employed to simulate the responses of healthy individuals and those genetically predisposed to inflammatory bowel disease (IBD) to environmental toxicants. Mice were exposed to metalaxyl, and an integrated multi-omics approach combining microbiome and metabolome profiling with machine learning was conducted to investigate the underlying mechanisms. Additionally, dietary tryptophan supplementation was administered to evaluate its protective effects.

RESULTS: Metalaxyl exposure induced low-grade colonic inflammation in wild-type mice and triggered severe colitis in IBD-susceptible mice. Multi-omics analysis revealed that metalaxyl significantly disrupted gut microbial composition, reduced the synthesis of endogenous tryptophan-derived metabolites, and inhibited aryl hydrocarbon receptor (AhR) signaling, ultimately initiating intestinal barrier dysfunction and inflammatory cascades. Notably, dietary tryptophan restored gut tryptophan metabolite levels, strengthened AhR signaling, mitigated intestinal inflammation, and repaired barrier defects.

DISCUSSION: This study identifies the gut microbiota as a central mediator of environmental pollutant-induced IBD and demonstrates that a high-tryptophan diet exerts beneficial effects against environmental colitis via the AhR axis. Furthermore, the stable phenotypes and high reproducibility of this dual-genotype mouse model underscore its utility as an ideal platform for investigating the enterotoxic effects of environmental pollutants.},
}

@article {pmid42694259,
year = {2026},
author = {Maslov, DE and Osipov, ID and Zabelina, DS and Demina, DS and Tomilova, YE and Berdieva, SB and Makukha, VV and Komissarova, TV and Agletdinov, EF and Netesov, SV},
title = {Molecular epidemiology of respiratory viral infections in hospitalized children in Novosibirsk, Russia, 2021-2023.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1882419},
pmid = {42694259},
issn = {2296-2360},
abstract = {BACKGROUND: Acute respiratory infections (ARIs) are among the leading global causes of morbidity and mortality in children. While viral agents of ARI are rigorously monitored, other pathogenic organisms and pathobionts - bacteria and fungi native to the host microbiome - remain largely neglected. Adenoviral types also warrant particular attention especially given the widespread use of adenoviral vector vaccines during the COVID-19 pandemic.

METHODS: Oro-nasal swabs collected from 1679 children under the age of 18 hospitalized in Novosibirsk, Russia between February 2021 and June 2023, were tested for the presence of nucleic acids by the diagnostic panel targeting 17 viruses, 12 bacteria and one yeast. Adenovirus-positive samples were additionally fine-typed by Sanger sequencing.

RESULTS: Overall, 79.15% of samples were positive for at least one of 17 viral pathogens, with RSV (22.87% positives) and RhV (24.54% positives) dominating the etiological structure. Oro-nasal presence for respiratory pathobionts and opportunistic pathogens was 67.96% and 11.49%, respectively. Generally, viral seasonality was typical for continental climate, with only two notable deviations: MpV absence in spring of 2022 followed by earlier December peaks in the same year; an earlier RSV maximum in October 2021 with extended circulation the next epidemic season. Overall, the epidemiology of the analyzed viruses was consistent with worldwide surveillance trends and largely stable between the two later epidemic seasons. In viral-bacterial association analysis we identified two significantly attracted pairs, in which virus is known to facilitate bacterial adherence to respiratory epithelium. Adenovirus fine-typing provided preliminary evidence that serotypes 1, 2, 3, and 7 are the most frequently detected among the typed samples, while vaccine serotype AdV-5 was identified in only two cases.

CONCLUSION: Broad target coverage allowed for a comprehensive analysis of epidemiological patterns, highlighting a trend toward stabilization of the etiological structure to pre-pandemic levels, and allowed for prioritization of clinically relevant viral-bacterial associations. Preliminary findings in adenoviral fine-typing are consistent with global trends in serotype prevalence and help address an important gap in regional adenoviral epidemiology.},
}

@article {pmid42694300,
year = {2026},
author = {Mojsak, P and Zmyslowska-Polakowska, E and Chmielewska, S and Sołowiej, K and Ploszaj, T and Skoczylas, S and Grzybowska-Adamowicz, J and Pienkowski, T and Kretowski, A and Zmyslowska, A and Ciborowski, M},
title = {Integrated Oral Microbiome and Metabolome Profiling Identifies Disease-Associated Multi-Omics Signatures in Alström and Bardet-Biedl Syndromes.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0211},
pmid = {42694300},
issn = {2001-0370},
abstract = {Background: Alström syndrome (ALMS) and Bardet-Biedl syndrome (BBS) are rare ciliopathies characterized by multisystem involvement, including obesity, insulin resistance, and type 2 diabetes. Systemic metabolic dysfunction may influence the oral microbiome; however, integrative analyses that combine microbial and metabolic profiles in these disorders remain limited. Methods: Saliva and gingival crevicular fluid (GCF) samples were collected from genetically confirmed ALMS and BBS patients, as well as from obesity and healthy control groups. Microbial communities were profiled using V3-V4 16S rRNA gene amplicon sequencing, and untargeted metabolomic profiling was performed by gas chromatography-mass spectrometry. Microbiome-metabolome associations were evaluated using Spearman's rank correlation analysis, followed by multi-omics integration using Multiple Co-Inertia Analysis (MCIA) and the supervised Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO) framework (mixOmics). Results: Integrated analysis identified distinct microbiome-metabolome association patterns in ALMS and BBS. Compared with controls, the ALMS+BBS group showed enrichment of Prevotella, Enterococcus, and Eikenella, alongside reduced Lactobacillus abundance. Metabolomic profiling revealed alterations in amino acid, fatty acid, and carbohydrate metabolism. GCF exhibited structured associations between metabolites and Firmicutes, Proteobacteria, and Actinobacteriota, whereas saliva showed broader interaction networks. These associations were absent or markedly weaker in obesity and healthy controls. MCIA demonstrated coordinated variation across the oral microbiome, salivary metabolome, and GCF metabolome, while DIABLO identified a shared multi-omics signature. Conclusions: Coordinated shifts in amino acid, lipid, and central carbon metabolism can be linked to oral microbial reorganization in ALMS and BBS. Integrative multi-omics analyses identified coordinated microbiome-metabolome signatures across the oral microbiome, saliva, and GCF. These findings warrant validation in larger longitudinal and functional studies.},
}

@article {pmid42694318,
year = {2026},
author = {Das, M and Thajuddin, N and Muralitharan, G and Pundeer, M and Ponnusamy, R and Mishra, A and Nayak, P},
title = {From Gut to Mind: Impact of Probiotics on Depression, Anxiety, Mood, Gut Microbiota, Sleep and Stress-A Systematic Review of RCTs.},
journal = {Annals of neurosciences},
volume = {},
number = {},
pages = {09727531261478458},
pmid = {42694318},
issn = {0972-7531},
abstract = {BACKGROUND: Probiotic supplementation may influence mental health through the gut-brain axis, with potential effects on depression, anxiety, sleep, cognition, stress hormones, and gut microbial composition. This systematic review aimed to evaluate the effects of probiotics on psychological, physiological, and gut microbiome-related outcomes across diverse populations.

SUMMARY: A comprehensive search of PubMed, MEDLINE, PsycINFO, and ScienceDirect identified randomized controlled trials evaluating probiotic supplementation. Twenty RCTs were included, of which 15 were assessed as having a low risk of bias and five as having a high risk of bias. Commonly assessed outcomes included depression (n = 17), anxiety (n = 10), sleep quality (n = 9), stress (n = 6), cortisol (n = 7), cognitive function (n = 5), quality of life (n = 5), gut microbial composition (n = 11), and other neuroendocrine and inflammatory markers. Overall, probiotics were associated with improvements in depression, anxiety, sleep quality, mood, cognition, quality of life, and beneficial gut microbial populations, although findings for cortisol and stress-related outcomes were inconsistent.

KEY MESSAGE: Probiotic supplementation may provide beneficial effects on psychological well-being and gut microbial composition. However, heterogeneity among interventions, populations, outcome measures, and study quality warrants further well-designed RCTs.},
}

@article {pmid42694357,
year = {2026},
author = {Chen, L and Ye, L and Li, X and Zhou, H},
title = {The relationship between C. psittaci infection and respiratory failure based on respiratory microbiota analysis: a retrospective cohort study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1899239},
pmid = {42694357},
issn = {2296-858X},
abstract = {OBJECTIVES: This study aimed to explore the impact of the pulmonary microbiota on the occurrence of respiratory failure in patients with psittacosis pneumonia.

METHODS: A total of 20 patients diagnosed with psittacosis pneumonia were enrolled in this study. Patients were divided into two groups according to the presence or absence of respiratory failure at admission. Clinical data, laboratory findings, and bronchoalveolar lavage fluid analyses were collected. Next-generation sequencing was employed to analyze the pulmonary microbiota.

RESULTS: In this cohort, patients with respiratory failure exhibited a significantly higher relative abundance sequences of C. psittaci compared with those without respiratory failure. Notably, Spearman correlation analysis indicated a significant negative correlation between C. psittaci relative abundance of sequences and CD4+ T-lymphocyte counts (r = -0.870, p = 0.002) and a positive correlation with the pulmonary arteriovenous oxygen partial pressure difference (r = 0.728, p = 0.017). Further analysis of the bacterial communities showed a negative association between Pseudomonas and C. psittaci (r = -0.509, p = 0.031), whereas Veillonella was positively correlated with C. psittaci (r = 0.533, p = 0.023).

CONCLUSIONS: The relative abundance sequences of C. psittaci was significantly higher in patients with respiratory failure than in those without respiratory failure, suggesting an association between C. psittaci load and disease severity. The significant negative correlation between relative abundance sequences of C. psittaci and CD4+ T-lymphocyte count suggests that C. psittaci may exacerbate disease progression by compromising the host immune response, but direction of this relationship cannot be determined. Furthermore, the negative correlation between the relative abundance sequences of Pseudomonas and C. psittaci suggests a possible competitive or protective interaction between these two organisms. In contrast, the positive correlation between Veillonella and C. psittaci may indicate a shared ecological niche. These findings provide preliminary evidence of a relationship between lung microbiota composition and the severity of psittacosis pneumonia, while the causal mechanisms remain to be elucidated in future studies.},
}

@article {pmid42694431,
year = {2026},
author = {Putignani, L and Marsiglia, R and Turco, L and Russo, A and Pane, S and Fusco, A and Lopetuso, L and Trecarichi, EM},
title = {The gut reservoir of carbapenem-resistant Enterobacterales: from dysbiosis and colonization to infection and decolonization, with a focus on patients with hematologic malignancies - a narrative review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1939690},
pmid = {42694431},
issn = {2235-2988},
mesh = {Humans ; *Hematologic Neoplasms/complications/microbiology ; *Dysbiosis/microbiology ; *Enterobacteriaceae Infections/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Probiotics ; },
abstract = {Carbapenem-resistant Enterobacterales (CRE) remain among the highest-priority antimicrobial-resistant pathogens worldwide, and intestinal colonization is increasingly recognized as the key precursor of invasive infections, particularly in patients with hematological malignancies. Increasing evidence indicates that disruption of the gut microbial ecosystem, reflected in reduced diversity, depletion of beneficial anaerobic taxa, intestinal barrier dysfunction, immune dysregulation, and expansion of Enterobacterales, plays a central role in the transition from colonization to infection. Consequently, restoring colonization resistance through microbiome-targeted interventions has emerged as a promising preventive strategy. This narrative review summarizes the current evidence on the epidemiology and clinical impact of CRE colonization and infection, with particular emphasis on the ecological alterations of the gut microbiome linking gut dysbiosis to epithelial barrier dysfunction, immune dysregulation, and loss of colonization resistance to CRE persistence and invasive infection. We critically discuss both conventional and emerging decolonization approaches, including selective digestive decontamination, probiotics, prebiotics and synbiotics, fecal microbiota transplantation (FMT), bacteriophage therapy, and CRISPR-Cas-based technologies, highlighting their mechanisms of action, available clinical evidence, and current limitations. Particular attention is given to patients with hematological malignancies, in whom the clinical need for effective decolonization strategies is greatest. Although FMT currently represents the most promising microbiome-based intervention, the available evidence remains heterogeneous and largely derived from small studies. Overall, durable and standardized decolonization strategies have yet to be established, underscoring the need for well-designed multicenter randomized clinical trials to define effective microbiome-directed approaches for preventing CRE-related infections in high-risk populations.},
}

Humans
*Hematologic Neoplasms/complications/microbiology
*Dysbiosis/microbiology
*Enterobacteriaceae Infections/microbiology/therapy
*Carbapenem-Resistant Enterobacteriaceae/drug effects
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation
Anti-Bacterial Agents/pharmacology/therapeutic use
Probiotics

@article {pmid42694482,
year = {2026},
author = {Ma, K and Thairu, M and Sankaran, K},
title = {Design, processing, and modeling for longitudinal multiomics microbiome data.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1837109},
pmid = {42694482},
issn = {2235-2988},
mesh = {*Multiomics/methods ; *Microbiota ; Humans ; Longitudinal Studies ; Research Design ; Machine Learning ; },
abstract = {Longitudinal multiomics studies can reveal mechanisms underlying microbiome dynamics. Though gathering such data has become increasingly accessible, challenges remain in experimental design, data processing, and interaction modeling. This mini-review surveys practical approaches for analyzing longitudinal multiomics microbiome data. We provide an overview of fundamental questions these experimental designs can address, discuss concepts for reducing confounding, review tools for data management, and describe statistical and machine learning methods for identifying interactions across time and biological layers. We conclude with emerging trends and open problems.},
}

*Multiomics/methods
*Microbiota
Humans
Longitudinal Studies
Research Design
Machine Learning

@article {pmid42694486,
year = {2026},
author = {Niu, Q and Mu, T and Zhang, J and Chen, Y and Guo, Z and Zhu, Y and Li, L},
title = {Gastrointestinal motility in microgravity: a critical review of multi-level mechanisms and model-dependent effects.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1930628},
pmid = {42694486},
issn = {1664-042X},
abstract = {BACKGROUND: Gastrointestinal motility disturbances rank among the most frequently reported medical complications of spaceflight. Astronauts experience delayed gastric emptying, erratic small intestinal transit and reduced colonic propulsion. The underlying mechanisms are multifactorial. Microgravity alters intra-abdominal physical mechanics, disrupts autonomic and enteric neural circuits, shifts gastrointestinal hormone secretion profiles, inflicts oxidative stress upon effector cells, and perturbs gut microbial communities. Cross-model comparisons reveal substantial disagreement, suggesting that no single ground-based analog fully captures the pathophysiology of orbital flight.

AIM: To critically review how weightlessness affects gastric emptying, small intestinal transit and colonic motility; to critically evaluate contradictory findings across simulation platforms; and to delineate the neural, humoral, cellular and microbiological mechanisms involved.

METHODS: We searched PubMed, Web of Science and the NASA Technical Reports Server for articles published between January 1990 and June 2026 (last search 30 June 2026). Search terms included: "microgravity", "weightlessness", "spaceflight", "gastrointestinal motility", "gastric emptying", "intestinal transit", "gut microbiome", "interstitial cells of Cajal" and "oxidative stress". Studies using head-down bed rest, hindlimb unloading, clinorotation, parabolic flight and actual spaceflight were included. The review follows a critical narrative design; the full search strategy and the framework used to appraise the evidence are described in Section 1.1.

RESULTS: Altered-gravity studies suggest that gastrointestinal dysmotility may involve neurohumoral dysregulation, oxidative injury to interstitial cells of Cajal and smooth muscle, barrier dysfunction and altered enteric signaling; however, most mechanistic evidence derives from simulated models and has not been directly validated during human spaceflight. Direct human motility measurements remain sparse, and the evidence comprises a mixture of direct observations, model-dependent inferences and testable hypotheses. Cross-study agreement is poor: some head-down bed rest trials report accelerated small-bowel transit, whereas tail-suspension models and limited flight observations suggest motor suppression. These divergences may reflect model-specific confounding rather than a uniform effect of microgravity.

CONCLUSION: Current ground-based models each capture only partial aspects of orbital GI pathophysiology. Future work should combine multi-omics profiling with next-generation simulation platforms to develop evidence-based countermeasures for long-duration missions.},
}

@article {pmid42694531,
year = {2026},
author = {Carvalho, A and Gschwendtner, S and Schloter, M and Gil, AM and Marques, CR},
title = {Stool microbiota variations along the adenoma-colorectal carcinoma sequence - robustness of disease-associated microbial features.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1822941},
pmid = {42694531},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) has been linked with gut microbiota dysbiosis, thereby fostering the discovery of disease-associated microbial signatures. However, the use of covariate-adjusted methods accounting for confounders effects on microbiome shifts is far from being a gold standard approach, leading to spurious microbial-disease associations. This study aimed to characterize stool microbiota alterations along the adenoma-carcinoma sequence in a Portuguese cohort, and assess the robustness of candidate microbial features.

METHODS: Stool samples from healthy individuals (HC), adenoma patients (AP), and CRC patients at early (SI/II) and advanced (SIII/IV) stages, were analyzed using 16S rRNA gene amplicon sequencing. Microbial features' profiles were compared with publicly available datasets from France, Ireland, Italy, and USA/Canada. Differential abundance (DA) analysis was conducted through multiple DA models (ANCOM-BC2, fastANCOM, MaAsLin2, limma voom, and LEfSe) and statistical approaches, including covariate (age, sex, and body mass index (BMI)) adjustment, prevalence filtering, and analysis of matched subsets.

RESULTS AND DISCUSSION: Among the altered taxa along de adenoma-carcinoma sequence, Sutterella and Desulfovibrio were generally enriched across different DA tools and matched subset analyses, while Parasutterella and Adlercreutzia were depleted. Sutterella, Parasutterella, and Adlercreutzia, were already altered in adenoma and early-stage CRC samples, maintaining or increasing their effect sizes towards advanced CRC stages. This pattern highlights the potential of these taxa as early microbial signatures of colorectal cancer progression. In contrast, Fusobacterium, which is a widely accepted CRC biomarker, was not detected after covariate adjustment. Cross-cohort comparison revealed a limited reproducibility of microbial features (i.e., Dialister was enriched in the Portuguese and French cohorts; Parasutterella and Terrisporobacter were depleted in the Portuguese and USA/Canada datasets), being most of them cohort-specific.

CONCLUSION: Overall, our results strengthen the importance of covariate control towards the identification of potentially robust and reproducible microbial markers of CRC onset and progression.},
}

@article {pmid42694632,
year = {2026},
author = {Ma, J and Li, S and Qiao, Y and Gao, Z and Liu, J and Song, Y and Liu, Y and Ji, X and Li, J and Zhang, J and Chang, L and Huo, B},
title = {Context-dependent functions of the aryl hydrocarbon receptor in gastrointestinal cancers: from microenvironmental regulation to precision targeted therapy.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1886657},
pmid = {42694632},
issn = {2296-634X},
abstract = {The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor with context-dependent roles in gastrointestinal (GI) tumor development. Depending on cellular context and microenvironment, AhR can preserve epithelial integrity, suppress inflammation, and inhibit tumor growth, but it can also promote immune evasion and metabolic reprogramming to drive tumor progression. Most existing reviews have focused on a single GI tumor type or functional dimension, and the concept of AhR as a context-dependent signaling hub has not been effectively linked to therapeutic stratification across the full spectrum of GI malignancies. No prior review has systematically compared AhR across five GI cancer types-esophageal, gastric, colorectal, hepatocellular, and pancreatic-or addressed the translational gap between preclinical data and clinical application. This review addresses these gaps in three key ways. First, it provides the first head-to-head comparative analysis of AhR functions across these five cancer types. Second, it adopts a functional stratification framework integrating five core mechanistic dimensions-tumor stemness, epithelial-mesenchymal transition, immune remodeling, metabolic reprogramming, and drug resistance-and proposes a three-dimensional AhR stratification model. Third, it systematically discusses emerging AhR-targeted therapeutic strategies-including antagonists, selective AhR modulators (SAhRMs), PROTACs, combination therapies, and microbiome-based interventions-while critically evaluating translational challenges. By establishing this context-informed framework, we aim to provide a conceptual basis for biomarker-guided evaluation of AhR-targeted strategies in GI cancers.},
}

@article {pmid42694728,
year = {2026},
author = {Bautista, J and Iñiguez-Ramírez, A and Villegas-Chávez, JA and Bunces-Larco, D and López-Cortés, A},
title = {Skin microbiome and cutaneous aging mechanisms and clinical implications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1917816},
pmid = {42694728},
issn = {1664-302X},
abstract = {The skin microbiome is an integral component of the cutaneous ecosystem and contributes to barrier, immune, and metabolic homeostasis. Available evidence is examined across three distinct levels: microbial community structure, functional activity, and host biological response. This ecological-functional distinction is necessary because taxonomic abundance alone does not establish microbial activity, biological effects, or causality. Age-associated microbial variation is considered within the physiological context of cutaneous aging, including reduced sebaceous activity, altered hydration and surface pH, impaired barrier recovery, chronic low-grade inflammation, oxidative stress, and extracellular matrix deterioration. Microbial alterations reported in acne, atopic dermatitis, and rosacea further illustrate how changes in the cutaneous environment can modify host-microbiome interactions and contribute to clinically relevant phenotypes. Translational developments in dermatology and aesthetic medicine include microbiome-compatible skincare, prebiotic and postbiotic formulations, live biotherapeutic approaches, and strategies intended to preserve microbial and barrier recovery after dermatological procedures. Interpretation of the available literature remains limited by low microbial biomass, anatomical and interpersonal heterogeneity, contamination risk, differences in sampling and sequencing methods, and limited functional and longitudinal resolution. Observed microbial remodeling should be interpreted within a bidirectional host-microbiome relationship. Physiological changes that accompany aging can reshape microbial ecology, whereas microbial products may modify barrier and immune responses. Current evidence does not establish whether these microbial alterations are causes, consequences, or correlates of cutaneous aging. Integration of strain-resolved microbiome data with microbial gene expression, metabolite measurements, host molecular responses, and clinical phenotypes will be required to identify biologically relevant microbial functions and determine their value in dermatological practice.},
}

@article {pmid42694733,
year = {2026},
author = {Zhao, X and Liu, Z and Yang, J and Xie, Q and Mao, T and Zhou, H and Wang, H and Zheng, P and Jiang, K and Gao, F},
title = {Causal AI for cancer immunotherapy: a narrative framework review of target trial emulation, treatment-effect learning and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1896755},
pmid = {42694733},
issn = {1664-3224},
mesh = {Humans ; *Neoplasms/therapy/immunology ; *Immunotherapy/methods ; *Artificial Intelligence ; Translational Research, Biomedical ; Treatment Outcome ; Clinical Trials as Topic ; },
abstract = {This narrative framework Review examines how artificial intelligence (AI) can move cancer immunotherapy research from outcome prediction toward target-trial-based treatment-effect learning. AI has produced increasingly accurate models for predicting response, survival and immune-related toxicity during cancer immunotherapy. Yet most models estimate outcome risk under observed care rather than the causal effect of choosing one strategy over another. We therefore frame immunotherapy AI as a causal digital-medicine problem: clinically useful AI should begin with a target-trial question that specifies eligibility, time zero, treatment strategies, comparators, outcomes, estimands and bias-control plans before model development. Within this framework, multimodal AI outputs from imaging, digital pathology, omics, microbiome data, electronic health records and clinical text can function as baseline confounders, candidate effect modifiers, longitudinal state variables or outcome-ascertainment tools. We distinguish established causal-inference approaches, such as target trial emulation, propensity-score weighting, g-methods, TMLE, DML and heterogeneous-treatment-effect estimation, from exploratory technologies such as reinforcement learning and digital twins that require prospective safety validation. We close by outlining validation, reporting, workflow, regulatory and lifecycle-monitoring requirements for moving from predictive biomarkers to trustworthy causal learning systems in immuno-oncology.},
}

Humans
*Neoplasms/therapy/immunology
*Immunotherapy/methods
*Artificial Intelligence
Translational Research, Biomedical
Treatment Outcome
Clinical Trials as Topic

@article {pmid42694775,
year = {2026},
author = {Shouq, MI and Saleem, HGM and Wang, Y and Sohail, M and Hussain, A and Zhang, H and Zheng, H},
title = {Lesion-specific oral microbiome signatures and predicted carcinogenic pathways in oral squamous cell carcinoma: a paired-site study in Pakistan.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2721025},
pmid = {42694775},
issn = {2000-2297},
abstract = {BACKGROUND: Oral squamous cell carcinoma accounts for over 90% of oral neoplasms. Despite therapeutic advances, the lack of reliable, non-invasive biomarkers and delayed diagnosis continues to impede effective clinical management. By combining paired lesion and non-lesion sampling with predictive metagenomics analysis, our study addresses this gap and advances the current understanding of microbiome‒tumor interactions.

METHODS: We analyzed 92 buccal swab samples from 39 OSCC patients and 14 healthy controls using 16S rRNA gene (V3-V4) sequencing. Taxonomic profiling was conducted using QIIME2 and SILVA/eHOMD databases, functional pathways were predicted using PICRUSt2, and hub taxa were identified through co-abundance network analysis.

RESULTS: Microbial community structure differed significantly across lesion, non-lesion, and healthy sites (PERMANOVA, p = 0.001). Lesions were enriched with Selenomonas infelix and Treponema vincentii, while healthy controls harbored Streptococcus oralis and Gemella haemolysans. Co-abundance network analysis revealed lesion-specific hub species, notably T. vincentii, strongly correlated with predicted activation of pyrimidine biosynthesis pathways (r = 0.69, q < 1E-6), suggesting predicted metabolic alterations in the tumor microenvironment. Non-lesion sites were also characterized by two hub species, Prevotella melaninogenica and Segatella oulorum.

CONCLUSION: Our findings define a lesion-specific microbial signature of OSCC characterized by the depletion of health-associated taxa, enrichment of pro-inflammatory pathobionts, and predicted associations with metabolic pathways implicated in carcinogenesis. These alterations reflect a predicted functionally altered tumor microenvironment.},
}

@article {pmid42694794,
year = {2026},
author = {Huang, TY and Chen, LL and Peng, FS and Chu, FY and Gau, ML},
title = {Effects of two different perineal preparations before vaginal birth on maternal and neonatal infections and hospital resources: A randomized controlled trial.},
journal = {European journal of midwifery},
volume = {10},
number = {},
pages = {},
pmid = {42694794},
issn = {2585-2906},
abstract = {INTRODUCTION: Perineal preparation during the second stage of labor may influence maternal and neonatal infection risk and healthcare resource utilization. Although povidone-iodine sterilization is traditionally used, microbial flora theory suggests that water cleansing may preserve normal flora without increasing infection while reducing workload and cost. This study compared water cleansing with povidone-iodine sterilization for perineal preparation at Far East Memorial Hospital, Taiwan, from 26 November 2024 to 5 June 2025.

METHODS: A randomized controlled trial design was employed, including 143 mothers randomly assigned to either the water cleansing group (n=72) or the povidone-iodine sterilization group (n=71). Outcome measures included maternal and neonatal infection parameters (maternal postpartum temperature, C-reactive protein, REEDA scores, neonatal temperature, and neonatal oral flora colonization), along with cleansing time and medical costs. Data were analyzed using t-tests, chi-squared tests, and generalized estimating equation (GEE).

RESULTS: GEE analysis revealed no significant differences between the two groups in maternal and neonatal infection indicators (REEDA, 95% CI: -0.53-0.18, p=0.337; maternal temperature, 95% CI: -0.06-0.21, p=0.278; neonate temperature, 95% CI: -0.12-0.19, p=0.636). The water group had significantly lower average medical costs than the povidone-iodine group (7.49 vs 110.92 TWD, t= -50.22, p<0.001), as well as a shorter cleansing time. Regarding neonatal flora colonization, the water group showed higher rates of normal flora (33.8% vs 15.5%) and lower rates of pathogenic bacteria (5.6% vs 12.7%, χ[2]=10.88, p=0.028).

CONCLUSIONS: Perineal preparation with water was not associated with an increased risk of maternal or neonatal infection or adverse neonatal oral microbial colonization at birth and was associated with lower medical costs. These findings suggest that water may be a safe and cost-effective alternative to povidone-iodine for perineal preparation among women with low-risk pregnancies in hospitals with high episiotomy rates. Further longitudinal studies are needed to determine the effects of intrapartum povidone-iodine exposure on neonatal microbiome development and its potential long-term health consequences.

CLINICAL TRIAL REGISTRATION: The study is registered on the official website of ClinicalTrials.gov.

IDENTIFIER: NCT06880445.},
}

@article {pmid42694997,
year = {2026},
author = {Abboud, E and Rossi, P and Crouzy, B and Evangeliou, N and Nenes, A and Violaki, K},
title = {Characterization of the atmospheric microbiome in a semi-rural area of Central Europe using flow cytometry.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag167},
pmid = {42694997},
issn = {2730-6151},
abstract = {Characterizing bioaerosols is important for understanding their potential impacts on the environment and public health. In this study, we developed a novel flow cytometry-based approach to determine the low nucleic acid (LNA), high nucleic acid (HNA), dead, and intact bioaerosol populations in samples collected with a wet cyclone at Payerne, Switzerland, during spring and summer 2024. We found that the average bioaerosol number concentration reached (2.47 ± 3.35)×10[4] m[-3]. The HNA and intact populations were the most abundant populations, representing the largest fraction of total bioaerosols within 65% and 97% of the samples, respectively. Our results show that the LNA can be composed of dead bioaerosols, which correlated strongly with atmospheric particulate mass. Quantitative Polymerase Chain Reaction (qPCR) and metagenomic analysis reveal significant correlations and associations (Spearman, PERMANOVA, and Mantel) between the different kingdoms analyzed, reflecting complex ecological interactions in the atmosphere among the communities. Despite this complexity, LNA was mainly associated with the archaea Nitrososphaerota and bacteria Actinomycetota, whereas HNA was enriched by fungal classes such as Pichiomycetes and Ustilaginomycetes. Pollen abundance was positively correlated with temperature and negatively correlated with relative humidity and pollution (NOx and NO2), as these conditions promote the formation of sub-pollen particles (pollen fragments) through osmotic (bursting) and oxidative stress. Factor analysis indicates a seasonal dynamics transition from plant-associated bioaerosols in the spring season, to other bioaerosol types to be co-emitted during summer. Overall, the integration of flow cytometry with molecular analysis provides a framework to characterize and quantify bioaerosols and provides new insights into the ecological structure, variability, and sources of the atmospheric microbiome.},
}

@article {pmid42695007,
year = {2026},
author = {Pan, Q and Tsompanidou, E and Hu, W and Khan, MT and van Dijl, JM},
title = {Faecalibacterium harmsenii sp. nov., an abundant but previously overlooked Faecalibacterium in the human gut.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag221},
pmid = {42695007},
issn = {2730-6151},
abstract = {Faecalibacterium is one of the most abundant anaerobes in the human colon. At the genus level, this bacterium shows a strong positive association with human health. Expanding collections of isolates and metagenome-assembled genomes have revealed its species diversity, yet species-level functions remain so far underexplored. Here, we describe a novel species, Faecalibacterium harmsenii. In addition, we reclassify another isolate as a member of the recently reported Faecalibacterium langellae species. Despite close genomic relatedness, these isolates exhibit distinct physiological and biochemical traits, including differences in carbohydrate utilization, stress tolerance, enzymatic activity, Gram-staining and fatty acid composition. Our present comparative genomics analyses further uncover extensive functional diversity and plasticity across type strains, with F. harmsenii being distinguished by an expanded carbohydrate gene repertoire and reduced defense systems, mobile genetic elements and antibiotic resistance genes. Extending to the species, we identify species-specific ecological niches across hosts and differential sensitivities to human diseases, highlighting certain species as reliable biomarkers of gut health. Together, these findings refine our understanding of Faecalibacterium diversity and provide a framework for its use in microbiome-based diagnostics and therapeutic development.},
}