@article {pmid41794765,
year = {2026},
author = {Wu, G and Zhang, J and Yan, S and Liu, N and Chen, W and Wu, F and Wang, Z and Zhang, J and Yang, Y and Deng, Y and Qiu, X and Liu, J and Shi, L and Cui, X and Wan, R and Li, X and Han, Y and Yang, G},
title = {Circadian rhythms and microbiota: molecular crosstalk and its implications for health and disease.},
journal = {Biology direct},
volume = {21},
number = {1},
pages = {},
pmid = {41794765},
issn = {1745-6150},
abstract = {UNLABELLED: Circadian rhythms, evolutionarily conserved 24-hour oscillations, exert precise regulatory control over microbial communities across host niches including the gastrointestinal tract, oral cavity, urinary bladder, and skin. This bidirectional interplay is critical to host physiology: host circadian clocks shape the composition and functional rhythms of resident microbiota, while microbiota-derived signals reciprocally modulate circadian entrainment and tissue-specific rhythmicity. Circadian disruption from shift work, irregular feeding, light pollution, or sleep deprivation trigger microbial dysbiosis and circadian misalignment, contributing to metabolic diseases, gastrointestinal disorders, neuropsychiatric conditions, cardiovascular diseases, and dermatological or reproductive disorders. Mechanistically, this crosstalk is mediated by rhythmic hormonal secretion, microbial metabolites, epigenetic regulation, and immune signaling. Therapeutic strategies such as time-restricted feeding, probiotics, melatonin, and polyphenol-rich diets show promise in restoring temporal homeostasis. This review synthesizes current evidence on circadian-microbiota interplay, elucidates its roles in physiology and disease, and highlights translational opportunities for chrono-microbiome-based interventions to optimize host health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13062-026-00748-w.},
}

@article {pmid41929220,
year = {2026},
author = {Pedreros, MB and Irigoyen, MF and Simoes-Barbosa, A and Riestra, AM and de Miguel, N},
title = {Chemotaxis and selective interactions of Trichomonas vaginalis with the vaginal bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41929220},
issn = {2692-8205},
abstract = {Trichomonas vaginalis is an extracellular parasite that inhabits the human genital tract, yet little is known about how it senses and responds to the complex vaginal microbial ecosystem. Here, we show that T. vaginalis exhibits chemotactic behavior on semisolid surfaces, forming multicellular assemblies that coordinate collective migration. Parasite colonies display both positive and negative chemotactic responses, indicating the ability to detect and react to diffusible signals. Different parasite strains display marked mutual avoidance between neighboring colonies, highlighting specific recognition mechanisms. Furthermore, we show that T. vaginalis is strongly attracted to acidic environments, revealing a niche-adapted pH taxis. Given that vaginal bacteria critically shape local pH, we examined parasite responses to representative members of the vaginal microbiota. T. vaginalis exhibited preferential chemotactic migration toward Lactobacillus gasseri, a hallmark species of eubiotic community state types (CSTs), over Gardnerella vaginalis, which is associated with dysbiotic CST-IV communities, while showing no detectable attraction to Escherichia coli. This selective migration correlated with a robust chemotactic response to lactic acid, a major metabolite produced by lactobacilli. Additionally, when the parasite is co-cultured with the equal number of L. gasseri and G. vaginalis, T. vaginalis exhibits a clear preferential binding to L. gasseri, as demonstrated by flow cytometry and fluorescent microscopy. We show that co-culture of T. vaginalis with either L. gasseri or G. vaginalis results in enhanced parasite growth only in the presence of L. gasseri. Collectively, these findings reveal pH taxis; bacteria-directed migration and preferential association with Lactobacillus as previously underappreciated behavioral traits of T. vaginalis. Such behaviors may destabilize protective microbial communities and drive the transition toward a CST-IV-type dysbiotic state which is frequently associated with trichomoniasis.},
}

@article {pmid41979573,
year = {2026},
author = {Serrage, HJ and Farrar, MD and McBain, AJ and Pennock, J and O'Neill, C},
title = {Skin Staphylococcus species differentially modulate keratinocyte cytokine secretion in response to UVB.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0154925},
doi = {10.1128/aem.01549-25},
pmid = {41979573},
issn = {1098-5336},
abstract = {Skin acts as the body's first line of defense against environmental insults including ultraviolet radiation (UVR) from sunlight and engages in a dynamic dialog with the resident skin microbiota, increasingly recognized for its role in shaping and educating the immune responses of the skin in both health and disease. However, how or indeed if the resident skin microbiota mediates inflammatory responses to sunlight remains unclear. To address this, we investigated the effects of five abundant members of the skin microbiota on cytokine secretion in human primary keratinocytes exposed to a single dose of UVB. Co-culture of primary keratinocytes with a defined five-species skin commensal community resulted in a broad increase in the secretion of innate immune mediators including interleukin-6 (IL-6), independent of UVB exposure. In the absence of UVB, Staphylococcus epidermidis was the dominant species, followed by Staphylococcus hominis within the five-species community. UVB induced a marked shift in community composition, characterized by increased proliferation of S. hominis and reduced S. epidermidis abundance, as confirmed by species-specific growth curve analyses. Assessment of species-specific effects using mono-associated host cells revealed S. epidermidis as the predominant contributor to the enhancement of immune mediator secretion. Without the presence of additional community members, UVB amplified S. epidermidis-induced cytokine secretion. However, co-culture of S. epidermidis with S. hominis attenuated the heightened inflammatory response to UVB typically associated with S. epidermidis, likely due to the reduced abundance of S. epidermidis following UVB exposure. These findings suggest that the resident skin microbiota may contribute to our inflammatory response to sunlight.IMPORTANCEThis study reveals that the skin microbiome may play a role in shaping inflammatory responses to UVB exposure. It provides evidence of organisms capable of both amplifying and mitigating inflammatory responses to UVB, highlighting the importance of microbial composition in photoprotection. These findings suggest individual responses to sunlight may be influenced not only by skin type but also by specific microbes present on the skin.},
}

@article {pmid41979582,
year = {2026},
author = {Smółka, L and Strugała, M and Kursa, K and Pomianowski, B and Blady, K and Bratek, K},
title = {The impact of the gut microbiome on the development of atherosclerosis and peripheral arterial disease: A narrative review.},
journal = {Przeglad epidemiologiczny},
volume = {79},
number = {4},
pages = {580-594},
doi = {10.32394/pe/214773},
pmid = {41979582},
issn = {0033-2100},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology ; *Peripheral Arterial Disease/microbiology ; *Dysbiosis ; },
abstract = {Atherosclerosis is a chronic, progressive process affecting medium and large arteries, while peripheral artery disease (PAD) represents one of its clinical manifestations in the limb arteries. Although classical risk factors such as poor diet, hypertension, diabetes, and smoking are well established, increasing evidence indicates that the gut microbiome is an important and modifiable contributor to vascular pathophysiology. This paper reviews current knowledge on the role of the gut microbiome in the initiation and progression of atherosclerosis and PAD, with emphasis on bacterial metabolites, proinflammatory mechanisms, and potential therapeutic interventions. Gut dysbiosis-an imbalance in the intestinal microbial community-has been associated with increased cardiovascular risk. Patients with vascular diseases show higher levels of pro-atherogenic taxa, including Enterobacteriaceae, Streptococcus spp., Lachnoclostridium, and Family XI, alongside a reduction of beneficial short-chain fatty acid (SCFA)-producing bacteria such as Roseburia, Faecalibacterium, Coprococcus2, and Ruminococcaceae. Two key microbial metabolites influence vascular health. Trimethylamine N-oxide (TMAO), formed from choline and L-carnitine via microbial and hepatic metabolism, promotes endothelial dysfunction, inflammation, and platelet reactivity, thereby accelerating atherosclerosis. Conversely, SCFAs-acetate, propionate, and butyrate-exert anti-inflammatory effects, improve insulin sensitivity, and enhance nitric oxide synthesis, resulting in vascular protection. Therapeutic strategies targeting the gut microbiota show promising potential. These include the use of probiotics and prebiotics (notably Lactobacillus rhamnosus GG), adherence to a Mediterranean diet, and fecal microbiota transplantation (FMT), all aimed at restoring eubiosis and a favorable intestinal metabolic profile. In summary, the gut microbiome appears to be a key modulator of the pathogenesis of atherosclerosis and PAD. Targeted modulation of gut microbial composition and activity may emerge as an innovative and effective strategy for the prevention and treatment of cardiovascular diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Atherosclerosis/microbiology
*Peripheral Arterial Disease/microbiology
*Dysbiosis

@article {pmid41979594,
year = {2026},
author = {Ager, EO and Nickodem, CA and Brown, J and Jendza, J and Neeno-Eckwall, E and Schuldes, M and Dittoe, DK and Hite, JL},
title = {Diet-vaccine interactions: SQM Iron and Salmonella vaccination shape poultry gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0012726},
doi = {10.1128/aem.00127-26},
pmid = {41979594},
issn = {1098-5336},
abstract = {UNLABELLED: Vaccines to prevent Salmonella are rapidly gaining traction in the poultry industry. Yet how these interventions interact with other management strategies to influence the broader gut microbial community, rather than Salmonella per se, remains poorly understood. Understanding these effects is critical because shifts in the microbiome can alter nutrient metabolism, immune function, and pathogen dynamics in ways that could either enhance or suppress management strategies aimed at improving bird health and food safety. Here, we examine how a live-attenuated Salmonella vaccine (AviPro Megan Vac 1) and iron supplementation, two widely adapted management strategies, individually and jointly shape the cecal microbiome of broiler chickens. Specifically, we compare standard iron supplements (FeSO4) with a polysaccharide-complexed iron supplement (SQM Iron) which uses a complexation process that "hides" iron from Salmonella via time- and tissue-specific release of this critical nutrient. Using 16S rRNA gene sequencing, we found that while overall microbial diversity was unchanged, both interventions induced reproducible shifts in community composition, including enrichment of taxa linked to fermentation and short-chain fatty acid production. Vaccination alone promoted Bacillota genera associated with gut homeostasis, whereas iron supplementation altered competitive dynamics by reducing Streptococcus and favoring several rare taxa. Strikingly, combining these treatments suppressed several beneficial fermentative genera, and Staphylococcus was markedly increased, revealing nonadditive effects. These findings illuminate the potential of integrated strategies, combining immune stimulation with precision micronutrient supplementation, to improve poultry health and food safety. However, these results also underscore the intricate microbial trade-offs that must be carefully navigated to avoid unintended consequences in modern production systems.

IMPORTANCE: Globally, non-typhoidal Salmonella (NTS) is a persistent food safety challenge and pre-harvest control is an industry priority. While Salmonella vaccines are rapidly gaining adoption, their interactions with other common management practices such as nutritional strategies remain unclear. Iron metabolism is particularly important, as it influences host immunity, pathogen colonization, and shapes the gut microbiome. This study investigates how live-attenuated Salmonella vaccine (AviPro Megan Vac 1) and iron-based nutritional management interact to shape the cecal microbiota of broiler chickens. Specifically, we focus on SQM Iron, with a complexation process that enables time- and tissue-specific release of this critical nutrient. Our findings indicate that targeted combinations of immune stimulation and micronutrient supplementation can selectively remodel the poultry gut microbiome, with potential implications for nutrient utilization, microbial metabolism, and integrated, non-antibiotic approaches to reduce Salmonella burden while supporting flock health.},
}

@article {pmid41979614,
year = {2026},
author = {Ibrahim, MN},
title = {The Immune Cost: How Virtual Life Becomes a Modifiable Risk Factor for Immune Dysregulation.},
journal = {Clinical laboratory},
volume = {72},
number = {4},
pages = {},
doi = {10.7754/Clin.Lab.2025.250624},
pmid = {41979614},
issn = {1433-6510},
mesh = {Humans ; Risk Factors ; *Stress, Psychological/immunology ; Gastrointestinal Microbiome/immunology ; *Immune System/immunology ; },
abstract = {BACKGROUND: The emergence of technology-based lifestyles has led to what may be called "virtual isolation," as people spend more and more time in front of screens and less and less time in the world. Though the psychological consequences of this isolation are broadly appreciated, the biological impact of such isolation, especially on the immune system, has not been well-studied.

METHODS: This letter synthesizes interdisciplinary research in neuroendocrinology, psychoneuroimmunology, and microbiome science to explore the biological implications of digital isolation on immune system regulation.

RESULTS: Long-term digital immersion has been linked to higher levels of the stress hormone cortisol, disrupted sleep and reduced oxytocin signaling - all which disarray both innate and adaptive immune function. The lack of social bonding in the real world limits the sharing of microbes and gut microbiome diversity, making immune homeostasis even worse. Digital addiction is also associated with raised inflammatory indicators and increased sus-ceptibility to infections and immune dysregulation.

CONCLUSIONS: The virtual bubble is nice, psychologically, but carries an insidious and deepening challenge to the integrity of the immune system. Tackling digital over exposure is essential to restore immunological balance, particularly in a post-pandemic society prone to stress-driven immunosuppression.},
}

Humans
Risk Factors
*Stress, Psychological/immunology
Gastrointestinal Microbiome/immunology
*Immune System/immunology

@article {pmid41979934,
year = {2026},
author = {Mertz, L},
title = {Suite of Ingestible Devices Opens Window to the Gut Nervous System, Microbiome.},
journal = {IEEE pulse},
volume = {17},
number = {1},
pages = {26-32},
doi = {10.1109/MPULS.2026.3659238},
pmid = {41979934},
issn = {2154-2317},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Optogenetics ; Animals ; *Gastrointestinal Tract/innervation ; },
abstract = {Ingestible capsules reveal gut neural signaling and microbiome dynamics through sensing and optogenetics.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Optogenetics
Animals
*Gastrointestinal Tract/innervation

@article {pmid41980076,
year = {2026},
author = {Liu, J and Zhang, J and Hu, S and Jiang, M and Lin, X and He, P and Peng, C},
title = {Endogenous Mechanisms of Selenium-Induced Antagonism against Cadmium Toxicity in Crops: Integration and Reconstruction of a Multilevel Defense Network.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17688},
pmid = {41980076},
issn = {1520-5118},
abstract = {Selenium (Se) orchestrates a multilevel endogenous defense network in crops against cadmium (Cd) toxicity. This network operates from rhizosphere immobilization (e.g., Cd-Se complexes, microbiome interactions, iron plaque, and root exudates) and subcellular sequestration via transporter regulation (e.g., OsNramp5, OsHMA3) to antioxidant enhancement and selenoprotein activation. Critically, Se acts as a signaling initiator, engaging pathways (e.g., GATA3-COMT1-melatonin) to systemically reprogram stress responses. This review highlights that Se's antagonistic efficacy is form-, dose-, and genotype-dependent, providing a mechanistic basis for precision agronomic strategies. Future efforts must bridge laboratory findings to field applications by elucidating molecular switches and developing integrated predictive technologies.},
}

@article {pmid41980084,
year = {2026},
author = {Aragón, M and Spyridis, H and Mostard, P and Reichelt, M and Gershenzon, J and Dicke, M and Kloth, KJ},
title = {Jasmonic and Salicylic Acid Pathways Shape the Rhizosphere Microbiome, affecting Aphid Herbivory and Soil-Mediated Insect-Plant Interactions in a density-dependent manner.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcag048},
pmid = {41980084},
issn = {1471-9053},
abstract = {Aboveground induction of plant defense pathways can shape root-associated microbial communities. However, whether these changes are pathway-specific and how they affect plant growth and resistance remains unclear. We evaluated how induction of the Jasmonic Acid (JA) and Salicylic Acid (SA) defense pathways shapes the root microbiome of Brassica oleracea, and whether these soil-mediated shifts affect plant growth and resistance to herbivory in a subsequent generation using a plant-soil feedback (PSF) approach. In the conditioning phase, defense pathways were induced either through foliar application of methyl jasmonate (MeJA) and SA solutions, or through herbivory by caterpillars (JA) and aphids (SA). Both pathways led to distinct shifts in microbial communities, with bacterial and fungal composition varying by pathway identity and induction method. JA induction resulted in more differentially abundant ASVs than SA, particularly with Proteobacteria depletion. Conversely, Planctomycetota (bacteria) and Mortierellomycota (fungi) were enriched under both pathways, suggesting that these represent general stress-responsive groups. In the feedback phase, JA- and SA-conditioned soils had no effect on resistance under high aphid pressure, whereas under low aphid density, plants grown in SA-conditioned soil exhibited reduced phloem feeding and lower aphid population development. Together, our results indicate that benefits provided by the defense-shaped root microbiome depend on pest pressure intensity and arise from overall community shifts rather than specific taxa enrichment. Our findings underscore the complex interactions between plant-defense pathways, rhizosphere microbes, and herbivores.},
}

@article {pmid41980215,
year = {2026},
author = {Zhang, L and Dove, A and Du, J and Yang, D and Su, Q and Huang, X and Wang, J and Yue, J},
title = {The Lung-Brain Axis in Cognitive Impairment and Dementia: Mechanisms and Therapeutic Prospects.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0095},
pmid = {41980215},
issn = {2152-5250},
abstract = {The lung-brain axis has been recognized as a critical interface linking lung health to cognitive disorders, including cognitive impairment, Alzheimer's disease, and dementia. Epidemiological and clinical evidence shows a close association between compromised lung health-including chronic obstructive pulmonary disease (COPD), asthma, obstructive sleep apnea (OSA), and pulmonary infections-and cognitive impairment and dementia. Potential mechanisms include established factors (systemic inflammation and immune crosstalk, hypoxic injury, and air-pollutant-induced neurotoxicity) and exploratory mechanisms (lung microbiome dysregulation). Notably, lung-centric strategies targeting the lung-brain axis involve repurposing pulmonary medications, intervening in shared mechanisms, and employing non-pharmacological strategies. Furthermore, realizing this promise will require future randomized controlled trials (RCTs) to develop comprehensive management strategies and alleviate the global burden of cognitive impairment and dementia.},
}

@article {pmid41980217,
year = {2026},
author = {Yagi, M and Mizukoshi, R and Ito, K and Isogai, N and Funao, H and Fujita, R},
title = {Microbiome-Linked Metabolic Architecture of Accelerated Biological Aging in Humans.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0237},
pmid = {41980217},
issn = {2152-5250},
abstract = {Biological aging is a major determinant of frailty, functional decline, and vulnerability to age-related diseases; however, its upstream metabolic and inflammatory signatures remain incompletely understood. We investigated biological aging using an integrated multi-omics approach in a clinically enriched human cohort. In this prospective study, 120 patients with adult spinal deformity (ASD) and 480 age- and sex-matched healthy controls were included for comparison of PhenoAge. Within the ASD cohort, high-resolution plasma metabolomics and targeted proteomics were performed to characterize metabolic and inflammatory correlates of biological aging. A composite trimethylamine N-oxide (TMAO) Pathway Index (TPI) was constructed using standardized methylamine-related metabolites. Biological age was significantly elevated in ASD compared with matched controls. Within the ASD cohort, metabolomic profiling revealed enrichment of methylamine-related and glycation-associated metabolites among the strongest correlations of PhenoAge. The TPI showed a strong, age-independent, near-linear association with PhenoAge. In sensitivity analyses adjusted for age, sex, BMI, smoking status, and eGFR, this association remained significant (β = 2.92, 95% CI 0.74-5.10, p = 0.009). Targeted proteomic analyses showed that tumor necrosis factor-α was selectively associated with both PhenoAge and the TPI, whereas associations with interleukin-1β, interleukin-6, and adiponectin were limited. Higher PhenoAge was also associated with reduced physical performance, increased frailty, and impaired health-related quality of life. These findings support an exploratory, hypothesis-generating framework in which methylamine-related metabolism and chronic inflammatory signaling are associated with biological aging in ASD. Because of the cross-sectional design, these results should be interpreted as associative rather than causal.},
}

@article {pmid41980282,
year = {2026},
author = {Sun, W and Wang, Y and Bao, J and Tong, Z and Zhang, J and Huang, M and Chen, H},
title = {Environmental concentration of chlorantraniliprole induces dysbiosis of gut microbiota and metabolism in crayfish (Procambarus clarkii).},
journal = {Ecotoxicology and environmental safety},
volume = {316},
number = {},
pages = {120139},
doi = {10.1016/j.ecoenv.2026.120139},
pmid = {41980282},
issn = {1090-2414},
abstract = {The widespread application of chlorantraniliprole (CAP) in rice-crayfish co-culture systems poses a potential threat to the health of the non-target crustacean Procambarus clarkii. However, the sub-chronic effects of environmentally relevant concentrations of CAP on intestinal health remain poorly understood. In this study, we conducted a 14-day exposure experiment at two environmentally realistic CAP doses (0.05 and 0.5 mg/L) to investigate its effects using an integrated approach combining histopathology, biochemical assays, 16S rRNA gene sequencing, and untargeted metabolomics. Our results demonstrated that CAP exposure induced dose-dependent intestinal damage, ranging from villi degeneration to severe enterocyte dissolution and cytoplasmic vacuolation. This structural compromise was accompanied by significant CAP accumulation and oxidative stress, as evidenced by the suppression of antioxidant enzymes (SOD, CAT) and the depletion of GSH, along with increased lipid peroxidation (MDA). Furthermore, CAP exposure caused significant gut microbiota dysbiosis, characterized by an increased Firmicutes/Proteobacteria ratio, reduced alpha diversity, and taxon-specific, dose-dependent shifts in genus abundance. Metabolomic analysis revealed substantial reprogramming of the host-associated metabolome, with the high-dose group exhibiting a distinct profile and a stronger disruption in amino acid metabolism pathways. Crucially, Mantel test analysis revealed a dose-dependent intensification of the microbiota-metabolite correlation, indicating that the dysbiotic gut microbiome actively mediated the host's metabolic dysfunction under high-level CAP exposure. Our findings provide a comprehensive perspective on the intestinal toxicity of CAP in crayfish, highlighting the gut microbiome as a key mediator of pesticide-induced metabolic dysregulation.},
}

@article {pmid41980294,
year = {2026},
author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Glucose metabolism's impact on Blastocystis presence in the human gut.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106647},
doi = {10.1016/j.clnu.2026.106647},
pmid = {41980294},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.

METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.

RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.

CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.},
}

@article {pmid41980384,
year = {2026},
author = {Ye, W and Yan, Y and Dai, J and Wang, P and Jiang, H and Yao, W and Zheng, W},
title = {Subacute dimethylated monothioarsenate (DMMTA) exposure induces hepatotoxicity and disrupts the gut microbiota-bile acid-liver axis: A multi-omics study in mice.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142031},
doi = {10.1016/j.jhazmat.2026.142031},
pmid = {41980384},
issn = {1873-3336},
abstract = {Dimethylated monothioarsenate (DMMTA), an emerging thiolated organic arsenical frequently detected in rice, exhibits in vitro cytotoxicity comparable to trivalent inorganic arsenic. However, its in vivo hepatotoxicity and underlying mechanisms remain largely unknown. Here, a 28-day subacute DMMTA exposure study was conducted in C57BL/6 mice, integrating hepatic transcriptomics, targeted bile acid metabolomics and 16S rRNA microbiome profiling to elucidate DMMTA-induced perturbations along the gut-liver axis. Phenotypically, DMMTA induced an atypical hepatotoxicity characterized by paradoxical liver atrophy coexisting with severe steatosis, alongside inflammatory infiltration and a non-monotonic elevation of liver ALT activity. Mechanistically, DMMTA critically impaired hepatic detoxification and redox homeostasis, evidenced by the inhibited nuclear translocation of Nrf2 and the concerted suppression of downstream xenobiotic-metabolizing genes (e.g., Gsts, Ugts). Targeted metabolomics revealed a profound disruption of enterohepatic circulation, marked by a 29% reduction in the primary to secondary bile acid ratio and 6.0-fold increase in toxic accumulation of 6,7-diketo LCA. Concurrently, microbiome profiling identified a highly selective dysbiosis driven by the massive expansion of Negativibacillus (71.1-fold) and the depletion of Blautia (20.3-fold). Multi-omics integration (Procrustes, M[2] < 0.46, P < 0.05) robustly linked these microbiota shifts to the accumulation of hepatotoxic secondary bile acids. Collectively, this study challenges the traditional "low toxicity" paradigm of organic arsenicals and highlights the gut-liver axis as a central mediator of DMMTA hepatotoxicity, providing vital mechanistic evidence to refine environmental risk assessment for rice-based diets.},
}

@article {pmid41980702,
year = {2026},
author = {Chlebicz, M and Reese, TA},
title = {The Trouble with "Clean" Mice: How Infection History Alters Host Immune Responses.},
journal = {Annual review of virology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-virology-092623-094931},
pmid = {41980702},
issn = {2327-0578},
abstract = {Laboratory mice are widely used in biomedical research due to their low cost, genetic tractability, and ease of manipulation. To reduce experimental variability, they are typically housed under specific pathogen-free (SPF) conditions that limit microbial exposure. While this approach minimizes confounding infections, it also creates an immunological environment that differs markedly from that of humans, reducing the translational relevance of mouse immune studies. This limitation has driven the development of alternative models known as "dirty" or microbially experienced (ME) mice. Despite methodological differences, ME models demonstrate that lifelong microbial exposure profoundly shapes immune development. Although immune maturation in these mice is often attributed to microbiome changes, persistent exposure to endemic rodent viruses and other pathogens also may drive sustained immune activation. Here, we review the immune implications of the various ME models and highlight the critical role the virome plays in aligning mouse immune responses more closely with those of humans. Through harnessing microbial experience as a complementary tool to traditional SPF housing conditions and germ-free models, researchers can more faithfully model a mature, pathogen-shaped immune system.},
}

@article {pmid41980780,
year = {2026},
author = {Dai, DLY and Manus, MB and Hoskinson, C and Jiang, J and Sbihi, H and Miliku, K and Campisi, SC and Korczak, DJ and Duan, Q and Moraes, TJ and Mandhane, PJ and Finlay, BB and Simons, E and Lishman, H and Patrick, DM and Subbarao, P and Azad, MB and Chawes, B and Bønnelykke, K and Sørensen, SJ and Thorsen, J and Stokholm, J and Petersen, C and Turvey, SE},
title = {Breastfeeding may lessen socioeconomic disparities in child health through differences in the infant gut microbiome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102755},
doi = {10.1016/j.xcrm.2026.102755},
pmid = {41980780},
issn = {2666-3791},
abstract = {Lower familial socioeconomic status (SES) is linked to increased childhood disease risk. Since SES has no inherent biological basis, identifying how it becomes physiologically embedded is essential for equitable intervention. Using data from the Canadian CHILD birth cohort (n = 2,752) with replication in the Danish Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010) cohort (n = 681), we analyze modifiable pathways linking SES to child health and find that the infant gut microbiota plays a key mediating role. Breastfeeding is associated with a stabilized infant microbiota, buffering against environmental impacts and reducing health risks in lower SES contexts. The presence of Bifidobacterium infantis, enriched through breastfeeding, is linked to protection against adverse outcomes from SES. Together, these results suggest that improving breastfeeding rates and restoring breastfeeding-enriched microbes, like B. infantis, may help buffer early biological impacts of social inequality and support healthier trajectories for children growing up in industrialized settings.},
}

@article {pmid41980904,
year = {2026},
author = {Bebelman, S and Artuyants, A and Nijmeijer, B and Fitzgerald, S and Henry, C and Blenkiron, C},
title = {Evaluating Sequencing Strategies for Endometrial Microbiome Profiling in Endometrial Cancer: A Comparative Study of Short- and Long-Read 16S rRNA Approaches.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {9},
number = {4},
pages = {e70540},
pmid = {41980904},
issn = {2573-8348},
support = {//Cancer Research Trust New Zealand/ ; //Cancer Society of New Zealand/ ; //Maurice and Phyllis Paykel Trust/ ; },
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/pathology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; New Zealand ; *Endometrium/microbiology/pathology ; Middle Aged ; Pilot Projects ; *High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/isolation & purification ; *Bacteria/genetics/isolation & purification/classification ; Aged ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Endometrial cancer (EC) is the most common gynaecological malignancy globally, with rising incidence and notable disparities in outcomes. In New Zealand, EC rates have increased significantly, particularly among Māori and Pacific women, who face higher risks of advanced disease and poorer outcomes. Microbial dysbiosis has been implicated in EC pathogenesis, but characterising the uterine microbiome is challenging due to low microbial biomass and high contamination risk.

AIMS: This study aimed to pilot a protocol that could inform the preparation of a larger cohort trial. Short-read Illumina MiSeq and long-read Oxford Nanopore Technologies (ONT) 16S rRNA gene sequencing were investigated to profile the uterine microbiome in people with EC.

METHODS AND RESULTS: Uterine and vaginal swabs were analysed to assess platform performance in terms of DNA recovery, sequencing success, diversity metrics, and taxonomic resolution. The impact of sample freezing or immediate lysis prior to DNA extraction was also evaluated. ONT sequencing provided enhanced species-level resolution and improved detection of low-abundance taxa but showed variable performance in low-yield samples. Freezing prior to cell DNA extraction modestly increased bacterial 16S copy numbers and improved community consistency. Contamination was a problem across both platforms, particularly in low-biomass samples, but can be minimised during data analysis.

CONCLUSION: This study provides practical guidance for sequencing platform selection and sample handling in uterine microbiome research. Our findings support future efforts to elucidate microbial contributions to EC pathogenesis and highlight the importance of rigorous contamination control. Importantly, this is the first presentation of a New Zealand cohort and contributes valuable data from an underrepresented population and informs future research in diverse clinical settings.},
}

Humans
Female
*Endometrial Neoplasms/microbiology/pathology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
New Zealand
*Endometrium/microbiology/pathology
Middle Aged
Pilot Projects
*High-Throughput Nucleotide Sequencing/methods
DNA, Bacterial/genetics/isolation & purification
*Bacteria/genetics/isolation & purification/classification
Aged
Dysbiosis/microbiology

@article {pmid41980940,
year = {2026},
author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z},
title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00986-w},
pmid = {41980940},
issn = {2055-5008},
support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.},
}

@article {pmid41980958,
year = {2026},
author = {Kim, NH and Oh, J and Lee, JH and Lee, S and Jung, ES and Suh, DH and Kang, HJ and Kim, B and Kim, HS and Jung, HR and Kim, H and Yun, INR and Ji, Y and Cho, SY and Lee, SW},
title = {A colon mimetic screening approach reveals Lactobacillus fermentum as a microbiome-based therapy for COPD.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00978-w},
pmid = {41980958},
issn = {2055-5008},
support = {RS-2024-00439165//Korean Health Industry Development Institute/ ; RS-2023-NR077159//National Research Foundation of Korea/ ; 2024ER080601//National Institute of Health research project/ ; },
abstract = {Chronic obstructive pulmonary disease (COPD) remains a major health burden with few effective therapies, particularly for emphysema. The gut-lung axis and microbial metabolites, such as short-chain fatty acids (SCFAs), have emerged as modulators of lung inflammation. We investigated the therapeutic effects of Lactobacillus fermentum HEM20792 (LF), identified through a colon mimetic personalized pharmaceutical meta-analytical screening (PMAS) platform using fecal samples from severe COPD patients. LF and Lactobacillus sakei HEM20224 (LS) were orally administered to smoke-exposed mice, followed by lung function testing, histopathology, RNA sequencing, single-cell transcriptomics, and fecal microbiome/SCFAs analyses. LF attenuated emphysematous changes, improved compliance, and reduced macrophage and IL-17+ lymphocyte infiltration. Single-cell analysis showed restoration of alveolar macrophages and reduction of pathogenic C1q[+] macrophages, while transcriptomics revealed normalization of NF-κB and arachidonic acid pathways and attenuation of IL-17- and SPP1-associated signaling. LF also increased fecal SCFAs levels. These findings provide preclinical evidence for LF as a promising microbiome-based therapeutic candidate for COPD.},
}

@article {pmid41980965,
year = {2026},
author = {Arp, G and Levy, S and Jiang, AK and Dufault-Thompson, K and Zhong, A and Grant, M and Li, Y and Jiang, X and Hall, B},
title = {SpiR is a gut microbial enzyme that drives cholesterol conversion.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41980965},
issn = {2041-1723},
support = {R35-GM155208//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Cholesterol/metabolism ; Humans ; Phylogeny ; *Eubacterium/enzymology/genetics ; *Bacterial Proteins/metabolism/genetics ; Oxidation-Reduction ; },
abstract = {The gut microbiota contributes to cholesterol homeostasis by converting cholesterol into coprostanol, a non-absorbable sterol excreted in the feces. However, the enzymes mediating this process remain poorly defined. Here, we identify spiR, a steroid Δ[5-4] isomerase/3-keto reductase from Eubacterium coprostanoligenes that catalyzes the initial oxidation of cholesterol to cholestenone, a requisite step in coprostanol production. We confirm that SpiR oxidizes both cholesterol and pregnenolone, and stereospecifically reduces 3-keto-steroids to 3β-hydroxylated forms. We show that SpiR preferentially binds to cholesterol over related steroids and functions as an NAD(H)-dependent homodimer. Through phylogenetic analysis, we show that spiR clusters with known Δ[5-4] isomerases and is restricted to an uncultured clade within Acutalibacteraceae, where it frequently co-occurs with species encoding ismA, a gene previously implicated in cholesterol conversion. We analyze a multi-omic dataset from three human cohorts and find that spiR homologs were strongly enriched in individuals exhibiting cholesterol conversion. We also show that spiR homologs have a greater predictive power for cholesterol conversion than ismA homologs, establishing them as superior markers of microbial cholesterol metabolism. Our findings refine the enzymatic model of cholesterol metabolism in the gut and establish spiR as a critical biomarker and mechanistic driver for microbiome-mediated cholesterol reduction.},
}

*Gastrointestinal Microbiome/physiology
*Cholesterol/metabolism
Humans
Phylogeny
*Eubacterium/enzymology/genetics
*Bacterial Proteins/metabolism/genetics
Oxidation-Reduction

@article {pmid41981035,
year = {2026},
author = {Faber, Q and Baker, CCM and West, JR and Doherty, SJ and Ernakovich, JG and Barbato, RA},
title = {Antimicrobial resistance varies with warming in active layer soil and permafrost.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46295-2},
pmid = {41981035},
issn = {2045-2322},
support = {PE 0602144A Program "Defense Resiliency Platform Against Extreme Cold Weather"//United States Department of Defense/ ; },
}

@article {pmid41981092,
year = {2026},
author = {Lenonyane, CK and Tsholo, K and Molale-Tom, LG and Bezuidenhout, CC and Olanrewaju, OS},
title = {Plant spatial compartmentalization buffers bacteriome structure and function under antibiotic stress.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46797-z},
pmid = {41981092},
issn = {2045-2322},
support = {D15022[CRP 2308]//International Atomic Energy Agency/ ; },
abstract = {Agricultural antibiotic contamination poses increasing threats to crop productivity and ecosystem stability through disruption of the plant-associated microbiome. While antibiotic impacts on bulk soil and rhizosphere communities are documented, the extent to which spatial compartmentalization across the plant-soil continuum buffers these effects remains poorly understood. Here, we investigated how compartment-specific selective pressures influence bacterial community assembly, functional resilience, and interaction networks under antibiotic stress. Lettuce (Lactuca sativa) was grown under five treatments in a completely randomized greenhouse design: T1 (sulfamethoxazole [SMX], 3 mg kg[-1] + manure + plant), T2 (trimethoprim [TMP], 3 mg kg[-1] + manure + plant), T3 (manure + plant, antibiotic-free control), T4 (manure only, plant-free control), and T5 (soil only, negative control). Bacterial communities were profiled across bulk soil, rhizosphere, and endosphere compartments using full-length 16 S rRNA gene sequencing. Spatial compartmentalization emerged as the primary driver of bacteriome structure and functional potential, surpassing antibiotic treatment effects across all analytical approaches. PERMANOVA revealed significant compartment-driven community structuring (R[2] = 0.189, P = 0.001), while treatment effects were non-significant (R[2] = 0.145, P = 0.116). Endosphere communities exhibited substantially lower alpha diversity than bulk soil and rhizosphere (P = 0.0001), with significant treatment × compartment interactions (P = 0.007). Antibiotic treatments selectively enriched xenobiotic degradation (P = 0.042) and secondary metabolism functions, particularly in bulk soil, without systematically increasing pathogen-associated or resistance-related functions. Network analysis revealed reduced bacterial connectivity under antibiotic pressure, yet cooperative interactions dominated across all treatments. Compositional differential abundance testing (ALDEx2) detected no significantly altered taxa for primary antibiotic contrasts (T1 vs. T3, T2 vs. T3), indicating context-driven rather than antibiotic-driven compositional changes. Functional diversity was significantly structured by compartment (Shannon P = 0.0017; richness P = 0.0039), while core plant-beneficial functions remained stable across treatments, with large effect sizes (Cohen's d ≥ 0.8) restricted to antibiotic degradation and secondary metabolism pathways. Our findings demonstrate that plant-microbe spatial structuring provides an ecological buffer that maintains core bacteriome functions against pharmaceutical disturbance, preserving plant-beneficial capabilities despite compositional shifts. The selective enrichment of antibiotic degradation pathways suggests potential for microbiome-assisted mitigation of pharmaceutical residues in agricultural systems. These results provide insights for developing compartment-specific microbiome management strategies that integrate with One Health approaches to enhance agricultural resilience under increasing pharmaceutical pressure in agroecosystems.},
}

@article {pmid41981263,
year = {2026},
author = {Zeng, S and Wang, S},
title = {Intergenerational dialogue via the gut microbiome and breast milk.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41981263},
issn = {1869-1889},
}

@article {pmid41981284,
year = {2026},
author = {Mukhopadhyay, M},
title = {Host-microbiome maps.},
journal = {Nature methods},
volume = {23},
number = {4},
pages = {679},
doi = {10.1038/s41592-026-03074-1},
pmid = {41981284},
issn = {1548-7105},
}

@article {pmid41981309,
year = {2026},
author = {},
title = {The gut microbiome as a fingerprint of antibiotic use history.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41981309},
issn = {1546-170X},
}

@article {pmid41981378,
year = {2026},
author = {Almohmadi, NH and Al-Kuraishy, HM and Hussein, KS and Turkistani, AM and Yousef, FM and Al-Gareeb, AI and Abdelaziz, AM and Elewa, YHA and Batiha, GE},
title = {The Gut-Brain Axis: A Critical Link between Type 2 Diabetes and Parkinson's disease.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41981378},
issn = {1867-1314},
}

@article {pmid41981415,
year = {2026},
author = {Byrd, MC and Han, S and Osazuwa-Peters, O and Bhaumik, D and Weatherspoon, D and Schlecht, NF and Osazuwa-Peters, N},
title = {Oral microbiome diversity, community- and taxon-level differences by oral human papillomavirus (HPV) and race/ethnicity.},
journal = {Infectious agents and cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13027-026-00757-4},
pmid = {41981415},
issn = {1750-9378},
}

@article {pmid41981426,
year = {2026},
author = {Muzhabaier, K and Li, Y and Wang, F and Guo, X and Chen, Q and Zhang, X and Cao, L},
title = {[Differential analysis of gut microbiome in patients with periprosthetic joint infection, aseptic failure, and osteoarthritis].},
journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery},
volume = {40},
number = {4},
pages = {548-556},
doi = {10.7507/1002-1892.202601002},
pmid = {41981426},
issn = {1002-1892},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Prosthesis-Related Infections/microbiology ; Female ; Middle Aged ; Aged ; *Osteoarthritis/microbiology ; Dysbiosis/microbiology ; Prosthesis Failure ; Arthroplasty, Replacement, Knee/adverse effects ; },
abstract = {OBJECTIVE: To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice.

METHODS: The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7±1) and (14±1); for the AF group, preoperatively and on postoperative day (7±1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota α-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm).

RESULTS: Analysis of gut microbiota diversity showed that the preoperative α-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7±1), the α-diversity indices in the PJI group on postoperative day (7±1) were lower, but the difference was not significant (P>0.05); by postoperative day (14±1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the α-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group.

CONCLUSION: Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.},
}

Humans
Male
*Gastrointestinal Microbiome
*Prosthesis-Related Infections/microbiology
Female
Middle Aged
Aged
*Osteoarthritis/microbiology
Dysbiosis/microbiology
Prosthesis Failure
Arthroplasty, Replacement, Knee/adverse effects

@article {pmid41981555,
year = {2026},
author = {Bangera, SR and Subbiah, R and Govindaraj, S and Ibegbu, C and Reznik, D and Read, TD and Hartman, TJ and Paul, S and Torres-Patarroyo, N and Lymon, KJ and Ciers-Davis, NA and Nguyen, ML and Bruner, DW and Flowers, L and Velu, V and Xiao, C},
title = {Characterizing Oral Microbiome and Periodontal Disease in Oral HPV-Positive (COMP-HPV) individuals with HIV: an observational longitudinal study protocol.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08193-x},
pmid = {41981555},
issn = {1472-6831},
support = {P51 OD011132/CD/ODCDC CDC HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; },
}

@article {pmid41981595,
year = {2026},
author = {Liang, L and Cao, S and Zhao, Y and Liu, B and Wang, J and Gong, P and Wang, Y and Hao, G and ZhangMu, X and Lu, N and Zhang, H and Wu, S and Kuang, F and Zhang, H},
title = {Neonatal sevoflurane exposure disrupts the lung-brain axis and drives microglial neuroinflammation and cognitive deficits.},
journal = {Journal of neuroinflammation},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12974-026-03808-0},
pmid = {41981595},
issn = {1742-2094},
support = {82101345//National Natural Science Foundation of China/ ; 82201414//National Natural Science Foundation of China/ ; 82271231//National Natural Science Foundation of China/ ; 82171170//National Natural Science Foundation of China/ ; 25YXYJYB00143//Science and Technology Plan in Xi'an of China/ ; },
abstract = {BACKGROUND: Neonatal sevoflurane exposure in mice induces microglial activation and long-term cognitive deficits, a finding that raises significant concerns for pediatric anesthesia. The lung-brain axis, a critical pathway mediating pulmonary-central nervous system communication, is indispensable for maintaining organismal homeostasis. However, existing research on anesthetic neurotoxicity has focused predominantly on central mechanisms, with insufficient attention to the lung-a major immune organ with extensive bidirectional crosstalk with the brain. Herein, we aim to explore the lung-brain interactions underlying long-term cognitive sequelae of neonatal sevoflurane exposure.

METHODS: C57BL/6J mice were selected and exposed to 3% sevoflurane for 2 h daily on postnatal days 6-8. Upon reaching adulthood, cognitive function and microglial activation status were evaluated. At 4 weeks post-exposure, 16S rRNA gene sequencing and metabolomic analysis were performed respectively to characterize the structure of the pulmonary microbiota and the metabolite profile. Proximity ligation assay (PLA), fluorescence lifetime imaging microscopy-fluorescence resonance energy transfer (FLIM-FRET), and co-immunoprecipitation (COIP) were employed to investigate the molecular mechanisms by which lung-derived metabolites mediate brain effects. Additionally, rescue experiments were conducted by administering the sphingosine-1-phosphate receptor modulator FTY720 and Moce to validate the aforementioned effects.

RESULTS: Repeated neonatal sevoflurane exposure impaired adult cognitive function, induced microglial activation, and was concurrent with pulmonary microbiome dysbiosis and metabolic alterations. Notably, sphingosine-a key membrane lipid-was significantly decreased. Intratracheal administration of FTY720, a sphingosine analog, alleviated neuroinflammation and ameliorated cognitive deficits. Mechanistically, sevoflurane exposure upregulated HDAC1 and downregulated KLF4, whereas FTY720 significantly rescued these sevoflurane-induced expression aberrations, implicating the HDAC1/KLF4 axis in the regulation of neuroinflammation. Additionally, MOCE significantly alleviated neuroinflammation and ameliorated cognitive deficits.

CONCLUSIONS: Developmental sevoflurane exposure induces microglial activation and cognitive decline via a pulmonary dysbiosis-sphingosine reduction cascade. The sphingosine-1-phosphate receptor modulator FTY720 mitigates this impairment by regulating microglial activation and neuroinflammation. These findings reveal novel mechanisms of anesthetic neurotoxicity and identify potential neuroprotective targets for pediatric anesthesia.},
}

@article {pmid41981681,
year = {2026},
author = {Brachmann, S and Kiesewetter, KN and Liddicoat, C and Wallace, KJ and Breed, MF and Eisenhauer, N and Barnes, AD},
title = {Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00896-6},
pmid = {41981681},
issn = {2524-6372},
support = {UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; },
abstract = {BACKGROUND: Forest restoration has primarily been evaluated through changes in aboveground communities, while belowground microbial communities-critical drivers of ecosystem functions-remain less understood. Moreover, studies of soil microbes have focused largely on community structure, which does not necessarily reflect the recovery of functional capacity and stability.

METHODS: To determine how forest restoration affects microbial community structure and function and how microbial diversity relates to ecosystem multifunctional potential and stability, we analysed soil microbial communities from 79 urban forest restoration sites across New Zealand, spanning 0-63 years since initial plantings. Shotgun metagenomic sequencing was used to characterize taxonomic composition and functional potential, with diversity quantified using alpha and beta metrics. To evaluate links between diversity and ecosystem function, we assessed ecosystem multifunctional potential (EMF) which describes the ecosystem's capacity to simultaneously provide multiple functions, and we developed a novel functional insurance (FI) index grounded in ecological theory as an indicator of functional stability and resilience. To calculate FI in microbial systems from sequencing data, we quantified functional overlap by estimating over 250 million species-function correlations per sample.

RESULTS: Contrary to our expectations, only beta diversity, not alpha diversity, was positively associated with EMF and FI, indicating that community composition and dissimilarity rather than species richness underpins microbial functional capacity and stability. EMF and FI were positively correlated, showing that high functional diversity and functional overlap can co-occur in microbial systems. In addition, archaeal turnover increased with closing forest canopies, contributing to higher EMF and FI, while bacterial turnover was only weakly associated with restoration parameters. Notably, restoration time did not play a role in shaping microbial diversity, EMF and FI.

CONCLUSIONS: Our findings demonstrate that microbial compositional turnover, rather than increases in species richness, are critical for restoring soil ecosystem functions. Incorporating microbial functional metrics like the FI index into restoration frameworks that recognise both above and belowground dynamics could promote resilient and multifunctional urban forests.},
}

@article {pmid41981684,
year = {2026},
author = {Clough, J and Mikac, KM},
title = {Metagenomic profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans).},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00564-7},
pmid = {41981684},
issn = {2524-4671},
}

@article {pmid41981689,
year = {2026},
author = {Zhang, Y and Li, H and Yu, F and Gao, M and Wang, Y and Xin, S and Yang, J and Wang, Z and Xiang, L and Ru, Q and Jiang, N},
title = {The role of Traditional Chinese Medicine in the management of liver disease: targeting gut microbiome.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {41981689},
issn = {1749-8546},
support = {ZDYN-2024-A-116//Clinical Collaboration Program on Viral Hepatitis between Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; GZY-ZJ-KJ-23070//The Science and Technology Department of the State Administration of Traditional Chinese Medicine and Zhejiang Provincial Administration of Traditional Chinese Medicine co-built the Science and Technology Plan Project/ ; },
abstract = {In recent years, liver disease have become a major contributor to global morbidity and mortality, with current clinical treatments often limited by late diagnosis and rapid progression. This review aims to explore the underexplored role of gut microbiota (GM) in liver disease pathogenesis, and to highlight how Traditional Chinese Medicine (TCM) offers a novel therapeutic approach through indirect modulation of the GM. While conventional pharmacological strategies focus on direct organ-targeting interventions, TCM emphasizes a holistic, multi-target approach that aligns with the complex GM-liver axis. Specifically, we examine the interactions between GM and various liver diseases (alcoholic liver disease, non-alcoholic fatty liver disease, cirrhosis, acute liver injury, autoimmune hepatitis, and hepatocellular carcinoma) and focuses on the indirect axis of "TCM-GM-liver," aiming to elucidate its scientific implications from the perspective of indirect pharmacology. Unlike current research that broadly addresses GM-derived metabolites, this review innovatively details how TCM and natural products regulate specific bacterial phyla and their representative genera to influence disease progression. In conclusion, we emphasize that GM metabolites serve as critical intermediate substances in TCM-mediated hepatoprotection. By elucidating these mechanisms, this review provides a theoretical foundation for developing microbiota-guided therapeutic strategies and advancing novel drug discovery for liver diseases.},
}

@article {pmid41981704,
year = {2026},
author = {Li, M and Wu, S and Zi, X},
title = {Identification of silage bacterial clusters and analysis of their microecological characteristics.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00891-x},
pmid = {41981704},
issn = {2524-6372},
abstract = {BACKGROUND: Enterotypes refer to the different bacterial clusters in the gut microecosystem, which are closely related to host physiology, digestion, disease, and other phenotypes. However, whether there are clear clusters in the silage microecosystem, and the fermentation quality and characteristics of unique cluster silage remain unknown. To determine whether distinct bacterial clusters exist in the silage microecosystem and to characterize their fermentation properties, we analyzed the bacterial community composition and fermentation quality of 156 silage samples, and further explored their underlying microbial ecological features.

RESULTS: We confirmed three distinct clusters in the silage microbiome, which were named according to their dominant bacterial taxa: the E-cluster (characterized by a higher abundance of unclassified Enterobacteriaceae (UG)), the P-cluster (enriched with Pseudomonas and Janthinobacterium), and the L-cluster (dominated by Lactobacillus). These microbial clusters were closely associated with fermentation quality: the L-cluster exhibited superior silage quality compared to the E- and P-clusters. Meanwhile, the microbial functional profiles differed significantly among the three clusters of silage. Numerous pathways were significantly enriched in the P-cluster, such as the Biosynthesis of other secondary metabolites, etc. Moreover, bacterial co-occurrence networks of three clusters silage displayed cooperative interactions mainly, P-cluster silage network was more complex and tighter, E-cluster silage has more functional microbial units and more stable. Furthermore, the assembly of microbial communities in the three silage clusters was dominated by stochastic processes. Specifically, the E-cluster and L-cluster were governed by ecological drift, while dispersal limitation was more influential in the P-cluster.

CONCLUSIONS: Overall, we found in our study that the silage microbiome can be divided into three clusters, and different clusters have significant differences in fermentation quality, microbial diversity and compositions, functional profiles, microbial network characteristics and community assembly mechanisms. These results could broaden our comprehension of the silage microbial ecology processes and also provide a scientific basis on which to develop a method to precisely regulate silage quality.},
}

@article {pmid41981741,
year = {2026},
author = {Chen, Y and Wang, YT and Hu, JY and Wang, EC and Jia, XH and Wang, J and Min, GT and Jin, WL and Jiang, L},
title = {Modulating the gut microbiota to enhance immune checkpoint inhibitor efficacy in colorectal cancer: mechanisms, therapeutic strategies, and clinical perspectives.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2652476},
pmid = {41981741},
issn = {1949-0984},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Colorectal Neoplasms/microbiology/immunology/drug therapy/therapy ; *Gastrointestinal Microbiome/drug effects ; Immunotherapy/methods ; Animals ; Bacteria/classification/metabolism/genetics ; Extracellular Vesicles ; },
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, yet their efficacy in colorectal cancer (CRC) remains limited to a minority of patients with microsatellite instability-high (MSI-H) tumors, leaving the majority with microsatellite stable (MSS) disease unresponsive. The gut microbiota, a key regulator of host immunity, has emerged as a pivotal determinant of ICI response. This review delineates the dual role of the gut microbiome-encompassing specific bacterial strains, their metabolites, and bioactive components such as extracellular vesicles (EVs) and outer membrane vesicles (OMVs)-in either enhancing or impairing ICI efficacy through complex interactions with the host immune system. We further explore the emerging concept of gut microbiota circadian rhythms and their potential to inform personalized chrono-immunotherapy paradigms. Furthermore, we synthesize promising microbiota-targeting strategies as adjunctive approaches to overcome resistance and augment ICI efficacy in CRC. Finally, we present selected clinical evidence and outline future perspectives to expand the clinical benefit of immunotherapy in CRC patients.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Colorectal Neoplasms/microbiology/immunology/drug therapy/therapy
*Gastrointestinal Microbiome/drug effects
Immunotherapy/methods
Animals
Bacteria/classification/metabolism/genetics
Extracellular Vesicles

@article {pmid41981758,
year = {2026},
author = {Murtaza, G and Hassan, NE and Ahmed, Z and Elmenofy, W and El-Mogy, MM and El-Ganainy, S and Kesba, HH and Hamed, LMM and Iqbal, R and Ullah, S},
title = {Microbiome-metabolite signaling drives aluminum stress alleviation in soybean under intercropping and selenium nanoparticle application.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2657733},
pmid = {41981758},
issn = {1559-2324},
mesh = {*Glycine max/drug effects/microbiology/metabolism/physiology ; *Aluminum/toxicity/metabolism ; *Selenium/pharmacology ; *Microbiota/drug effects ; *Nanoparticles/chemistry ; *Stress, Physiological/drug effects ; Rhizosphere ; *Signal Transduction/drug effects ; Oxidative Stress/drug effects ; },
abstract = {Aluminum (Al) toxicity and soil-borne pathogens severely constrain legume productivity in acidic soils, yet the signaling mechanisms underlying intercropping-mediated stress alleviation remain insufficiently understood. Here, we investigated whether soybean-sorghum intercropping under Al stress (SSAl), alone or combined with selenium nanoparticles (SSAl + Se), modulates rhizosphere signaling networks and plant defense responses. Integrated 16S rRNA microbiome sequencing and rhizosphere metabolomics were employed to decipher microbe‒metabolite interactions associated with Al detoxification and disease suppression. Compared with monoculture soybean under Al stress (MSAl), SSAl and SSAl + Se significantly reduced Al accumulation (16.9% and 57.4%, respectively) and Fusarium wilt incidence (10.9% and 34.4%, respectively), accompanied by enhanced root growth. These treatments attenuated oxidative stress, as evidenced by decreased O2[-], H2O2, and malondialdehyde (MDA) levels, while stimulating antioxidant enzyme activities (SOD, POD, and APX), indicating reinforcement of redox homeostasis. In the rhizosphere, NH4[+]-N and available K levels increased, with NH4[+]-N positively correlated with urease activity and negatively correlated with Al accumulation, suggesting nitrogen-mediated modulation of Al dynamics. Microbiome analysis revealed enrichment of beneficial taxa, including Streptomyces, Intrasporangium, and Sphingomonas, which are positively associated with antimicrobial and stress-related metabolites such as 15-methyl palmitate, lactucin, and sordarin. These coordinated shifts in the microbial community structure and metabolite profiles indicate that the activation of rhizosphere chemical signaling restricts pathogen proliferation and enhances Al detoxification. Collectively, our findings demonstrate that selenium nanoparticles potentiate intercropping-induced rhizosphere reprogramming, linking redox regulation, nitrogen transformation, and microbiome-metabolite signaling to improve aluminum stress tolerance and disease resistance in soybean. This study provides mechanistic insight into how nano-enabled agronomic strategies influence plant signaling networks under edaphic stress.},
}

*Glycine max/drug effects/microbiology/metabolism/physiology
*Aluminum/toxicity/metabolism
*Selenium/pharmacology
*Microbiota/drug effects
*Nanoparticles/chemistry
*Stress, Physiological/drug effects
Rhizosphere
*Signal Transduction/drug effects
Oxidative Stress/drug effects

@article {pmid41981872,
year = {2026},
author = {Janković, SM},
title = {Clinically significant interactions between drugs, microbiome, and sex.},
journal = {Expert opinion on drug metabolism & toxicology},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/17425255.2026.2660706},
pmid = {41981872},
issn = {1744-7607},
abstract = {INTRODUCTION: There are multiple interactions between drugs and the human microbiome that can influence drug effects and pharmacokinetics, but few clinical studies have examined the influence of sex on these interactions.

AREAS COVERED: Literature for this narrative review was searched in PubMed and Google Scholar without language restrictions and for the time period from 2015 to the present. Focus of the search was on clinical trials and observational studies in the human population.

EXPERT OPINION: Current knowledge about the clinically significant effects of microbiomes on drug metabolism and treatment outcomes in humans is very scarce, while the question of sex differences remains unanswered. Both population pharmacokinetic studies, including microbiome composition and sex as covariates, and clinical studies of treatment outcomes will be necessary to fill this knowledge gap.},
}

@article {pmid41981895,
year = {2026},
author = {Bright, R and Macowan, MG and Tian, K and Fitzsimmons, T and Wilson, RL and Roberts, CT and Christophersen, CT and Bartold, PM and Kidd, SP and Zilm, PS},
title = {Periodontitis during pregnancy: The effect on the gut microbiome and intestinal inflammation.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70132},
pmid = {41981895},
issn = {1943-3670},
support = {190-2027//Australian Dental Research Foundation/ ; },
abstract = {BACKGROUND: Periodontitis has been epidemiologically associated with adverse pregnancy outcomes, but causality remains difficult to establish in humans due to confounding factors. This study uses a controlled murine model to examine the effects of experimentally induced periodontitis on the composition of the gut microbiota and gastrointestinal inflammation during pregnancy.

METHODS: Periodontitis was induced in pregnant BALB/c mice via oral inoculation with Porphyromonas gingivalis and Fusobacterium nucleatum before conception (n = 20 per group). Pregnancy outcomes, gut histology, systemic inflammatory markers, and microbiome composition, assessed by 16S rRNA sequencing, were evaluated at gestational Day 18.

RESULTS: Periodontitis was confirmed by significant alveolar bone loss. While fetal and placental weights were modestly increased in periodontitis-positive mice, there were no changes in implantation rates or placental efficiency. Systemic inflammatory markers, including C-reactive protein and interleukin-33, were reduced, suggesting pregnancy-specific immunomodulation. Histological analysis revealed significant inflammation in the jejunum and colon of periodontitis-exposed mice. Despite this, alpha and beta diversity metrics of the gut microbiota remained essentially unchanged. Taxonomic shifts were observed at the genus level, with reductions in protective taxa, such as Akkermansia muciniphila and increases in potentially pro-inflammatory genera, like Desulfovibrio.

CONCLUSIONS: Periodontitis during pregnancy alters gut microbial composition and increases gastrointestinal inflammation without overtly impairing pregnancy outcomes in mice. These findings suggest an association between oral inflammation, intestinal inflammatory changes, and systemic inflammatory modulation during pregnancy. Further studies are warranted to explore long-term maternal and offspring consequences and their relevance to human pregnancy.

PLAIN LANGUAGE SUMMARY: This study explored how periodontitis during pregnancy can influence the gut and immune system. Periodontitis is already associated with poor pregnancy outcomes, but establishing cause and effect in humans is difficult. To investigate this, the researchers used a controlled mouse model. We induced periodontitis in pregnant mice and examined its impact on the gut microbiome, intestinal health, and immune responses. The results revealed that periodontitis does not stay confined to the mouth; it disrupts gut bacterial balance, causes gut inflammation, and modifies immune pathways. Notably, these effects occurred during pregnancy, a time when the immune system is already adapting. The findings suggest that oral infections during pregnancy can have widespread effects, impacting gut health and immune regulation. This may help explain the link between periodontitis and human pregnancy complications. Overall, the study underscores the importance of oral health during pregnancy and supports the idea that treating periodontitis might also safeguard gut and immune health, leading to better outcomes for both mothers and their babies.},
}

@article {pmid41982387,
year = {2026},
author = {Huang, P and Du, M and Liu, Y and Han, Z and Wan, Q and Liang, F and Han, W},
title = {Phase variation in Bacteroides fragilis governs susceptibility to a microvirus and drives its evolution.},
journal = {Engineering microbiology},
volume = {6},
number = {1},
pages = {100252},
pmid = {41982387},
issn = {2667-3703},
abstract = {The interaction and co-evolution between human gut bacteria and their phages shape the dynamic gut microbiome, exerting a significant impact on human health. However, the underlying mechanisms are largely unexplored. In particular, a bacteria-phage interaction model of the Bacteroidota phylum and the Microviridae phages is lacking, limiting our understanding of their ecological roles in human gut. In this study, we isolated a Bacteroidota-infecting Microviridae phage φHBP1 from human feces. Infection of its host Bacteroides fragilis with φHBP1 drives multiple genomic structural variations, which are correlated with host resistance to φHBP1. In turn, our phage evolution assay in B. fragilis H1 obtained φHBP1 mutants that carry mutations within the capsid and pilot proteins and can reinfect the resistant bacterial population. Together, our findings provide novel insights into an antagonistic co-evolution mechanism between gut phage and bacteria, and hold important implications for diversifying phages through evolution to target resistant bacteria in phage therapy.},
}

@article {pmid41982457,
year = {2026},
author = {Shi, S and Wang, S and Li, S and Lu, R and Pan, S and Chen, F and He, X},
title = {Severe periodontitis patients with well-controlled type 2 diabetes display a distinct subgingival microbiome with increased Saccharibacteria compared to systemically healthy controls.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1814983},
pmid = {41982457},
issn = {2235-2988},
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Periodontitis/microbiology/complications ; *Gingiva/microbiology ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; DNA, Ribosomal/chemistry/genetics ; Dental Plaque/microbiology ; Aged ; },
abstract = {INTRODUCTION: Type 2 diabetes mellitus (T2DM) is a major systemic risk factor that exacerbates periodontitis, with microbial dysbiosis recognized as an important mechanism. However, whether a well-controlled diabetic state still exerts a distinct influence on the subgingival microbiome remains to be fully elucidated.

METHODS: This study compared the subgingival microbiota composition in patients with generalized Stage III/IV periodontitis, categorized into a systemically healthy Control group (n = 30) and a well-controlled T2DM group (HbA1c < 8%, n = 30). Subgingival plaque samples were collected using curettes from the deepest diseased sites. The V4 hypervariable region of the 16S rRNA gene was sequenced using Illumina NovaSeq 6000 platform.

RESULTS: Demographic characteristics and periodontal parameters were comparable between groups, except for glycemic indices. Alpha and beta diversity analyses demonstrated no significant differences in overall microbial diversity or community structure (ANOSIM, P > 0.05). However, the T2DM group exhibited a distinct diabetic-associated microbial signature. The T2DM group showed a significant enrichment of the phylum Saccharibacteria (formerly TM7), particularly Nanosynbacter lyticus. In contrast, the phylum Actinomycetota, predominantly represented by the genus Actinomyces, was significantly reduced in the T2DM group. Notably, classical "Red Complex" pathogens were not identified as discriminative biomarkers between the groups. Additionally, correlation analysis revealed that Saccharibacteria abundance was positively associated with HbA1c and fasting blood glucose levels.

DISCUSSION: These findings demonstrate that even with adequate glycemic control, the diabetic microenvironment exerts a unique selective pressure on the subgingival microbiome, favoring the expansion of specific epibiotic bacteria like Saccharibacteria while reducing commensal Actinomyces.},
}

Humans
*Diabetes Mellitus, Type 2/complications/microbiology
Middle Aged
Female
Male
RNA, Ribosomal, 16S/genetics
*Microbiota
*Periodontitis/microbiology/complications
*Gingiva/microbiology
Adult
*Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA
DNA, Ribosomal/chemistry/genetics
Dental Plaque/microbiology
Aged

@article {pmid41982475,
year = {2026},
author = {Wang, Y and Wang, Y and Jin, H},
title = {Update on the Etiology and Pathogenesis of Erythrodermic Psoriasis.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {581723},
pmid = {41982475},
issn = {1178-7031},
abstract = {Erythrodermic psoriasis(EP) is a rare, life-threatening variant affecting 75%-90% of the body surface area. Characterized by widespread erythema and potential systemic symptoms like fever and lymphadenopathy, it severely impairs patient quality of life. The pathogenesis of erythrodermic psoriasis is not fully understood. It is a multifactorial, multistep process suspected to result from an abnormal immune response induced by both genetic and environmental factors. Key contributors to erythrodermic psoriasis onset include specific gene polymorphisms, altered expression of adhesion molecules, dysregulated cytokine activity, and abnormal activation of T cell subsets. Additionally, imbalances in the skin microbiota and external factors, such as infections and medications, play important roles in disease onset and progression. Distinct from prior reviews that primarily emphasize clinical features and treatment, this review integrates recent mechanistic advances across genetic, immune, environmental, and microbiome domains to provide an updated, systems-level framework for understanding erythrodermic psoriasis and to highlight potential therapeutic implications.},
}

@article {pmid41982769,
year = {2026},
author = {Zhang, D and Sheng, J and He, P and Wang, J and Zhou, M and Sun, Y and Cao, Y and Jiang, Y and Jia, H and Wang, L and Xu, X and Teng, Y},
title = {Dietary fiber supplementation mitigates gestational diabetes risk and preterm birth via gut microbiota modulation: a randomized controlled trial.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1794560},
pmid = {41982769},
issn = {1664-2392},
mesh = {Humans ; Female ; Pregnancy ; *Dietary Fiber/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Diabetes, Gestational/prevention & control/microbiology/diet therapy ; Adult ; *Dietary Supplements ; *Premature Birth/prevention & control/microbiology/epidemiology ; Gestational Weight Gain ; Infant, Newborn ; Pregnancy Outcome ; },
abstract = {BACKGROUND: Gestational Diabetes Mellitus (GDM) poses severe health risks to mother and child, yet effective, non-invasive preventive strategies remain elusive. While the gut microbiota is known to influence glucose metabolism, its potential as a therapeutic target and predictive biomarker in high-risk pregnancies is underexplored. This study investigated whether soluble dietary fiber supplementation could remodel the gut microbiome to prevent GDM and improve pregnancy outcomes.

METHODS: We performed a single-center, randomized controlled trial with 98 pregnant women at elevated risk for GDM. For 5 weeks, from 20 to 24[+6] weeks of pregnancy, participants were randomly assigned to either a fiber group (getting soluble fiber supplements every day) or a control group (getting normal care). Clinical outcomes encompassed OGTT results, gestational weight gain (GWG), and delivery outcomes. We used 16S rRNA sequencing to look at changes in gut flora. Furthermore, we developed a novel nomogram integrating clinical variables with microbial signatures to predict GDM risk.

RESULTS: Although GDM incidence did not statistically differ, the fiber group exhibited significantly improved glycemic excursions (predominantly lower 1h-PG, and reduced whole-OGTT glucose AUC and iAUC), reduced GWG during the 5-week intervention period (1.83 vs. 2.54 kg; P = 0.016), and a complete absence of preterm births (0% vs. 12.0%; P = 0.040). Microbiome analysis revealed that fiber intake enriched Bifidobacterium and Limosilactobacillus while suppressing Phascolarctobacterium. Functional prediction indicated a downregulation of inflammation-related pathways (HIF-1, AMPK) in the Fiber group. Crucially, a prediction model combining clinical factors with a specific "micro-balance" (Bifidobacterium ratio) achieved superior predictive accuracy (AUC 0.821) compared to clinical factors alone.

CONCLUSIONS: Preliminary findings suggest that dietary fiber supplementation serves as a potent "biotic" intervention in high-risk pregnancies, improving 1-hour postprandial glucose homeostasis and eliminating preterm birth in this cohort. The mechanism appears associated with the specific enrichment of Bifidobacterium. Additionally, we validated a novel clinical-microbial nomogram, suggesting that integrating gut microbiome data can significantly enhance GDM risk stratification. Future extensive research is need to confirm these results.},
}

Humans
Female
Pregnancy
*Dietary Fiber/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Diabetes, Gestational/prevention & control/microbiology/diet therapy
Adult
*Dietary Supplements
*Premature Birth/prevention & control/microbiology/epidemiology
Gestational Weight Gain
Infant, Newborn
Pregnancy Outcome

@article {pmid41982876,
year = {2026},
author = {Ren, J and Lan, Z and Wang, C and Zhu, J and Li, M and Xu, J and Lu, Y and Tu, J and Zhang, X and Boskovic, L and Huang, J and Hu, X},
title = {Metagenomic next-generation sequencing and conventional microbiology for microbial profiling in biliary tract infections: a comparative study with clinical stratification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1799474},
pmid = {41982876},
issn = {1664-302X},
}

@article {pmid41982878,
year = {2026},
author = {Yu, Y and Li, X and Shahzad, AS and Zhuang, S},
title = {Short-term calcium peroxide application promotes soil microbial interactions to improve peanut yield in acidic soils.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780622},
pmid = {41982878},
issn = {1664-302X},
abstract = {The deterioration of soil microorganisms stands as a key barrier to the sustainable cultivation of peanut. Peroxides such as hydrogen peroxide (H2O2) and calcium peroxide (CaO2) with antimicrobial efficacy may inhibit soil pathogens and improve microbial community, but their effects on the soil properties, microbiome and peanut yield are still unclear. In this study, a field experiment was conducted to investigate the effects of CaO2 (CP, with application rate of 4.5 t ha[-1]) and H2O2 (HP, with application rate of 22.5 t ha[-1]) and no peroxide application (CK) on physicochemical properties, microbial communities and network structures of acidic soils in which peanut had been cultivated for 13 years. Compared with CK, calcium peroxide application significantly increased soil pH. Hydrogen peroxide showed a similar trend, but not significant. Principal co-ordinates analysis (PCoA) indicated that peroxides application significantly affected the fungal community structure, while it had a weaker impact on the bacterial community. With peroxides application, soil harmful fungus Fusarium and the fungal functional group associated with plant pathogen declined. Network co-occurrence analysis showed that peroxides enhanced bacterial network interactions, with bacterial stability increasing markedly by 2.19- and 1.40-fold in calcium peroxide and hydrogen peroxide treatments, respectively. Peanut yield was correlated with the microbial network properties, and significantly increased by 31.7% in calcium peroxide. Random forest model analysis further revealed that bacterial stability, soil pH, bacterial negative cohesion, and complexity were key factors for peanut yield. In conclusion, short-term calcium peroxide application increased soil pH and bacterial stability, thereby promoting peanut yield in acidic soils.},
}

@article {pmid41982910,
year = {2025},
author = {Santos, S and Salinas, I and Almeida, N and Caicedo, A},
title = {The role of microbiota dysbiosis in Parkinson's disease: Pathophysiology and therapeutic opportunities.},
journal = {Engineering microbiology},
volume = {5},
number = {3},
pages = {100222},
pmid = {41982910},
issn = {2667-3703},
abstract = {Parkinson's disease (PD) is a chronic, progressive neurodegenerative disorder characterized by debilitating motor and non-motor symptoms. Its etiology is multifactorial, with no single definitive cause identified, although aging is a significant risk factor. Additional risks include genetic predisposition, family history, and environmental factors such as pesticide exposure and Helicobacter pylori infection. Dysbiosis of the gut microbiota, and in particular bacterial imbalances, has been implicated in the disruption of the gut-brain axis, contributing to both systemic and neuroinflammation. Environmental factors such as antibiotic exposure and toxins can precipitate microbial dysregulation, potentially accelerating PD progression. Understanding the mechanisms of the gut-brain axis and identifying strategies to preserve a healthy microbiome are essential for developing novel therapeutic approaches. This review synthesizes current therapeutic strategies and ongoing research focused on restoring gut-brain balance to combat PD. These approaches include fecal microbiota transplantation, dietary interventions, and probiotic therapies, all of which show promise in mitigating both motor and non-motor symptoms. Furthermore, we emphasize the urgent need for continued research into probiotics and innovative therapeutic approaches for gut-brain axis modulation, presenting novel opportunities for effective PD management.},
}

@article {pmid41982913,
year = {2025},
author = {Hu, M and Xu, S and Xu, R and Qi, X and Yu, X and Wang, J and Li, Y and Liu, Y and Xi, G and Yu, J and Shi, M},
title = {Analysis of single-cell RNA sequencing data to examine the gastric inflammation-to-cancer transition and evaluation of the effect of probiotic on precancerous lesions.},
journal = {Engineering microbiology},
volume = {5},
number = {3},
pages = {100208},
pmid = {41982913},
issn = {2667-3703},
abstract = {Gastric cancer (GC) is the fifth most prevalent malignancy globally. However, its heterogeneity and asymptomatic early-stage development hinder timely diagnosis and effective treatment. Here, we employed single-cell RNA sequencing to delineate the transitional features of pit mucous cells (PMCs) during the gastritis-to-cancer transition and identified 100 core genes. Characterization of the gene set revealed the role of ribosomal protein small subunit and ribosomal protein large subunit in inflammation-to-cancer transition, which promoted ribonucleoprotein complex biogenesis and cytoplasmic translation. External validation using independent cohorts confirmed that this core gene set discriminated disease progression (AUC > 0.7) and was significantly enriched in GC tissues (p < 0.01). Moreover, we evaluated the therapeutic intervention effects of C. butyricum and synbiotics (Weichanghao®) using a rat model of gastritis and demonstrated the targeted suppression of inflammation-to-cancer transition genes. Our findings establish the basis for early diagnosis of GC through PMC-driven molecular dynamics. Additionally, we propose microbiota-based strategies to prevent the inflammation-to-cancer transition in preneoplastic stages. Furthermore, our results highlight that dysbiosis of the gastric microbiome can be addressed using probiotic supplementations and the core gene set may provide labeling for the evaluation of probiotics-based treatment.},
}

@article {pmid41965542,
year = {2026},
author = {Priya, S and Sridhar, SB and Shareef, J and Wadhwa, T and Balusamy, B and Meenakshi, DU and Sundram, S and Malviya, R},
title = {Epidemiology, diagnosis and emerging therapies for Lyme disease of the Northern Hemisphere.},
journal = {International journal of emergency medicine},
volume = {19},
number = {1},
pages = {},
pmid = {41965542},
issn = {1865-1372},
abstract = {BACKGROUND: Lyme disease is the most widespread tick-borne infection in the Northern Hemisphere and is challenging to diagnose and treat due to its changing clinical presentation, antigenic variation, tissue tropism, and the expanding distribution of vectors. This review includes ecology, pathogenesis, diagnostics, treatment, post-treatment, prevention, and novel translational approaches.

METHODS: A literature review was conducted to include literature published between January 2000 and March 2026 in PubMed/MEDLINE, Scopus, and Web of Science, with landmark studies used where applicable. Original research, clinical trials, systematic reviews, and major public health reports were prioritised.

RESULTS: Two-tier serology is the most common diagnostic technique, but it has limited sensitivity in early infection and does not distinguish between active and past infection. Culture and PCR are only useful in a few instances. The use of new technologies such as multiomics biomarkers, metagenomics, T-cell assays, and AI-enhanced diagnostics is promising but has not yet been tested in a prospective multicentre study. Most of the early and disseminated disease can be treated with standard antibiotics, whereas the long-term therapy of PTLD is not justified and can cause more adverse effects. These preventive and curative advancements involve VLA15 vaccination, anti-tick and reservoir-specific approaches, microbiome-engineered vectors, and anti-persister/ biofilm.

CONCLUSION: Lyme disease requires combined prevention, improved diagnostics, enhanced biomarker research, and well-designed PTLD trials. The short-term benefits will be based on the optimisation of existing diagnostics and vector control, and the long-term benefits will be based on rigorous validation of vaccines, biomarkers, and specific therapies.},
}

@article {pmid41975041,
year = {2026},
author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , },
title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41975041},
issn = {1532-1827},
support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; },
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).

METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.

RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa -notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.

CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.

PROSPERO: CRD42023433704.},
}

@article {pmid41975112,
year = {2026},
author = {Liu, J and Sun, X and Yuan, P and Qin, Y and Wu, W and Fan, Y and Zhang, Y and Zou, L and Ren, C and Li, S},
title = {Clinical response and risk factors of fecal microbiota transplantation in children: a systematic review and meta-analysis.},
journal = {European journal of pediatrics},
volume = {185},
number = {5},
pages = {},
pmid = {41975112},
issn = {1432-1076},
support = {No.ZF2025046//the Hebei Provincial Department of Finance/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/adverse effects/methods ; Child ; Risk Factors ; *Clostridium Infections/therapy ; *Inflammatory Bowel Diseases/therapy ; *Autism Spectrum Disorder/therapy ; Treatment Outcome ; },
abstract = {UNLABELLED: The objective of this study is to investigate the clinical response and incidence of adverse events (AEs) following fecal microbiota transplantation (FMT) in children, across various diseases, populations, and treatment protocols. A systematic search was conducted across eight major Chinese and English databases, identifying 47 studies up to August 28, 2025, for inclusion. Study quality was assessed using the Quality Assessment with Diverse Studies (QuADS) tool. Single-arm rates were pooled via meta-analysis employing the Freeman-Tukey double arcsine transformation, followed by extensive subgroup comparisons to identify influencing factors. FMT demonstrated efficacy in pediatric recurrent Clostridium difficile infection (rCDI), inflammatory bowel disease (IBD), and autism spectrum disorder (ASD), although a higher incidence of AEs was observed in children with IBD. Subgroup analyses revealed that the use of donor feces from relatives or friends was associated with a higher clinical response rate in rCDI. The presence of comorbidities such as IBD diminished the response rate in rCDI patients. Younger age in rCDI and IBD patients showed a trend towards higher clinical response rates, though this did not reach statistical significance. No statistically or clinically significant differences were found in other subgroup comparisons. Meta-regression suggested IBD to be a risk factor for FMT-related AEs.

CONCLUSION: This study innovatively delineates the efficacy-safety profile of pediatric FMT and outlines a pathway for optimizing individualized treatment regimens, providing crucial evidence-based guidance for clinical practice.

TRIAL REGISTRATION: This study has been registered on the PROSPERO database (CRD42024614196).

WHAT IS KNOWN: • Fecal Microbiota Transplantation (FMT) demonstrates preliminary therapeutic potential in several pediatric diseases. • Existing evidence remains fragmented, with limited systematic data on factors modifying efficacy and safety in children.

WHAT IS NEW: • The study revealed FMT's high efficacy across rCDI, IBD, and ASD, and identified IBD as a risk factor for elevated FMT-related adverse events in pediatric patients. • Notably, related/friend donors improved rCDI response rates, while comorbidities like IBD reduced rCDI treatment efficacy.},
}

Humans
*Fecal Microbiota Transplantation/adverse effects/methods
Child
Risk Factors
*Clostridium Infections/therapy
*Inflammatory Bowel Diseases/therapy
*Autism Spectrum Disorder/therapy
Treatment Outcome

@article {pmid41975182,
year = {2026},
author = {Kleinbölting, N and Fiore, A and Cangioli, L and Visca, A and Huang, L and Hett, J and Costanzo, M and Sevi, F and Tabacchioni, S and Aprea, G and Mengoni, A and Pihlanto, A and Neuhoff, D and Sczyrba, A and Schlüter, A and Bevivino, A},
title = {Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47528-0},
pmid = {41975182},
issn = {2045-2322},
support = {818431//Horizon 2020 Framework Programme/ ; },
abstract = {Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha[- 1], and 200 kg nitrogen ha[- 1]) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.},
}

@article {pmid41975257,
year = {2026},
author = {Tang, Z and Zhuang, D and Duan, X and Gong, Q and Tian, C and Jiang, P and Yu, J and Li, F and Zhao, F and Shi, G and Yang, H and Du, Q and Li, T and Ye, Z and Zhang, Z},
title = {MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06444-w},
pmid = {41975257},
issn = {1471-2105},
}

@article {pmid41975274,
year = {2026},
author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN},
title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655793},
pmid = {41975274},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolome ; Female ; Male ; Middle Aged ; Feces/microbiology/chemistry ; Adult ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Liver Cirrhosis, Biliary/microbiology/metabolism/pathology ; *Cholangitis, Sclerosing/microbiology/metabolism/pathology ; Aged ; },
abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.},
}

Humans
*Gastrointestinal Microbiome
*Metabolome
Female
Male
Middle Aged
Feces/microbiology/chemistry
Adult
*Bacteria/classification/genetics/isolation & purification/metabolism
*Liver Cirrhosis, Biliary/microbiology/metabolism/pathology
*Cholangitis, Sclerosing/microbiology/metabolism/pathology
Aged

@article {pmid41975478,
year = {2026},
author = {Zhang, H and Mao, W and Lai, Z and Zhu, Y and Dong, J and Li, L and Xie, F and Zhu, W and Shen, J and Mao, S},
title = {Integrated metatranscriptomics identifies Lachnospiraceae as keystone taxa regulating rumen biohydrogenation and milk ω-6/ω-3 polyunsaturated fatty acids ratio in dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02397-7},
pmid = {41975478},
issn = {2049-2618},
support = {2022YFD1301001//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Enhancing milk nutritional quality through increased ω-3 polyunsaturated fatty acid (PUFA) content and a reduced ω-6/ω-3 PUFA ratio represents a significant opportunity for improving dairy products. While ruminal biohydrogenation substantially influences milk fatty acid (FA) composition, the specific microbial mechanisms regulating the milk fat ω-6/ω-3 PUFA ratio remain poorly characterized. This study aimed to identify key microbial taxa and metabolic pathways controlling this nutritionally relevant parameter, thereby establishing a foundation for targeted microbiome interventions to optimize milk FA profiles.

RESULTS: Analysis of 95 Holstein cows revealed that rumen bacterial community composition explained 41.0% of the variation in the milk ω-6/ω-3 PUFA ratio. Comparative analysis of cows with contrasting phenotypes (high-ratio, HFR; low-ratio, LFR) demonstrated distinct FA profiles across rumen fluid, serum, and milk, with α-linolenic acid (ALA, C18:3 C9,12,15) and linoleic acid (LA, C18:2 C9,12) emerging as critical determinants. Integrated metatranscriptomic and amplicon sequencing identified members of the family Lachnospiraceae, particularly Butyrivibrio and Eubacterium genera, as central regulators of PUFA metabolism. Notably, HFR-associated microbiomes showed enrichment of FA isomerase gene transcripts. Experimental validation using isolated strains demonstrated that B. hungatei preferentially hydrogenated ALA, while Eubacterium_I efficiently metabolized LA, establishing a mechanistic basis for differential substrate biohydrogenation that influences the final ω-6/ω-3 PUFA ratio.

CONCLUSIONS: Collectively, these results indicate that rumen microbial community structure and transcriptional activity are closely associated with variation in the milk ω-6/ω-3 PUFA ratio. Members of Lachnospiraceae appear to contribute to substrate-specific biohydrogenation processes that may influence downstream milk FA composition. These findings provide a multi-omics framework for understanding microbiome-lipid interactions and support future efforts to develop microbiome-targeted strategies for improving dairy nutritional quality. Video Abstract.},
}

@article {pmid41975790,
year = {2026},
author = {Goh, CJ and Park, J and Kim, Y and Park, D and Kim, J and Kwon, SJ and Kim, MJ and Lee, MS},
title = {Machine Learning-Based Lung Cancer Classification Using Blood-Derived Microbial DNA: A Comparative Analysis of Taxonomic Profiling Strategies.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {7},
pages = {},
pmid = {41975790},
issn = {2075-4418},
abstract = {Background: Blood-derived circulating cell-free microbial DNA (cfmDNA) has emerged as a potential non-invasive biomarker source for cancer detection. However, low biomass and high susceptibility to analytical variability raise concerns regarding the stability and interpretability of inferred microbial signatures. This study aimed to evaluate how different taxonomic profiling strategies influence downstream machine learning-based classification and feature interpretation in lung cancer. Methods: cfDNA sequencing data from 168 individuals (80 lung cancer patients and 88 non-cancer controls) were analyzed using two taxonomic profiling workflows: a Bracken-based abundance estimation approach and a BLAST-refined alignment-based strategy. Microbial profiles derived from each pipeline were evaluated using supervised machine learning models within a nested cross-validation framework. Feature stability and fold-change trends were compared across profiling strategies. Results: A Random Forest model achieved robust classification performance under both workflows (AUC 0.852 for Bracken-derived data and 0.906 for BLAST-derived data). However, substantial pipeline-dependent variation was observed in feature selection patterns and quantitative fold-change directionality. Although 13 genera were consistently selected across cross-validation folds in both workflows, the magnitude and direction of abundance differences were not uniformly concordant. Conclusions: Blood-derived microbial DNA profiles can support machine learning-based lung cancer classification; however, feature-level interpretation remains sensitive to taxonomic assignment strategy. These findings underscore the importance of pipeline-aware interpretation and methodological transparency in low-biomass blood microbiome research.},
}

@article {pmid41975843,
year = {2026},
author = {Koskinas, N and Gouva, M and Konstanti, Z and Sintou, E and Mantzoukas, S and Zagorianakou, N},
title = {Oral Self-Care as a Preventive Strategy in Medicated Older Adults: Biological Mechanisms, Genetic Susceptibility, and Public Health Implications.},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {41975843},
issn = {2227-9032},
abstract = {Global population aging has led to a substantial increase in the number of older adults receiving long-term pharmacological treatment, often involving polypharmacy. Long-term medication use is often linked to negative oral health outcomes, such as xerostomia, periodontal disease, dental caries, and changes in the oral microbiome, even if it is necessary for treating systemic conditions. The general health, nutritional state, and quality of life of elderly people are all significantly impacted by these diseases. This narrative review integrates recent data on biological causes, genetic vulnerability, and public health consequences to investigate oral self-care as a preventive strategy in older persons on medication. The effects of long-term medication therapy on oral tissues, salivary function, inflammatory responses, and microbial balance are given special attention, as is the role of genetic variants linked to immunological and inflammatory pathways on individual variability. The review also evaluates oral self-care interventions aimed at reducing medication-related oral complications, such as the use of fluoride, mechanical plaque control measures, and caregiver-assisted oral care practices. Oral self-care is viewed from a public health perspective as a scalable and affordable strategy for reducing oral health disparities in older populations. The results highlight the significance of preventative, individualized, and integrated oral health interventions within larger healthcare frameworks for older persons taking long-term medications.},
}

@article {pmid41975975,
year = {2026},
author = {Szala, Ł and Staninska-Pięta, J and Piotrowska-Cyplik, A},
title = {Microbiome of Bovine Milk and Factors Influencing Its Composition.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41975975},
issn = {2076-2615},
support = {MEiN/2023/DPI/2870//Ministry of Science and Higher Education/ ; },
abstract = {The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.},
}

@article {pmid41975980,
year = {2026},
author = {Idowu, PA and Chauke, C and Mpofu, TJ},
title = {Integrated Stress Physiology and Mitigation Strategies for Heat Stress in Layer Chickens-Review.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41975980},
issn = {2076-2615},
abstract = {Heat stress is a major constraint to global egg production, as rising temperatures increasingly challenge the physiological limits of commercial layer chickens. This review integrates current advances in stress physiology to demonstrate that heat stress is not merely a thermoregulatory problem but a multi-systemic disruption involving neuroendocrine overload, metabolic imbalance, oxidative damage, immune suppression, and gastrointestinal barrier breakdown. These interacting pathways collectively impair egg production, shell quality, feed efficiency, and hen welfare. The review also synthesizes emerging mitigation strategies across environmental control, nutritional interventions, genetic and breeding innovations, welfare-oriented housing systems, and precision monitoring technologies. Studies indicate that targeted cooling, antioxidant, and electrolyte supplementation, the selection of heat-tolerant strains, enriched environments, and sensor-based early-warning systems can significantly enhance egg-laying hen resilience. Remaining gaps include a limited understanding of multi-stressor interactions, microbiome-mediated thermal tolerance, and the large-scale implementation of precision tools. The review provides a forward-looking framework for improving heat resilience in modern layer systems.},
}

@article {pmid41976013,
year = {2026},
author = {Srisa, A and Kamonpatana, P and Promhuad, K and Wongphan, P and Seubsai, A and Klinmalai, P and Harnkarnsujarit, N},
title = {Plant-Derived Functional Ingredients in Pet Nutrition: Phytochemical Classification, Mechanisms, Efficacy, and Application in Dogs and Cats.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41976013},
issn = {2076-2615},
support = {project no. FF(KU) 51.67//Kasetsart University Research and Development Institute (KURDI)/ ; },
abstract = {This review classifies plant-derived functional ingredients in pet food according to phytochemical groups and application forms, including direct oral supplementation and incorporation into complete diets. Polyphenols and plant extracts exert prominent antioxidant (singular), anti-inflammatory, immunomodulatory, and microbiome-regulating effects. Microalgae and omega-3 sources support lipid metabolism, cardiovascular function, and skin integrity. Cannabinoids demonstrate dose-dependent responses in dogs, while cats generally tolerate long-term administration and exhibit notable benefits in chronic pain management. Combinations of botanical extracts with complementary bioactives and fermented botanical preparations exhibit multi-target functionality, with dogs showing pronounced biochemical and microbiome modulation, whereas cats display more behavioral and functional improvements. Phytochemicals operate through integrated multi-level regulation, including activation of antioxidant enzymes, modulation of inflammatory cytokines and T-lymphocyte ratios, microbial metabolic shifts toward short-chain fatty acid production, and regulation of lipid metabolism. Dogs demonstrate marked effects on hepatic function, reproductive resilience, microbiome diversity, CD4+/CD8+ balance, and cholesterol control. In contrast, cats show greater benefits in inflammation reduction, pain relief, intestinal integrity, and long-term safety. These species-specific responses underscore the importance of precision formulation and highlight the emergence of plant-based "pharma-pet nutrition" integrating nutritional and biochemical strategies for targeted health promotion.},
}

@article {pmid41976101,
year = {2026},
author = {Wang, E and Han, X and Sun, W and Zheng, C and Du, W},
title = {Replacing up to 50% of Corn Silage with Triticale Silage Alters the Fecal Microbiome but Not Milk Yield or Composition in Mid-Lactation Holstein Cows.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41976101},
issn = {2076-2615},
abstract = {Diversifying forage sources may improve the sustainability and flexibility of dairy production. In a 60 d feeding trial, 72 mid-lactation Holstein cows were assigned to three treatments (24 cows/group) and fed a total mixed ration in which corn silage represented 41.16% of dietary dry matter in the control diet; 25% or 50% of this corn silage fraction was replaced with triticale silage (TS) on a dry matter basis. The study evaluated whether partial TS substitution could maintain lactational performance while affecting fecal fermentation and microbiota. Replacing corn silage with TS did not affect milk yield, 4% fat-corrected milk, major milk components, or metabolic indicators. However, 50% replacement increased fecal bacterial richness and diversity, as reflected by ACE, Chao1, and Shannon indices, and altered the overall microbial community structure. This treatment also changed fecal volatile fatty acid profiles, including increasing the proportions of branched-chain volatile fatty acids. Overall, TS can replace up to 50% of the corn silage fraction in the ration of mid-lactation cows without compromising milk production or composition, while modifying hindgut microbial ecology and fermentation patterns, thereby offering greater ration flexibility when corn silage availability is limited or costly.},
}

@article {pmid41976282,
year = {2026},
author = {Klus, W and Ossowska, J and Kowalcze, K and Kiliszczyk, A and Paziewska, A},
title = {Pathogenesis, Diagnostic Pathways, and New Therapeutic and Nutritional Strategies for Pancreatic Cancer-Associated Cachexia.},
journal = {Cancers},
volume = {18},
number = {7},
pages = {},
pmid = {41976282},
issn = {2072-6694},
abstract = {Background/Objectives: Pancreatic cancer-associated cachexia (CAC) is a complex, multifactorial and multi-organ metabolic syndrome affecting approximately 80% of patients with pancreatic ductal adenocarcinoma (PDAC). Recent epidemiological data show that cachexia is a primary cause of mortality in PDAC, directly accounting for approximately 30% of cancer-related deaths and significantly limiting the tolerability of cancer therapy and is associated with adverse effects of treatment. It is defined by systemic weight loss, skeletal muscle atrophy (sarcopenia), and adipose tissue depletion, often driven by systemic inflammation and metabolic dysregulation. Methods: The literature was searched in PubMed and Scopus using combinations of keywords. The search covers the literature between 2016 and 2026, but papers before this period were also included because of their historical importance. Studies with higher evidential value, such as prospective studies, randomized controlled trials, and meta-analyses, were prioritized and emphasized in our analysis. Results: CAC in PC arises from a systemic inflammatory response driven by tumor-host interactions and the release of pro-inflammatory mediators, such as growth differentiation factor 15 (GDF-15) and parathyroid hormone-related protein (PTHrP), which promotes anorexia and weight loss. The most commonly used diagnostic criteria include unintentional weight loss of more than 5% of body mass within 6 months, a body mass index (BMI) below 20 kg/m[2], or weight loss greater than 2% in the presence of sarcopenia. Emerging evidence supports the use of AI-based body composition analysis and novel biomarkers, including GDF-15 levels, to improve the detection and monitoring of cachexia. This review highlights that, despite the absence of pharmacological agents specifically approved for CAC in the United States and Europe, current guidelines recommend multimodal supportive care, including low-dose olanzapine, nutritional support, and exercise-based interventions. Furthermore, we identify recent phase 2 trials targeting the GDF-15 pathway, such as the GDF-15 inhibitor ponsegromab, which have demonstrated significant improvements in body weight and physical activity, suggesting a potential breakthrough in targeted therapies for CAC. Conclusions: CAC in PDAC represents a critical unmet medical need in oncology. It manifests as a lethal systemic pathology that demands early identification and targeted personalized pharmacological and nutritional interventions. Early diagnosis and targeted intervention represent promising strategies for improving survival and quality of life in this high-risk patient population.},
}

@article {pmid41976434,
year = {2026},
author = {Li, X and She, M and Yi, L and Zhou, G and Lian, Y and Yang, C and Wu, Y and Liu, Y and Han, Y and Li, J},
title = {Surfactin-Producing Bacillus velezensis A1 Inhibits Lactic Acid Bacteria in Jiang-Flavor Baijiu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976434},
issn = {2304-8158},
support = {32021005//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; BK20233003//Jiangsu Basic Research Center for Synthetic Biology/ ; BK20202002//Natural Science Foundation of Jiangsu Province/ ; JUSRP124034//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Lactic Acid Bacteria contribute to heightened acidity in the fermentation process of Jiang-flavor Baijiu due to their production of lactic acid. High-temperature Daqu may act as a reservoir for beneficial microorganisms and antimicrobial compounds. In this study, we utilized 16S rRNA and ITS amplicon sequencing to identify microbial taxa in high-temperature Daqu that inhibit the primary lactic acid bacterium involved in Jiang-flavor Baijiu fermentation, Acetilactobacillus jinshanensis, followed by the selection of antagonistic strains. The strain exhibiting the strongest antagonistic activity was identified as Bacillus velezensis based on whole-genome sequencing. Genome analysis revealed 12 secondary metabolite biosynthetic gene clusters, from which one lipopeptide was identified. This lipopeptide was demonstrated to antagonize A. jinshanensis AJS1 by disrupting the cell membrane and inducing leakage of intracellular contents. Collectively, strain A1 and its secondary metabolites exhibit considerable promise as antagonistic agents to mitigate acidity increases triggered by A. jinshanensis AJS1 during the fermentation of Jiang-flavor Baijiu.},
}

@article {pmid41976554,
year = {2026},
author = {Liu, M and Kong, W and Zhang, T and Wu, Z and Zeng, X and Guo, Y and Pan, D},
title = {Alcohol-Induced Acute Liver Disease in Mice: A Comparison of the Preventive Effects of Fermented Milk from Lactobacillus delbrueckii Subsp. bulgaricus or Lacticaseibacillus casei.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976554},
issn = {2304-8158},
support = {32272339, 32372355//National Natural Science Foundation of China/ ; D26C200002//Natural Science Foundation of Zhejiang Province/ ; BF2025322//Jiangsu Provincial Frontier Technology Research and Development Program/ ; },
abstract = {Fermented milk is rich in probiotics, peptides, vitamins, and minerals, which are used as routine food supplements and are of great benefit for regulating human health. This study explored the mechanism of Lactobacillus delbrueckii ssp. bulgaricus CGMCC 21287 or Lacticaseibacillus casei CGMCC 15956 fermented milk for alleviating acute alcoholic liver injury. We found that fermented milk was associated with reduced activation of TLR4/NF-κB pathways, alleviating alcohol-induced liver inflammation. Meanwhile, the two probiotics regulated different intestinal microbial communities in mice. The LC group specifically increased the abundance of probiotics such as Roseburia, unidentified_Lachnospiraceae, and Allobaculum, and decreased the abundance of pathogenic bacteria such as Enterococcus and Shigella. The LB group increased the abundance of Adlercreutzia and Ruminococcus, thereby increasing butyric acid, acetic acid, and valeric acid levels and decreasing lipopolysaccharide (LPS) production. These results suggest that daily intake of fermented milk can attenuate alcohol-induced acute liver injury in mice via the gut-liver axis, though differences exist in the mechanisms of action and areas of emphasis.},
}

@article {pmid41976908,
year = {2026},
author = {Oommen, TT and Philips, CA and Ahamed, R and Theruvath, AH and Tharakan, A and Rajesh, S and Augustine, P},
title = {Palliative Healthy Donor Stool Transplantation (pFMT) in Patients with End-Stage Alcohol-Related Cirrhosis and Severe Unstable Decompensations-A Cohort Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {7},
pages = {},
pmid = {41976908},
issn = {2077-0383},
abstract = {Background and Aims: Severe alcohol-associated hepatitis (SAH) can trigger unstable decompensations in cirrhosis patients. They experience high rates of emergency department visits and hospitalization. We evaluated real-world clinical outcomes following palliative-faecal microbiota transplantation (pFMT) compared to best supportive care (BSC) in this critically ill population. Patients and Methods: From July 2021 to April 2024, 28 patients on pFMT were compared with 37 on BSC. Patients on pFMT received nasoduodenal healthy donor stool infusion daily for 5-days. Patients were followed up for portal hypertension-related events, infections, hospitalizations, extrahepatic organ failure and 6- and 12-months survival. 16S rRNA sequencing on stool samples collected at baseline and on follow up were analysed for changes in relative abundance (RA) of bacterial communities. Results: Patients were matched for age, type of decompensation and liver disease severity at enrolment. Twelve-month survival was 64.3% in pFMT versus 51.4% in BSC groups. pFMT dramatically reduced hospital readmissions (mean 0.76 ± 0.76 vs. 2.29 ± 1.27, p < 0.001). Unstable decompensations beyond 3 months occurred in 14.3% of pFMT versus 64.9% of BSC (p < 0.001). Organ failures were lesser with pFMT: acute kidney injury 7.7% versus 93.8% (p < 0.001), hepatic encephalopathy 7.1% versus 68.2% (p < 0.001). Infection burden was significantly lower (53.6% vs. 83.8%, p = 0.008), particularly infections requiring admission (17.4% vs. 66.7%, p < 0.001) with pFMT. Microbiome analysis revealed progressive expansion of Gram-negative genera in BSC, and beneficial Actinobacteria in pFMT-treated patients at 3, 6, and 12 months. Conclusions: Palliative FMT represents a unique disease-modifying intervention in end-stage alcohol-related cirrhosis, preventing organ failure progression, reducing healthcare utilization, and improving survival trajectories.},
}

@article {pmid41977084,
year = {2026},
author = {Crișan, IM and Crețu, A and Bucur, SM},
title = {Observational Study of the Association Between Oral Helicobacter pylori, Fixed Orthodontic Appliances, and Gastric Cancer Risk.},
journal = {Journal of clinical medicine},
volume = {15},
number = {7},
pages = {},
pmid = {41977084},
issn = {2077-0383},
abstract = {Background:Helicobacter pylori is a well-established risk factor for gastric carcinogenesis. Increasing evidence suggests that the oral cavity may serve as an extragastric reservoir for the bacterium, potentially contributing to persistent infection and reinfection. Orthodontic appliances can modify oral biofilm ecology and may facilitate bacterial colonization. This study aimed to investigate the association between oral H. pylori colonization and gastric cancer, while exploring the potential modifying role of fixed orthodontic appliances. Materials and Methods: In this cross-sectional observational study, 212 participants were recruited from gastroenterology and dental clinics between January 2023 and March 2025. Oral samples were collected and analyzed for H. pylori DNA using polymerase chain reaction (PCR). Gastric diagnoses were established through endoscopic examination and histopathological evaluation, classifying participants into gastric cancer, precancerous gastric lesions, non-atrophic gastritis, and control groups. Demographic, clinical, and oral health variables were recorded. Multivariable logistic regression models were used to evaluate the association between oral H. pylori detection and gastric cancer while adjusting for potential confounders, including age, sex, smoking status, oral hygiene indicators, and socioeconomic factors. Results: Oral Helicobacter pylori DNA was detected in 35/54 (64.8%) patients with gastric cancer, 30/56 (53.6%) with precancerous lesions, 21/52 (40.4%) with non-atrophic gastritis, and 15/50 (30.0%) controls. Gastric H. pylori infection was identified in 41/54 (75.9%) gastric cancer cases compared with 18/50 (36.0%) controls. Oral H. pylori positivity was more frequent among patients undergoing active orthodontic treatment (22/36, 61.1%) than among those without orthodontic appliances (79/188, 42.0%). In multivariable analysis, oral H. pylori positivity remained independently associated with gastric cancer (adjusted OR 3.02, 95% CI 1.51-6.03, p = 0.002). Conclusions: Our findings support an association between oral-gastric microbial interactions and H. pylori-associated disease, and suggest that the oral cavity may serve as a potential reservoir for gastric infection dynamics. The presence of orthodontic appliances may be associated with altered oral microbial ecology and could be linked to sustained H. pylori colonization.},
}

@article {pmid41977121,
year = {2026},
author = {Kamiński, J and Piotrowicz-Cieślak, AI},
title = {Effects of Inorganic Fluoride and the Fluoroquinolone Antibiotic Pefloxacin on the Growth and Microbiome Structure of Eruca sativa L.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977121},
issn = {1422-0067},
support = {UMO-2019/35/B/NZ7/04394//National Science Centre/ ; },
mesh = {*Microbiota/drug effects ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Pefloxacin/pharmacology ; Rhizosphere ; *Fluorides/pharmacology ; Soil Microbiology ; Bacteria/genetics/drug effects/classification ; *Sodium Fluoride/pharmacology ; Plant Roots/microbiology/drug effects/growth & development ; },
abstract = {Environmental contamination with fluorinated compounds has increased markedly due to their widespread use in industry, medicine, and agriculture. Fluoride ions and fluoroquinolone antibiotics may enter soils through fertilizers, wastewater, and manure application, where they can interact with plant-associated microbial communities. In the present study, we investigated the effects of inorganic fluoride (applied as sodium fluoride, NaF) and the fluoroquinolone antibiotic pefloxacin on the growth and microbiome composition of Eruca sativa L. Plants were cultivated under controlled conditions and exposed for four weeks to NaF or pefloxacin at equimolar concentrations of 10 and 20 µM/kg soil. Morphological parameters, including biomass accumulation, root length, leaf dimensions, and leaf area, were not significantly affected by either treatment. Nevertheless, increased variability of growth traits was observed, particularly in plants exposed to NaF. High-throughput sequencing of the 16S rRNA gene revealed pronounced, treatment-specific alterations in both rhizosphere and phyllosphere bacterial communities. The rhizosphere microbiome was relatively stable at higher taxonomic levels but exhibited selective enrichment of Actinomycetota, including the class Thermoleophilia, under NaF exposure. In contrast, the phyllosphere microbiome showed strong sensitivity to fluoride, with a marked increase in Betaproteobacteria, dominated by Burkholderiales. Changes induced by pefloxacin were weaker and more diffuse. Our results demonstrate that plant-associated microbiomes respond to fluorinated compounds at concentrations that do not induce visible plant stress. The phyllosphere microbiome, in particular, represents a sensitive indicator of fluoride exposure and may serve as an early-warning system for environmental contamination.},
}

*Microbiota/drug effects
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Pefloxacin/pharmacology
Rhizosphere
*Fluorides/pharmacology
Soil Microbiology
Bacteria/genetics/drug effects/classification
*Sodium Fluoride/pharmacology
Plant Roots/microbiology/drug effects/growth & development

@article {pmid41977129,
year = {2026},
author = {Liu, Z and Wang, X and Li, L},
title = {Lysine Propionylation as a Metabolically Coupled PTM: Mechanisms, Functional Consequences, and Therapeutic Potentials.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977129},
issn = {1422-0067},
support = {32570698//the National Natural Science Foundation of China/ ; DUT24YG126//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; *Lysine/metabolism ; *Protein Processing, Post-Translational ; *Acyl Coenzyme A/metabolism ; Animals ; Acylation ; Acetylation ; Fatty Acids, Volatile/metabolism ; },
abstract = {Lysine propionylation (Kpr) is a metabolically coupled lysine acylation that links propionyl-CoA availability to the molecular regulation of gene expression and protein function. Although lysine acetylation (Kac) is the most extensively characterized, recent proteomic and metabolic studies suggest that Kpr is more frequent than previously appreciated, occurs at defined lysine sites, and displays tissue-resolved and context-dependent patterns. Kpr often co-varies with other short-chain acylations such as Kac and lysine butyrylation (Kbu); however, emerging genomic-scale evidence indicates mark-biased genomic distributions and functional associations, suggesting that Kpr is not simply an extension or alternative to Kac. Notably, propionyl-CoA, the direct acyl donor for Kpr, can be influenced by microbiome-derived short-chain fatty acids (SCFAs), implying that interventions modulating SCFA availability (e.g., dietary manipulation) may provide an actionable route to tune Kpr and related acylations. Here, we summarize recent advances in propionyl-CoA sources and compartmentalization, the enzymatic writers/erasers/readers, the molecular mechanisms underlying Kpr, and the functional consequences of Kpr in physiology and disease.},
}

Humans
*Lysine/metabolism
*Protein Processing, Post-Translational
*Acyl Coenzyme A/metabolism
Animals
Acylation
Acetylation
Fatty Acids, Volatile/metabolism

@article {pmid41977159,
year = {2026},
author = {Suturina, L and Belkova, N and Sidorova, T and Smurova, N and Igumnov, I and Lazareva, L and Danusevich, I and Nadeliaeva, I and Sholokhov, L and Belenkaia, L and Atalyan, A},
title = {Gut Microorganisms as Markers of Hyperandrogenemia in Premenopausal Women with Polycystic Ovary Syndrome.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977159},
issn = {1422-0067},
support = {126020216231-0//Ministry of Science and Higher Education of the Russian Federation/ ; 1022040800022-7-3.2.2;3.2.24//Ministry of Science and Higher Education of the Russian Federation/ ; АААА-А20-120120790036-3//Ministry of Science and Higher Education of the Russian Federation/ ; АААА-А18-118011990043-5//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/microbiology/complications ; *Gastrointestinal Microbiome ; Adult ; Premenopause ; *Hyperandrogenism/microbiology ; RNA, Ribosomal, 16S/genetics ; Biomarkers ; Case-Control Studies ; Young Adult ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Previously, the role of decreased biodiversity of gut microbiota in polycystic ovary syndrome (PCOS) was demonstrated, but the objective criteria for assessing the representation of microorganisms associated with hyperandrogenemia (HA) were limited. A total of 175 premenopausal women (26 women with PCOS and HA and 149 women without HA, including 19 healthy controls) were recruited during the Eastern Siberia PCOS Epidemiology and Phenotype (ESPEP) Study (2016-2019). Methods included a questionnaire survey, clinical examination, pelvic U/S, blood and feces sampling. Gut microbiome was analyzed by high-throughput sequencing of the V1-V3 of the variable regions of the 16S rRNA gene (Illumina MiSeq, San Diego, CA, USA). Amplicon libraries of 16S rDNA were processed using the QIIME2 bioinformatics pipeline. All data were analyzed using R 3.6.3. The gut microbiocenosis in women with HA was characterized by a higher representation of Lactobacillus and a lower prevalence of the Clostridia class. For Faecalibacterium, Christensenellaceae_R-7_group, and [Eubacterium] eligens group the cut-off values of their relative presence, associated with HA, were estimated as: ≤0.043%, ≤0.039%, and ≤0.02%, respectively. Conclusions: Women with PCOS-associated HA demonstrate a lower prevalence, predominantly, of Clostridia class gut microorganisms, compared with those without any forms of HA. The study presents the quantitative criteria for assessing the representation of gut microorganisms, negatively associated with hyperandrogenic phenotypes of PCOS. The threshold values proposed may be useful to justify the administration of probiotics in PCOS patients with HA.},
}

Humans
Female
*Polycystic Ovary Syndrome/microbiology/complications
*Gastrointestinal Microbiome
Adult
Premenopause
*Hyperandrogenism/microbiology
RNA, Ribosomal, 16S/genetics
Biomarkers
Case-Control Studies
Young Adult
Feces/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid41977176,
year = {2026},
author = {Wang, X and Wu, F and Liu, J and Hong, X and Dong, S},
title = {Application and Potential of Local Drug Delivery Systems for Antibacterial Treatment of Periodontitis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977176},
issn = {1422-0067},
support = {jcsz2023481-10//the Healthcare Talent Development Project of the Finance Department of Jilin Province/ ; },
mesh = {Humans ; *Periodontitis/drug therapy/microbiology ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; *Drug Delivery Systems/methods ; Animals ; Nanoparticles/chemistry ; Biofilms/drug effects ; },
abstract = {Periodontitis (PD) is a chronic inflammatory disease characterized by the progressive destruction of periodontal supporting tissues. As one of the most prevalent chronic diseases, PD affects more than 743 million people globally, some with serious systemic health implications. Plaque accumulation constitutes the key driver of periodontitis, initiating host inflammatory cascades and compromising periodontal microbiome equilibrium. Conventional treatment methods, such as scaling and root planing, are limited by a constrained operative field, resulting in blind spots that impede the complete eradication of bacterial biofilms and the modulation of the inflammatory microenvironment. Therefore, employing new therapeutic strategies (e.g., drug delivery systems) is essential. This review focuses on local drug delivery systems for the treatment of PD, including fibers, strips and films, microspheres, gels, nanoparticles, and vesicle systems, to deliver drugs directly into the periodontal pockets, targeting inflammation and providing sustained antibacterial effects while reducing systemic side effects. The characteristics and clinical implications of each type of local drug delivery system are discussed, along with emerging technologies such as 3D printing and nanotechnology.},
}

Humans
*Periodontitis/drug therapy/microbiology
*Anti-Bacterial Agents/administration & dosage/therapeutic use
*Drug Delivery Systems/methods
Animals
Nanoparticles/chemistry
Biofilms/drug effects

@article {pmid41977259,
year = {2026},
author = {Amaradasa, BS and Chretien, RL and Lowman, S and Mei, C},
title = {Transcriptomic and Root Microbiome Responses of Lettuce to Beneficial Endophytic Bacteria in Hydroponic Systems.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977259},
issn = {1422-0067},
support = {2021B-570//the U.S. Department of Agriculture's (USDA) Agricultural Marketing Service/ ; },
mesh = {*Lactuca/microbiology/genetics/growth & development ; *Plant Roots/microbiology/genetics/growth & development ; Hydroponics/methods ; *Microbiota/genetics ; *Transcriptome ; *Endophytes/physiology ; *Pseudomonas/physiology ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; },
abstract = {Controlled environment agriculture (CEA) relies on hydroponic systems to achieve high yields, yet optimizing plant performance remains a challenge. Beneficial endophytic bacteria offer a sustainable solution by promoting growth and nutrient uptake. Here, we investigated the mechanistic basis of growth enhancement in lettuce (Lactuca sativa) inoculated with Pseudomonas psychrotolerans IALR632 in a nutrient film technique (NFT) system. Growth measurements showed significant increases in shoot and root biomass and leaf greenness. RNA-seq profiling at 4, 10, and 15 days after transplanting revealed dynamic transcriptional reprogramming, with 38, 796, and 7642 differentially expressed genes, respectively. MapMan and GO analyses indicated up-regulation of pathways related to cell wall remodeling, lipid metabolism, nitrogen assimilation, and stress adaptation, alongside modulation of ethylene signaling. Root bacterial microbiome through 16S metabarcoding sequencing demonstrated distinct community shifts, confirmed by analysis of similarity (ANOSIM) (R = 1, p = 0.028), with enrichment of genera linked to nutrient cycling and plant growth promotion. These findings provide integrated molecular and ecological evidence that IALR632 enhances lettuce growth by coordinating host gene expression and rhizobiome restructuring, offering a mechanistic framework for microbial inoculant strategies in hydroponic horticulture.},
}

*Lactuca/microbiology/genetics/growth & development
*Plant Roots/microbiology/genetics/growth & development
Hydroponics/methods
*Microbiota/genetics
*Transcriptome
*Endophytes/physiology
*Pseudomonas/physiology
Gene Expression Regulation, Plant
Gene Expression Profiling

@article {pmid41977298,
year = {2026},
author = {Cycoń, M},
title = {Molecular Monitoring in Soil Bioremediation: From Genetic Potential to Verified Pathway Operation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977298},
issn = {1422-0067},
mesh = {*Biodegradation, Environmental ; *Soil/chemistry ; *Soil Pollutants/metabolism ; *Soil Microbiology ; },
abstract = {Sequence-based tools have greatly improved the molecular description of soil bioremediation, but detection alone cannot confirm that a contaminant is being degraded by a defined pathway. In soils, bioavailability limitations, redox microsites, relic DNA, gene mobility, and community restructuring can decouple gene presence from reaction flux. This review synthesizes an operational framework that separates three inferential levels: pathway potential, in situ activity, and verified pathway operation. The framework links inoculant fate, functional gene abundance, gene expression, pathway reconstruction, stable isotope probing, and targeted chemical analysis under explicit quality assurance, quality control, and decision rules. Particular attention is given to distinguishing parent compound loss from mineralization and detoxification and to using isotopic attribution when functional redundancy or inoculant-native overlap obscures agency. Instead of being presented as conceptually new, these principles are organized into a practical workflow for soil systems. This structure clarifies what can be discerned from genes, transcripts, proteins, metabolites, and transformation products at each evidentiary tier and provides a conservative basis for integrating multi-omics with mechanistic and quantitative interpretation.},
}

*Biodegradation, Environmental
*Soil/chemistry
*Soil Pollutants/metabolism
*Soil Microbiology

@article {pmid41977315,
year = {2026},
author = {Prasad, YM and Gowda, SR and Shantamurthy, N and Sehar, AEJS and Razack, SA and Srichairatanakool, S and Ravikumar, Y},
title = {Computational Identification of Triphala-Derived Sterol Compounds as Putative Agonists of the Human Takeda G Protein-Coupled Receptor (TGR5).},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977315},
issn = {1422-0067},
support = {11/2025//Chiang Mai University/ ; },
mesh = {Humans ; *Receptors, G-Protein-Coupled/agonists/chemistry/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; *Sterols/chemistry/pharmacology ; Plant Extracts/chemistry/pharmacology ; },
abstract = {The presence of an unbalanced gut microbiome and the dysregulation of bile acid signalling are considered pivotal causes of various inflammation-based diseases. The Takeda G protein-coupled receptor (TGR5), TGR5 is a bile acid-responsive receptor that modulates inflammatory signalling pathways, making it an enticing molecular target for the discovery of novel anti-inflammatory agents. Herein, a comprehensive in silico approach was employed to identify potential TGR5 agonists from sterol-rich phytocompounds present in Triphala, a traditional polyherbal formulation. Using in silico computational methods, such as molecular docking and molecular dynamics simulations (MDS), we screened the putative agonistic potential of 10 phytocompounds obtained from Terminalia chebula, Terminalia bellirica, and Phyllanthus emblica against the crystal structure of human TGR5 (PDB ID: 7XTQ). Based on binding energy and molecular interactions, ergosterol (-12.34 ± 0.17 kcal/mol) and stigmasterol (-10.35 ± 0.04 kcal/mol) were predicted to be the top and best compounds. Furthermore, the stability of these two compounds in the docked complex was analysed using MDS for 200 ns. The mean Cα RMSD values were 0.22 ± 0.02 nm for both ergosterol- and stigmasterol-bound complexes, compared to 0.21 ± 0.02 nm for the unbound apo protein. Further, the molecular mechanics/Poisson-Boltzmann surface area (MMPBSA) analysis revealed that ergosterol exhibited binding free energy (-139.868 ± 12.318 kJ/mol) comparable to that of the co-crystallised ligand R399 -93.424 ± 8.919 kJ/mol. In silico ADMET predictions indicated acceptable drug-like properties and low toxicity for both compounds. Collectively, these computational findings suggest that ergosterol is a promising putative TGR5 agonist, warranting further experimental validation of its potential role in modulating inflammation-related pathways.},
}

Humans
*Receptors, G-Protein-Coupled/agonists/chemistry/metabolism
Molecular Docking Simulation
Molecular Dynamics Simulation
*Sterols/chemistry/pharmacology
Plant Extracts/chemistry/pharmacology

@article {pmid41977345,
year = {2026},
author = {Ifrach, C and Levy-Turgeman, R and Szitenberg, A and Kesten, I and Pitashny, M and Levin-Iaina, N and Segev, Y and Yagil, Y},
title = {Gut Microbiome Signatures Distinguish Susceptibility from Disease Development in Type 2 Diabetes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977345},
issn = {1422-0067},
support = {N/A//Institutional funds/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology/etiology ; Rats ; Disease Susceptibility ; RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; *Diabetes Mellitus, Experimental/microbiology ; Disease Models, Animal ; },
abstract = {Individuals may be prone or resistant to the development of type 2 diabetes. The basis for susceptibility is in part genetic, but environmental factors are likely to come into play. The gut microbiome stands at the interface of genetics and the host microenvironment. Its role in mediating susceptibility to diabetes, however, has not been resolved. Here we investigated whether the gut microbial composition contributes to susceptibility to diabetes, as distinct from disease development. We hypothesized that distinct microbial signatures modulate sensitivity or resistance to a diabetogenic diet (DD) and that separate signatures are linked to disease development. To test this hypothesis, we studied the Cohen diabetic rat model, comprising a diabetes-sensitive strain (CDs/y) and a diabetes-resistant strain (CDr/y). When exposed to DD, diabetes develops in CDs/y but not in CDr/y rats; on a regular diet (RD), both strains remain metabolically normal. To establish the contribution of the gut microbiome to susceptibility, we studied the fecal microbial composition in young, metabolically healthy CDs/y and CDr/y rats, using 16S rRNA gene sequencing, measures of α- and β-diversity, and differential taxonomic abundance. We found distinct, strain-specific gut microbiota profiles that differentiated diabetes-sensitive from -resistant animals, indicating an association between microbial composition and susceptibility. To test causality, we co-housed sensitive and resistant animals to allow passive microbial cross-transfer and fed the animals with DD. Co-housing led to partial convergence of microbial communities and significantly attenuated the diabetic phenotype in CDs/y rats, supporting a contributory and causal role for the gut microbiome in modulating sensitivity to diabetes. The resistance phenotype, on the other hand, remained unchanged. To distinguish between the contribution of the gut microbiome to susceptibility to diabetes as opposed to the development of the disease, we studied the gut microbial profiles across strains after feeding with DD or RD and the development of diabetes in CDs/y but not in CDr/y. We found distinct taxonomic signatures that differentiated diabetic from non-diabetic animals. These findings demonstrate that the gut microbiome contributes to susceptibility to diabetes with separate pathways from those linked to the development of diabetes and may represent an important modifiable determinant of diabetes risk and a target for early intervention.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Diabetes Mellitus, Type 2/microbiology/etiology
Rats
Disease Susceptibility
RNA, Ribosomal, 16S/genetics
Male
Feces/microbiology
*Diabetes Mellitus, Experimental/microbiology
Disease Models, Animal

@article {pmid41977499,
year = {2026},
author = {Shetty, S and Luca, R and Rodriguez, SH and Skondra, D},
title = {A Potential Gut-Retina Axis in Retinopathy of Prematurity: Emerging Perspectives on Microbiome-Mediated Modulation of the IGF-1-VEGF Pathway.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
pmid = {41977499},
issn = {1422-0067},
mesh = {Humans ; *Retinopathy of Prematurity/metabolism/microbiology/pathology/etiology ; *Gastrointestinal Microbiome ; *Insulin-Like Growth Factor I/metabolism ; Animals ; *Vascular Endothelial Growth Factor A/metabolism ; Signal Transduction ; *Retina/metabolism/pathology ; Infant, Newborn ; Dysbiosis ; },
abstract = {Retinopathy of prematurity (ROP) is a leading cause of childhood blindness characterized by disrupted physiologic vascularization followed by pathologic neovascularization, classically organized around the insulin-like growth factor-1 (IGF-1)-vascular endothelial growth factor (VEGF) axis in the retina. Increasing evidence suggests that early-life gut dysbiosis may act as an upstream modifier of this biphasic process. In this review, we synthesize human cohort studies, multi-omics analyses, and experimental animal models examining associations between the neonatal gut microbiome and ROP. Preterm infants who develop severe ROP demonstrate enrichment of facultative anaerobes and reduced acquisition of obligate anaerobes, alongside altered predicted metabolic capacity. Microbiome-derived metabolites, including short-chain fatty acids, bile acid derivatives, and lipid mediators, have been shown in experimental systems to influence systemic IGF-1 production, hypoxia-inducible factor-1α stabilization, and VEGF signaling. Rodent oxygen-induced retinopathy models offer a translation framework to assess the functional link between microbial perturbation and retinal angiogenic responses. Collectively, these findings support a conceptual microbiome-IGF-1-VEGF-retina axis in which early intestinal dysbiosis may modulate inflammatory tone, metabolic signaling, and retinal vascular development. Although current evidence remains largely associative, integrating microbiome profiling with mechanistic and longitudinal studies may clarify potential causal pathways and identify novel biomarkers or preventive strategies for severe ROP.},
}

Humans
*Retinopathy of Prematurity/metabolism/microbiology/pathology/etiology
*Gastrointestinal Microbiome
*Insulin-Like Growth Factor I/metabolism
Animals
*Vascular Endothelial Growth Factor A/metabolism
Signal Transduction
*Retina/metabolism/pathology
Infant, Newborn
Dysbiosis

@article {pmid41978089,
year = {2026},
author = {Singar, S and Kachouei, AA and Lantigua-Somoano, L and Manley, D and Cardinale, A and Sadikan, MZ and Kadyan, S and Shahamati, D and Dias, L and Wood, A and Chavarria, C and Rosenkranz, SK and Akhavan, NS},
title = {Ultra-Processed Foods and the Cardiovascular-Kidney-Metabolic Continuum: Integrating Epidemiological, Multi-Omics, and Translational Evidence.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978089},
issn = {2072-6643},
mesh = {Humans ; *Cardiovascular Diseases/epidemiology/etiology ; *Fast Foods/adverse effects ; *Metabolic Syndrome/epidemiology/etiology ; Metabolomics ; *Kidney Diseases/epidemiology/etiology ; Translational Research, Biomedical ; *Food Handling ; Proteomics ; Food, Processed ; Multiomics ; },
abstract = {Cardiovascular-kidney-metabolic (CKM) syndrome integrates excess adiposity, metabolic dysfunction, kidney impairment, subclinical cardiovascular diseases, and clinical events along a staged continuum that invites unified prevention and treatment. Ultra-processed foods (UPFs) are a complex, high-prevalence exposure that may influence risk across CKM stages through nutrient profiles, additives, processing-induced compounds, and packaging-related contaminants. This review synthesizes epidemiologic, mechanistic, and translational evidence with attention to exposure definition and analytic rigor. We summarize NOVA-based UPF operationalization across dietary assessment tools, highlighting misclassification of mixed dishes, brand heterogeneity, and energy under-reporting, and we propose further examination of energy-adjusted models, calibration, and harmonized metrics. Observational studies consistently associate higher UPF intake with adiposity, diabetes, chronic kidney disease, cardiovascular events, and mortality, with modest to moderate effect sizes that are heterogeneous across populations. Mechanistic data from metabolomics, lipidomics, proteomics, and the gut microbiome converge on pathways of inflammation, lipid metabolism, oxidative and metabolic stress, and intestinal barrier dysfunction; in selected cohorts, multi-omics modules account for a substantial minority of UPF-outcome associations. We outline quality-control pipelines, batch-effect prevention/correction, and multiple-testing control necessary for reproducible diet-omics. Translationally, targeted lipidomic and proteomic panels show promise for CKM risk stratification and monitoring but require validation, clinical thresholds, and guideline endorsement. Equity and global context, including differences in product mix, food systems, and care capacity, modify population impact. We conclude with a research agenda prioritizing harmonized exposure metrics, error-aware modeling, standardized multi-omics workflows, and adequately powered, stage-specific interventions capable of testing mediation and prognostic utility.},
}

Humans
*Cardiovascular Diseases/epidemiology/etiology
*Fast Foods/adverse effects
*Metabolic Syndrome/epidemiology/etiology
Metabolomics
*Kidney Diseases/epidemiology/etiology
Translational Research, Biomedical
*Food Handling
Proteomics
Food, Processed
Multiomics

@article {pmid41978103,
year = {2026},
author = {Lim, MJS and Parlindungan, E and See, E and Gan, CH and Yap, R and Yong, GJM},
title = {Diet, the Gut Microbiome, and Estrogen Physiology: A Review in Menopausal Health and Interventions.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978103},
issn = {2072-6643},
support = {C240314055//Agency for Science, Technology and Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; *Menopause/physiology ; *Estrogens/physiology/metabolism ; *Diet ; Phytoestrogens/administration & dosage ; Probiotics/administration & dosage ; Women's Health ; },
abstract = {Menopause represents a key transitional phase in women's health, characterized by declining estrogen levels and increased risk for cardiometabolic, musculoskeletal, and urogenital disorders. Beyond its endocrine roots, emerging evidence highlights the gut microbiome as a critical modulator of systemic hormonal balance. This review synthesizes current understanding of the bidirectional relationship between estrogen and the gut microbiome and its implications for women's health during menopause. Evidence from current studies reveals distinct findings across populations, reflecting the complexity of estrogen regulation in part by the gut microbiome (i.e., estrobolome). While no ideal gut microbial composition has been identified for women across stages of perimenopause, likely due to geographically unique gut microbiome profiles among healthy women, greater microbial diversity has been positively associated with improved estrogen regulation. Conversely, reduced diversity and altered Firmicutes/Bacteroidetes ratios have been linked to biomarkers of inflammation during perimenopause, which is a key driver across many perimenopausal symptoms. Although hormone replacement therapy remains the primary clinical intervention during perimenopause, we highlight emerging evidence on the adjuvant potential of diet, synbiotics, phytoestrogens, and strain-specific probiotics in modulating the estrogen-gut microbiome axis for improved health span trajectories and better symptom management. Future longitudinal studies integrating diet, gut microbiome profiles and symptom trajectories are essential to clarify these mechanisms across ethnicity and geography. Ultimately, understanding localized diet-microbiome interactions will enable the development of accessible, personalized, and non-hormonal strategies to complement and increase agency in proactive management during the perimenopausal transition.},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
*Menopause/physiology
*Estrogens/physiology/metabolism
*Diet
Phytoestrogens/administration & dosage
Probiotics/administration & dosage
Women's Health

@article {pmid41978124,
year = {2026},
author = {Matera, M and Biagioli, V and Palazzi, CM and Meocci, M and Pedaci, F and Besostri, A and Zerbinati, N and Di Pierro, F},
title = {A One Health Decalogue for Breastfeeding: Microbiota-Targeted Strategies for Infant Gastrointestinal and Neurodevelopmental Health.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978124},
issn = {2072-6643},
mesh = {Humans ; *Breast Feeding ; Infant ; Probiotics/administration & dosage ; Female ; *Gastrointestinal Microbiome/physiology ; Milk, Human/microbiology ; *Infant Health ; Infant, Newborn ; *Child Development ; Maternal Nutritional Physiological Phenomena ; *Gastrointestinal Tract/microbiology ; Infant Nutritional Physiological Phenomena ; },
abstract = {Background/Objectives: Breastfeeding represents a critical developmental window during which maternal biology, environmental exposures, and nutrition converge to influence infant gastrointestinal health and long-term developmental trajectories. From a One Health perspective, breastfeeding can be conceptualized not as a static nutritional act, but as a dynamic and modifiable biological system in which maternal factors shape early-life microbiota assembly and immune programming. This narrative review explores how microbiota-oriented strategies during breastfeeding may foster a favorable trajectory of infant health, potentially extending to transgenerational outcomes. Methods: This narrative review is structured around a ten-point decalogue addressing interconnected domains relevant to the maternal-milk-infant microbiota axis, including maternal diet, microbial diversity, environmental exposures, psychological stress and probiotic use. Current mechanistic and clinical evidence was examined to evaluate how these domains may modulate microbiota composition and function during breastfeeding. Attention was given to probiotic supplementation, including strain specificity, timing of administration, and clinical context, as well as to the broader implications of a One Health framework. Results: Available evidence suggests that maternal nutritional patterns, environmental and psychosocial exposures, and targeted microbiota-modulation strategies may influence the composition and functional properties of human milk and the developing infant microbiota. Probiotic use during breastfeeding appears to have strain-specific and context-dependent effects, with potential benefits in selected clinical scenarios. However, findings remain heterogeneous, and uncertainties persist regarding optimal strains, timing, and long-term outcomes. Conclusions: Breastfeeding can be understood as a dynamic biological interface shaped by maternal and environmental factors. Integrating microbiota-oriented strategies within a One Health framework may support infant gastrointestinal health and possibly contribute to longer-term developmental trajectories. Nevertheless, careful interpretation of the current evidence is warranted to avoid reductionist, supplement-centered approaches and to prevent maternal overmedicalization or blame.},
}

Humans
*Breast Feeding
Infant
Probiotics/administration & dosage
Female
*Gastrointestinal Microbiome/physiology
Milk, Human/microbiology
*Infant Health
Infant, Newborn
*Child Development
Maternal Nutritional Physiological Phenomena
*Gastrointestinal Tract/microbiology
Infant Nutritional Physiological Phenomena

@article {pmid41978132,
year = {2026},
author = {van Wees-Jansen, ERPC and Hutten, BA and Nieuwdorp, M},
title = {The Broad Effect of Iodine in Graves' Hyperthyroidism and Its Relationship with the Gut Microbiota.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978132},
issn = {2072-6643},
mesh = {Humans ; *Graves Disease/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Iodine/administration & dosage ; Diet ; Thyroid Hormones/biosynthesis ; },
abstract = {Thyroid disorders are among the most common endocrine disorders worldwide and are classified as noncommunicable diseases. These disorders are associated with significant morbidity, impaired quality of life, and considerable socioeconomic burden. Like other noncommunicable diseases, thyroid disorders arise from complex interactions between genetic susceptibility and environmental factors, including diet and lifestyle. Despite growing interest in lifestyle-based approaches to noncommunicable disease prevention and management, thyroid disorders have received comparatively limited attention in this context. Graves' disease, the most common cause of hyperthyroidism, is a relevant condition for exploring dietary interventions. Current treatment strategies-anti-thyroid drugs, radioactive iodine and thyroidectomy-have remained largely unchanged for decades. Long-term remission following drug therapy is achieved in no more than approximately 50% of patients, while all treatment modalities carry potential adverse effects. These limitations underscore the need for alternative or adjunctive therapeutic strategies. Iodine intake plays a central role in thyroid hormone synthesis. Indeed, observational studies have shown inverse associations between iodine intake and remission rates, as well as achievement of euthyroidism, medication requirements and thyroid autoantibody titers. These findings suggest that dietary iodine restriction may enhance treatment efficacy and reduce medication-related risks. Beyond its direct effects on thyroid hormone synthesis, iodine may influence Graves' disease through indirect mechanisms involving the lipid profile and the gut-thyroid axis. Autoimmune thyroid diseases are associated with a dyslipidemic profile and with gut microbiota dysbiosis; the latter characterized by increased potentially pathogenic bacteria and reduced beneficial bacteria such as Lactobacillus and Bifidobacterium.},
}

Humans
*Graves Disease/microbiology
*Gastrointestinal Microbiome/drug effects
*Iodine/administration & dosage
Diet
Thyroid Hormones/biosynthesis

@article {pmid41978138,
year = {2026},
author = {Kase, BE and Liese, AD and Zhang, J and Murphy, EA and Steck, SE},
title = {Association Between the Dietary Index for Gut Microbiota (DI-GM) and Colorectal Cancer in the PLCO Cohort.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978138},
issn = {2072-6643},
support = {U01 CA272977-01/CA/NCI NIH HHS/United States ; P20 GM155896/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/epidemiology/microbiology/prevention & control ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; *Diet ; Aged ; Incidence ; Risk Factors ; Proportional Hazards Models ; Follow-Up Studies ; Cohort Studies ; },
abstract = {OBJECTIVES: The study aimed to examine the association between a dietary index for gut microbiota (DI-GM) and the risk of incident colorectal cancer (CRC). Clarifying the role of diet-induced alterations in the composition and function of gut microbiota on the development of CRC can contribute to prevention efforts.

METHODS: Participants from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening trial enrolled in the intervention arm and who completed baseline assessments were included in the analysis (n = 55,685). The DI-GM is a literature-derived index used to score diet quality in terms of maintaining healthy gut microbiota. A time-dependent Cox model stratified by follow-up years (<5 and ≥5 person-years) was used to evaluate the relationships between the dietary patterns and risk of incident CRC.

RESULTS: A total of 735 incident CRC were identified over 650,470 person-years of follow-up. During < 5 years of follow-up, those with higher diet quality (DI-GM scores above 67th percentile) had an 18% lower risk of incident CRC (HRadjusted = 0.82, 95% CI: 0.63, 1.07) compared with those with lower diet quality (DI-GM scores below the 67th percentile), though effect estimates were imprecise. During ≥ 5 years of follow-up, there was no association between incident CRC and DI-GM (HRadjusted = 1.01, 95% CI: 0.80, 1.26).

CONCLUSIONS: Diet quality measured using the DI-GM was associated with the risk of CRC in the first five years of follow-up in a large prospective cohort study. A diet that enhances the composition and function of gut microbiota may contribute to reduction in CRC risk.},
}

Humans
*Colorectal Neoplasms/epidemiology/microbiology/prevention & control
*Gastrointestinal Microbiome/physiology
Female
Male
Middle Aged
*Diet
Aged
Incidence
Risk Factors
Proportional Hazards Models
Follow-Up Studies
Cohort Studies

@article {pmid41978161,
year = {2026},
author = {Gala, RM and Schoeman, J and Revuelta Iniesta, R and van den Brink, M and Lovell, AL and Huibers, MHW and , },
title = {Establish Global Nutrition Research Strategies: The Meeting Report of the First SIOP Nutrition Research Forum.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978161},
issn = {2072-6643},
mesh = {Humans ; *Neoplasms/therapy ; Nutritional Status ; Child ; Global Health ; *Biomedical Research ; Pediatrics ; *Medical Oncology ; *Nutritional Sciences ; Congresses as Topic ; },
abstract = {Despite strong evidence linking nutritional status to treatment efficacy and survival in pediatric cancer, significant knowledge gaps and practice variation persist globally. On 24th October 2025, the International Society of Paediatric Oncology (SIOP) Nutrition Network, in collaboration with Prinsess Máxima Center for Paediatric Oncology and the International Initiative for Pediatrics and Nutrition (IIPAN), convened the first global SIOP Nutrition Network Research Forum. The forum brought together 54 international experts from high-income countries and low- and middle-income countries to define global nutrition research strategies for pediatric oncology. The forum addressed six emerging domains: body composition and treatment outcomes; microbiome, micronutrient status and metabolic health; prehabilitation and rehabilitation strategies; validation of nutritional assessment tools, guideline development for high-income settings; insights from international multicentric research initiatives-the International Atomic Energy Agency (IAEA), SIOP Nutrition Network, the Adapted Resource and Implementation Application (ARIA) guide nutrition portal, the International Collaboration on Nutrition in Cancer (ICONIC) WHO knowledge portal; and IIPAN and the World Cancer Research Fund (WCRF) for funding strategies. Delegates identified three priority working groups, namely prehabilitation optimization, pharmacokinetics, and advocacy, with each outlining collaborative nutrition research priorities for the next five years. This forum represents a critical point in pediatric oncology nutrition research as it established the first coordinated and internationally endorsed roadmap to bridge gaps in cancer care and ensure standard nutrition care worldwide. The research priorities and collaborations will help in creating evidence to improve cancer treatment and survival rate for children globally.},
}

Humans
*Neoplasms/therapy
Nutritional Status
Child
Global Health
*Biomedical Research
Pediatrics
*Medical Oncology
*Nutritional Sciences
Congresses as Topic

@article {pmid41978176,
year = {2026},
author = {Frye, BM and Cooper, H and Negrey, JD and Sutphen, C and Nagpal, R and Kim, J and Barcus, RA and Lockhart, SN and Whitlow, CT and Tooze, JA and Yadav, H and Craft, S and Register, TC and Shively, CA},
title = {Dietary Pattern-Induced Gut Microbiota Differences Are Associated with White Matter Volume Changes in Middle-Aged Female Macaques.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978176},
issn = {2072-6643},
support = {R01 HL122393/HL/NHLBI NIH HHS/United States ; RF1 AG077443/AG/NIA NIH HHS/United States ; P30CA012197//National Cancer Institute's Cancer Center/ ; USDA-ARS-447044//United States Department of Agriculture/ ; USDA-ARS-448763//United States Department of Agriculture/ ; USDA-ARS-440658//United States Department of Agriculture/ ; FDOH-24A05//Florida Department of Health/ ; FDOH-23A02//Florida Department of Health/ ; IDSA-ALZ-ID-0000000028//Infectious Diseases Society of America/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; *Diet, Western/adverse effects ; *Diet, Mediterranean ; *White Matter/diagnostic imaging ; Amino Acids, Branched-Chain/blood ; Fatty Acids, Volatile/metabolism ; Macaca fascicularis ; Insulin/blood ; Insulin Resistance ; Feces/microbiology/chemistry ; Lipopolysaccharide Receptors/blood ; },
abstract = {Background/Objectives: Western and Mediterranean diets have divergent effects on the brain. The gut microbiome may mediate diet effects, and specific microbes may be particularly significant contributors to these processes. Oscillospira, a genus of gut-dwelling bacteria, has been implicated as a key microbial target. Other peripheral contributors may include short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), insulin resistance, and microbial translocation. Methods: We determined the effects of long-term (31 months, ~9 human years) consumption of a Mediterranean or Western-type diet on Oscillospira abundance, fecal SCFAs, plasma BCAAs, soluble CD14 (sCD14), and insulin responses in a randomized trial of 38 middle-aged female cynomolgus macaques (Macaca fascicularis). We determined diet effects and associations between dependent variables. For variables that were affected by diet composition and significantly associated with Oscillospira, we tested whether Oscillospira abundance mediated the effects of diet. Results: The Mediterranean diet resulted in higher Oscillospira (p = 0.004) and SCFAs (acetate p = 0.002; propionate p = 0.049) and lower BCAAs (isoleucine p = 0.035; leucine p = 0.007; valine p < 0.001). The Western diet increased insulin resistance (p = 0.040) and WM loss (p = 0.011). Oscillospira abundance was negatively associated with BCAAs (leucine p = 0.007; valine p = 0.005) and insulin resistance (insulin AUC: p = 0.024; increase in insulin AUC from pretreatment: p = 0.020), with trends for isoleucine (p = 0.066) and sCD14 (p = 0.103). Oscillospira abundance was positively associated with acetate (p = 0.032) and WM volume changes (p = 0.012). Oscillospira abundance significantly mediated the effects of diet on white matter volume changes (p = 0.020) and on insulin resistance (insulin AUC: p = 0.012 at study end; increase in insulin AUC during study: p = 0.020), presenting potential pathways through which diet may influence the brain. Conclusions: These findings suggest that diet-driven differences in Oscillospira are linked to metabolic regulation and white matter integrity, and Oscillospira may mediate the relationships. The results highlight a potential role for diet-microbiome interactions in shaping metabolic and brain aging trajectories.},
}

Animals
Female
*Gastrointestinal Microbiome/physiology
*Diet, Western/adverse effects
*Diet, Mediterranean
*White Matter/diagnostic imaging
Amino Acids, Branched-Chain/blood
Fatty Acids, Volatile/metabolism
Macaca fascicularis
Insulin/blood
Insulin Resistance
Feces/microbiology/chemistry
Lipopolysaccharide Receptors/blood

@article {pmid41978177,
year = {2026},
author = {Chan, MX and Hoh, CY and Teh, YY and Toh, XY and Ismail, NAS},
title = {Effects of Probiotic Supplementation on Core Symptoms of Autism Spectrum Disorder in Children.},
journal = {Nutrients},
volume = {18},
number = {7},
pages = {},
pmid = {41978177},
issn = {2072-6643},
support = {no//Faculty of Medicine, Universiti Kebangsaan Malaysia/ ; },
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; *Autism Spectrum Disorder/therapy/microbiology ; Child ; Adolescent ; *Dietary Supplements ; Gastrointestinal Microbiome ; Treatment Outcome ; Male ; Child, Preschool ; Female ; Randomized Controlled Trials as Topic ; },
abstract = {Background/Objectives: Increasing evidence implicates the microbiome-gut-brain axis in Autism Spectrum Disorder (ASD) pathophysiology, prompting interest in probiotics as a therapeutic strategy, although findings remain inconsistent. This systematic review aimed to evaluate the clinical efficacy of probiotic supplementation on core ASD symptoms, examine the outcome measures used, and provide insights into optimal probiotic interventions. Methods: This review was conducted in accordance with PRISMA 2020 guidelines. PubMed, Scopus, Web of Science, Ovid, ProQuest, and Wiley Online Library were searched for studies published between January 2015 and July 2025. Randomized, non-randomized, and open-label clinical studies evaluating oral probiotic supplementation in children and adolescents with ASD were included. Outcomes assessed core symptom domains using validated instruments. Study selection, data extraction, and risk-of-bias assessment (RoB 2 and ROBINS-I) were performed independently by multiple reviewers. Due to methodological heterogeneity, the findings were synthesized narratively. Results: Fourteen studies involving 924 children and adolescents with ASD across seven countries or regions were included, of which ten were randomized controlled trials. Eight studies reported significant improvement in core ASD symptoms, predominantly within the social and communication domain. The most frequently used assessment tools were the Social Responsiveness Scale (SRS), Autism Treatment Evaluation Checklist (ATEC), and Autism Diagnostic Observation Schedule (ADOS). Lactobacillus reuteri supplementation for at least three months was consistently associated with improvement in social behavior. Conclusions: L. reuteri supplementation possibly improves social and communication function in children with ASD. However, there is limited high-quality evidence on this. Evidence for other core domains remains limited and inconsistent, highlighting the need for well-designed, multicenter trials using standardized outcome measures and strain-specific hypotheses.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
*Autism Spectrum Disorder/therapy/microbiology
Child
Adolescent
*Dietary Supplements
Gastrointestinal Microbiome
Treatment Outcome
Male
Child, Preschool
Female
Randomized Controlled Trials as Topic

@article {pmid41978283,
year = {2026},
author = {Sun, Y and Fu, C and Wang, Y and Peng, L and Li, S and Zhao, M and Wang, S and Shen, J and Cheng, L},
title = {ZmPHR1 and ZmPHR2 Mediate Metabolic and Microbial Regulation of Maize Adaptation to Phosphorus Heterogeneity.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70527},
pmid = {41978283},
issn = {1365-3040},
support = {328017493//Deutsche Forschungsgemeinschaft (DFG)/ ; 2366//Deutsche Forschungsgemeinschaft (DFG)/ ; 2023YFD1700203//National Natural Science Foundation of China and the National Key Research and Development Program of China/ ; 31972496//National Natural Science Foundation of China and the National Key Research and Development Program of China/ ; 32130094//National Natural Science Foundation of China and the National Key Research and Development Program of China/ ; },
abstract = {Spatial heterogeneity of soil phosphorus (P) severely constrains maize productivity, yet the regulatory mechanisms underlying plant adaptation to heterogeneous P supply remain poorly understood. This study reveals the distinct roles of the transcription factors ZmPHR1 and ZmPHR2 in mediating metabolic and rhizosphere microbial responses to heterogeneous P supply in maize (Zea mays L.). Using split-root systems combined with multi-tissue metabolomics and microbiome analysis, we show that mutation of ZmPHR2 severely impaired shoot development, photosynthetic efficiency and systemic P allocation. In contrast, ZmPHR1 mainly influenced root morphological plasticity. Loss of ZmPHR2 led to widespread repression of leaf metabolites, including organic acids and glutathione, and disrupted key pathways such as alanine, aspartate and glutamate metabolism. In root exudates, sphingolipid and histidine metabolism were critical for asymmetric root proliferation. Both mutations abolished differential root growth in P-rich patches and altered bacterial and fungal community composition and network structure. Our findings decipher a ZmPHR1/2-mediated adaptive framework integrating metabolic reprogramming and microbiome assembly, providing a mechanistic basis for breeding P-efficient maize suited to heterogeneous soils.},
}

@article {pmid41978401,
year = {2026},
author = {Wen, Q and Zhang, L and Qin, A and Li, X},
title = {[Small intestinal bacterial overgrowth and inflammatory factor expression levels in patients with asymptomatic hyperuricemia].},
journal = {Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences},
volume = {58},
number = {2},
pages = {313-318},
pmid = {41978401},
issn = {1671-167X},
mesh = {Humans ; *Hyperuricemia/microbiology/blood/complications ; Interleukin-6/blood ; C-Reactive Protein/metabolism/analysis ; Male ; Female ; Interleukin-1beta/blood ; Tumor Necrosis Factor-alpha/blood ; Middle Aged ; Adult ; *Intestine, Small/microbiology ; Breath Tests ; Case-Control Studies ; Aged ; *Blind Loop Syndrome/epidemiology ; },
abstract = {OBJECTIVE: To analyze the incidence of small intestinal bacterial overgrowth (SIBO) in patients with asymptomatic hyperuricemia (HUA) and the serum levels of C-reactive protein (CRP), interleukin-1β (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) in patients with asymptomatic HUA and SIBO.

METHODS: A total of 87 asymptomatic HUA patients and 40 healthy controls from Shanxi Fenyang Hospital from June 2023 to June 2024 were selected as the study subjects, and the baseline data, laboratory indicators were collected. Lactulose methane-hydrogen breath test (LHBT) was used to detect the occurrence of SIBO, and the asymptomatic HUA patients was divided into SIBO-positive group and SIBO-negative group according to the test results of LHBT. The positive rate of SIBO in the asymptomatic HUA patients was analyzed, and the concentrations of H2 and CH4, the levels of CRP, IL-1β, IL-6 and TNF-α at each time point between the asymptomatic HUA patients and the healthy controls were compared, and the levels of CRP, IL-1β, IL-6 and TNF-α were compared between the SIBO-positive group and the SIBO-negative group. Multivariate Logistic regression analysis was performed to analyze the influencing factors of SIBO in asymptomatic HUA. Spearman rank correlation analysis was used to analyze the correlation between CRP, IL-1β, IL-6 and TNF-α levels and SIBO in asymptomatic HUA patients.

RESULTS: The positive rate of SIBO in the asymptomatic HUA patients was 58.62%, which was higher than that in the healthy controls (20.00%), and the difference was statistically significant (χ[2]=16.431, P < 0.001). There were significant differences in exhaled H2 concentration between the asymptomatic HUA patients and the healthy controls at 0, 30, 60 and 90 min (P < 0.05), and there was no significant difference in exhaled CH4 concentration at each time point (P>0.05). The levels of CRP, IL-1β, IL-6 and TNF-α in the asymptomatic HUA patients were significantly higher than those in the healthy controls (P < 0.05). The serum levels of CRP, IL-1β and IL-6 in the SIBO-positive group were significantly higher than those in the SIBO-negative group (P < 0.05), while the levels of TNF-α were not significantly different between the two groups (P>0.05). Multivariate Logistic regression ana-lysis of the influencing factors of SIBO in the asymptomatic HUA showed that increased IL-1β (OR=1.332, 95%CI: 1.005-1.764, P=0.046) and increased IL-6 (OR=1.586, 95%CI: 1.216-2.069, P=0.001) were independent risk factors for SIBO in the HUA patients. In asymptomatic HUA patients with SIBO, the LHBT set value was positively correlated with serum IL-1β (r=0.594, P < 0.001).

CONCLUSION: Asymptomatic HUA patients are more likely to develop SIBO than healthy people, and SIBO in asymptomatic HUA patients is closely related to the level of inflammatory factors, so attention should be paid to the detection and intervention of SIBO in asymptomatic HUA patients.},
}

Humans
*Hyperuricemia/microbiology/blood/complications
Interleukin-6/blood
C-Reactive Protein/metabolism/analysis
Male
Female
Interleukin-1beta/blood
Tumor Necrosis Factor-alpha/blood
Middle Aged
Adult
*Intestine, Small/microbiology
Breath Tests
Case-Control Studies
Aged
*Blind Loop Syndrome/epidemiology

@article {pmid41979145,
year = {2026},
author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA},
title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.},
journal = {Research report (Health Effects Institute)},
volume = {},
number = {237},
pages = {1-58},
pmid = {41979145},
issn = {1041-5505},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Feces/chemistry/microbiology ; Female ; *Metabolome/drug effects ; Infant ; Male ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; Particulate Matter/adverse effects/analysis ; *Environmental Exposure/adverse effects ; California ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; },
abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.

METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter ≤2.5 µm and ≤10 µm in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.

RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.

CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Feces/chemistry/microbiology
Female
*Metabolome/drug effects
Infant
Male
*Air Pollution/adverse effects/analysis
*Air Pollutants/adverse effects/analysis
Pregnancy
Particulate Matter/adverse effects/analysis
*Environmental Exposure/adverse effects
California
Prenatal Exposure Delayed Effects
Infant, Newborn

@article {pmid41979351,
year = {2026},
author = {Zhang, R and Li, Y and Zhao, X and Degen, AA and Liu, X and Lian, J and Li, Y and Wu, Y and Shang, Z},
title = {Five-year fertilization alters soil microbial composition and functionality in sandy grassland.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0296325},
doi = {10.1128/spectrum.02963-25},
pmid = {41979351},
issn = {2165-0497},
abstract = {UNLABELLED: The impacts of reclamation and fertilization of sandy grassland on soil microbial communities and functional groups related to carbon (C) and nitrogen (N) cycling are not well understood. To fill this gap, three types of fertilizers, namely, chemical fertilizer (CF), manure (M), and chemical fertilizer plus manure (CF_M), were applied annually for five years to reclaimed sandy cropland planted to maize. Nearby sandy grassland without fertilizer and maize was included as a control. Soil microbial communities and processes, soil properties, and aboveground biomass (AGB) were determined. Soil microbial Chao richness was lowest in soil without fertilizer and maize. Fungal Shannon diversity was lowest with chemical fertilizer plus manure, while soil microbial Chao richness and bacterial Shannon diversity were not influenced by fertilization. Reclamation and fertilization increased AGB, which was greatest with chemical fertilizer plus manure and was more than seven times greater than that of sandy grassland. Soil extracellular enzyme activities increased with chemical fertilizer plus manure. Fertilization enhanced C cycle functional groups by decreasing soil bulk density and elevating soil total N, total carbon, Firmicutes abundance, and bacterial Chao richness, but lessened N cycle functional groups by decreasing Nitrospirota abundance. Microbial functional category groups associated with C and N cycles responded differently to reclamation and fertilization of sandy soil, which, in turn, affected soil carbon sequestration and nutrient availability.

IMPORTANCE: Reclamation and fertilization of sandy grassland altered biogeochemical functions by influencing microbial communities and functional category groups related to carbon (C) and nitrogen (N) cycling. Reclamation and fertilization could lead to the reduction of soil C content and insufficient soil N by altering functional category groups, which would be a potential risk leading to sandy grassland degradation. These findings not only improve our understanding of the consequences of sandy grassland reclamation and fertilization on ecosystem processes, but are also important for predicting soil C sequestration and nutrient cycling and for developing strategies to prevent degradation of sandy grassland.},
}

@article {pmid41979517,
year = {2026},
author = {Pioppi, A and Gomes, SIF and Nicolaisen, M and Xu, X and Kovács, ÁT},
title = {Successive cultivation under drought selects for specific microbiome members in the wheat rhizosphere.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag037},
pmid = {41979517},
issn = {1574-6941},
abstract = {Growing knowledge on plant microbiomes demonstrates the contribution of the host plant during microbiome assembly, especially under stress conditions commonly threatening crops. To dissect the influence of a plant on its microbiome, repeated cycling of microbiomes can be utilized to enhance functional properties in the enriched microbial communities. We used such a successive cultivation approach for wheat (Triticum aestivum) microbiome under drought conditions and selected lineages for drought resilience and susceptibility, with and without enriching the starting community with a library of bacterial isolates obtained from wheat. Significant differences in the rhizosphere microbiome between selection regimes were confirmed through 16S rRNA gene amplicon sequencing. Notably, replicate lineages of each selection regime showed convergence to similar microbiomes. Specific genera were abundant depending on the selection regimes; Stenotrophomonas under drought resilience, while Rahnella under drought conditions when the strain library was added initially. Applying Stenotrophomonas or Rahnella as single inoculum did not improve drought resilience in wheat. We hypothesize that complex microbiome dynamics take place during successive cultivation, which underscores the importance of considering complex plant-microbiome systems for studying plant stress resilience. Successive cultivation remains a valuable approach for observing rhizosphere microbiome changes under different conditions.},
}

@article {pmid41787255,
year = {2026},
author = {Wang, J and Yang, F and Hao, S and Dong, C and Tian, Y and Xu, Y and Yang, S and Yang, H and Xiao, X and Zheng, T and Zuo, H and Pei, X and Zhao, X},
title = {Machine learning model integrating oral microbiota and clinical features for predicting osteoporosis and bone loss in high-altitude populations.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41787255},
issn = {1471-2180},
support = {2024YFHZ0043//Science and Technology Department of Sichuan Province/ ; 2024YFFK0184//Science and Technology Department of Sichuan Province/ ; 2024NSFSC0563//Science and Technology Department of Sichuan Province/ ; XZ202301ZY0049G//Science and Technology Department of Tibet Autonomous Region/ ; HN240302C//the Project of Institute of Health New Productivity/ ; 2023SY-04//the Discipline Revitalization Project of Public Health Laboratory Sciences/ ; },
abstract = {BACKGROUND: Osteoporosis and bone loss (OP&BL) are major public health challenges, especially in high-altitude environments with chronic hypoxia. Current diagnostic methods, based on low-altitude populations, are impractical for large-scale screening in resource-limited, high-altitude settings. This study developed a machine learning-based predictive model for OP&BL by integrating oral microbiota data with clinical and questionnaire variables.

METHODS: We analyzed data from 560 Tibetan adults residing at high altitudes. Bone health status (OP&BL vs. normal) was determined by dual-energy X-ray absorptiometry. Oral microbiota profiles were characterized via 16 S rRNA sequencing. After feature selection using elastic net regression, five machine learning models, namely Logistic Regression (LR), Naïve Bayes (NB), Random Forest (RF), Support Vector Machine (SVM), and Extreme Gradient Boosting (XGB), were trained (60%, 337/560) and validated (40%, 223/560).

RESULTS: Feature selection identified nine predictors: Age, Gender, BMI, oral microbial genera Abiotrophia, Frequency of spicy food consumption (H23), Tooth brushing frequency (J5), Frequency of sweet-drink consumption (J3b), Current marital status (Separated/Divorced, A5_3), and frequency of numbing food consumption (H27). The LR model demonstrated good and stable performance with an AUC of 0.885 (95% CI: 0.823–0.937) on the test set, along with good calibration and the highest net clinical benefit. SHAP analysis indicated that oral factors Abiotrophia and Tooth brushing frequency together accounted for nearly 10% of the model’s total predictive contribution.

CONCLUSIONS: We developed a machine learning model integrating oral microbiota and clinical data for predicting OP&BL in people living above 3500 m. This model could offer a promising non-invasive tool for early screening in resource-limited settings and highlights the potential role of oral factors in high-altitude bone health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04718-0.},
}

@article {pmid41969125,
year = {2026},
author = {van der Molen, MK and van de Sande, M and Zandt, MI' and Saccomandi, T and Baartman, SL and Zhao, H and de Arellano, JV},
title = {Declining Ecosystem Respiration Linked to Nitrogen Deposition: Insights From a 26-Year FLUXNET Record.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70849},
pmid = {41969125},
issn = {1365-2486},
support = {NWO 2025//Ruisdael Observatory/ ; 184.034.015//Ruisdael Observatory/ ; },
mesh = {*Nitrogen/metabolism/analysis ; Netherlands ; *Soil/chemistry ; *Ecosystem ; *Soil Microbiology ; *Carbon Cycle ; *Forests ; Hydrogen-Ion Concentration ; Pinus ; Carbon/metabolism ; },
abstract = {Long-term carbon flux measurements at the FLUXNET site Loobos, a Pine forest in the Netherlands, reveal a counter-intuitive decline in total ecosystem respiration (TER) by tens of percents between 1997 and 2021. This trend cannot be explained by temperature variability or methodological changes alone. Instead, our findings point to a biogeochemical mechanism: despite a doubling of soil organic matter stocks, ecosystem respiration appears limited by decomposition rates rather than substrate availability. Soil incubation experiments indicate that microbial activity is limited by substrate quality and strongly acidic conditions (pH = 2.9), associated with large nitrogen deposition. Glucose addition experiments confirm the presence of an active microbiome, but its activity is suppressed under the present acidic soil conditions. These results raise concerns about ecosystem health under conditions of nitrogen deposition and the long-term sustainability of the observed carbon sink. Loobos may serve as an early indicator of broader ecosystem responses to environmental disturbances, as similar negative TER trends have been observed at other long-term FLUXNET sites. To advance understanding of the global carbon cycle, it is essential that observed flux trends are attributed and corroborated by changes in carbon and nitrogen stocks, and that models are continuously confronted with observational data. We therefore discuss the need of periodically measuring pH as soil acidification can be a limiting factor and suggest the need to introduce this variable in model representations of TER near regions sensitive to nitrification.},
}

*Nitrogen/metabolism/analysis
Netherlands
*Soil/chemistry
*Ecosystem
*Soil Microbiology
*Carbon Cycle
*Forests
Hydrogen-Ion Concentration
Pinus
Carbon/metabolism

@article {pmid41969207,
year = {2026},
author = {Saha, P and Roy, S and More, M and Bose, D and Trivedi, A and Brooks, BW and Syn, WK and Diehl, AM and Chatterjee, S},
title = {Underlying MASLD-induced gut microbiome dysbiosis and intestinal inflammation are key to poor outcomes in vibriosis infections in a preclinical model.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2652474},
doi = {10.1080/19490976.2026.2652474},
pmid = {41969207},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Mice ; Disease Models, Animal ; *Vibrio Infections/microbiology/pathology/complications ; Vibrio vulnificus/physiology ; Mice, Inbred C57BL ; Male ; Humans ; Inflammation/microbiology ; *Non-alcoholic Fatty Liver Disease/microbiology/complications ; Intestines/microbiology/pathology ; Female ; Liver/pathology ; Anti-Bacterial Agents ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of chronic liver disease globally, especially in developed countries, including the United States. The etiology of MASLD is closely associated with several other cardiometabolic conditions and can further aggravate to more severe stages of liver disease, including steatohepatitis and cirrhosis. Moreover, patients with underlying MASLD conditions have altered gut microbiome signatures and intestinal homeostasis, leading to gut barrier dysfunction, thereby making them more vulnerable to acute gastrointestinal infections like non-cholera vibriosis. However, the exact role of the gut microbiome and intestinal pathophysiology in increasing susceptibility to infection in patients with MASLD remains poorly understood. In this study, we used oral inoculation of the bacterium Vibrio vulnificus to investigate the pathophysiological outcomes in both control and diet-induced MASLD mouse cohorts. Our results showed that non-cholera vibriosis in mice with underlying MASLD caused increased liver damage, an inflammatory surge, followed by the onset of fibrotic lesions compared to the chow-diet fed control mice, depicting a worsened outcome. Depletion of the gut bacteriome by antibiotic treatment and following fecal microbiota transplantation in these mouse cohorts showed decreased pathophysiology in the livers, indicating that an altered gut microbiome in MASLD could be a key factor in the increased likelihood of non-cholera vibriosis in patients with MASLD.},
}

Animals
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Mice
Disease Models, Animal
*Vibrio Infections/microbiology/pathology/complications
Vibrio vulnificus/physiology
Mice, Inbred C57BL
Male
Humans
Inflammation/microbiology
*Non-alcoholic Fatty Liver Disease/microbiology/complications
Intestines/microbiology/pathology
Female
Liver/pathology
Anti-Bacterial Agents

@article {pmid41969232,
year = {2026},
author = {Du, Y and Zhao, M and Zuo, Z and Sun, Y},
title = {Bioelectric Profiling of Atopic Dermatitis: From Molecular Barrier Defects to Closed-Loop Theranostic Strategies.},
journal = {Experimental dermatology},
volume = {35},
number = {4},
pages = {e70250},
doi = {10.1111/exd.70250},
pmid = {41969232},
issn = {1600-0625},
support = {81741128//the National Natural Science Foundation of China/ ; 81401553//the National Natural Science Foundation of China/ ; //National Innovation and Entrepreneurship Program of Northwestern Polytechnical University/ ; W007101//Innovation Program for the Undergraduate International Student of the School of Life Science and Technology, NPU/ ; 23JRRA701//Gansu Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *Dermatitis, Atopic/physiopathology/diagnosis/therapy ; Filaggrin Proteins ; Dielectric Spectroscopy ; Cytokines/metabolism ; Skin ; Theranostic Nanomedicine ; Animals ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory dermatosis characterised by skin barrier disruption and immune dysregulation. Current clinical scoring systems (e.g., SCORAD) often fail to quantify subclinical pathophysiology or characterise the biopharmaceutical interface. This review synthesises the 'bioelectric profile' of AD, integrating electrical impedance spectroscopy (EIS) and current perception threshold (CPT) to construct a precision phenotyping framework. Evidence indicates that EIS non-invasively quantifies barrier integrity, with specific parameters (e.g., EIS[diff]) that correlate positively with terminal differentiation proteins such as filaggrin, serving as a surrogate marker of molecular permeability. Concurrently, neuroselective CPT assessment reveals abnormal C-fibre sensitisation in non-lesional skin, distinguishing extrinsic from intrinsic AD phenotypes. Furthermore, we explore reciprocal interactions between bioelectric parameters, Th2/Th22 cytokines (e.g., IL-31, IL-13) and the microbiome. Finally, we discuss translating these signatures into closed-loop theranostic strategies for feedback-controlled drug delivery. This bioelectric panorama provides a unique biophysical perspective on AD pathogenesis and a theoretical foundation for future precision medicine.},
}

Humans
*Dermatitis, Atopic/physiopathology/diagnosis/therapy
Filaggrin Proteins
Dielectric Spectroscopy
Cytokines/metabolism
Skin
Theranostic Nanomedicine
Animals

@article {pmid41969349,
year = {2026},
author = {Cheng, L and Wang, J and Sun, J and Xu, S and Zhao, G and Li, M},
title = {Integrated multi-omics of the ruminal microbiome and host metabolome reveals compensatory growth in response to dietary energy restriction and re-alimentation in growing beef bulls.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {265-281},
pmid = {41969349},
issn = {2405-6383},
abstract = {Understanding the mechanisms of dietary energy on compensatory growth in beef cattle is crucial for improving feed efficiency and mitigating the environmental footprint of beef production. The objectives of the study were to investigate the effects of dietary energy restriction and subsequent re-alimentation on growth performance, nutrient digestibility, ruminal microbiome, plasma metabolites, and nitrogen metabolism in growing beef bulls. Twelve 6-8-month-old Simmental crossbred bulls (initial body weight: 226 ± 24 kg) were randomly allocated to two groups (n = 6 per group): the dietary energy restriction group (REC) was fed a diet containing 9.25 MJ/kg metabolizable energy (ME) for 4 weeks (energy restriction period), followed by a 2-week re-alimentation period with a 10.29 MJ/kg ME diet, while the control group (CON) was fed the 10.29 MJ/kg ME diet consistently throughout the experimental period. Dietary energy restriction significantly decreased body weight and average daily gain (ADG) compared to CON (P < 0.05). However, no significant differences were observed by the end of the re-alimentation period (P > 0.05), demonstrating successful compensatory growth through dietary energy modulation. Ruminal propionate, total volatile fatty acids, ammonium nitrogen, and microbial crude protein (MCP) concentrations significantly decreased in the energy restriction treatment compared to CON (P < 0.05), but MCP exceeded the levels in CON after dietary energy re-alimentation (P < 0.05). Energy restriction also significantly increased urinary nitrogen excretion (P = 0.002), driven by imbalanced amino acid metabolism and significantly increased urinary urea (P = 0.038), which significantly reduced protein synthesis and nitrogen retention (P = 0.017). Metagenomics analysis revealed that energy restriction significantly increased the relative abundances of Limosilactobacillus, Enterococcus, and Aliarcobacter (P < 0.05), while decreasing those of Gemmatirosa and Mesorhizobium (P < 0.05). Dietary energy re-alimentation significantly increased the relative abundance of Gramella, Acetobacter, Phaeobacter, and Flammeovirga (P < 0.05). These bacteria are associated with pathways related to amination, transamination, and microbial protein synthesis. Integrated multi-omics revealed shifts in the ruminal microbiome and host metabolome, particularly in pathways related to ruminal urea hydrolysis, biosynthesis of glutamate, glutamine, and alanine, and post-absorptive amino acid metabolism, which collectively enhanced protein synthesis and compensatory growth. These findings establish a practical feeding strategy to optimize feed efficiency and enhance compensatory growth in beef bulls via short-term dietary energy manipulation.},
}

@article {pmid41969353,
year = {2026},
author = {Wei, Y and Wei, Y and Liu, C and He, Y and Ruan, S and Huang, Y and Wang, L and Yang, X and Yi, H},
title = {Biosynthetic reuterin improved the intestinal health in pigs.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {212-227},
pmid = {41969353},
issn = {2405-6383},
abstract = {This experiment aimed to study the effects of dietary supplementation with biosynthetic reuterin (RT) from Escherichia coli cells on the growth performance and intestinal health of pigs. A total of 72 pigs (Duroc × Landrace × Yorkshire, 21 d old, 5.7 ± 0.3 kg weight) were randomly divided into basal diet group (CON), basal diet supplemented with 5 × 10[10] colony-forming unit (CFU)/kg Lactobacillus reuteri group (LR), and basal diet supplemented with 50 mg/kg reuterin group (RT) with 6 pens (4 pigs per pen) per group for a 14-d period. One piglet was randomly selected from each pen on the 15th d for sampling. The results showed that the addition of RT to the diet significantly improved the growth performance of piglets, specifically increasing average daily gain (ADG; P = 0.004), and reduced diarrhea rate (P = 0.012), improved the intestinal morphology by significantly increasing villus height and the villus height to crypt depth ratio (P < 0.05), and enhanced intestinal barrier and immune functions by upregulating the expression of related genes (ZO1, MUC1, pBD2, and PR39; P < 0.05). Simultaneously, RT upregulated TLR gene expression and activated the MAPK signaling pathway (P < 0.05). Combined analysis of microbiome and non-targeted metabolomics showed that RT improved metabolism by affecting the relative abundance of Phascolarctobacterium succinatutens YIT12067 (known for succinate production and impacting energy metabolism) and Holdemanella (implicated in carbohydrate metabolism and immune modulation) in pigs (P < 0.05). In addition, RT significantly reduced the deposition of intestinal collagen (P < 0.05). In conclusion, this study demonstrated that biosynthetic RT effectively improved the growth and intestinal health of pigs, which may provide some theoretical basis for the RT production as a feed additive.},
}

@article {pmid41969354,
year = {2026},
author = {Dayan, J and De Cesare, A and Soglia, F and Zampiga, M and Indio, V and Antenucci, EL and Petracci, M and Sirri, F},
title = {Nutritional alternatives to commercial lipid sources: Impact of the dietary inclusion of black soldier fly (Hermetia illucens) larvae oil on broiler chicken productivity, breast meat quality traits and caeca microbiome.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {255-264},
pmid = {41969354},
issn = {2405-6383},
abstract = {Protein production from poultry, particularly broiler chickens, is considered a key component of future global food security, due to its relatively high sustainability. However, the use of resources such as soybean oil remains a concern. Black soldier fly (Hermetia illucens [HI]) larvae oil represents a promising alternative due to a relatively rapid rearing cycle and ability to utilize organic waste as growth substrates. This study investigated how replacing a commercial lipid source such as soybean oil, with HI larvae oil affects broiler growth performance, meat quality traits, fatty acid (FA) profile, and caeca microbiome. A total of 552 one-d-old male Ross 308 broilers, with equal initial weights (48.89 ± 0.18 g; P = 0.597), were allocated to three dietary treatments with 8 replicate pens per group (23 birds/pen). All birds received the same commercial basal diet, formulated to be isoenergetic and with the same amino acid profile, differing only in the source of the supplemented oil: 100% soybean oil group (CON), 50% soybean oil + 50% HI larvae oil group (MIX), or 100% HI larvae oil group (HIO). Growth performance parameters were recorded at the end of each feeding phase (14, 28, and 42 d). At slaughter (42 d), 10 breasts (pectoralis-major muscle) and thighs (extensor-iliotibialis muscle) samples per group were collected for meat quality assessment, and caecal content samples were obtained from 8 birds/group for microbiome analysis. Growth performance metrics showed an improvement in feed conversion ratio during the starter phase for HI larvae oil-fed groups (1.54 vs. 1.45 vs. 1.46 for CON, MIX, and HIO, respectively; P < 0.001) and comparable performance across the trial. Meat quality traits remained within commercially acceptable ranges, with minimal effects observed, apart from variations in breast fillet redness and thigh protein oxidation. FA analysis indicated higher levels of saturated FAs in the HI groups, with a concurrent reduction in omega (n)-6 levels and a more balanced n-6 to n-3 ratio (16.47 vs. 15.18 vs. 11.60 for CON, MIX, and HIO, respectively; P < 0.001). The caecal microbiome revealed stable diversity across groups, with only minor shifts in relative abundance. Overall, the findings showed that HI larvae oil is an effective alternative to conventional vegetable lipid sources in poultry nutrition, with added potential to enhance growth performance during the early growth stages.},
}

@article {pmid41969555,
year = {2026},
author = {Attard, TM and St Peter, SD and Kats, A and Lagemann, DR and Lawson, CE and Roy, BC and Yusuf, K and Harvey, L and Bhanja, P and Chugh, RM and Saha, S and Washburn, MP and Umar, S},
title = {Molecular and regional characterization of colorectal polyps: insights from proteomics, phosphoproteomics, and immune profiling.},
journal = {Translational gastroenterology and hepatology},
volume = {11},
number = {},
pages = {44},
pmid = {41969555},
issn = {2415-1289},
abstract = {BACKGROUND: Familial adenomatous polyposis (FAP) is an inherited predisposition to colorectal cancer and characterized by profuse colorectal adenomas starting from the second decade of life. Regional (left vs. right) differences in the colonic microbiologic and immunologic microenvironment may impact adenoma evolution but are poorly understood. We aimed to characterize regional molecular, microbial, DNA damage, and immune differences in pediatric FAP polyps to test the hypothesis that polyps in pediatric FAP exhibit distinct regional and molecular features that contribute to differential growth and genomic instability.

METHODS: Colonic polyps and adjacent non-polyp mucosa were harvested from pediatric FAP patients undergoing colonoscopy. Tandem mass tag-based proteomic and phosphoproteomic profiling was performed and were followed by functional assays including colony formation, spheroid growth, and patient-derived organoid culture. γH2AX staining was used to quantify induction of DNA double-strand breaks (DSBs) in HCT116 colon cancer cells cultured in Fusobacterium nucleatum conditioned media (FnCM). Immunohistochemistry and immunofluorescence were used to assess ATR, CDK4, γH2AX, and oxidative damage (8-OxoG). Immune profiling was performed by flow cytometry, focusing on CD103[+] tissue-resident memory T cells (TRMs).

RESULTS: Right-sided polyps exhibited increased ATR and CDK4 expression compared with left-sided lesions and adjacent mucosa. FnCM exposure induced a marked increase in γH2AX staining in HCT116 cells, consistent with our in vivo findings of elevated DSB burden in proximal versus distal FAP polyps. Biofilm enrichment and higher microbial staining were observed in right-sided lesions, whereas distal polyps were enriched with CD103[+] TRM populations. Pharmacologic inhibition of ATR or CDK4 significantly suppressed both colony formation and spheroid growth. Organoids derived from proximal colon polyps exhibited accelerated growth and crypt budding, with higher expression of stemness markers (CD44, CD133, Lgr5, BMI-1) compared with distal polyps.

CONCLUSIONS: Integrated proteomic, phosphoproteomic, and immune-microbiome profiling reveals regional heterogeneity of adenomas in pediatric FAP. Right compared to left sided polyps harbor greater DNA damage, elevated ATR/CDK4 kinase activity, reduced immune surveillance, and increased stem-like growth. These findings identify ATR and CDK4 as potential therapeutic targets and suggest that regional microenvironmental differences can impact chemoprevention strategies in pediatric FAP.},
}

@article {pmid41969565,
year = {2026},
author = {Kavagutti, VS and Beavogui, A and Wiart, N and Wincker, P and Oliveira, PH},
title = {Defensomes, counter-defensomes, and the remodeling of microbial communities.},
journal = {PNAS nexus},
volume = {5},
number = {4},
pages = {pgag073},
pmid = {41969565},
issn = {2752-6542},
abstract = {Bacteria and mobile genetic elements (MGEs) have coevolved for billions of years in an enduring evolutionary arms race, leading to the emergence and diversification of a vast arsenal of defense and counter-defense systems. In the last recent years, high-throughput screening methods and genome-resolved metagenomics have markedly enhanced our understanding of the diversity and abundance of immune systems across cultured and uncultured microorganisms. This fueled subsequent interest in better understanding the dynamic tri-kingdom interplay between bacteria, bacteriophages, and eukaryotic cells, and led to renewed efforts to improve alternative antibacterial phage-based therapies. Here, we discuss the evolutionary and ecological dynamics underlying the bacteria-MGE arms race, recent findings on bacterial defensomes, MGE counter-defensomes, holodefensomes, and their key role in the development of microbiome-targeted therapies. To this end, we argue why and how highly conserved anti-MGE defense systems should be prioritized as promising targets for the development of next-generation bacterial inhibitors with broad biomedical relevance, supported by a comprehensive analysis of their distribution and diversity across bacteria.},
}

@article {pmid41969649,
year = {2026},
author = {Ryan, LK and Duran-Pinedo, AE and Irelan, DW and Mulcahy, B and Galeas-Pena, M and Glover, SC and Frias-Lopez, J and Diamond, G},
title = {Vitamin D deficiency in mice modulates oral microbiome stability over time and leads to changes in host inflammatory gene expression pathways.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1775097},
pmid = {41969649},
issn = {2235-2988},
mesh = {Animals ; *Vitamin D Deficiency/microbiology/complications ; Mice, Inbred C57BL ; Mice ; *Microbiota ; Disease Models, Animal ; *Inflammation ; *Mouth/microbiology ; Male ; Vitamin D ; },
abstract = {INTRODUCTION: We previously showed that vitamin D deficiency leads to gingival inflammation and alveolar bone loss in mice, and that topical vitamin D3 administration prevents that bone loss and inflammation and fosters a health-associated oral microbiota in a murine ligature model of periodontal disease. To understand the relationship between vitamin D, the oral microbiome, and host factors, we performed taxonomic profiling of the oral microbiome from C57Bl/6 mice fed either a vitamin D-deficient diet or a standard diet.

METHODS: This was a 13-week study, with a group crossover period at week 7. Oral microbiomes were sampled weekly. At the end of the 13 weeks, single-cell analysis was performed on the gingival and buccal tissues.

RESULTS: During the first 6 weeks, the vitamin D3-deficient group 1 showed higher diversity at the start of the experiments but was more volatile in alpha-diversity values, with a notable dip in diversity at week 8. Group 2 showed lower initial diversity but was more stable by mid-study and remained relatively higher during the period where group 1 diversity crashes (weeks 6-8). The most striking feature occurs around weeks 6-8, coinciding with the change in vitamin D diet, group 1 plummets while group 2 either remained stable or rose.

DISCUSSION: This showed that elimination of vitamin D3 in the diet altered the diversification of bacterial species in favor of an oral microbiome associated with inflammation and bone loss. This persistent dysbiosis contrasts with the transcriptomic changes, which showed mice on a vitamin D deficient diet displayed an overall enrichment of gene sets involved in epithelial development, suggesting that re-introduction of vitamin D into the diet may help improve mucosal barrier health in the face of persistent microbiome dysbiosis.},
}

Animals
*Vitamin D Deficiency/microbiology/complications
Mice, Inbred C57BL
Mice
*Microbiota
Disease Models, Animal
*Inflammation
*Mouth/microbiology
Male
Vitamin D

@article {pmid41969652,
year = {2026},
author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X},
title = {Correction: Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1826950},
doi = {10.3389/fcimb.2026.1826950},
pmid = {41969652},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1726935.].},
}

@article {pmid41969654,
year = {2026},
author = {Kubba, R and Kejriwal, S and Razzouk, J and Evans, JR},
title = {Megasphaera in the gut microbiome and cancer: from Megasphaera elsdenii dysbiosis to Megasphaera sp. XA511 in tumor microenvironments.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1766220},
pmid = {41969654},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Tumor Microenvironment ; *Dysbiosis/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Neoplasms/microbiology ; Lung Neoplasms/microbiology ; },
abstract = {Growing evidence suggests that the gut microbiome and specific gut microbes influence carcinogenesis both within the gastrointestinal tract and in distant organs through immune, metabolic, and inflammatory pathways. Megasphaera elsdenii, a gram-negative-staining, strictly anaerobic member of the Veillonellaceae family, has been implicated in disruption of colonic epithelial homeostasis and may exert systemic effects beyond the intestine. While much attention has focused on the gut-brain axis, this mini-review synthesizes current evidence linking intestinal dysbiosis, microbial metabolite signaling, and immune crosstalk along the gut-lung axis. By integrating findings from studies on microbial translocation, mucosal immunity, and metabolite-mediated inflammation, we present a hypothesis-generating model in which M. elsdenii-driven gut dysbiosis may shape lung cancer pathogenesis through short-chain fatty acid-dependent immunometabolic signaling and hypothesized lymphatic and outer membrane vesicle-mediated pathways, recognizing that existing lung data derive solely from non-causal, genus-level 16S rRNA surveys. We further distinguish viable colonization from detection of immunogenic DNA and vesicular debris in distal tissues and discuss the context-dependent roles of the genus, contrasting the systemic pathogenicity of M. elsdenii in the gut-lung axis with the divergent, protective metabolic profile of a distinct gut-derived strain, Megasphaera sp. XA511, in pancreatic tumor microenvironments. This framework highlights Megasphaera as an understudied but potentially actionable modulator of cancer immunobiology.},
}

Humans
*Gastrointestinal Microbiome
*Tumor Microenvironment
*Dysbiosis/microbiology
Animals
RNA, Ribosomal, 16S/genetics
*Neoplasms/microbiology
Lung Neoplasms/microbiology

@article {pmid41969655,
year = {2026},
author = {Sohrabi, A and Sadeghi, F and Zagai, U and Andreasson, A and Vieth, M and Agréus, L and Talley, NJ and Ye, W},
title = {Duodenal microbiota profiling and its effects on gastrointestinal tract dysfunction.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1761015},
pmid = {41969655},
issn = {2235-2988},
mesh = {Humans ; Middle Aged ; Female ; *Duodenum/microbiology/pathology ; Male ; Cross-Sectional Studies ; Adult ; RNA, Ribosomal, 16S/genetics ; Aged ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Diseases/microbiology ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; Young Adult ; Biodiversity ; *Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: Duodenal microbiota has been proposed to be associated with gastrointestinal dysfunction, but population-based data are sparse. Profiling duodenal microbiota using 16S rRNA approach would appear to be a powerful tool for better understanding its role in gastrointestinal manifestations.

METHODS: In a population-based cross-sectional study, 265 adult subjects chosen randomly underwent symptom assessment, upper endoscopy, and gastroduodenal biopsies, with collection of duodenal brushing specimens. The 16S rRNA gene (V3-V4 region) sequencing was conducted using Illumina[©] MiSeq platform. The microbiome taxonomy was constructed and classified to identify the microbiota composition. The diversity and composition were compared among subjects categorized based on gastrointestinal dysfunction, histopathological features, and demographic characteristics.

RESULTS: The five most abundant genera in individuals with a normal duodenum were Streptococcus (33%), Veillonella (12%), Prevotella (11%), Rothia (5%), and Actinomyces (5%). Alpha diversity metrics showed that there were no significant differences among the participants with different demographic or histopathological features. However, the beta diversity of the duodenal microbiota differed significantly between current smokers and non-smokers, and across education level, BMI, as well as age groups. Furthermore, alteration of duodenal microbiota diversity was strongly associated with the presence of non-H. pylori gastritis or the co-occurrence of gastroesophageal reflux and functional dyspepsia based on Adonis R² (PERMANOVA) test (P < 0.05). Differential abundance of duodenal microbiota composition analysis at genus level illustrated that known pathogens and commensal bacteria, such as Sphingomonas, Lactobacillus, Streptococcus, Sphingomonas, Neisseria, Veillonella, Staphylococcus, Haemophilus, Gemellacea, and Intrasporangiaceae, were related to different histopathological manifestations.

CONCLUSION: Alterations of duodenal microbiota signatures are linked to smoking, aging, BMI, education and gastroduodenal disorders. Further mechanistic studies are warranted to further explore the potential effects of duodenal microbiota on gastrointestinal health.},
}

Humans
Middle Aged
Female
*Duodenum/microbiology/pathology
Male
Cross-Sectional Studies
Adult
RNA, Ribosomal, 16S/genetics
Aged
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Diseases/microbiology
Sequence Analysis, DNA
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/chemistry/genetics
Young Adult
Biodiversity
*Gastrointestinal Tract/microbiology

@article {pmid41969757,
year = {2026},
author = {Anderson, SM and Cing, Z and Drewes, JL and White, JR and Southward, T and Beauregard, H and Ferri, JT and Wanyiri, JW and Roslani, A and Vadivelu, J and Tang, SN and Queen, J and Sears, CL},
title = {Clostridioides difficile Detection in a Human CRC Cohort.},
journal = {Open forum infectious diseases},
volume = {13},
number = {4},
pages = {ofag169},
pmid = {41969757},
issn = {2328-8957},
abstract = {BACKGROUND: The role of the gut microbiome and specific enteric bacteria in influencing the development of colorectal cancer (CRC) remains incompletely understood. Recently, it was shown that human CRC-derived strains of Clostridioides difficile were capable of inducing colonic tumorigenesis in a susceptible mouse model. We hypothesized that C. difficile contributes to the pathogenesis of human CRC and would be enriched in CRC tumors compared to paired normal tissues from the same individual.

METHODS: We analyzed matched tumor/normal tissue samples from a cohort of 108 individuals presenting to a tertiary care hospital in Kuala Lumpur, Malaysia, for CRC resection between 2013 and 2014. We assessed the prevalence of C. difficile detection using 16S rRNA amplicon sequencing with high-resolution taxonomic assignment as well as culture and PCR.

RESULTS: We found that detection of C. difficile was prevalent (38% of individuals), but of low abundance (tumor median relative abundance 0.01%, paired normal 0.006% [P = .4]). Detection of C. difficile was more prevalent in individuals with biofilm-positive tumor tissues than biofilm-negative (ie, 81% of C. difficile-positive individuals were biofilm-positive vs 63% of C. difficile-negative individuals [P = .04]). Additionally, in exploratory analyses, we describe patterns of taxonomic and inferred functional pathway differences between C. difficile-positive and C. difficile-negative groups.

CONCLUSIONS: These findings suggest that C. difficile is frequently present in low abundance in the tumor microbiome with a potentially significant impact on community composition and function.},
}