@article {pmid41774605,
year = {2026},
author = {Wang, T and Lu, S and Sun, L and Cheng, Y},
title = {Skin Barrier Compromise: A Central Early Event in Ultraviolet Radiation-Induced Skin Pathogenesis.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000551027},
pmid = {41774605},
issn = {1421-9832},
abstract = {Ultraviolet radiation (UVR) is a major environmental stressor to the epidermal barrier, extending beyond erythema or photoaging. Emerging evidence reframes barrier impairment as an early and central event, integrating DNA and oxidative injury with inflammatory, immune, and microbial disturbances in a self-reinforcing cycle of fragility. This perspective challenges the traditional view of UVR damage as isolated mechanisms and highlights the need for barrier-focused research. Sunscreens remain essential, and recent formulations now extend beyond optical filtering by incorporating biologically active components such as antioxidants and photolyase that enhance photostability and support DNA lesion clearance. Emerging research also suggests that microbiome-preserving compositions may help maintain commensal balance during UVR exposure. Together, these developments point to a shift toward multifunctional photoprotection, although evidence is still accumulating. This review synthesizes recent advances alongside remaining gaps in the field. By integrating mechanistic evidence on UVR-induced barrier injury, it identifies directions that can support the design of more biologically grounded photoprotective strategies and delineates priority topics for future research.},
}

@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}

@article {pmid41774188,
year = {2026},
author = {Yadav, A and Melkani, GC},
title = {Microbes, mood, and metabolism/obesity: Pharmacological insights into the gut-obesity-depression triad.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-025-06022-y},
pmid = {41774188},
issn = {1420-9071},
support = {AG065992//National Institute of Aging/ ; },
}

@article {pmid41773937,
year = {2026},
author = {Wang, A and Dao, LQ and Ramos-Gomez, F and Wang, Y},
title = {Maternal influences on oral microbiome development and implications for early childhood health: a systematic review.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0058525},
doi = {10.1128/iai.00585-25},
pmid = {41773937},
issn = {1098-5522},
abstract = {A deeper understanding of how maternal-infant interactions shape the establishment and diversification of the oral microbiome could have significant clinical applications; however, relatively few studies emphasize early maternal-infant microbial connections. This systematic review provides a longitudinal analysis of oral microbiome development from birth to five years, focusing on the relationship between maternal and infant microbiomes. We conducted a systematic search (June 2025) using keywords "mother," "children," "oral microbiome," and "longitudinal" across PubMed, Cochrane Library, and Embase. Twelve studies fulfilled the inclusion criteria: longitudinal design, healthy mother-child dyads, saliva sample collection, and relevant age range. We excluded review articles, non-English publications, and studies with overlapping data. Results were synthesized by developmental stage and topic. Overall, current literature agrees that the mother is an important source of exposure for initial colonization of the newborn's oral microbiome. Several studies indicated that the oral microbiome at birth is diverse and unspecialized, composed mostly of maternally derived strains. Rapid selection occurs over the first few weeks, as the relative abundances of typical oral bacterial species increase. Throughout the first year, increases in diversity strengthen the resemblance between infant and maternal microbiomes. The microbiome appears to stabilize around 3-5 years. In conclusion, maternal-infant connections play a significant role in influencing oral microbiome development during the first 5 years of life. This review highlights the need for future studies to incorporate larger, longitudinal designs with metadata and advanced tools to clarify the roles of delivery mode, tooth eruption, and parental lifestyle habits in shaping early oral microbiome development.},
}

@article {pmid41773902,
year = {2026},
author = {Vidal, VM and Montes-Cobos, E and Canto, FB and Bozza, MT},
title = {The different meanings of tolerating the gut microbiome.},
journal = {mBio},
volume = {},
number = {},
pages = {e0173624},
doi = {10.1128/mbio.01736-24},
pmid = {41773902},
issn = {2150-7511},
abstract = {Multicellular life arose in a world dominated by microorganisms, a reality that has imposed a constant and pervasive selective pressure on all subsequent complex organisms. The immune system has been historically defined by its role in pathogen clearance through resistance mechanisms. However, a complementary and equally critical strategy is to enable the peaceful and inevitable coexistence with microorganisms, allowing each host species to shelter a unique associated microbiome. The term tolerance holds multiple meanings in immunology, yet all underlie a balanced and cooperative host-microorganism relationship. Each represents a different aspect of how the immune system limits tissue damage while maintaining functionality in the presence of microbial or inflammatory stimuli. Using the intestinal mucosa as a paradigm, we explore how epithelial barrier integrity, toxin neutralization, tissue repair, and stress response underpin disease tolerance; how microbial exposure calibrates innate immunity via epigenetic and metabolic reprogramming (LPS tolerance); and how the gut microenvironment fosters the generation of tolerogenic antigen-presenting cells and microbe-specific regulatory T cells to enforce immunological tolerance. We further explore how the microbiota itself is a potent inducer of these tolerogenic pathways and highlight IL-10 as a major hub, connecting different tolerogenic circuits. Finally, we examine the hygiene hypothesis, arguing that lifestyle changes during the Anthropocene disrupt these finely tuned tolerance mechanisms, thereby contributing to the rising incidence of immune-mediated diseases. We posit that these tolerance programs are fundamental prerequisites for engendering host-microbiota symbiosis, a relationship forged over millennia of co-evolution and endangered in the contemporary world.},
}

@article {pmid41773862,
year = {2026},
author = {Makori, TO and Gicheru, ET and Mburu, MW and Sada, MS and Nyawa, O and Mutunga, M and Lewa, C and Cheruiyot, R and Kiguli, S and Olupot-Olupot, P and Muhindo, R and Mogaka, C and Williams, TN and Agoti, CN and Maitland, K and Sande, CJ},
title = {Nasopharyngeal Microbiome Composition and its Clinical Correlates in Children Hospitalized with Severe Pneumonia in East Africa.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag093},
pmid = {41773862},
issn = {1537-6613},
support = {P46493//Imperial College London/ ; //Medical Research Council Department for International Development/ ; MR/L004364/1/WT_/Wellcome Trust/United Kingdom ; 102231/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: Pneumonia remains the leading cause of infectious mortality in children under 5, with the highest burden in sub-Saharan Africa. Dysbiosis in nasopharyngeal (NP) microbiota may influence pneumonia susceptibility and progression, but little is known about its composition or clinical relevance in low- and middle-income countries. We characterized the NP microbiota of children hospitalized with severe pneumonia in East Africa and investigated associations with clinical outcomes.

METHODS: We performed 16S rRNA partial gene sequencing of NP swabs collected at hospital admission from 876 children enrolled in the COAST trial across 5 sites in Kenya and Uganda. Clinical, demographic, and virological data were prospectively collected. Microbial profiles were analyzed using hierarchical clustering, nonmetric multidimensional scaling, and multivariable regression to assess associations with respiratory viral infections, sepsis, cyanosis, bacteremia, coma, HIV status, malnutrition, sickle cell disease, malaria, and mortality.

RESULTS: The NP microbiome was structured in 6 distinct clusters, each dominated by different genera, including Staphylococcus, Streptococcus, Haemophilus, Dolosigranulum, Corynebacterium, and Moraxella. Multivariable models adjusting for study site and age showed a positive association between Corynebacterium and early mortality. Temporal analysis showed elevated Corynebacterium abundance in children who died within 48 hours of admission, then declined over longer 56 survival intervals, approaching levels observed in survivors. However, time-continuous models did not support this persistent association, suggesting a subgroup effect.

CONCLUSIONS: We provide one of the largest high-resolution surveys of the pediatric upper airway microbiome in Africa, identifying microbial patterns associated with viral infection, HIV status, early death, and bacteremia.},
}

@article {pmid41773858,
year = {2026},
author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M},
title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0222025},
doi = {10.1128/spectrum.02220-25},
pmid = {41773858},
issn = {2165-0497},
abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.

IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.},
}

@article {pmid41773303,
year = {2026},
author = {Ma, H and Hu, K and Wang, Y},
title = {Dynamic changes of cervical microbiome during pregnancy for preterm birth risk prediction: A prospective cohort study.},
journal = {African journal of reproductive health},
volume = {30},
number = {4},
pages = {50-63},
doi = {10.29063/ajrh2026/v30i4.5},
pmid = {41773303},
issn = {1118-4841},
abstract = {This prospective cohort study investigated the dynamic changes in the cervical microbiome during pregnancy and developed a predictive model for preterm birth risk. Ninety-three singleton pregnant women were enrolled, including 41 with preterm birth and 52 with term delivery. Cervical secretions were collected at four gestational stages and analyzed using 16S rRNA sequencing, alongside ELISA testing for inflammatory markers. The preterm group exhibited significantly lower microbial diversity and a progressively increasing ratio of Lactobacillus iners to Lactobacillus crispatus throughout pregnancy. Early pregnancy IL-6 levels were also significantly elevated in this group. Logistic regression identified the L. iners/L. crispatus ratio, IL-6, history of preterm birth, and short cervical length as independent risk factors. The integrated prediction model demonstrated high accuracy (AUC 0.847), with even stronger performance in predicting births before 34 weeks (AUC 0.892). These findings suggest that microbiome patterns and inflammatory markers can effectively predict preterm birth risk, supporting early clinical intervention.},
}

@article {pmid41773092,
year = {2026},
author = {Lamanna, OK and Hu, R and Khemmani, M and Wolfe, AJ and Groah, SL and Forster, CS},
title = {Differential Effects of Uropathogenic and Non-Uropathogenic E. coli on the Mouse Urobiome and Urine NGAL Levels.},
journal = {Research and reports in urology},
volume = {18},
number = {},
pages = {580953},
pmid = {41773092},
issn = {2253-2447},
abstract = {OBJECTIVE: To determine whether urine neutrophil gelatinase-associated lipocalin (uNGAL) or urobiome alterations can differentiate urinary tract infections (UTI) from asymptomatic bacteriuria (ASB).

METHODS: Female 8-week-old C57BL/6 mice were instilled with either Escherichia coli CFT073 (UTI model, n=12), E. coli 83972 (ASB model, n=12), or saline (control, n=3). uNGAL was measured daily for 3 days post-instillation. Urobiome composition was assessed pre- and post-instillation using 16S rRNA sequencing. At day 3, kidneys were harvested for culture. Comparisons were made across groups for uNGAL levels and urobiome diversity.

RESULTS: Baseline β diversity did not differ between groups. Post-instillation, β diversity significantly differed across groups (p=0.01), driven by increased relative abundance of E. coli in UTI mice compared to ASB mice. Median uNGAL levels increased significantly in both UTI and ASB groups relative to controls, but no significant difference was observed between UTI and ASB groups.

CONCLUSION: Introduction of a uropathogenic E. coli strain reduced urobiome diversity, while a non-uropathogenic strain did not, suggesting strain-specific effects on microbial ecology. Bladder instillation itself also altered the urobiome. Elevated uNGAL levels were observed in both UTI and ASB models, indicating that while uNGAL reflects bacterial exposure, it does not distinguish between uropathogenic and non-uropathogenic E. coli. These findings highlight urobiome analysis as a potential tool for differentiating UTI from ASB, whereas uNGAL alone is insufficient.},
}

@article {pmid41772961,
year = {2026},
author = {Li, M and Zong, H and Yang, X and Liu, Q and Wang, J and Wang, M and Wu, D and Zheng, S and Wang, H and Long, Q},
title = {A flavonoid-rich medicinal herb extract ameliorates high-fat diet-induced obesity and insulin resistance in mice.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2026007},
pmid = {41772961},
issn = {1745-7270},
abstract = {Obesity has emerged as a critical global health challenge, contributing to severe metabolic and neoplastic complications. However, most existing anti-obesity drugs exhibit significant adverse effects, necessitating the development of safer therapeutic alternatives. In this study, we evaluate the efficacy and safety of a flavonoid-rich medicinal herb extract (MHE) in a high-fat diet (HFD)-induced murine obesity model. Daily oral administration of MHE does not alter food intake or induce hepatic injury but significantly attenuates HFD-induced weight gain (P < 0.05) and adiposity accumulation. Furthermore, MHE treatment improves systemic insulin sensitivity and glycemic control. Notably, MHE enhances whole-body energy expenditure, as evidenced by elevated oxygen consumption (VO 2), carbon dioxide production (VCO 2), and heat generation (P < 0.01). Mechanistically, MHE selectively promotes the proliferation of beneficial gut microbiota, including Lactobacillus, Akkermansia, and Bifidobacterium species, resulting in increased production of the short-chain fatty acid propionate (PA). Elevated circulating PA levels subsequently stimulate the browning/beiging of inguinal white adipose tissue (iWAT) and upregulate thermogenic pathways. Collectively, our findings demonstrate that MHE exerts anti-obesity effects through gut microbiota modulation and adipose tissue remodeling, offering a promising natural alternative for obesity management.},
}

@article {pmid41772824,
year = {2026},
author = {Ndhlovu, A and von der Heyden, S},
title = {Spatial Patterns and Overlap of Sedimentary and Rhizosphere Microbiomes of the Seagrass Zostera capensis.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70313},
pmid = {41772824},
issn = {1758-2229},
support = {//African Research Universities Alliance/ ; //National Research Foundation/ ; },
abstract = {Seagrasses are important nature-based solutions for climate change mitigation and adaptation due to their carbon stocks and ecosystem service co-benefits. Characterising microbial communities in seagrass sediments and rhizospheres is essential for understanding their roles in biogeochemical cycling, seagrass health, and potential contributions to ecosystem functioning. However, the extent to which seagrass microbiomes are shared at different spatial scales is not well understood. We utilised 16S rRNA metabarcoding to characterise prokaryotic communities in the sediments of the seagrass Zostera capensis at three estuaries spanning the environmental gradient of South Africa. In addition, we characterised the rhizosphere microbiome (rhizobiome) to better understand rhizosphere and sediment community dynamics. Overall, after accounting for community in adjacent seawater, we found that Z. capensis sediment and rhizosphere microbiomes largely overlap, sharing 34 genera but also harbour core genera. The sediment microbiome and rhizobiome showed significant spatial variability, suggesting that both local-scale and broader estuary-specific factors shape site-level microbial signatures. Further, predictive functional analysis showed that the rhizobiome was enriched for nutrient cycling pathways potentially beneficial to Z. capensis. Our findings support the exploration of sediment and rhizosphere microbial communities for monitoring ecosystem health and assessing impacts from threats such as pollution and climate change.},
}

@article {pmid41772743,
year = {2026},
author = {He, J and Wang, MN and Chen, HJ and Zuo, GY and Li, JL and Yin, WF and Pan, XG and Cheng, YC and Xia, CY and Xu, JK and Zhang, WK},
title = {Muribaculum intestinale alleviates depressive-like behaviors by inhibiting Th17 cell differentiation and M1 microglia polarization.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02354-4},
pmid = {41772743},
issn = {2049-2618},
support = {ZRZC2025-KCC03//National High Level & Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; 2025-NHLHCRF-JBGS-A-WZ-10; ZRJY2024-BJ01//National High Level & Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; 82474100//National Natural Science Foundation of China/ ; 82474100, 82273815, 82273809, 82073731//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in the pathogenesis of depression. Our previous studies identified loganin as a potential antidepressant agent; however, its oral bioavailability is low. Whether loganin alleviates depression via modulation of the gut microbiota remains unclear.

METHODS: Chronic unpredictable stress mice model was used to evaluate the antidepressant-like effects of loganin. To determine the role of gut microbiota, mice were treated with an antibiotic cocktail (ABX) to deplete microbiota. Fecal microbiota transplantation (FMT) from loganin-treated donors and Muribaculum intestinale (M. intestinale) were performed to assess microbial contributions.

RESULTS: Loganin exerted antidepressant-like effects by modulating gut microbiota, as evidenced by reduced efficacy in ABX-treated mice and behavioral improvements in recipients of FMT from loganin-treated donors. Loganin modulated gut microbiota composition particularly increasing the abundance of Muribaculum, and increased short-chain fatty acids (SCFAs). M. intestinale alleviated depressive-like behaviors, prompted the butyrylation of RORγt, inhibited Th17 cells differentiation, and suppressed M1 microglia polarization. Importantly, overexpression of RORγt attenuated the behavioral benefits of M. intestinale.

CONCLUSION: Loganin exerts antidepressant-like effects by enriching Muribaculum and SCFAs, thereby inhibiting Th17 cell differentiation and M1 microglia polarization. M. intestinale may represent a promising microbial-based therapeutic strategy for depression.},
}

@article {pmid41772715,
year = {2026},
author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD},
title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02362-4},
pmid = {41772715},
issn = {2049-2618},
support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.

RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.

CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.},
}

@article {pmid41772405,
year = {2026},
author = {Luo, H and Kamer, AR and Xu, Z and Qi, X and Liu, R and Wu, B},
title = {Moderating Effects of Oral Bacteria and Tooth Loss on Cognitive Performance.},
journal = {JDR clinical and translational research},
volume = {},
number = {},
pages = {23800844261423487},
doi = {10.1177/23800844261423487},
pmid = {41772405},
issn = {2380-0852},
abstract = {INTRODUCTION: The oral microbiome may influence brain health and contribute to cognitive decline. However, little evidence exists on the potential modifying role of the oral microbiome in the relationship between tooth loss and cognitive performance. This study aimed to investigate the interaction effects between tooth loss and oral dysbiotic status on cognitive performance.

METHODS: Data were from the 2011-2012 National Health and Nutrition Examination Survey. The sample included 677 adults aged 60 to 69 y. Cognitive performance was assessed by the Consortium to Establish a Registry for Alzheimer's Disease, the Animal Fluency Test (AFT), and the Digit Symbol Substitution Test. Significant tooth loss was defined as a loss of ≥10 permanent teeth out of 28. A high dysbiotic index was defined as being in the upper tertile of the ratio of periodontal disease-associated bacteria (Treponema, Porphyromonas, and Tannerella) to healthy bacteria (Rothia and Corynebacterium).

RESULTS: A multivariable linear regression model showed a significant interaction effect between tooth loss and dysbiotic index on the AFT (b = -1.87, P = 0.03), indicating that participants with a higher dysbiosis index and fewer missing teeth scored lower on the AFT.

CONCLUSIONS: The effect of tooth loss on verbal fluency depends on oral bacterial imbalances: if there is significant tooth loss, bacterial imbalances may not be important. However, when fewer teeth are lost, high bacterial imbalances may account for lower verbal fluency. These findings suggest that maintaining periodontal health aimed at decreasing oral dysbiosis should be promoted among older adults in the community.Knowledge Transfer Statement:Our findings highlight the importance of preserving the health of the teeth and not just retaining the teeth. Oral health awareness and good oral hygiene practice should be further promoted among older adults in the community.},
}

@article {pmid41771971,
year = {2026},
author = {Deng, S and Wu, X and Xu, W and Wu, X and Cai, H and Wang, S and Liu, J and Cao, J},
title = {Multi-dimensional immunoprotection of Ganoderma lucidum spore oil in immunosuppressed mice via microbiome-proteome-metabolome network analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40137-x},
pmid = {41771971},
issn = {2045-2322},
support = {JCYJ20220530153201003//Science and Technology Planning Project of Shenzen Municipality/ ; GDRC202119//Natural Science Foundation of Top Talent of SZTU/ ; 82104362//National Natural Science Foundation of China/ ; 20211063010055//Research Founding of Post-doctor who came to Shenzhen/ ; SDAIT-20-05//Shandong Province Traditional Chinese Medicine Industry Project/ ; 2022ZDJS119//Guangdong Province Key Discipline Construction Research Project/ ; },
}

@article {pmid41771954,
year = {2026},
author = {Nicotra, D and Mosca, A and Dimaria, G and Tessitori, M and Vetukuri, RR and Catara, V},
title = {Temporal dynamics of the tomato rhizosphere microbiome in response to synthetic communities of plant growth-promoting rhizobacteria.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41771954},
issn = {2045-2322},
abstract = {UNLABELLED: The rhizosphere microbiome plays a crucial role in plant health and productivity, yet intensive agriculture has diminished soil microbial diversity, increasing reliance on chemical inputs. Plant growth-promoting rhizobacteria offer a sustainable alternative, enhancing nutrient uptake, stress tolerance, and pathogen resistance. While single-strain inoculants have shown promise, microbial consortia may improve resilience through functional diversity. However, their impact on resident microbial communities remains understudied. In this study, three SynComs (four, six, and ten strains) were assembled from taxonomically diverse native PGPR strains identified as part of the tomato core microbiome, including Bacillus, Pseudomonas, Glutamicibacter, Paenarthrobacter, Chryseobacterium and Leclercia. All consortia significantly enhanced tomato growth, with the six- and ten-strain SynComs (containing Pseudomonas) exhibiting the most pronounced effects, increasing plant height by up to 94% in the indeterminate-growth variety ‘Proxy’. High-throughput sequencing revealed that while temporal factors were the primary drivers of community assembly, SynCom application triggered dynamic, time-dependent shifts specifically targeting the bacterial “rare biosphere”. Early-stage (T1) responses were characterized by the enrichment of rare bacterial taxa involved in key biogeochemical processes, such as the sulphur (Sulfurovum, Desulfosporosinus) and nitrogen (Azospirillum) cycles. By four weeks post-inoculation, community responses converged, primarily through the depletion of rare taxa and a predicted functional redirection toward xenobiotic degradation pathways. While SynCom strains showed a decline in absolute abundance over time, the persistence of growth-promoting effects suggests that these consortia act through early-stage indirect microbiome modulation rather than long-term high-density colonization. Furthermore, the consortia exerted a subtle cross-kingdom influence, modulating fungal succession by sustaining Basidiomycota and Mucoromycota populations. These findings demonstrate that small, host-derived, taxonomically diverse SynComs can enhance tomato growth and restructure rhizosphere microbial communities, especially impacting rare bacterial taxa and metabolic potential of the communities, with Pseudomonas-containing consortia exerting the most pronounced effects. These insights support the use of tailored, core-based microbial communities to improve crop productivity and soil health, though further research is needed to optimize SynCom design for agricultural applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41114-0.},
}

@article {pmid41771940,
year = {2026},
author = {Li, Y and Azman, EA and Ismail, R and Deng, X and Dhar, S and Noviardi, R and Citraresmini, A and Zi, T and Yang, L},
title = {Effect of root promoter on tobacco (Nicotiana tabacum L.) growth and nutrient accumulation at Hunan Province, China.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40215-0},
pmid = {41771940},
issn = {2045-2322},
}

@article {pmid41771883,
year = {2026},
author = {Mao, C and Jin, W and Dou, L and Guo, T and Huang, J and Wang, Y and Liu, X and Wu, S and Qiao, W and Xiang, Y and Zhu, Y and Wu, J and Yeung, KWK},
title = {Bioengineered ROS-tolerant probiotic reshapes gut microbiota-host axis to ameliorate type 2 diabetes in male mice.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70138-3},
pmid = {41771883},
issn = {2041-1723},
support = {2023YFB3810200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 21200592//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; 22210832//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; 23220952//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; },
abstract = {The pandemic-scale progression of type 2 diabetes mellitus (T2DM) necessitates innovative interventions targeting the pathogenic triad of insulin resistance, dysregulation of lipid metabolism, and gut microbiome dysbiosis. Here, we report a synthetically bioengineered probiotic consortium (REcN-F/Ca) developed through directed metabolic adaptations of Escherichia coli Nissle 1917 (EcN) under iterative hydrogen peroxide selection, subsequently functionalized with fructooligosaccharide-calcium carbonate composites. REcN-F/Ca exhibits enhanced reactive oxygen species tolerance through upregulated antioxidant enzymes and hydrogen sulfide-mediated redox balancing, alongside improved gastrointestinal survivability. In high-fat diet-induced obese male mice, REcN-F/Ca restores gut microbiota diversity, enriches butyrogenic taxa (Lachnospiraceae and Blautia), and rescues short-chain fatty acids depletion. Transcriptomic profiling reveals PPAR signaling activation, driving lipid metabolism and suppressing adipose inflammation. These effects translate to systemic metabolic improvements with attenuated weight gain (-25.4%), restored glucose homeostasis, and reduced insulin resistance (HOMA-IR: -73.2%) in the obesity and T2DM murine model. Our findings establish REcN-F/Ca as a synthetically engineered probiotic that simultaneously corrects intestinal ecological perturbations and reverses host metabolic dysfunction, proposing a paradigm for metabolic syndrome management.},
}

@article {pmid41771597,
year = {2026},
author = {Payne, T and Shaw, A and Hanjani, LS and Homes, R and Giddens, F and Ravuri, HG and Yap, CX and Walsh, J and Kumar, V and Garton, FC and Rhee, H and Huang, A and Francis, RS and Reid, N and McAdams-DeMarco, M and Gordon, E and Midwinter, M and Hubbard, R},
title = {ReFIT study (reversing frailty in transplantation): protocol for a longitudinal study to assess clinical and biomedical changes in frailty through kidney transplantation.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e100158},
doi = {10.1136/bmjopen-2025-100158},
pmid = {41771597},
issn = {2044-6055},
abstract = {INTRODUCTION: Losses of functional reserve across multiple physiological systems have been identified in frail patients, yet the exact aetiology of frailty remains unclear. Although strongly associated with chronological age, frailty often develops at a younger age in patients with organ failure. Frailty is prevalent in patients with kidney failure; however, individuals experience improvements in physical frailty measures following kidney transplantation. This makes younger patients with kidney failure a unique population for studying both the accelerated onset of frailty and its reversal. This research project aims to test the hypothesis that frailty secondary to organ failure and age-related frailty are associated with similar molecular and physiological measures.

METHODS AND ANALYSIS: This longitudinal study will recruit 150 patients in three groups. Group A (kidney transplant recipients aged ≥40 years; n=50) and Group B (patients aged ≥40 years active on the kidney transplant waitlist; n=50) will comprise younger adults with frailty from organ failure. Group C (adults aged ≥65 years (or ≥55 years for Aboriginal and Torres Strait Islander patients); n=50) will comprise older community dwellers. The primary outcome is the Frailty Index (FI). Secondary outcomes include the change in FI over time, and at baseline when considering various clinical metadata, immune parameters, kidney function and nutrition intake which will be measured at baseline and 12-month time points. Longitudinal changes in frailty will be analysed using linear mixed models with multiple testing corrections for false discovery rates.Endocrine profiles and metabolomics, measures of immune function and microcirculatory dysfunction, will be measured by liquid chromatography-mass spectrometry and/or gas chromatography-mass spectrometry. The gut microbiome will be sequenced via shotgun metagenomics (Illumina NextSeq500, 150 bp paired-end, [3]Gbp/sample). Circulating cell-free DNA/mitochondrial DNA will be quantified through droplet digital PCR. Microcirculation will be assessed via sublingual dark field videomicroscopy with glycocalyx markers measured by ELISA.

ETHICS AND DISSEMINATION: This study will be conducted with all stipulations of this protocol, and the conditions of the ethics committee approval. Ethical principles have their origin in the Declaration of Helsinki, all Australian and local regulations and in the spirit of the standard of Good Clinical Practice (as defined by the International Conference on Harmonisation). Organs/tissues will be sourced ethically and will not be sourced from executed prisoners or prisoners of conscience or other vulnerable groups.Ethics approval was received by the Metro South Health Research Ethics Committee (HREC/2023/QMS/95392) and ratified by the University of Queensland.Results will be disseminated through peer-reviewed publications, academic conferences, participant newsletters and health organisation collaboration.},
}

@article {pmid41771438,
year = {2026},
author = {Lynch, SV and Nagler, CR and Rachid, R},
title = {Microbial Therapeutics for the Prevention and Treatment of Food Allergy.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2026.02.024},
pmid = {41771438},
issn = {2213-2201},
abstract = {Food allergy affects approximately 8% of children and 11% of adults in the United States. Available treatment including oral immunotherapy and anti-IgE are not known to lead to remission. There is now increasing evidence implicating the gut microbiome as a key regulator of allergic inflammation. Distinct microbial and metabolomic alterations characterize food-allergic individuals, and gnotobiotic mouse models show that fecal microbiota from food-allergic donors transfers allergic sensitization, whereas microbiota from healthy donors protects from anaphylaxis through induction of tolerogenic Foxp3[+]RORγt[+] regulatory T cells. Goblet cell-derived resistin-like molecule beta (RELM β) induces food allergy through modulation of the gut microbiome and depletion of indole-producing species. These findings have inspired the development of five microbial therapeutics approaches: probiotics, rationally defined bacterial consortia, fecal microbiota transplantation, metabolite-based approaches, and biologics targeting dysbiosis-associated pathways. Early-phase clinical studies support feasibility, yet long-term safety, durability, and reproducibility remain uncertain. Major challenges include inter-individual variability, ecological complexity, and regulatory standardization. Microbiome-directed therapeutics hold promise to transform food allergy management from temporary desensitization toward remission and durable immune tolerance. The application of systems biology approaches integrating metabolomics, transcriptomics, and immune phenotyping will be essential to unravel the complex host-microbial interactions that underlie the efficacy of these approaches.},
}

@article {pmid41771260,
year = {2026},
author = {Vaughn, SN and Pavlovsky, JC and Jackson, CR},
title = {Bacterial Communities in Sand and Seawater of Northern Gulf Coast Beaches: Temporal, Spatial, and Environmental Influences.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70309},
pmid = {41771260},
issn = {1758-2229},
support = {//U.S. Department of the Treasury/ ; //Mississippi Department of Environmental Quality/ ; //Mississippi Based RESTORE Act Center of Excellence/ ; },
abstract = {Coastal microbial communities play critical roles in marine food webs and biogeochemical cycling, yet their diversity and function remain poorly characterised in many regions. This is especially evident along the northern Gulf coast, a dynamic system with substantial freshwater influences. We used high throughput 16S rRNA sequencing to characterise bacterial communities in sand and seawater collected every 3 months (March 2024 through March 2025) from 10 beaches along a 53 km stretch of the Mississippi coast. The diversity and composition of these communities were related to environmental variation and to biogeochemical function as determined from the activity of enzymes related to carbon, nitrogen, and phosphorus mineralisation. Our findings revealed distinct bacterial communities in sand and seawater, with the microbiome of each habitat showing greater temporal variation over the course of the study than spatial variation between beaches. Patterns in bacterial community structure and proportions of abundant taxa were strongly linked to physicochemical variables, while enzyme activities suggested how microbial communities may contribute to biogeochemical processes in these habitats. Collectively, these findings provide critical information for understanding microbial ecology in this system and highlight the central role of bacteria in mediating ecosystem function along a dynamic and understudied coastline.},
}

@article {pmid41771225,
year = {2026},
author = {Maria-Alexia, P and Cristina, R and Andreea-Ramona, T and Octavian, A and Viorica, R},
title = {Familial colorectal cancer: risk factors, screening strategies and personalized medicine.},
journal = {Cancer genetics},
volume = {302-303},
number = {},
pages = {166-175},
doi = {10.1016/j.cancergen.2026.02.008},
pmid = {41771225},
issn = {2210-7762},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, with approximately 25-30 % of cases exhibiting a familial component driven by germline mutations in DNA mismatch repair genes (Lynch syndrome) or the APC gene (familial adenomatous polyposis). Despite advances in screening and early detection, significant challenges persist in identifying at-risk individuals, optimizing surveillance strategies and addressing disparities in access to genetic testing and preventive care. This narrative review synthesizes current evidence on the genetic underpinnings, modifiable risk factors and personalized screening approaches for familial CRC. We highlight the critical interplay between hereditary predisposition and environmental exposures including diet, obesity, smoking and gut microbiome alterations, which cumulatively influence disease penetrance and clinical outcomes. Emerging predictive models integrating family history, polygenic risk scores and proteomic biomarkers offer unprecedented opportunities for risk stratification, enabling tailored screening initiation and intervals that balance clinical efficacy with cost-effectiveness. Novel non-invasive biomarkers, such as circulating tumor DNA and stool RNA tests, demonstrate promising sensitivity and specificity, potentially enhancing patient adherence while complementing gold-standard colonoscopy. Furthermore, artificial intelligence-assisted endoscopy and comprehensive genetic panels are reshaping precision oncology by improving adenoma detection rates and guiding targeted therapies. Addressing social determinants of health and implementing structured genetic counseling remain essential to achieving equitable CRC prevention. By transitioning from age-based to individualized, risk-adapted screening paradigms, healthcare systems can significantly reduce CRC incidence and mortality, particularly among genetically predisposed populations.},
}

@article {pmid41771203,
year = {2026},
author = {Khan, SM and Hussain, JM and Khan, B and Saad, A and Mehboob, J and Rukh, G and Manzoor, M and Mughal, AW and Kayani, A and Baig, MA and Khan, SRM and Saleem, Z and Hashim, R},
title = {Dark side of nocturnal eating: Unraveling the emerging axis between meal timing, gut microbiota, and early-onset cancer risk.},
journal = {Nutrition research (New York, N.Y.)},
volume = {148},
number = {},
pages = {1-14},
doi = {10.1016/j.nutres.2026.01.007},
pmid = {41771203},
issn = {1879-0739},
abstract = {The worldwide increase in early-onset metabolic disorders and digestive system cancers has elicited serious concern about lifestyle and diet as contributors to chronic disease risk. Disruption of circadian rhythms, particularly through nocturnal eating, is implicated in the development of various malignancies. This narrative review explored the emerging interplay between nocturnal eating, gut microbiota disruption, and early-onset cancer risk. Literature was sourced from PubMed, Scopus, Google Scholar, and Elsevier databases, emphasizing mechanistic studies and key findings in chrononutrition, microbiome research, and oncology. Nocturnal eating desynchronizes central and peripheral clocks, alters clock-gene expression, and provokes gut dysbiosis and inflammatory signaling that promote tumorigenic pathways. In contrast, daytime-aligned time-restricted eating (TRE) has shown potential to restore circadian synchrony, enhance metabolic resilience, and improve gut health even in the absence of caloric restriction. While TRE's role in cancer prevention remains hypothetical, its circadian benefits warrant further investigation. Overall, meal timing represents a modifiable factor influencing metabolic health and possibly early carcinogenesis. Aligning eating behavior with intrinsic circadian rhythms may help mitigate cancer risk and improve long-term well-being.},
}

@article {pmid41771182,
year = {2026},
author = {Carrillo, MP and Berrojalbiz, N and Sánz, C and Iriarte, J and Trilla-Prieto, N and Calbet, A and Saiz, E and Barata, C and Dachs, J and Vila-Costa, M},
title = {Copepod-associated microbiome responses to organophosphate ester plasticizers and other bioaccumulative organic pollutants in the ocean.},
journal = {Water research},
volume = {296},
number = {},
pages = {125640},
doi = {10.1016/j.watres.2026.125640},
pmid = {41771182},
issn = {1879-2448},
abstract = {Organic pollutants pose a growing threat to ocean ecosystems, largely due to their persistence, bioaccumulation potential, and toxicity. Yet, directly measuring the full spectrum of pollutants in situ remains unfeasible, and thus there is a dearth of alternative indicators of exposure. Host-associated microbiomes offer a promising but underexplored approach to fill this gap. Along a latitudinal transect of the Atlantic Ocean (40°N - 52°S), we observed significant correlations between the relative abundance of Enterobacterales in copepod-associated bacterial communities and seawater concentrations of organophosphate esters (OPEs), polycyclic aromatic hydrocarbons (PAHs) and with some perfluoroalkyl acids (PFAAs). All these chemicals bioaccumulate in marine zooplankton. Laboratory exposures of the copepod Paracartia grani to environmentally relevant OPE concentrations revealed similar microbiome composition shifts and decreased fecundity, revealing active depuration processes, including microbial degradation and fecal pellet production. These findings establish the basis for exploring host-associated microbiomes as sensitive indicators of bioaccumulative contaminant exposure in marine ecosystems, offering a novel avenue for large-scale pollution monitoring.},
}

@article {pmid41770930,
year = {2026},
author = {Bai, X and Li, Z and Chen, B and Qian, X and Guo, Y and Wang, Q and Chen, C and Chen, W and Shen, X and Liu, J and Jin, J and Zhang, W and Liu, Q and Chen, S and Yang, S and Xu, L and van der Heijden, MGA and Tiedje, JM and Jiao, S and Wei, G},
title = {High bacterial diversity drives the suppression of a soilborne plant disease.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {10},
pages = {e2509303123},
doi = {10.1073/pnas.2509303123},
pmid = {41770930},
issn = {1091-6490},
abstract = {The rhizosphere microbiome plays a crucial role in the resistance to soilborne plant diseases. However, the principles needed to explain and predict which microbiota will be effective against soilborne pathogens are still lacking due to the complexity of the soil microbial community. We hypothesized that, independent of particular microbial strains, a high diversity is associated with, or increases the probability of, effective suppression. We tested this hypothesis by demonstrating that random combinations of rhizosphere microbial isolates, with the same bacterial diversity, had an equal impact on suppressing root diseases. The incidence of root rot was significantly reduced when soil bacterial diversity was high. We further investigated how high-diversity bacterial communities suppress root rot by constructing synthetic bacterial communities (SynComs). The results suggest that high bacterial diversity suppresses pathogens through mechanisms potentially including nutrient competition and the formation of physical barriers on the root surface. Our study highlights that high bacterial diversity is beneficial for suppressing soilborne plant diseases, offering a nonchemical and sustainable approach for crop disease management.},
}

@article {pmid41770903,
year = {2026},
author = {Wang, X and Sun, H and Tan, Y and Xu, S and Liu, Z and Ji, K and Qiu, D and Deng, J and Feng, B and Wu, X and Iwakura, Y and Chen, M and Feng, R and Huang, C and Tang, C},
title = {Colonic Engyodontium fungus triggers neutrophil antimicrobial activity to suppress Lactobacillus johnsonii-derived glutamic acid-maintained Tregs.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI196788},
pmid = {41770903},
issn = {1558-8238},
abstract = {Isolating commensal fungi from mouse intestines has been challenging, limiting our understanding of their role in intestinal immune homeostasis and diseases. Using an Fc fusion protein of the C-type lectin Dectin-2, we successfully purified the commensal Ascomycota fungus Engyodontium sp. from mouse feces. Engyodontium enhances the antimicrobial activity of colonic neutrophils via CARD9 pathway, and exacerbates colitis by impairing the colonization of intestinal Lactobacillus johnsonii (L. johnsonii) WXY strain. L. johnsonii produces high levels of L-glutamic acid by expressing the glutaminase-encoding gene glsA to facilitate Treg expansion via enhancing IL-2 receptor signaling. Patients with Crohn's disease (CD) and ulcerative colitis harbored increased Engyodontium and decreased L. johnsonii abundance. Engyodontium directly induced calprotectin in human colonic neutrophils, and CD patients exhibited lower levels of L-glutamic acid which also promoted human Treg expansion. These findings highlight the Engyodontium-calprotectin axis against the Lactobacillus-glutamate-Treg cascade to aggravate colitis, suggesting commensal Engyodontium-triggered signaling as a therapeutic target for mucosal inflammatory diseases.},
}

@article {pmid41770693,
year = {2026},
author = {Lin, A and Bik, EM and Costello, EK and Dethlefsen, L and Haque, R and Relman, DA and Singh, U},
title = {Correction: Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0343568},
pmid = {41770693},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0053838.].},
}

@article {pmid41770447,
year = {2026},
author = {Sosanya, ME and Temple, JL},
title = {Two Sides of a Coin: Molecular, metabolic, and Phenotypic Convergence in Pediatric Undernutrition and Obesity.},
journal = {Current obesity reports},
volume = {15},
number = {1},
pages = {},
pmid = {41770447},
issn = {2162-4968},
abstract = {PURPOSE OF REVIEW: This narrative review juxtaposes the metabolic and molecular consequences of pediatric under- and overnutrition, highlighting the similarities and differences between these two nutritional states occurring simultaneously in different parts of the world.

RECENT FINDINGS: Numerous biological changes in pediatric acute undernutrition and obesity have been linked to elevated risks of chronic metabolic disorders. We summarize recent evidence on pathophysiological pathways and outcomes common to both conditions. Despite etiological divergence, early-life nutritional imbalances converge on shared mechanisms and consequences with intergenerational implications.

SUMMARY: Both acute undernutrition and obesity in childhood have intersecting long-term outcomes including insulin resistance, type 2 diabetes, cardiovascular diseases, hepatic steatosis, cancers, and others, mediated through endocrine, immunological, epigenetic, and gut microbiome pathways, albeit via diverse specific mechanisms. Robust, longitudinal studies in varied geopolitical settings are needed to further elucidate the complex mechanisms, long-term phenotypic consequences, and therapeutic effects in these twin conditions.},
}

@article {pmid41770016,
year = {2026},
author = {Martins, I and Silva, JM and Almeida, JR},
title = {HYMET: A Hybrid Metagenomic Pipeline for Accurate and Efficient Taxonomic Classification.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag024},
pmid = {41770016},
issn = {2047-217X},
abstract = {BACKGROUND: Reliable taxonomic classification of metagenomic sequences remains constrained by high mutation rates, fragmented assemblies, and large heterogeneous reference databases. HYMET (Hybrid Metagenomic Tool) was developed to overcome these challenges through a two-stage hybrid design combining adaptive Mash-based screening with Minimap2 alignment and a coverage-weighted Lowest Common Ancestor (LCA) classifier. Its sample-adaptive thresholds and on-the-fly reference database construction enable efficient, domain-agnostic classification while maintaining accuracy across divergent genomes.

RESULTS: Across seven CAMI assembly datasets in contig mode, HYMET achieved a mean F1 of 83.89%, with genus-level F1 of 76.75% and species-level F1 of 60.18%, while averaging 115.93 s runtime and a mean peak memory of 6.24 GB. Performance remained stable under mutation rates up to 30% for most domains (F1 ≥ 0.8), with viral sequences showing the expected decline (F1 ≈ 0.5 at 30%). Read and contig inputs produced nearly identical results when sharing reference caches, and real-world datasets confirmed robustness with the human gut metagenome reproduced typical anaerobic profiles, while in the ZymoBIOMICS mock community HYMET recovered all bacterial members; a further ground-truth evaluation on the ZymoBIOMICS Gut Microbiome Standard (D6331) yielded near-perfect genus-level concordance (Pearson r = 0.998, Bray-Curtis =0.04) across bacteria, fungi, and archaea.

CONCLUSIONS: HYMET achieves a practical balance of accuracy, efficiency, and scalability for metagenomic classification. Its adaptive candidate selection, alignment-anchored taxonomy, and reproducible reference caching collectively enhance performance across domains. HYMET source code is fully available at https://github.com/ieeta-pt/HYMET.},
}

@article {pmid41769660,
year = {2026},
author = {He, X and Chen, C and Shen, L and Su, X and Xie, H and Yang, M and Jiang, W},
title = {Retrospective insights into probiotic and prebiotic interventions: associations with gut microbiota profiles and nutritional outcomes.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1729480},
pmid = {41769660},
issn = {2296-861X},
abstract = {BACKGROUND: Probiotics and prebiotics are known to regulate the gut microbiota, however, their relations with the metabolic and nutritional outcomes in adults are under-investigated in practical environments.

OBJECTIVE: To provide light on microbiome-targeted metabolic health initiatives, this retrospective study investigates relationships among probiotic and prebiotic therapies, gut microbiota profiles, and nutritional outcomes.

METHODS: Clinical and nutritional history (n = 350 adults) in probiotic (n = 140), prebiotic (n = 120), and control (n = 90) were compared. The microbiota data were obtained with the help of 16S rRNA sequencing in the stool samples at baseline and 4-12 weeks of the intervention. Alpha (Shannon, Simpson) and beta diversity (Bray-Curtis) was evaluated by means of PERMANOVA, and the relative abundance of the main taxa (Lactobacillus spp., Bifidobacterium spp., Faecalibacterium prausnitzii) was determined. The adjusted ANCOVA and multivariate regression models adjusted to the difference between baseline were used to analyze the anthropometric and biochemical outcomes, including body mass index (BMI) and lipid profiles.

RESULTS: Alpha diversity (Shannon index: probiotics 3.4-4.2, p < 0.01; prebiotics 3.3-4.0, p < 0.01) and beta diversity clustering (PERMANOVA R2 = 0.12, p < 0.001 in probiotics) were significantly increased by the use of probiotics and prebiotics, respectively. Lactobacillus (2.1-4.8%, p < 0.01) and Bifidobacterium (3.5-7.9%, p < 0.001) were increased due to probiotic supplementation, whereas Bifidobacterium (3.7-6.8%, p < 0.001) and F. prausnitzii (6.1-8.3%, p = 0.04) were increased due to prebiotics supplementation. The two interventions were better than controls in terms of BMI and lipid levels (reduction of BMI: probiotics -1.6 + - 0.4 kg/m2, prebiotics -2.0 + - 0.5 kg/m2; total cholesterol: probiotics -18 + -5 mg/dL, prebiotics -17 + -6 mg/dL; all p < 0.05).

CONCLUSION: The use of probiotic and prebiotic supplementation was found to be related to an augmented gut microbial and better metabolic results in grown-ups. Such results point to possible advantages of the dietary microbiota modulation, but due to the retrospective design, it is not possible to make causal conclusions.},
}

@article {pmid41769659,
year = {2026},
author = {Alhodieb, FS},
title = {Microbial biofortification of fermented foods: a review of probiotic-mediated nutrient enhancement.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1754233},
pmid = {41769659},
issn = {2296-861X},
abstract = {Microbial biofortification via probiotic fermentation is a unique solution to reducing micronutrient deficiencies worldwide and it is a sustainable approach to prevention and German fermentation is widely applicable for plant-based diets as these micronutrients, such as B12 and K, are hardly present. Fermentative microbes such as Lactobacillus, Bifidobacterium, Propionibacterium synthesis of the vitamins like folate, riboflavin, vitamin K. They also facilitate the accessibility of minerals and increase the quality of proteins in many foods. This process not only enhances vitamins and minerals as a result of antinutrient such as phytate breakdown, but also bioactive peptides and short-chain fatty acids are produced. These are beneficial compounds for gut health and are helpful to the health of the immune system. Studies in labs, animals, and humans indicate that consumption of biofortified fermented foods increases micronutrient levels, promotes gut microbial balance, and increases immunity. In order to exploit this approach to its fullest potential, there are hurdles to overcome, ensuring that the strain remains viable, enhancing product taste, and overcoming regulatory hurdles. Future advances will require engineering strains of probiotics to produce even greater amounts of vitamins and implementing personalized microbiome information, as well as their public health interventions, in resource-limited situations.},
}

@article {pmid41769655,
year = {2026},
author = {Ray, S and Shankaran, P},
title = {Nutrition and the gut microbiome: a symbiotic dialogue influencing health and disease.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1761992},
pmid = {41769655},
issn = {2296-861X},
abstract = {The gut microbiome, a complex consortium of trillions of microorganisms, significantly influences human health through its metabolic activities, immune modulation, and interaction with the nervous system. Diet plays a significant role in shaping the gut microbiome, with plant-based diets promoting the colonization of beneficial bacteria and fiber fermentation, whereas meat-based diet may encourage harmful microbial shifts associated with systemic inflammation. Gut bacteria produce short-chain fatty acids (SCFAs) from dietary fibers and those are crucial for energy metabolism, intestinal integrity, and immune modulation. Certain neurotransmitters like GABA and serotonin produced by gut bacteria, play a vital role in the gut-brain axis. Dysbiosis in the gut microbiota have been linked to various psychiatric and neurological disorders like anxiety, depression, bipolar disorder, Schizophrenia, Alzheimer's and Parkinson's. Beyond neurological implications, the gut microbiota also linked to metabolic and cardiovascular diseases, including obesity, hypertension, and coronary artery disease, as well as colorectal cancer. Imbalances in bacterial ratios, such as Firmicutes to Bacteroidetes, can impact metabolism and inflammation. This review (i) elucidates the complex interplay between nutrition and the gut microbiome, emphasizing its implications for human health and disease; (ii) critically examines the methodological and analytical limitations inherent in current metagenomic studies; and (iii) proposes an integrated, multi-layered, systems-level framework for developing predictive models of host-microbe interactions and their pathological significance.},
}

@article {pmid41769611,
year = {2026},
author = {Li, X and Xu, S and Li, Y and Wang, R and Qin, C and Wang, X},
title = {Research Progress on the Mechanisms of Gut Microbiota Dysbiosis Associated With Idiopathic Pulmonary Fibrosis: A Review.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e102429},
pmid = {41769611},
issn = {2168-8184},
abstract = {Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic interstitial lung disease with an incompletely understood pathogenesis. In recent years, growing evidence has highlighted the critical role of gut microbiota dysbiosis in the onset and progression of IPF. This review comprehensively summarizes the characteristics of gut microbiota alterations associated with IPF, explores the underlying mechanisms driving these changes, and examines their impact on disease development. Particular emphasis is placed on the emerging concept of the "gut-lung axis," which elucidates the bidirectional communication between the intestinal microbiome and pulmonary health. The review further discusses microbial metabolites and immune modulation as key mediators linking gut dysbiosis to pulmonary fibrosis. Additionally, current advances in microbiota-targeted therapeutic strategies, including probiotics, prebiotics, and fecal microbiota transplantation, are analyzed for their potential in IPF management. By systematically integrating recent findings, this article aims to deepen the understanding of IPF pathophysiology and provide a theoretical foundation for novel treatment targets centered on gut microbiota regulation.},
}

@article {pmid41769608,
year = {2026},
author = {Beniwal, P and Singla, M and Kar, DP and Bhargava, V and Chandra, N and Sinha, DK and Ruhela, V and Jha, R and Joseph, R and Rs, V and Bhosle, N and Mehta, K and Bajpai, S},
title = {Multispecies Probiotic Supplementation in Chronic Kidney Disease (CKD): Insights From Indian Nephrology Experts.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e102520},
pmid = {41769608},
issn = {2168-8184},
abstract = {Chronic kidney disease (CKD) is a progressive condition leading to the accumulation of uremic toxins and systemic complications, eventually resulting in loss of kidney function. One of the major mechanisms behind the CKD complications is gut dysbiosis, a commotion in the gut micro-ecology that aggravates systemic inflammation and worsens the CKD management. Probiotics, through their ability to restore gut micro-ecology, strengthen the intestinal barrier integrity, modulate the immune system, and mitigate systemic inflammation, offer a promising add-on therapy to traditional CKD therapies. Specific probiotic strains, including Streptococcus thermophilus, Lactobacillus acidophilus, Bifidobacterium longum, and Bacillus coagulans, have demonstrated antimicrobial effects by promoting commensal bacterial growth and inhibiting pathogenic bacterial growth. Studies indicate that these probiotics reduce uremic toxin levels, such as indoxyl sulfate and p-cresyl sulfate, blood urea nitrogen, urea, and creatinine levels, enhance gut integrity, alleviate inflammation, and are beneficial for patients with CKD stages 3 to 5. While the evidence for probiotic supplementation is promising, further studies are required to establish their long-term benefits, especially in patients with immune deficiency or kidney transplants. Overall, this consensus article provides insights from Indian nephrology experts on the potential benefits of multispecies probiotic supplementation in CKD patients, focusing on improving their quality of life, delaying disease progression, and ultimately augmenting survival outcomes.},
}

@article {pmid41769348,
year = {2026},
author = {Sun, M and Zang, D and Zhou, H and Che, YL and Chen, J},
title = {Epistemic compression in large language model explanations of the gut-liver axis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1773593},
pmid = {41769348},
issn = {2235-2988},
abstract = {BACKGROUND: The gut-liver axis integrates intestinal barrier function, microbial ecology, metabolism, immune regulation, and hepatic feedback, yet remains causally non-closed and strongly context dependent. As large language models (LLMs) increasingly mediate biomedical explanation, their ability to preserve evidentiary structure within such epistemically open frameworks requires systematic evaluation.

METHODS: We conducted a cross-platform, mixed-methods infodemiology analysis of five widely accessible LLMs. Twenty clinically grounded questions spanning five hierarchical domains from basic mechanisms to intervention and evaluation generated 100 single-turn responses. Linguistic accessibility was assessed using seven established readability indices, while epistemic integrity was evaluated using the Journal of the American Medical Association Benchmark Criteria, Global Quality Score, and a modified DISCERN framework.

RESULTS: Linguistic complexity increased as prompts progressed toward intervention and evaluation, without corresponding gains in transparency, reliability, or educational quality. Informational integrity clustered primarily by platform rather than domain. Readability indices showed strong internal concordance, whereas integrity metrics aligned only moderately and correlated weakly with readability. Item-level analysis revealed consistently high narrative clarity but systematic under-signaling of source attribution and uncertainty, resulting in over-coherent explanations that compressed conditional associations into mechanism-like claims.

CONCLUSIONS: LLM explanations of the gut-liver axis are susceptible to epistemic compression driven by narrative fluency rather than factual error. Readability does not reliably indicate epistemic robustness in decision-adjacent contexts. These findings support shifting evaluation and governance from platform comparison toward concept-conditioned requirement engineering that enforces provenance, calibrated uncertainty, and explicit separation of correlation, mechanism, and actionability as generative outputs approach clinical relevance.},
}

@article {pmid41769343,
year = {2026},
author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y},
title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1688580},
pmid = {41769343},
issn = {2235-2988},
abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.

METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).

RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in α-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.

CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.},
}

@article {pmid41769336,
year = {2026},
author = {Wu, Y and Han, B and Zhang, B and Li, J and Ren, B and Su, Z},
title = {Metabolic crosstalk between oral microbiota and the host in OSCC: emerging roles of microbial metabolites in tumor initiation and progression.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1778329},
pmid = {41769336},
issn = {2235-2988},
abstract = {Oral squamous cell carcinoma (OSCC) is an aggressive malignancy characterized by profound metabolic reprogramming and a persistently poor clinical outcome. Beyond genetic and environmental risk factors, growing evidence indicates that dysbiosis of the oral microbiome is associated with metabolic perturbations observed in OSCC and may contribute to tumor initiation and progression. Microbiome-derived metabolites represent a previously underappreciated layer of cancer metabolism, linking microbial activity to host metabolic states, epigenetic regulation, and immune dysfunction within the tumor microenvironment. In this review, we provide a comprehensive synthesis of current evidence highlighting how microbial metabolites shape metabolic vulnerabilities in OSCC through the microbiome-metabolite-host axis. We focus on key metabolite classes, including short-chain fatty acids, tryptophan-derived metabolites, sulfur-containing compounds, and other emerging metabolic intermediates, and discuss their roles in modulating cellular energy metabolism, epigenetic remodeling, oxidative stress responses, and immune evasion. Particular emphasis is placed on the context-dependent and often dualistic functions of metabolites such as butyrate, which can exert tumor-suppressive or tumor-promoting effects depending on microbial source, concentration, and local inflammatory conditions. By integrating insights from metabolomics, microbial functional profiling, and mechanistic studies, this review underscores microbial metabolism as an integral component of OSCC pathobiology. Recognizing microbial metabolites as active metabolic regulators rather than passive byproducts provides a conceptual framework for identifying novel biomarkers and metabolic intervention strategies in OSCC.},
}

@article {pmid41769334,
year = {2026},
author = {Zhong, L and Zhou, X and Su, J and Zhang, Y and Zhang, D and Wan, H},
title = {Microbiome dysbiosis and therapeutic restoration in atopic dermatitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1693905},
pmid = {41769334},
issn = {2235-2988},
abstract = {Atopic dermatitis (AD) is increasingly recognized as a chronic inflammatory skin disease driven by a self-reinforcing vicious cycle involving skin barrier dysfunction, immune dysregulation, and cutaneous microbiome dysbiosis. A hallmark of this dysbiosis is the overrepresentation of pathogens like Staphylococcus aureus and Malassezia species, alongside a marked loss of microbial diversity, particularly during disease flares. This review systematically dissects the host-derived factors-such as altered lipid profiles, reduced antimicrobial peptides, and elevated skin pH-that facilitate S. aureus colonization. We further examine how bacterial virulence factors amplify type 2 inflammation and impair barrier integrity, thereby sustaining the pathological loop. We also explore the emerging roles of the skin virome, particularly the phageome, and discuss how microbiome-targeted interventions, including bacteriotherapy with commensal bacteria and precision phage therapy, offer promising avenues for ecological restoration. Finally, we argue that future research must leverage multi-omics to understand strain-specific functions, ultimately guiding the development of personalized microbiome interventions for AD.},
}

@article {pmid41768933,
year = {2025},
author = {Ameer, A and Saleem, F and Keating, C and Afzal, F and Irshad, H and Ahmed, K and Sattar, S and Ijaz, UZ and Javed, S},
title = {Avian cecal microbiome response and resilience to Newcastle disease are dictated by breed background.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1659648},
pmid = {41768933},
issn = {2674-0702},
abstract = {A wide range of viral infections threaten the long-term sustainability of poultry production. Newcastle disease (ND), caused by Newcastle disease virus (NDV), is endemic in most Asian countries, including Pakistan, causing 50%-100% mortality in young and mature chickens. Some local chicken breeds show resistance to certain diseases and have greater survival probability. The chicken gut microbiome is linked to immune response against infections and to production performance parameters. The present study aims to comprehend disease resistance patterns in multiple chicken breeds with respect to gut microbial communities. Day-old Naked Neck, Black Australorp, Rhode Island Red, white layer, and broiler chicks were raised on an antibiotic-free diet in a semi-controlled setup. Vaccinated and non-vaccinated birds were challenged with NDV. Disease onset was delayed in breeds other than broilers, in which disease symptoms appeared at day 3 post-challenge with maximum severity and mortality. Other breeds, irrespective of vaccination, survived through the challenge period. Naked Neck showed the least variation in clinical features and growth parameters. A lower diversity in broiler groups with a significant decrease after NDV challenge was revealed by 16S rRNA amplicon sequencing of cecal DNA. Furthermore, broiler cecal core microbiome membership was found to be more variable than other breeds. Moreover, differentially abundant genera were observed across treatment groups and breeds with a similar effect on the predicted metabolic pathways, indicating varied energy metabolism responses. Shotgun metagenomics revealed a higher abundance of functional genes, including antimicrobial resistance (AMR) genes, stress genes, virulence genes, and amino acid degradation genes in the broiler NDV-infected group compared to the control group. The gut microbiota in chickens affects immunity to infections, health, and productivity. Compared to broilers, local chicken breeds, specifically Naked Neck, are found to have high immune competence in resisting ND while maintaining most performance metrics. Broilers show lower alpha diversity with an unstable core microbiome. Therefore, stable core microbiome maintenance may help the birds cope with the viral infection. The results support the farming of resistant chicken breeds over broilers to reduce production losses from NDV outbreaks.},
}

@article {pmid41768524,
year = {2026},
author = {Hirano, T and Wagatsuma, K and Shimomori, Y and Akita, K and Nakamura, T and Yamakawa, T and Yokoyama, Y and Kurumi, H and Ishigami, K and Nagaishi, K and Nakase, H},
title = {Loss of Nonhematopoietic Osteopontin Weakens the Intestinal Barrier and Alters the Microbiome and Metabolome in Mice.},
journal = {Gastro hep advances},
volume = {5},
number = {4},
pages = {100883},
pmid = {41768524},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Inflammatory bowel disease (IBD) is characterized by intestinal barrier disruption and dysregulated interactions between host immunity and gut microbiota. Osteopontin (OPN) is considered a proinflammatory mediator in IBD, but nonhematopoietic cell-derived OPN may exert barrier-protective functions. This study aimed to determine the effects of OPN in a murine model of acute colitis.

METHODS: We examined wild-type and OPN knockout mice under steady-state conditions and in dextran sulfate sodium-induced colitis, including bone marrow chimeras to distinguish the effects of hematopoietic and nonhematopoietic OPN.

RESULTS: Overt colitis did not occur under steady-state conditions. Compared with wild-type mice, OPN knockout mice exhibited crypt elongation, goblet cell hyperplasia, and increased epithelial proliferation. Gene expression analysis revealed reduced interleukin (IL)-22, IL-23, and IL-13 levels alongside increased interferon-γ, IL-1β, and IL-17A levels. 16S rRNA sequencing revealed increased alpha diversity, expansion of Akkermansia and Prevotellaceae, and reduced Lactobacillus abundance. Functional prediction identified enrichment of microbial sulfur metabolism pathways, and metabolomic analysis demonstrated increased L-proline and L-(-)-fucose levels and reduced β-sitosterol levels. These shifts indicate enhanced mucinolytic activity and altered energy metabolism, consistent with a latent "preinflammatory state." Bone marrow chimera experiments demonstrated that OPN deficiency in the recipients reproduced changes in the microbiota composition and lipocalin-2 expression at the steady state and conferred heightened susceptibility to dextran sulfate sodium-induced acute colitis, irrespective of donor genotype.

CONCLUSION: These findings indicate that nonhematopoietic cell-derived "guardian-type" OPN preserves barrier integrity, sustains IL-22/IL-23 production, and maintains microbiota-metabolome balance, whereas its loss induces a preinflammatory state that predisposes to acute mucosal injury. These findings provide a conceptual basis for stage- and source-specific therapeutic strategies in IBD.},
}

@article {pmid41768503,
year = {2025},
author = {Lundberg, HE and Kafel, J and Holo, H and Larsen, SE},
title = {Daily cheese intake positively affects serum osteocalcin levels, vitamin K status and bone turnover markers in elderly men and women.},
journal = {BMJ nutrition, prevention & health},
volume = {8},
number = {2},
pages = {e000933},
pmid = {41768503},
issn = {2516-5542},
abstract = {INTRODUCTION: Daily intake of vitamin K2-rich Jarlsberg cheese is shown to positively affect bone turnover markers (BTMs) in fertile women. How do postmenopausal women and adult men respond to a cheese intervention?

PURPOSE: To estimate the optimal daily efficacy dose (OED) of Jarlsberg cheese to increase serum osteocalcin level in postmenopausal females and males past 55 years of age and estimate the effect on BTMs.

METHODS: Ten expected healthy postmenopausal females and 10 healthy males past 55 years voluntarily participated in a two-dimensional response surface pathway designed dose-response study with three design levels. The duration of each design level was 4 weeks. Blood samples were taken at baseline and the end of each design level for measurements of osteocalcin (OC), vitamin K2, the BTMs procollagen type 1 N-terminal propeptide (P1NP) and serum cross-linked C-telopeptide type I collagen (CTX-1) and other biochemical parameters.

RESULTS: In the female group, the OC level increased significantly (p<0.01) during the first design level but decreased slightly during the second and third design levels. Among males, the OC level increased monotonously during the study and significantly in the second and third design levels (p<0.01). There was no significant change in P1NP, but CTX decreased significantly (p≤0.05) in both sex groups. The ratio P1NP/CTX increased significantly (p≤0.05) in the female group. S-phosphate and s-urea increased significantly (p≤0.02) while s-calcium and s-magnesium were unchanged. After the study, four of the participating women received a diagnosis of osteoporosis.

CONCLUSION: Estimated OED of Jarlsberg cheese was 47 and 67 g/day for postmenopausal females and adult males, respectively. The development in OC and BTMs suggests an anabolic effect of Jarlsberg cheese on bone tissue.},
}

@article {pmid41768492,
year = {2025},
author = {Vignal, L and de Lahondès, R and Gillibert, A and Tavolacci, MP and Prifiti, E and Formstecher, E and Ribet, D and Quillard, M and Coeffier, M and Déchelotte, P},
title = {Metagenomic analysis of salivary microbiota in patients with anorexia nervosa and association with functional digestive disorders (ORMICAN pilot study).},
journal = {BMJ nutrition, prevention & health},
volume = {8},
number = {2},
pages = {e001112},
pmid = {41768492},
issn = {2516-5542},
abstract = {BACKGROUND: Patients with anorexia nervosa (AN) have intestinal dysbiosis and are frequently affected by oral and upper gastrointestinal disorders. Until now, no metagenomic sequencing data were available on oral microbiota in AN.

DESIGN: This observational study enrolled 46 patients with restrictive/purging AN and 20 controls. Salivary samples were performed after fasting. DNA of oral microbiota from salivary samples was analysed by whole genome shotgun deep sequencing. The primary objective was to compare the diversity of oral microbiota between patients with AN and healthy individuals. Secondary endpoints were to assess the associations between the diversity of oral microbiota and the severity of functional digestive disorders, between patients with a restrictive type of AN and patients with a mixed/purging type and between the diversity of oral microbiota and the severity of AN.

RESULTS: We observed not only a significant decrease in the alpha diversity of oral microbiota in AN patients (4.47 (4.05; 4.75)) versus controls (4.81 (4.68; 5.04)) (p=0.001) but also in gene richness (p=0.00023). There was no significant correlation (95% CI) between oral microbiota diversity and functional digestive disorders nor between patients with a restrictive type of AN and patients with a mixed/purging type of AN, nor between the diversity of oral microbiota and the severity of AN. In addition, we observed four bacterial taxa that were decreased in AN patients.

CONCLUSION: Our study highlights a decreased diversity of oral microbiota in AN patients. Future larger studies may help identify the prognostic and therapeutic value of oral microbiota in AN.},
}

@article {pmid41768489,
year = {2025},
author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Iwasaki, M and Dinassing, A and Senthilkumar, R and Preethy, S and Abraham, SJK},
title = {Randomised trial of Aureobasidium pullulans-produced beta 1,3-1,6-glucans in patients with Duchenne muscular dystrophy: favourable changes in gut microbiota and clinical outcomes indicating their potential in epigenetic manipulation.},
journal = {BMJ nutrition, prevention & health},
volume = {8},
number = {2},
pages = {e000776},
pmid = {41768489},
issn = {2516-5542},
abstract = {OBJECTIVE: Duchenne muscular dystrophy (DMD) is an X-linked neuromuscular disorder that leads to increasing muscle weakening and early death. Steroids, the standard treatment of choice in slowing down disease progression, are plagued with adverse effects. Anti-inflammatory, antifibrotic effects and enhancement of muscle regeneration biomarkers after oral consumption of Aureobasidium pullulans strain N-163-produced beta 1,3-1,6-glucan (Neu REFIX) having been demonstrated in clinical and preclinical studies of DMD; in this study, we have investigated the effects on the gut microbiome in patients with DMD.

DESIGN: Twenty-seven patients with DMD were included in the study (control (n=9), N-163 (n=18)). Whole-genome metagenomic sequencing was performed in pre-N-163 and post-N-163 intervention faecal samples of each of these participants.

RESULTS: After N-163 beta-glucan administration, the constitution of the gut microbiome in all the participants was modified to one with positive outcomes on health. There was an increase in butyrate-producing species such as Roseburia and Faecalibacterium prausnitzii. There was a decrease in harmful bacteria associated with inflammation such as enterobacteria and Alistipes.

CONCLUSION: Beneficial reconstitution of the gut microbiome after Neu REFIX beta-glucan administration and its safety have been confirmed. These outcomes correlating with the anti-inflammatory, anti-fibrotic effects along with increase in dystrophin in skeletal muscle and plasma, reported earlier make us recommend further in-depth exploration on its role in epigenetic manipulation which when found encouraging might help other genetic diseases as well.

TRIAL REGISTRATION NUMBER: CTRI/2021/05/033346.},
}

@article {pmid41768415,
year = {2026},
author = {Panda, A and Adhikari, M and Nasker, SS and Nayak, AK and Das, D and Nayak, SK and Dash, SK and Nayak, S},
title = {Enhanced formulation of precision probiotics through active machine learning.},
journal = {Biology methods & protocols},
volume = {11},
number = {1},
pages = {bpag007},
pmid = {41768415},
issn = {2396-8923},
abstract = {The human gut microbiome is crucial to health, with dysbiosis increasingly linked to disease. Precision probiotics offer a promising approach to restoring microbial balance, but ensuring probiotic viability through gastrointestinal transit remains a challenge. This study applies an advanced active machine learning (ML) approach to predict how excipients affect the growth of Lactobacillus plantarum, a commonly used probiotic. State-of-the-art experiments were carried out to complement the ML study. Starting with five known excipient-probiotic interactions, we apply active ML over three rounds to predict the effects of 116 excipients, iteratively refining model certainty and accuracy. Five ML models-neural networks, gradient boosting, logistic regression, random forest, and support vector machines-were trained and evaluated, with the final model achieving certainty levels close to 90%. Unlike previous methods, which retrained new models per iteration, our approach continuously optimized a single model, enhancing prediction stability and reducing uncertainty spread. These results highlight the potential of active ML to support accurate excipient selection in probiotic formulations.},
}

@article {pmid41768127,
year = {2026},
author = {Alsaid, F and Davila, B and He, B},
title = {Plant-derived extracellular vesicles and nanoparticles: origins, functions, and applications.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1758558},
pmid = {41768127},
issn = {2296-4185},
abstract = {Plant-derived extracellular vesicles (PDEVs) and plant-derived nanoparticles (PDNPs) are emerging plant-based nanomaterials with growing relevance in biotechnology, agriculture, and health. Although often grouped together, they arise from distinct origins: PDEVs are actively secreted vesicles with selective cargo loading, whereas PDNPs form during tissue disruption and reflect the lipid-metabolite composition of plant biomass. This review summarizes recent progress in distinguishing these systems, including advances in biogenesis, isolation, biomarkers, and functional characterization. We highlight mechanistic insights into PDEV-mediated cross-kingdom RNA communication in plant immunity and the strong translational potential of PDNPs in oral drug delivery, immunomodulation, and microbiome regulation. Remaining challenges include standardization, scalable purification, and deeper mechanistic clarity. By clarifying their differences and complementary strengths, this review outlines a foundation for developing reliable plant-derived nanovesicle technologies.},
}

@article {pmid41768053,
year = {2026},
author = {Lv, M and Tian, D and Wang, G and Hou, C and Fan, T and Li, W},
title = {Salinity gradients alter root-zone soil microbiome structure and nitrogen-related functional potential in alfalfa (Medicago sativa L.): a pot experiment.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1753229},
pmid = {41768053},
issn = {1664-462X},
abstract = {INTRODUCTION: Soil salinization constrains agricultural sustainability in arid and semi-arid regions. This study examined integrated soil-plant-microbe responses of alfalfa (Medicago sativa L.) to a salinity gradient.

METHODS: A pot experiment was conducted with control, low-, and moderate-salinity treatments. Root-zone soil and plants were sampled to measure soil EC, pH, and inorganic nitrogen forms, and to assess plant growth traits. Shotgun metagenomics was used to characterize microbial community composition and metagenome-inferred functional potential.

RESULTS: Salinity increased soil EC and pH and altered inorganic nitrogen forms, with higher NO3 [-]-N under moderate salinity and lower NH4 [+]-N under salinity compared with the control. Plant height peaked under low salinity, whereas fresh and dry biomass decreased under both salinity treatments. Microbial β-diversity differed among treatments, while α-diversity showed limited responses. Functional annotations indicated treatment-associated trends in nitrogen- and stress-related categories and KEGG level 3 pathways; however, most differences were not significant after FDR correction.

DISCUSSION: This integrative root-zone assessment links salinity-driven soil chemistry changes with alfalfa performance and suggests coordinated shifts in soil chemistry, microbiome structure, and plant growth under salinity stress.},
}

@article {pmid41767851,
year = {2026},
author = {Khanehzar, E and Shams, F and Jafari, A and Poustforoosh, A},
title = {Next-generation AI-assisted drug design against cancer: large language models meet conventional in silico methods.},
journal = {In silico pharmacology},
volume = {14},
number = {1},
pages = {76},
pmid = {41767851},
issn = {2193-9616},
abstract = {UNLABELLED: Cancer remains a leading cause of death, with limited effective therapies. The AXL-GAS6 pathway promotes tumor growth, invasion, metastasis, and resistance to apoptosis. Large Language Models (LLMs) can predict drug-target interactions, generate novel molecular scaffolds, and optimize lead compounds. This study aims to design novel small molecules through a computational pipeline integrating commercial LLMs, molecular docking, molecular dynamics (MD), and ADMET evaluation. We combined DeepSeek LLM with conventional computational methods to design AXL inhibitors via three strategies: natural product-based, microbiome-derived, and FDA-approved drug-inspired scaffolds. Structured prompt engineering generated novel candidates, filtered for drug-likeness, synthetic feasibility, and docking score (Glide, Schrödinger). Top hits underwent 100 ns MD simulations and ADMET evaluation (SwissADME, ADMETLab3). AIC1 showed the highest binding affinity (- 10.079 kcal/mol), surpassing clinical-stage bemcentinib (- 8.234 kcal/mol). MD confirmed stable complexes (RMSD < 3 Å), with AIC1 and AIC4 forming extensive hydrogen bonds. ADMET profiling indicated favorable pharmacokinetics for all, with AIC2 exhibiting the lowest toxicity (hERG inhibition: 34.2%, hematotoxicity: 36.8%) and optimal drug-like properties. This work pioneers LLM-driven in silico design of AXL inhibitors, offering a scalable blueprint for accelerated anticancer drug development.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40203-026-00582-y.},
}

@article {pmid41767845,
year = {2026},
author = {Ortutu, BF and Okin, AO and Darkwah, KO and Onuorah, UM and Maigoro, AY and Iheme, GO},
title = {Gut microbiota and brain aging: a comparative review of African and western populations.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1740408},
pmid = {41767845},
issn = {1663-4365},
abstract = {As the population ages, cognitive decline and neurodegenerative diseases have become major public health concerns. The human gut microbiota plays a major role in regulating neurodevelopment, neuroinflammation, and cognitive decline through the gut-brain axis. Emerging evidence reveals a possible association between alterations in gut microbial diversity and age-related neurological disorders, including Alzheimer's disease and neurodegeneration. Regional and dietary differences shape the gut microbiome. These variations may, in turn, be associated with differences in brain aging across populations. Several cross-sectional studies indicate that rural African communities consuming predominantly fiber-rich diets exhibit distinct gut microbiota profiles characterized by increased abundance of genera, including Prevotella, Faecalibacterium, and Ruminococcus. These microbial configurations have been associated with improved gut barrier integrity, reduced systemic inflammation, and enhanced production of short-chain fatty acids in some preclinical and human studies. All these factors have been studied as potential mechanisms linked to delayed brain aging. Furthermore, epidemiological reports suggest lower prevalence rates of dementia and other neurodegenerative disorders in these populations, although such comparisons may be influenced by differences in study design, diagnosis, and case ascertainment across regions. This narrative review synthesized current understanding of the gut microbiota's role in brain aging, summarized available data on gut microbiota composition in African versus Western populations, and explored the pathways by which traditional African diets may contribute to neuroprotection. By critically examining this evidence and highlighting major research gaps, the review advocates for region-specific investigations and future longitudinal studies to validate causal links.},
}

@article {pmid41767840,
year = {2026},
author = {Kost, E and Kundel, D and Barthel, M and Conz, RF and Werner, RA and Ghiasi, S and Bublitz, TA and Mäder, P and Krause, HM and Six, J and Hartmann, M and Mayer, J},
title = {Drought increases root and rhizodeposition carbon inputs into soils.},
journal = {Plant and soil},
volume = {519},
number = {1},
pages = {103-127},
pmid = {41767840},
issn = {0032-079X},
abstract = {AIMS: Increasing droughts affect crop yield and health. Plants can respond to drought by adapting their root biomass, root morphology, and quality and quantity of rhizodeposition to improve water and nutrient uptake. Besides droughts, agricultural management influences roots and rhizodeposition; however, it is not well studied how agricultural management can affect the response of roots and rhizodeposition to drought.

METHODS: A semi-continuous [13]CO2 isotope labelling experiment was performed in a long-term field experiment comparing biodynamic, mixed conventional, and mineral conventional cropping systems. Rainout shelters were installed to induce drought. Root, net rhizodeposition, and the rhizosphere microbiome were determined at ripening of wheat.

RESULTS: Drought enhanced the total root carbon mainly through the increase of fine roots. Fine root carbon under drought was primarily enhanced in the mixed conventional and biodynamic cropping system, both receiving farmyard manure, whereas no increase was measured in the mineral fertilized conventional system. Net rhizodeposition carbon was enhanced in all cropping systems under drought, particularly in the first 0.25 m. While some plant-growth-promoting genera such as Streptomyces and Rhizophagus showed relative increases under drought, other plant growth-promoting genera often involved in nitrogen fixation such as Rhodoferax and Mesorhizobium were decreased.

CONCLUSION: This field trial suggests that drought increases total belowground carbon input via fine root and net rhizodeposition carbon inputs. Since fine root carbon increased under drought in cropping systems with farmyard manure, adding manure under future drought periods could be advantageous to increase soil carbon inputs and improve nutrient foraging.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-08021-1.},
}

@article {pmid41767763,
year = {2026},
author = {Samara, P and Athanasopoulos, M and Athanasopoulos, I},
title = {Benign, persistent, and invasive: mechanistic and translational approaches to middle‑ear cholesteatoma.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {7},
number = {},
pages = {1002359},
pmid = {41767763},
issn = {2692-3114},
abstract = {Acquired middle-ear cholesteatoma is a histologically benign keratinizing squamous epithelial lesion that paradoxically exhibits locally destructive, recurrent, and invasive behavior, often resulting in ossicular erosion, hearing loss, labyrinthine fistula, and, rarely, intracranial complications. Surgical excision remains the primary management strategy; however, recurrence is common due to persistent microenvironmental drivers. Recent mechanistic studies-including single-cell transcriptomics, spatial proteomics, and epigenetic profiling-reveal a multifactorial pathogenesis orchestrated by chronic inflammation, proteolytic extracellular-matrix remodeling, osteoclast activation via RANKL and activin A, epithelial plasticity with partial epithelial-to-mesenchymal transition (EMT), and a dysbiotic, biofilm-forming microbiome. Emerging evidence further implicates oxidative stress, RNA and epigenetic modifications, miRNA dysregulation, and immune cell infiltration as central modulators of lesion chronicity and bone resorption. Collectively, these processes establish a self-sustaining pro-osteolytic microenvironment that drives bone erosion and postoperative recurrence. Cholesteatoma recapitulates several features of malignant lesions-hyperproliferation, local invasion, and stromal/immune cell recruitment-yet remains fundamentally benign, lacking metastatic potential and genomic instability. Its aggression is ecological rather than genetic, highlighting the potential for microenvironment-directed, precision-based strategies. Adjunctive approaches may include local delivery of modulatory agents, targeted interference with inflammatory, proteolytic, osteoclastogenic, and microbial axes, and biomarker-guided patient stratification. Preclinical and early-phase experimental studies assessing target engagement, radiologic stabilization, and molecular surrogates of efficacy could inform safer, mechanism-driven interventions that complement surgery, reduce recurrence, and preserve hearing. Integrating molecular pathobiology with clinical strategy positions cholesteatoma as a model for benign yet locally aggressive, microenvironment-driven disease, providing a roadmap for translational therapies with direct relevance to surgical practice.},
}

@article {pmid41767584,
year = {2025},
author = {Dang, Y and Xu, S and Huang, J and Peng, X and Yang, Y and Wang, Y and Yan, Y and Jiang, F and Wang, J and Liu, J},
title = {Comprehensive identification of microbial and metabolomic factors impacting ICC recurrence.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1703182},
pmid = {41767584},
issn = {2234-943X},
abstract = {INTRODUCTION: Intrahepatic cholangiocarcinoma (ICC) originates from intrahepatic bile duct epithelial cells and its global incidence is rising. Surgery remains the primary treatment, but postoperative recurrence rates remain high.

METHODS: We analyzed ICC patients' gut microbiota at four stages (preoperative, 7 days postoperative, 1 month postoperative, and during recurrence) using 16S rRNA sequencing and their serum metabolome via LC-MS/MS. Correlations among gut microbiota, metabolome, and clinical indicators were investigated, and candidate microorganisms and metabolites were integrated for multiomics clustering and staging.

RESULTS: This revealed significant increases in Bacteroides, Veillonella, and Enterococcus in ICC patients compared to healthy controls across all stages, suggesting these bacteria as potential markers of ICC progression. Microbial and metabolite changes were observed, with gut microbes influencing ICC development through kynurenic acid, linoleic acid, creatine, cholic acid, L-arginine, and the tumor microenvironment. Multiomics analysis showed that cholangiocarcinoma staging improves patient prognosis, particularly highlighting bile acids' role in type II hepatic phenotypes related to cholesterol metabolism.

DISCUSSION: Our study provides insights into ICC microbiome and metabolome associations with clinical features and survival.},
}

@article {pmid41767576,
year = {2026},
author = {Luppi, S and Topouzova, GA and Campisciano, G and Giolo, E and Bulfone, T and Rossi, F and Zito, G and Ricci, G and Comar, M and Andreuzzi, E},
title = {Impact of hormonal treatments for endometriosis on the reproductive microbiome: a systematic review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755725},
pmid = {41767576},
issn = {1664-302X},
abstract = {INTRODUCTION: The reproductive microbiome plays a key role in disease progression and fertility in women with endometriosis. Vaginal and endometrial dysbiosis has been increasingly linked to inflammation, impaired reproductive outcomes, and symptom severity. Although estro-progestins, progestins, and GnRH agonists are widely used, their impact on microbial communities remains poorly understood, highlighting the need to clarify microbiome-therapy interactions. This systematic review aims to comprehensively synthesize current evidence on how hormonal therapies influence the reproductive microbial environment and to offer insights for optimizing clinical management of endometriosis.

METHODS: Literature screening and data extraction followed PRISMA guidelines using PubMed, Scopus, and Google Scholar. The search combined terms on endometriosis, hormonal therapy, and reproductive microbiome. Non-English studies, reviews, and those without original data were excluded. Risk of bias was assessed with ROBINS-I-V2, and microbial composition and diversity were analyzed and synthesized qualitatively.

RESULTS: The literature search retrieved 577 publications, of which 6 met eligibility criteria and were analyzed. The evidence collected through sequencing or culture-based methods suggested that the use of hormonal therapies to treat endometriosis may impact both vaginal and endometrial microbiome, favoring the colonization of bacterial species associated with infertility. GnRHa resulted to foster the dominance of potentially pathogenic bacteria, as Gardnerella and Streptococcaceae, in the endometrium, and supporting bacterial vaginosis by increasing intermediate flora (Nugent score 4-6). A similar effect on the vaginal environment has been reported upon the use of oral contraceptive pills, which was shown to prompt the increase of Prevotella, Ureaplasma, Streptococcus anginosus and Streptococcus agalactiae, among other pathogenic microbes, and to enhance the Bacillota/Bacteroidota ratio.

DISCUSSION: Despite affected by several limitations and heterogeneity of included studies, this review provides a preliminary overview of the possible pejorative effect of hormonal therapy on the reproductive microbiome of endometriosis patients. While further investigations are required to consolidate these findings, the observations raised offer a valuable basis for opening a discussion about improving management strategies for affected women. By highlighting confounding factors overlooked in the selected papers, the present work will also be functional to optimize the design of future studies.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251042858, identifier PROSPERO (CRD420251042858).},
}

@article {pmid41767572,
year = {2026},
author = {Pattapulavar, V and S, SK and Ramanujam, S and Subburaj, S and John, GC},
title = {Probiotic-based therapeutics for a One Health future: redefining antibiotic dependency to combat antimicrobial resistance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1736436},
pmid = {41767572},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) has become a major One Health concern, affecting the interconnected microbial systems shared by humans, animals, and the environment. Decades of antibiotic-driven control have disturbed ecological stability and contributed to the expansion of the global resistome. This Perspective approaches AMR mitigation through an ecological restoration lens, outlining a three-part strategy that brings together probiotic therapeutics, microbiome-focused public awareness, and integrated surveillance. Probiotics are presented as biologically compatible tools that promote microbial stability through competitive niche occupation, immune support, and environmental biodegradation, thereby reducing selective pressures that favor resistance. In parallel, strengthening microbiome literacy can guide behavioral choices that support stewardship and reduce unnecessary antimicrobial use. The proposed One Health Microbiome Intelligence Framework (OH-MIF) adds a data-driven layer by linking genomic, clinical, agricultural, and environmental information through AI-enabled analytics. Together, these components form an adaptable system that shifts AMR management from reactive dependence on antibiotics toward a more resilient, coexistence-based approach. By aligning ecological interventions with education and policy intelligence, this Perspective positions microbial balance as a practical foundation for sustainable AMR control within broader planetary health goals.},
}

@article {pmid41767565,
year = {2026},
author = {Doku, TE and Belford, JDE and Sylverken, AA},
title = {Rhizosphere microbiome assembly drives metal sequestration in Leucaena leucocephala during tailing phytoremediation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1745018},
pmid = {41767565},
issn = {1664-302X},
abstract = {INTRODUCTION: Ghana's water and soil resources face severe challenges due to heavy metal contamination from gold mining operations. Although Leucaena leucocephala exhibits potential for phytoremediation, little is known about the contribution of its rhizosphere microbiomes to metal uptake and tolerance in multiple-metal contaminated tailings in field conditions.

METHODS: We investigated the rhizosphere bacterial community dynamics in L. leucocephala across three soil treatments (garden soil, 1:1 soil-tailings mixture, and pure tailings) using 16S rRNA amplicon sequencing and atomic absorption spectrophotometry. Briefly, transplanted seedlings of L. leucocephala were harvested at three-month intervals for three consecutive harvests to assess metal accumulation and changes in the microbiome.

RESULTS AND DISCUSSION: Leucaena leucocephala demonstrated notable tolerance to elevated metal concentrations (>10,000 mg/kg Fe and Mn) under acidic conditions (pH 4.57-5.97). Maximum metal uptake occurred at final harvest, with Fe reaching 14,605 ± 1.40 mg/kg in shoots and Mn reaching 12,279 ± 1.13 mg/kg in roots. The elevated concentrations of metals reduced overall bacterial diversity, except for selected metal-tolerant Actinobacteria, Proteobacteria, and Acidobacteria, which dominated bacterial communities across all treatments. The initial proliferation of Nocardioides and Streptomyces corroborated nutrient and metal-induced stress, while key genera such as Arthrobacter, Gaiella, Skermanella, and Chelatococcus showed strong positive associations with metal accumulation and maintained essential ecological functions.

CONCLUSION: Rhizosphere bacterial communities undergo stress-specific assembly processes, with specific taxa facilitating L. leucocephala's exceptional phytoremediation capacity. These findings provide insights into microbiome-enhanced strategies for mine site rehabilitation.},
}

@article {pmid41767558,
year = {2026},
author = {Song, L and Yu, QY},
title = {Stratified management of residual gastric cancer risk after Helicobacter pylori eradication.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779490},
pmid = {41767558},
issn = {1664-302X},
abstract = {Despite the established efficacy of Helicobacter pylori eradication in reducing gastric cancer (GC) incidence, a significant residual risk persists in successfully treated individuals, driven by lasting pathological alterations termed "oncogenic memory," including irreversible mucosal damage (e.g., intestinal metaplasia), residual pro-inflammatory and epigenetic "molecular scars," and gastric microbiome dysbiosis. This perspective synthesizes current evidence to advocate for a paradigm shift from a singular focus on pathogen clearance towards a comprehensive, risk-adapted management strategy. We propose a novel, dual-dimensional framework centered on a multidimensional risk assessment that integrates OLGA/OLGIM staging, demographic, lifestyle, and genetic factors to stratify post-eradication individuals into distinct risk categories. The framework subsequently outlines tailored surveillance protocols-specifying endoscopy frequency and advanced biomarker application-leverages technological support from AI-assisted endoscopy and molecular testing, and details differentiated resource allocation models based on regional GC incidence and economic development. This integrated approach provides a practical roadmap for implementing precision prevention, aiming to mitigate the lingering GC risk and ultimately reduce the global disease burden through a dynamic, lifelong management system beyond eradication. To facilitate implementation, we provide a user-ready risk calculator that operationalizes the multidimensional score for cohort-level application.},
}

@article {pmid41767542,
year = {2026},
author = {Effendi, RMRA and Witkam, WCAM and Dwiyana, RF and Suwarsa, O and Kraaij, R and Murad, C and Thio, HB and Nijsten, T and Pardo, LM},
title = {Profiling skin microbiota in an underrepresented population: Indonesian children with atopic dermatitis and controls.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1697420},
pmid = {41767542},
issn = {2296-858X},
abstract = {INTRODUCTION: The skin microbiome plays a central role in the pathogenesis of atopic dermatitis (AD), but most studies have focused on high-income populations of European ancestry. Microbiome data from tropical and developing regions remains limited. In Asia, microbiome research has similarly centered around developed countries, leaving populous developing countries like Indonesia underrepresented. The aim was to profile the cutaneous bacterial microbiota of children with AD from Indonesia and compare it with controls.

METHODS: Skin swabs were collected from lesional sites of 111 children aged 4-18 years with AD and from the forearms of 107 controls, all attending Pediatric Dermatology Clinic of Dr. Hasan Sadikin General Hospital, an urban tertiary-care referral center in Bandung, West Java, Indonesia. AD was diagnosed using Hanifin-Rajka criteria, while controls had non-atopic, non-inflammatory dermatological conditions. Cutaneous bacterial microbiota was profiled using 16S rRNA sequencing with amplicon sequence variant (ASV) level analysis using DADA2 pipeline. Data was analyzed after quality control to estimate alpha and beta diversities, the later using, permutational multivariate analysis of variance (PERMANOVA) to assess contribution of individual variables to the variation in microbiota composition. Univariable differential abundance was done to analysis the composition of specific bacteria in cases versus controls. Analysis of core microbiota compositions and phylogenetic relationships were explored to identify key taxa associated with AD.

RESULTS: Most children came from families with higher household incomes, and children with AD were younger than controls (mean age 8.35 ± 3.51 vs. 9.91 ± 3.79 years, P = 0.002). Lesional AD skin showed a significantly reduced alpha diversity and a marked overrepresentation of Staphylococcus aureus and Staphylococcus epidermidis. Less commonly reported genera, including Acetobacter and Gluconobacter, were enriched in cases, potentially reflecting environmental exposure in this cohort. PERMANOVA revealed that case-control status, family income, maternal atopy, maternal education and DNA concentration significantly influenced microbial composition. Phylogenetic analysis showed a clear lineage-level distinction between Staphylococcus ASVs.

CONCLUSION: Our findings reveal distinct microbial profiles in children with AD from a tropical, underrepresented population with predominantly higher household incomes, and underscore the role of environmental and sociodemographic factors associated with skin microbiota. While generalizability to lower-income or rural populations may be limited, the value of ASV-level analysis lies in its ability to capture both known and less characterized microbial signals.},
}

@article {pmid41767378,
year = {2026},
author = {Xu, Y and Cao, Y and Zou, L and Wulanna, and Liu, X and Yan, S and Liu, C and Gao, M and Zhan, J and Wang, Q and Wu, C},
title = {Protective role of aqueous Coriandrum sativum seed extract in diet-induced glucolipid metabolic disorder through gut-liver axis regulation.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1744741},
pmid = {41767378},
issn = {1664-2392},
abstract = {OBJECTIVE: To elucidate the protective effects of aqueous Coriandrum sativum seed extract against high-fat, high-sugar diet (HSFD)-induced glucolipid metabolic disorder in mice, with particular focus on gut-liver axis regulation involving hepatic metabolism, oxidative stress, inflammation, and gut microbiota composition.

METHODS: Male mice were fed an HSFD and orally treated with Coriandrum sativum seed extract (1.0 or 2.0 g/kg/day) for eight weeks. Biochemical parameters, histopathology, hepatic gene expression, oxidative stress markers, and gut microbial profiles were assessed via standard assays, RT-qPCR, Western blot, histological staining, and full-length 16S rRNA gene sequencing with functional prediction.

RESULTS: The extract significantly ameliorated HSFD-induced metabolic impairments, including hyperglycemia, hyperlipidemia, insulin resistance, and hepatic steatosis. Histological improvements were observed in the liver, pancreas, and colon. Hepatic expression of FAS, NF-κB, and IL-6 was suppressed, while PPARα and LDLR expression was restored. Antioxidant defenses were enhanced by reducing malondialdehyde and increasing superoxide dismutase activity. Microbiota analysis revealed partial restoration of beneficial taxa such as Lactobacillus murinus and Lachnospiraceae_UCG-006, alongside enrichment of microbial pathways related to energy and carbohydrate metabolism.

CONCLUSION: Aqueous Coriandrum sativum seed extract exerts systemic metabolic benefits in diet-induced glucolipid dysregulation by targeting the gut-liver axis. Its multi-targeted actions on hepatic metabolism, inflammatory signaling, oxidative balance, and gut microbiota composition support its potential as a natural therapeutic agent for metabolic disorders.},
}

@article {pmid41767368,
year = {2026},
author = {De Pasquale, C and Harrison, LC},
title = {Early-life antibiotic exposure and type 1 diabetes risk: a systematic review and meta-analysis.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1764522},
pmid = {41767368},
issn = {1664-2392},
abstract = {OBJECTIVE: Antibiotic exposure impacts the gut microbiome and potentially, in an infant, the developing immune system, with implications for the emergence of immune disorders such as type 1 diabetes (T1D). Reports of early-life antibiotic exposure on risk for T1D are inconsistent. We aimed to perform a systematic review and meta-analysis of the association between antibiotic exposure in early life and the development of T1D.

METHODS: Observational studies were assembled that reported an association between early-life antibiotic exposure and the development of T1D. Four early-life periods were covered: 12 months preconception, prenatal (in pregnancy), neonatal and up to 24 months postnatal. Medline, Embase, Web of Science Core Collection, and Scopus were searched from inception to August 28, 2024. All records were imported into Covidence for automated deduplication, abstract screening and full-text screening by two independent reviewers. Data from 20 studies and 10, 960 T1D cases were extracted and analysed using a random effects meta-analysis. Pooled odds ratios (ORs) and hazard ratios (HRs) with associated 95% confidence intervals (CIs) were calculated.

RESULTS: In the preconception period, maternal exposure to macrolide (OR = 1.23 [95% CI: 1.02-1.48]), sulfonamide/trimethoprim (OR = 1.34 [95% CI: 1.07-1.69]) or tetracycline (OR = 1.26 [95% CI: 1.11-1.44]) antibiotics was associated with an increased odds of T1D. Prenatal, neonatal and postnatal antibiotic exposure was not significantly associated with T1D.

CONCLUSION: Preconception exposure to specific antibiotic classes may represent a modifiable maternal risk factor for T1D in the offspring. This would have implications for antibiotic prescribing guidelines but requires validation by the further study of defined antibiotic classes and their exact timing of preconception exposure.

The protocol was pre-registered on PROSPERO (CRD42024589374) and followed PRISMA guidelines.},
}

@article {pmid41767236,
year = {2026},
author = {Tavassol, ZH and Farsi, F and Ettehad-Marvasti, F and Ejtahed, HS and Hasani-Ranjbar, S},
title = {Gut Microbiota Alterations in Hypothyroidism: A Pilot Study Revealing Increased Abundance of Specific Bacterial Genera.},
journal = {Journal of nutrition and metabolism},
volume = {2026},
number = {},
pages = {9988966},
pmid = {41767236},
issn = {2090-0724},
abstract = {BACKGROUND: Hypothyroidism (HT) is a prevalent thyroid disorder characterized by insufficient thyroid hormone production, leading to metabolic complications. Emerging research suggests a link between gut microbiota and thyroid regulation, positing that alterations in gut bacterial populations may contribute to HT's development and progression. This study aimed to investigate these associations by comparing gut microbiota compositions between individuals with HT and healthy adults, potentially refining diagnostic tools and therapeutic strategies.

METHODS: In this pilot study conducted between 2019 and 2023, 15 hypothyroid patients and 15 age- and gender-matched healthy controls participated in the study. Exclusion criteria were applied to eliminate confounding factors. Anthropometric data were collected, and stool samples underwent microbial analysis. Total bacterial DNA was extracted, and quantitative real-time PCR targeting 16S rRNA genes across eight bacterial genera was performed. The Mann-Whitney U test was used for statistical analyses.

RESULTS: No significant differences were observed in baseline demographic and anthropometric characteristics between groups. However, hypothyroid patients exhibited significantly elevated levels of Bacteroides, Bifidobacterium, Escherichia, Fecalibacterium, and Prevotella (p values < 0.001-0.030). No significant differences were found in levels of Akkermansia, Lactobacillus, or in the Bacteroides/Prevotella ratio.

CONCLUSION: This pilot study provides preliminary indications of a possible role of gut microbiota in the pathophysiology of HT. Variations in bacterial composition suggest a significant influence of gut health on thyroid regulation. Future studies with larger cohorts are needed to explore the biological pathways linking the gut microbiome to thyroid function, which may lead to novel microbiota-targeted therapeutic approaches.},
}

@article {pmid41767117,
year = {2026},
author = {Hu, T and Chen, Z and Yin, Z and Zhou, L and Chen, Q and Han, Y and Li, K},
title = {New concept in wound infection management: From bacterial eradication to microbiome modulation.},
journal = {APL bioengineering},
volume = {10},
number = {1},
pages = {010901},
pmid = {41767117},
issn = {2473-2877},
abstract = {Wound infection represents a significant challenge in clinical practice. Traditional wound management, targeting sterility and relying on strategies of broad-spectrum bactericidal activity and antibiotic dependence, achieves partial infection control but induces severe complications, including exacerbated bacterial resistance and skin microbiota dysbiosis. With the continuous advancement of microbiome research, a novel consensus has emerged: the key to wound healing lies not in the complete eradication of all microorganisms but in maintaining the dynamic balance of the microbial ecosystem. This review aims to elaborate on the paradigm shift from "bactericidal eradication" to "microbial modulation" in wound care, analyze the inherent limitations of conventional antibacterial strategies, and systematically summarize the critical roles of skin commensal microbiota in promoting wound healing through core mechanisms such as competitive inhibition, metabolic regulation, and immune modulation. Furthermore, it proposes that the core strategy of future wound care should focus on precision microbial modulation and discusses the application prospects of cutting-edge technologies, including probiotics, postbiotics, and individualized precision interventions. The innovative significance of this paradigm in wound dressing design is envisaged, emphasizing the development of novel materials integrating microbiota-specific regulatory capabilities and smart responsive functions. This work provides theoretical support for the precision prevention and control of wound infections, the improvement of healing quality, and technological innovation in the field of wound care.},
}

@article {pmid41767020,
year = {2026},
author = {Alachraf, K and Trouten, P and Thayer, J},
title = {Zoonotic Streptococcus canis Bacteremia Following a Dog Scratch in an Elderly Patient With a Nonconditional Pacemaker.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {2485747},
pmid = {41767020},
issn = {2090-6625},
abstract = {Streptococcus canis is a β-hemolytic Group G streptococcus commonly found in the microbiome of dogs and cats and is an uncommon cause of invasive human infection. Although typically regarded as a veterinary pathogen, S. canis has been reported to cause bacteremia, endocarditis, and other severe infections in humans, particularly in older adults with significant comorbidities or implanted medical devices. We describe a case of Streptococcus canis bacteremia in an 89-year-old woman with multiple comorbidities and a nonconditional permanent pacemaker who presented with fever, dyspnea, and severe lower back pain. Blood cultures grew S. canis, identified using standard microbiologic techniques. The clinical course raised concern for metastatic infection and pacemaker involvement. Imaging of the thoracic and lumbar spine demonstrated no evidence of discitis or osteomyelitis, and both transthoracic and transesophageal echocardiography showed no valvular or pacemaker lead vegetations. Further history revealed a dog scratch several weeks prior to presentation that resulted in skin disruption, representing a plausible portal of entry. The patient was treated with intravenous ceftriaxone with rapid clinical improvement, resolution of hypoxia, clearance of bacteremia, and declining inflammatory markers. She was discharged to inpatient rehabilitation to complete a 2-week course of antimicrobial therapy and recovered without evidence of recurrent infection. This case underscores Streptococcus canis as an uncommon but clinically relevant zoonotic pathogen and highlights the importance of detailed exposure history, appropriate microbiologic identification, and careful evaluation for device-related infection in high-risk patients.},
}

@article {pmid41766754,
year = {2026},
author = {Devinsky, O and Leitner, DF and Kamondi, A and Wisniewski, T},
title = {Epilepsy and Alzheimer Disease: Epidemiologic, Clinical, Molecular, and Neuropathologic Convergences and Divergences.},
journal = {Neurology. Clinical practice},
volume = {16},
number = {2},
pages = {e200589},
pmid = {41766754},
issn = {2163-0402},
abstract = {PURPOSE OF REVIEW: Alzheimer disease (AD) and epilepsy are major causes of neurologic disability and are reciprocally related: epileptiform discharges, subclinical seizures, and epilepsy are more prevalent in patients with AD compared with controls; progressive cognitive impairment commonly afflicts epilepsy patients; and late-onset epilepsy patients have higher rates of new-onset dementia.

RECENT FINDINGS: Epidemiologic studies support shared risk factors (e.g., genetic variants, vascular disease, sleep disorders, microbiome) with notable divergences. AD and epilepsy have some overlapping anatomic (e.g., hippocampus, entorhinal, and association cortex), clinical (e.g., memory, attentional, and executive) impairments, and neuropathologic (e.g., amyloid, tau, neurofibrillary tangles) features. Shared clinical and translational challenges include underlying mechanisms (e.g., genetic variants, neuroinflammation, metabolic and mitochondrial dysfunction, excitatory/inhibitory imbalance, microbiome, and sociodemographic factors) and identifying valid and reliable biomarkers (e.g., total tau and phosphorylated tau (p-tau), amyloid deposition, Aβ42/Aβ40 ratio) to assess disease progression, predict outcomes, and assess potentially disease-modifying interventions.

SUMMARY: Identifying convergences and divergences between epilepsy and AD may inform our understanding. The clinical, neurophysiologic, neuropathologic, and molecular pathologic changes in AD and epilepsy may reveal pathophysiologic insights and therapeutic opportunities.},
}

@article {pmid41766731,
year = {2026},
author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF},
title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73172},
pmid = {41766731},
issn = {2045-7758},
abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.},
}

@article {pmid41766653,
year = {2026},
author = {Jiang, Z and Zhai, C and He, C and Shen, L and Tang, G and Xu, L and Yang, H and Hu, H and Han, J},
title = {Effects and mechanisms of probiotics supplement on hypertension.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000004258},
pmid = {41766653},
issn = {1473-5598},
abstract = {The global population of individuals suffering from hypertension is estimated to surpass 1.28 billion. Uncontrolled hypertension makes contributions to the development of cardiovascular and cerebrovascular diseases. Emerging evidence indicates a significant correlation between hypertension and gut microbiota. As an intestinal regulator, which could confer health benefits to the host in adequate amounts, probiotics may become a novel approach to regulating blood pressure without side effects. Therefore, we overview the antihypertensive effects and the potential mechanisms of probiotics supplement on hypertension.},
}

@article {pmid41766520,
year = {2026},
author = {Wallander, K and Beijer, G and Eliasson, E and Giske, CG and Ponzer, S and Söderquist, B and Eriksen, J},
title = {Is current guidance for cloxacillin prophylaxis dosages in hip and knee arthroplasty adequate? Evidence from a prospective Swedish cohort.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {3},
pages = {},
doi = {10.1093/jac/dkag067},
pmid = {41766520},
issn = {1460-2091},
support = {//Region/ ; FoUI-954900//Stockholm/ ; FoUI-973467//Stockholm/ ; FoUI-974859//Stockholm/ ; 2021-02699//Stockholm/ ; OLL-983304//Region Örebro County/ ; },
abstract = {OBJECTIVES: Perioperative antibiotic prophylaxis is crucial for preventing detrimental postoperative prosthetic joint infections (PJIs). Guidelines aim to prevent infection with methicillin-susceptible staphylococci-in Sweden through administering cloxacillin, at fixed doses with minimal consideration to kidney function or patient weight. Over- and under-dosing could have adverse effects, negative effects on the microbiome, or increase the risk of PJI. We aimed primarily to evaluate whether the current uniform prophylactic regimen of cloxacillin in hip and knee arthroplasty is adequate.

PATIENTS AND METHODS: Patients subjected to elective prosthetic joint surgery (N = 204) were included in a prospective study. Free plasma concentrations of cloxacillin were measured on three occasions throughout arthroplasty surgery. Samples were analysed using a validated HPLC-MS/MS method. A free concentration of <2 mg/L was deemed a theoretically appropriate concentration to suppress growth of methicillin-susceptible staphylococci in bone. A sensitivity analysis with values of 1 and 4 mg/L was included.

RESULTS: Potentially subtherapeutic concentrations (≤2 mg/L) at the end of surgery were found in 31 cases (15%). The corresponding numbers for 1 and 4 mg/L were 3 and 88 (1% and 43%). In multivariable logistic regression analysis, an ASA (American Association of Anesthesiologists physical status) score of I (relatively healthy patients), estimated glomerular filtration rate >90 mL/min/1.73 m2, body weight >100 kg and long duration of surgery significantly predicted suboptimal concentrations.

CONCLUSIONS: Current cloxacillin dosing in hip and knee arthroplasty surgery results in a risk for subtherapeutic levels in patients with high body weight and preserved renal function. Therefore, dosing guidelines for cloxacillin prophylaxis in arthroplasty should be reviewed.},
}

@article {pmid41766340,
year = {2026},
author = {Kovner, A and Kapushchak, Y and Pakharukova, M},
title = {Liver flukes and kidney injury: systematic review of human and animal data (from 1950 to 2025).},
journal = {Journal of helminthology},
volume = {100},
number = {},
pages = {e24},
doi = {10.1017/S0022149X26101187},
pmid = {41766340},
issn = {1475-2697},
support = {grant number 24-44-00048//Russian Science Foundation/ ; },
abstract = {Foodborne trematodes, particularly from families Opisthorchiidae and Fasciolidae, significantly impact human health. Research on trematode-related diseases has primarily focused on the hepatobiliary system and carcinogenic potential of these flukes. Nonetheless, chronic infection by these parasites likely affects other organ systems. This review emphasises the need to expand studies beyond the hepatobiliary system to fully understand the pathogenesis of liver fluke infections and advocates for a systematic approach to the management of affected humans. This review analyses scientific data from 1950 to 2025, including studies on laboratory animals, wild animals, and humans. Databases such as PubMed, Google Scholar, WHO, IARC, Rospotrebnadzor, and eLibrary were utilised. Common kidney injuries from trematode infections include glomerular and tubular damage, interstitial inflammation, and fibrosis. These injuries are influenced by liver damage and gut microbiome imbalances. Interspecies differences highlight the complexity of host-parasite interactions. Research indicates that foodborne-trematode-associated nephropathy exists in both humans and animals and involves immune complexes, oxidative stress, and biomarkers like KIM1. The documented renal damage underscores the need for further investigation into the mechanisms of the trematode-associated renal pathologies.},
}

@article {pmid41766326,
year = {2026},
author = {Troielli, P and Moreno, J and Cortes, A and Cardenas, P and Kerob, D and Gamarra, A and Dreno, B},
title = {Integrating Dermocosmetics Into Acne Care in Latin America.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {3},
pages = {e70776},
pmid = {41766326},
issn = {1473-2165},
support = {//La Roche-Posay Laboratoire Dermatologique, L'Oreal Dermatological Beauty Division/ ; },
abstract = {BACKGROUND: Prescription acne products have proven efficacy and safety, yet management can pose a challenge. This review discusses the benefits of adding dermocosmetics to acne management.

METHODS: We add expert consensus with review of the literature to provide guidance for clinicians managing patients with acne in Latin America.

RESULTS: There is increasing evidence that dermocosmetics (over-the-counter cleansers, moisturizers, and sunscreens that contain acne-targeting ingredients) can be a good alternative to prescription acne treatments as well as adjuncts. Milder forms of acne may be present in any age patient, but prepubertal acne and acne cosmetica may be particularly well suited to a dermocosmetic approach. More severe acne may need a dermocosmetic added if there is sensitive skin or poor tolerance to prescription medications, and when the patient or family does not wish to use antibiotics or other acne prescription treatments. Dermocosmetics may be used as adjuncts to any type of prescription therapy, but may be most effective when used with products associated with skin irritation such as topical retinoids or benzoyl peroxide. Appropriate dermocosmetics can also fortify the skin barrier and help to protect the skin microbiome.

CONCLUSIONS: Acne management is complex and there can be adherence, tolerability, and efficacy problems. Dermocosmetics alone can be used in milder forms of acne or in maintenance post treatment, as a good compromise between efficacy and tolerability. As adjuncts, dermocosmetics can also decrease skin irritation and thereby increase adherence, can enhance the efficacy of prescription therapies, and can normalize dysbiosis in acne.},
}

@article {pmid41766111,
year = {2026},
author = {Zhao, C and Ye, S and Chen, M and Qian, J and Xu, J},
title = {First-line immunotherapy for advanced HER2-negative gastric cancer: differences between Asian and non-Asian patients.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0398},
pmid = {41766111},
issn = {2095-3941},
support = {2024ZD0520600//Non-communicable Chronic Diseases-National Science and Technology Major Project/ ; },
abstract = {Emerging evidence suggests that the efficacy of immunotherapy in patients with advanced HER2-negative gastric cancer differs between Asian and non-Asian populations. This review examines potential factors contributing to these disparities, including differences in demographic and clinicopathologic characteristics, somatic mutations, molecular subtypes, tumor immunity, Helicobacter pylori (H. pylori) infection, dietary habits, and gut microbiome composition. These factors may serve as predictors of immunotherapy response in gastric cancer patients. For example, the prevalence of molecular subtypes and somatic mutations have been linked to variations in immunotherapy efficacy between Asian and non-Asian populations. In addition, differences in H. pylori infection rates, dietary habits, and gut microbiota composition may influence systemic immune responses, and consequently, immunotherapy outcomes. Understanding the factors contributing to these disparities in immunotherapy response is crucial for optimizing treatment strategies and improving outcomes for patients with gastric cancer. Further research into the mechanisms underlying racial and ethnic disparities in immunotherapy response is needed to identify potential biomarkers predictive of immunotherapy response in diverse patient populations.},
}

@article {pmid41766018,
year = {2026},
author = {You, Y and Peng, H and Gu, A and Liu, Y},
title = {High-throughput sequencing-based profiling of endophytic bacterial community composition and diversity in seeds of Yunnan cytoplasmic male-sterile rice.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {3},
pages = {},
pmid = {41766018},
issn = {1572-9699},
support = {Y20240210, QN2021105002L//the National Foreign Expert Program of China/ ; 20250484961, 20220484220//the Beijing Nova Program/ ; FM2025-09//the Opening Project of Food Microbiology Key Laboratory of Sichuan Province/ ; },
abstract = {As an important food crop in China, hybrid rice is of significant importance for national food security and supply. Cytoplasmic male-sterile (CMS) rice is a key component of hybrid rice technology, while plant endophytes, especially seed endophytes, play a crucial role in promoting plant growth and reproduction. Therefore, understanding the diversity and community structure of seed endophytes in CMS rice is essential for hybrid rice technology. However, relevant research in this area remains scarce. This study systematically analyzed the diversity and community structure characteristics of seed endophytic bacteria in 14 Yunnan CMS rice varieties (totaling 42 samples) based on Illumina NovaSeq 6000 high-throughput sequencing technology, aiming to elucidate the core microbial community structure and diversity. A total of 503 operational taxonomic units (OTUs) were identified. At the phylum level, the dominant microbial groups in all samples were Proteobacteria (relative abundance 91.53-99.95%). At the genus level, the core microbial community consisted of Pantoea (64.29-93.11%), Xanthomonas (1.08-16.97%), and Kosakonia (0.46-12.66%). Both α- and β-diversity analyses revealed no significant inter-line differentiation, indicating a highly stable and conserved endophytic bacterial community across the Yunnan CMS rice germplasm. This study provides the first comprehensive characterization of the seed-associated core microbiome of Yunnan CMS rice lines.},
}

@article {pmid41765557,
year = {2026},
author = {Wang, M and Zhao, J and Gao, J and Cai, S and Gu, Y and Liu, Y and Gao, L and Xu, Y and Wu, Y and Zhou, Z and Zhang, J and Tian, W},
title = {Deciphering the potential of Bacillus cereus HS-9 in cadmium bioremediation and ensuring rice safety.},
journal = {Journal of environmental sciences (China)},
volume = {162},
number = {},
pages = {573-583},
doi = {10.1016/j.jes.2025.05.044},
pmid = {41765557},
issn = {1001-0742},
abstract = {Cadmium (Cd) contamination in agricultural soils poses significant environmental and health risks due to its non-degradable and bio-magnifying nature. With the global imperative for eco-friendly Cd remediation strategies, microbial bioremediation emerges as a promising approach. Here, Bacillus cereus HS-9 was isolated from Cd-contaminated paddy soil using LB medium supplemented with 5 mg/L of Cd. HS-9 exhibited an impressive Cd removal efficiency of 95.44 % at a concentration of 5 mg/L. A rice pot experiment was conducted using Cd-contaminated soil, with HS-9 inoculation as the treatment group and non-inoculated soil as the control. The treatment group resulted in a 38.99 % reduction in soil Cd availability and a 34.33 % decrease in rice Cd content without affecting rice yield. The microbial community of the rice rhizosphere was analyzed using metagenome sequencing. The results revealed an increased abundance of czcA, frnE, and irlS genes in the soil microbiome, indicating enhanced Cd resistance and efflux capabilities. Microbial community showed significant shifts towards a beneficial microbial consortium, particularly marked by increases in Lysobacter and Sphingomonas genera which are known for their roles in heavy metal resistance and bioremediation. B. cereus HS-9 demonstrated significant potential for the bioremediation of Cd-contaminated soil. This study provides foundation for the development of microbial-based strategies for the eco-friendly remediation of heavy metal-polluted agricultural lands.},
}

@article {pmid41765175,
year = {2026},
author = {Clarke, BC and Ordinola-Zapata, R and Noblett, WC and Gould, M and Staley, C},
title = {Taxonomy and Virulence Factors in the Root Canal Microbiome: Metagenomic Insights by Lesion Size and Clinical Factors in Primary Endodontic Infections.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.02.016},
pmid = {41765175},
issn = {1878-3554},
abstract = {INTRODUCTION: This study aimed to investigate the taxonomic and functional profiles of the root canal microbiome in teeth with large versus small periapical lesions, examining the influence of clinical variables on microbial composition and functional pathways.

METHODS: Samples from 25 teeth with large (>8mm) and 20 with small periapical lesions (<2mm) were analyzed. Quantitative PCR, 16S next-generation and whole genome sequencing (WGS) were used to assess microbial load, diversity, and composition. Functional predictions were performed using the KEGG and MetaCyc databases. Alpha diversity was calculated using Shannon and Chao1 indices. Beta diversity was assessed using ANOSIM and PERMANOVA. Significant variables were explored using MaAsLin3. Kruskal-Wallis tests were used for univariate comparisons.

RESULTS: Teeth with large lesions exhibited significantly higher bacterial load (p = 0.011), but comparable alpha diversity and number of species per group in 16S and Whole genome analysis (P > 0.05). Lesion size showed significance by ANOSIM (p = 0.04) but not in PERMANOVA (p = 0.36). Age was significant in both beta diversity tests, but the effect size only explained 3.6% of the variance. All clinical variables were not significant in 16S analysis for beta diversity. MetaCyc pathway analysis identified percussion sensitivity as the most influential clinical variable in both tests (ANOSIM R = 0.182, p = 0.012; PERMANOVA R[2] = 0.063, p = 0.046). MaAsLin3 modeling revealed enrichment of enzymatic pathways involved in methionine and cysteine-related metabolism.

CONCLUSIONS: Large periapical lesions contain significantly higher bacterial load, but similar diversity compared to small lesions. Functional predictions suggest bacterial metabolic activity may contribute to mechanical allodynia in endodontic infections.},
}

@article {pmid41765047,
year = {2026},
author = {Himmerich, H and Keeler, JL and King, JA and Ehrlich, S and Kaufmann, LK and Bulik, CM and Cohen-Woods, S and Wade, T and Steiger, H and Booij, L and Monteleone, P and Cascino, G and Monteleone, AM and Cuntz, U and Voderholzer, U and Tessema, SA and Lewis, YD and Sjögren, M and Hebebrand, J and Seitz, J and Tyszkiewicz-Nwafor, M and Karpenko, O and Mutwalli, H and Fetissov, SO and Mack, I and Dhopatkar, N and Mörkl, S and Kan, C and Uribe, MM and Yoshiuchi, K and Abuobeid, N and Kapogiannis, D and Stein, D and Bektas, S and Müller, DJ and Gorwood, P and Duriez, P and Montcel, CTD and Paszyńska, E and McElroy, SL and Wranik, WD and Fernandez-Aranda, F and Mehler, PS and Papežová, H and Roubalová, R and Procházková, P and Morris, R and Lewczuk, P and Hiemke, C and Berk, M and Karwautz, A and Treasure, J and Kasper, S and , and , },
title = {World Federation of Societies of Biological Psychiatry (WFSBP) consensus statement on candidate biomarkers for anorexia nervosa.},
journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry},
volume = {},
number = {},
pages = {1-92},
doi = {10.1080/15622975.2026.2626934},
pmid = {41765047},
issn = {1814-1412},
abstract = {OBJECTIVES: This World Federation of Societies of Biological Psychiatry (WFSBP) consensus paper aims to summarise and evaluate the published study results on objectively measurable biological markers associated with anorexia nervosa (AN).

METHODS: The relevant literature was reviewed by the WFSBP Task Forces on Eating Disorders and on Biological Markers, and a consensus regarding the significance of the published evidence was reached.

RESULTS: Candidate biological markers that have been associated with AN include clinical (e.g. body weight), molecular (e.g. genetic, epigenetic, hormonal, immunological, metabolomic), cellular (e.g. leukocytes), neuroimaging (e.g. structure, function, connectivity), digital, cardiac and neurophysiological parameters. Some clinical and laboratory parameters are risk markers in clinical practice. Biological markers have pathophysiological relevance in understanding the biological and metabolic pathophysiology of AN and its physical health consequences. Few studies have examined pharmacogenetics or therapeutic drug monitoring as tools to monitor and guide the treatment of AN.

CONCLUSIONS: Biological markers will hopefully soon enable clinicians to intervene earlier in a more targeted manner to mitigate treatment resistance. However, the current scientific basis for most biological markers are group comparisons only. Studies on sensitivity, specificity and the prognostic value of these markers are lacking.},
}

@article {pmid41764962,
year = {2026},
author = {Kong, J and Han, C and Shao, G and Feng, K and Song, C and Xie, Q},
title = {Virulence attenuation of intestinal pathogenicity via combined gene deletion in duck enteritis vaccine strain restores gut microbiota balance and enhances safety.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106633},
doi = {10.1016/j.psj.2026.106633},
pmid = {41764962},
issn = {1525-3171},
abstract = {There is an increasing need for a new generation of effective and safe vaccines, in the context of large-scale poultry farming and the prevalence of infectious diseases. With this in mind, we developed, for the first time, a duck enteritis virus (DEV) mutant, ΔTK-ΔgI/gE-ΔgG/gJ, through the deletion of multiple virulence genes. The resulting gene-deletion strain exhibited replication kinetics similar to those of the parent strain and was found to be safe in various animal models, offering a strategy for rapidly generating attenuated DEV strains. Previously, our team reported that DEV infection leads to intestinal dysbiosis; however, the impact of DEV vaccines on the gut microbiota remains unclear. This study aimed to characterize the gut microbiota of ducks, chicks, and mice immunized with DEV strains using microbiome analysis, assess the effects on microbial composition, and compare the outcomes. Both two strains caused significant shifts in gut microbiota diversity. Both strains restored the diversity of the microbiota, whereas the parental vaccine caused the enrichment of potential pathogens in chicks. Moreover, the conventional DEV vaccine disrupted gut microbiota and morphology, but the gene-deleted strain largely reversed these changes. These findings may improve the safety of vaccine through gene editing, thereby enhancing the protection of target animals.},
}

@article {pmid41764831,
year = {2026},
author = {Peng, X and Zhang, L},
title = {Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {2},
pages = {117321},
doi = {10.1016/j.diagmicrobio.2026.117321},
pmid = {41764831},
issn = {1879-0070},
abstract = {Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagnostic methods such as culture, PCR, and immunological assays are widely used, they are limited by long processing times, narrow detection scopes, and poor capability for identifying unknown pathogens. untargeted shotgun metagenomic sequencing (mNGS), as a non-targeted, high-throughput detection technology, enables broad-spectrum identification of diverse microorganisms and functional gene annotation, making it an increasingly important complement in infectious disease diagnostics. This review summarizes the clinical value of mNGS in key scenarios such as neurological, respiratory, and bloodstream infections. It also discusses its utility in antimicrobial resistance (AMR) monitoring and personalized therapy, highlights current challenges in sensitivity, bioinformatics analysis, and result interpretation, and briefly explores future directions involving artificial intelligence (AI), multi-omics integration, and healthcare information system integration. The goal is to provide a reference for the standardized application of mNGS in infectious disease diagnosis and treatment.},
}

@article {pmid41764596,
year = {2026},
author = {Yao, W and Du, H and Kulyar, MF and Pan, H and Ren, H and Luo, Q and Bhutta, ZA and Liu, S and Fang, R and Li, J},
title = {Probiotic efficacy of Bacillus amyloliquefaciens TL106 from Tibetan pigs in metabolic syndrome: modulation of gut microbiota and metabolic in sows and suckling piglets.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02328-y},
pmid = {41764596},
issn = {2049-2618},
abstract = {BACKGROUND: Metabolic syndrome disrupts metabolic resilience in periparturient sows and compromises piglet growth. As intestinal microbes govern host energy homeostasis, microbiome-directed feed additives represent a practical solution. We therefore evaluated the Tibetan‑pig isolate Bacillus amyloliquefaciens TL106, previously validated in weanlings for its capacity to alleviate sow-associated metabolic syndrome.

RESULTS: In a 43‑day trial (20 sows per group), dietary TL106 (5 × 10[9] CFU kg[-1]) increased digestibility of crude fiber (+ 12.5%, p < 0.05) and crude fat (+ 9.3%, p < 0.01), lowered serum IL‑1β (- 34%) and TNF‑α (- 28%), and boosted antioxidant enzymes and immunoglobulins (all p < 0.05). Litter performance improved, with a two‑thirds reduction in diarrhea and heavier piglets at 21 days (+ 15%, aggregate n = 300). Multi‑omics profiling revealed higher cecal α‑diversity, enrichment of butyrate‑producing Ruminococcus and Butyricicoccus (log2C 2.1 and 1.8; FDR < 0.05), and activation of histidine‑metabolism and ABC‑transporter pathways (q ≤ 0.03) in piglets, while pathways for amino‑acid biosynthesis, lipid utilization, and steroidogenesis were favored in sows.

CONCLUSIONS: Bacillus amyloliquefaciens TL106 simultaneously enhanced maternal metabolic health and neonatal development by reshaping gut microbiota and host metabolism, positioning it as a micro‑ecological tool for managing metabolic syndrome in Landrace × Yorkshire sows and Duroc × Landrace × Yorkshire suckling piglets. Video Abstract.},
}

@article {pmid41764594,
year = {2026},
author = {Geng, M and Zheng, Y and Tang, S and Fang, Z and Wang, T and Li, K and Chen, H and Zhang, J and Zhou, N and Wei, X and Yang, J},
title = {Gut T cell-microbiota crosstalk orchestrates antibacterial immunity and mucosal homeostasis in teleost.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02370-4},
pmid = {41764594},
issn = {2049-2618},
support = {2025T180854//China Postdoctoral Science Foundation/ ; 24ZR1419700//Natural Science Foundation of Shanghai Municipality/ ; 32373165//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: T cells cooperate with the intestinal microbiota to coordinate antimicrobial defense, but whether this crosstalk arose as an independent innovation in mammals or represents an evolutionarily conserved feature of vertebrate immunity remains unknown.

RESULTS: Using the teleost Nile tilapia as a model, we demonstrate that both systemic and localized infection with Edwardsiella piscicida induce enteritis, correlated with robust intestinal T cell responses. Selective T cell depletion triggered excessive expression of proinflammatory cytokines, impaired mucosal architecture, and diminished host resistance to infection, underscoring the essential role of T cells in gut immunity. Strikingly, T cell depletion also caused profound alterations in gut microbial composition, characterized by a sharp decline in beneficial taxa such as Cetobacterium and the expansion of opportunistic pathogens including Klebsiella and Acinetobacter, indicating that T cells are required to maintain microbiome homeostasis. Conversely, broad-spectrum antibiotic eradication of the microbiota provoked hyperproliferation of intestinal T cells and barrier disruption, revealing reciprocal regulation between T cells and commensals. From the gut content, we isolated a C. somerae strain SH518, whose dietary supplementation for 6-8 weeks enhanced the activation, proliferation, and effector function of intestinal T cells, preserved mucosal homeostasis during E. piscicida challenge, and even boosted systemic T cell immunity in the spleen.

CONCLUSIONS: Collectively, these findings demonstrate that teleost T cells engage in bidirectional interactions with gut microbiota to orchestrate both antimicrobial defense and mucosal homeostasis. We therefore propose that T cell-microbiota cooperation represents an evolutionarily ancient strategy predates terrestrial adaptation, offering new insights into the coevolution of mucosal T cell immunity and microbiome. Video Abstract.},
}

@article {pmid41764576,
year = {2026},
author = {Li, J and Ren, J and Xu, J and He, J and Xu, J and Yin, Q and Yao, J and Wu, S},
title = {Ability of the Chinese herbal residue to alleviate short-distance transportation stress in sheep through the remodeling of the rumen microbiome-metabolism axis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41764576},
issn = {1674-9782},
support = {2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 32573272//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
abstract = {BACKGROUND: Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota‒metabolism axis.

RESULTS: Twenty first-lambing East Friesian × Hu sheep hybrids weighing 54.49 ± 7.94 kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet + 50 g/d CMR) feeding at 4 h after approximately 300 km of short-distance transport. Results indicated that 4 h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, α-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.

CONCLUSION: This study confirmed that 4 h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.},
}

@article {pmid41764274,
year = {2026},
author = {ElNaggar, S and Chen, WC and Prodehl, LM and Marumo, TK and Khan, MU and Mathew, CG and Ruff, P and Jin, Z and Neugut, AI and Rustgi, AK and Uhlemann, AC and Korem, T and Abrams, JA},
title = {A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01468-y},
pmid = {41764274},
issn = {2730-664X},
abstract = {BACKGROUND: Esophageal squamous cell carcinoma (ESCC) has a poor prognosis and limited tools for early detection. Saliva is easily accessible and its microbiome composition can serve as a marker for upper gastrointestinal tract disease. This study aims to evaluate the potential of an oral microbiome signature for classifying ESCC.

METHODS: In a cross-sectional study of 48 ESCC patients and 110 controls from South Africa, a region with high ESCC incidence, we studied the potential utility of an oral microbiome signature for the disease. We built models using nested cross-validation to evaluate whether this signature is generalizable to held-out samples and further evaluated generalizability in studies from China, a distinct geographic region.

RESULTS: We find significant alterations in the oral microbiome in patients with ESCC including significantly reduced α diversity and increased abundance of Fusobacterium nucleatum. We also find that logistic regression models based on microbiome data can better classify ESCC in held-out samples (auROC=0.96) compared to clinical and demographic data (auROC = 0.69; DeLong p < 1 x 10[-8]). Lastly, we find that microbiome-based models trained across multiple studies can generalize well to geographically distinct studies.

CONCLUSIONS: Our results show that the oral microbiome in individuals with ESCC is distinct from controls and that this signal can generalize across unseen samples, suggesting the potential of saliva to serve as a non-invasive screening tool for ESCC.},
}

@article {pmid41764142,
year = {2026},
author = {Brayley, ODM and McCready, K and Liu, S and Convey, P and Chen, Y and Ullah, S and Teets, N and Hayward, SAL},
title = {The Microbiome of an Invasive Antarctic insect, Eretmoptera Murphyi (Diptera: Chironomidae), and its Potential Role in Nutrient Cycling.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02706-5},
pmid = {41764142},
issn = {1432-184X},
support = {NE/S007350/1//NERC CENTA2/ ; NE/S007350/1//NERC CENTA2/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; OPP-1850988//National Science Foundation/ ; 700545//USDA National Institute of Food and Agriculture Hatch Project/ ; RF-2024-396/2//Leverhulme Research Fellowship/ ; },
}

@article {pmid41764137,
year = {2026},
author = {Zhao, S and Zou, Y and Wang, Z and Ye, L and Chen, Y and Cao, Z and Xu, X and Gao, A and Ying, X and Chen, M and Qin, K and Zhang, Y and Gu, W and Wang, J and Ning, G and Wang, W and Liu, R and Jin, J and Hong, J},
title = {Gut Microbiota and Bile Acid Profiles as Predictors of PCOS Remission: Findings from a Sleeve Gastrectomy Treatment Study.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {41764137},
issn = {1708-0428},
}

@article {pmid41764092,
year = {2026},
author = {Kurbanova, DI and Gurov, AV and Romanenko, SG and Pavlikhin, OG and Lesogorova, EV and Krasilnikova, EN and Zemlyanov, VA and Eliseev, OV and Teplykh, EA and Safyannikova, EA},
title = {[Features of the laryngeal mucosa microbiota in patients with chronic hyperplastic laryngitis (literature review)].},
journal = {Vestnik otorinolaringologii},
volume = {91},
number = {1},
pages = {64-69},
doi = {10.17116/otorino20269101164},
pmid = {41764092},
issn = {0042-4668},
abstract = {The literature review analyzed the data concerning studies of the microbiome of the laryngeal mucosa in patients with chronic hyperplastic laryngitis. It remains a matter of discussion whether the inflammatory process in the larynx is primary with subsequent dysbiosis and excessive growth of pathogenic microorganisms, or whether changes in the structure of the normal microbial landscape become an inducer of the disease. The article reflects the results of basic research on the role of bacterial, fungal, and viral pathogens detected on the mucous membrane of the larynx in patients with chronic hyperplastic laryngitis, conducted by Russian and foreign scientists using various technological approaches.},
}

@article {pmid41764036,
year = {2026},
author = {Salaün, C and Huré, M and Guérin, C and Bôle-Feysot, C and Valentin, A and Léon, F and Lenoir, S and do-Rego, JL and do-Rego, JC and Langlois, L and Ribet, D and Achamrah, N and Coëffier, M},
title = {Intestinal epithelial TLR4 knock out induces sex-specific effects on gut barrier and microbiome in an activity-based anorexia model.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2637316},
doi = {10.1080/19490976.2026.2637316},
pmid = {41764036},
issn = {1949-0984},
abstract = {The role of the microbiota‒gut‒brain axis in the pathophysiology of anorexia nervosa has emerged in recent decades. Increased expression of Toll-like receptor 4 (TLR4) has been reported in the intestinal epithelial cells (IEC) of activity-based anorexia (ABA) mice. The inducible TLR4 knockout in IEC (TLR4[IEC][-/-]) was subsequently associated with behavioral and energy balance changes in ABA mice. Our study aimed to assess the intestinal response to TLR4[IEC][-/-] in both male and female ABA mice by focusing on three components: inflammation, the gut barrier, and the gut microbiota composition. After 12 d of undernutrition with free wheel access, the colonic expression of 43 markers was measured by RT-qPCR. The gut microbiota composition was analyzed by Illumina sequencing of the 16S rRNA gene. First, TLR4[IEC][-/-] was associated with more marked alterations in male control mice compared to females. Indeed, a reduction in the mRNA expression of eight inflammatory factors, seven tight junction proteins and fecal calprotectin levels was observed in males. Control TLR4[IEC][-/-] females showed increased expression of four inflammatory markers and one target involved in the gut barrier. The levels of the Bacillota phylum and the Deltaproteobacteria class and their subdivisions, up to the Desulfovibrio genus, increased in the control TLR4[IEC][-/-] males compared to wt. In females, only an increase in the Alcaligenaceae genus, which ranks from the Betaproteobacteria phylum, was observed. Interestingly, in both males and females, these alterations were not observed in response to ABA model in TLR4[IEC][-/-] mice. Similarly, ABA increased Tjp1 expression and Lactobacillus abundance, both of which were decreased by TLR4[IEC][-/-]. Our study shows for the first time the impact of inducible TLR4[IEC][-/-] on the intestinal response. TLR4[IEC][-/-] induced sex-specific colonic alterations and changes in the gut microbiota, which disappeared after the ABA model. Further studies are warranted to decipher the underlying mechanisms.},
}

@article {pmid41763984,
year = {2026},
author = {Amirsultan, S and Odunayo, A},
title = {From Diagnosis to Resolution: A Practical Guide to Acute Diarrhea in Veterinary Patients.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cvsm.2025.12.003},
pmid = {41763984},
issn = {1878-1306},
abstract = {This review emphasizes that most cases of acute diarrhea (AD) in dogs and cats are self-limiting and primarily managed with supportive care, including hydration and nutrition. Diagnostic testing should be tailored to individual cases, focusing on ruling out systemic illness or infectious causes. Recent evidence advocates against routine antibiotic use in uncomplicated AD to prevent antimicrobial resistance and microbiome disruption. Instead, targeted therapy is reserved for systemic or bacterial infections. Additional treatments such as antiemetics and careful hygiene are discussed. Clinicians should prioritize supportive care and judicious diagnostics, adhering to antimicrobial stewardship principles to optimize patient outcomes and combat resistance.},
}

@article {pmid41763967,
year = {2026},
author = {Boix-Amorós, A and Bu, K and Blank, RB and Cantor, A and Gutiérrez-Casbas, A and Rodríguez-Lago, I and Marin-Jimenez, I and Sanz, J and Masmitja, JG and Trujillo, E and Muñoz, MC and Vivar, MLG and Carrillo, M and Hernández, MVH and Calvet, X and Salaet, MA and Romero, MI and García, AB and Pérez, S and Llorente, JFG and Gonzalez-Lama, Y and Argumánez, CM and Plaza, Z and Domínguez, M and Cañete, JD and Diaz-Gonzalez, JF and Scher, JU and Clemente, JC},
title = {Microbial signatures in psoriatic arthritis distinguish disease phenotypes and newly diagnosed inflammatory bowel disease independent of faecal calprotectin.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ard.2026.01.018},
pmid = {41763967},
issn = {1468-2060},
abstract = {OBJECTIVES: There is growing evidence of microbial involvement in immune-mediated inflammatory diseases, including psoriatic arthritis (PsA) and inflammatory bowel disease (IBD). However, it remains unclear whether different PsA phenotypes exhibit distinct microbial profiles. Furthermore, up to 4% of patients with PsA have comorbid IBD, which often remains undiagnosed. We hypothesised that the gut microbiome distinguishes PsA subphenotypes and serves as a biomarker of IBD in patients with PsA independent of faecal calprotectin (fCAL).

METHODS: We obtained samples from 192 patients with axial or peripheral PsA and no prior diagnosis of IBD enrolled in the EISER study. Patients with elevated fCAL and subclinical IBD symptoms underwent colonoscopy with intestinal biopsy. Stool samples were used to measure fCAL, and gut microbiome was characterised using shotgun metagenomics. Serum samples were used for cytokine profiling.

RESULTS: Axial PsA had lower alpha diversity and loss of several commensals compared with peripheral PsA, as well as a depletion of microbial biotin and arginine metabolism and higher levels of IL-23, IL-17F, and IL-8. Five subjects had newly diagnosed IBD which was characterised by a depletion of tryptophan and vitamin B6 metabolism. They also showed significant enrichment of several taxa compared to non-IBD and with a larger effect size than fCAL.

CONCLUSIONS: Our results identify a distinct microbiome and immune profile in axial PsA, with lower microbiome diversity, a depletion of commensals and protective microbial mechanisms, and higher levels of some proinflammatory cytokines. In patients with newly diagnosed IBD, we identified microbial taxa associated with the condition yet independent of fCAL, the current clinical standard.},
}

@article {pmid41763775,
year = {2026},
author = {Li, S and Liu, S and Yu, Y and Huang, X and Yang, M and Tian, L and Zhang, T and Liu, J and Li, Y and Du, Z},
title = {Bifunctional nanoparticles based on esterified hydroxypropyl β-cyclodextrin/quaternary ammonium chitosan for ulcerative colitis intervention.},
journal = {Food research international (Ottawa, Ont.)},
volume = {229},
number = {},
pages = {118450},
doi = {10.1016/j.foodres.2026.118450},
pmid = {41763775},
issn = {1873-7145},
abstract = {Developing oral nanoparticles (NPs) that combine anti-inflammatory effects with gut microbiome modulation enables an effective strategy for integrated ulcerative colitis (UC) therapy. Yet, the complex and dynamically evolving nature of the gastrointestinal milieu presents formidable challenges to the consistency and specificity of NP interventions. To address this challenge, this study designed and developed gastrointestinal microenvironment-adaptive NP via self-assembly, utilizing curcumin (Cur) for anti-inflammatory effects and anthocyanin (Cy) for microbiome regulation to achieve dual functional therapeutic outcomes. Employing the esterification strategy, hydroxypropyl-β-cyclodextrin (HPCD) was modified using citric acid (CA) and sulfonic acid (SA) to synthesize CACD (CA-modified HPCD) and SACD (SA-modified HPCD), respectively, which self-assembled in the presence of quaternary ammonium chitosan (HTCC), Cur, and Cy to yield NPs. NPs demonstrated high Cur encapsulation efficiency (EE) and encapsulation capacity (EC) across pH 2.0-7.0, highlighting their high gastrointestinal adaptability. In vivo experiments showed clear amelioration of colitis symptoms, including downregulation of pro-inflammatory cytokines and attenuation of tissue damage. HTCC-Cy-CACD-Cur NPs enriched Eubacterium siraeum_group and Prevotellaceae, HTCC-Cy-SACD-Cur NPs favored Peptococcus expansion, potentially contributing to improved immune regulation and attenuation of UC. These bifunctional NPs offer innovative UC therapy and precision nutrition interventions.},
}

@article {pmid41763459,
year = {2026},
author = {Xu, X and Wei, X and Yang, X and Lin, S},
title = {Inflammaging in Geriatric Liver Disease: Mechanistic Insights and Therapeutic Frontiers.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112165},
doi = {10.1016/j.mad.2026.112165},
pmid = {41763459},
issn = {1872-6216},
abstract = {The rising prevalence of chronic liver disease in older adults necessitates a deeper understanding of the mechanisms driving hepatic vulnerability to aging. This review proposes a mechanistic framework positioning hepatic "inflammaging"-a chronic, low-grade inflammatory state-as a key driver of geriatric liver pathology. This review synthesizes evidence linking three interconnected processes: hepatocellular senescence, innate immune dysregulation, and gut-liver axis impairment. Senescent hepatocytes secrete senescence-associated secretory phenotype (SASP) factors that activate Kupffer and stellate cells, forming self-sustaining inflammatory loops. The NLRP3 inflammasome functions as a central integrator of stress and metabolic dysfunction, while age-related intestinal barrier decline continuously supplies inflammatory stimuli such as lipopolysaccharides. These converging pathways perpetuate a pathological hepatic microenvironment characterized by oxidative stress, fibrogenesis, and impaired regeneration. Emerging therapeutics-validated primarily in preclinical murine models-include senolytic CAR-T cells, inflammasome inhibitors, and microbiome-targeted interventions, illustrating the translational potential of this paradigm. However, clinical validation in human cohorts remains a critical next step. This mechanistic framework redefines geriatric liver disease as an active, targetable pathology rather than a passive consequence of chronological aging, highlighting new avenues for precision therapies.},
}

@article {pmid41763351,
year = {2026},
author = {Murillo-Saich, JD and Mannochio-Russo, H and Sala-Climent, M and Argel, N and Quan, A and Hose, MK and Paz-Gonzalez, R and Akkati, M and Chang, E and Cutuk, A and Gentry, E and Coras, R and Lane, NE and Dorrestein, PC and Guma, M},
title = {Potential Role of Bile Acids as a Microbiome-Derived Mechanism in Synovitis of Knee Osteoarthritis Synovitis.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2026.02.011},
pmid = {41763351},
issn = {1522-9653},
abstract = {OBJECTIVE: To evaluate the relationship between bile acids (BAs) and synovitis in knee osteoarthritis (KOA).

METHODS: Radiographic KOA patients with complete datasets were included. WOMAC total and subscores were calculated. Synovitis was assessed by ultrasound or Krenn score. BAs were profiled in plasma (N=28) or synovial fluid (SF, N=29) using liquid chromatography-tandem mass spectrometry. OA synovial explants, OA fibroblast-like synoviocytes (FLS), and bone marrow-derived macrophages (BMDM) were used for in vitro experiments. Data analysis was performed using R and MetaboAnalyst.

RESULTS: Sixteen KOA participants had low-grade (0-1) and twelve had high-grade synovitis (2-3). Glycohyodeoxycholic acid (1.198 ± 0.983 vs. 1.954 ± 0.686, 0.76[95% CI: 0.04 to 1.89]) and lithocholic acid (0.19 ± 0.53 vs. 0.825 ± 0.866, 0.63[95% CI: 0.00 to 1.58]) were elevated in subjects with high-grade synovitis. LPS-binding protein (LBP) (rho = 0.58, p = 0.037, [95% CI: -0.807 to 0.46]) correlated with synovitis but only in obese participants (BMI ≥ 30). LBP, lithocholic acid, and glycohyodeoxycholic acid predicted high synovitis (92% sensitivity, 75% specificity, AUC = 0.875[95% CI: 0.99 to 1.05], p < 0.001). In SF, taurodeoxycholic and glycohyodeoxycholic acids correlated positively with WOMAC pain and stiffness subscores and the total WOMAC score. The BA receptors, TGR5 and LXR, were present in synovial tissue. In vitro, BAs reduced cytokine secretion in FLS and BMDM.

CONCLUSION: Detection of BAs and their receptors in synovial tissue, together with their modulatory effects on synovial cells, supports a potential biological role for BAs in KOA.},
}

@article {pmid41763194,
year = {2026},
author = {Chi, F and Han, S and Yilmaz, ÖH},
title = {Purified diets enable experimental rigor through compositional control in animal research.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2026.01.010},
pmid = {41763194},
issn = {1932-7420},
abstract = {Purified diets offer compositionally defined platforms that improve causal inference in nutrition studies. When aligned with the biological question, they enable targeted nutrient loss- and gain-of-function experiments, systematic lipid-source swaps, and the discovery of diet-microbiome-drug interactions. We recommend complementary validation in grain-based chow or human-relevant diets to maximize translational relevance.},
}

@article {pmid41762976,
year = {2026},
author = {Hao, D and Han, H and Li, D and Sun, Y and Wang, Y and Yan, H and Li, G and Liu, H and Li, B and Li, F and Liu, W},
title = {Lactobacillus salivarius SNK-6 improves egg quality, yolk nutrient composition, and yolk flavor profile in laying hens via modulation of tissue metabolites and Cecal microbiomes.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106649},
doi = {10.1016/j.psj.2026.106649},
pmid = {41762976},
issn = {1525-3171},
abstract = {This study aimed to investigate the effects of Lactobacillus salivarius SNK-6 (L.a-SNK-6) supplementation on the laying performance, egg quality and yolk nutrition composition, including amino acid (AAs), fatty acids, and flavor profile, of Wenshang Barred hens. A total of 432 healthy 40-week-old hens were randomly assigned to three groups with 6 replicates each: control group (CON), a group supplemented with 2.0 × 10[8] CFU/kg L.a-SNK-6 (T1), and a group supplemented with 2.0 × 10[9] CFU/kg L.a-SNK-6 (T2). Compared with the CON group, both the T1 and T2 groups showed a reduction in the broken egg rate and increases in serum alkaline phosphatase, calcium (Ca) and calcitonin levels (P < 0.05). These groups also exhibited higher Haugh unit, eggshell strength and eggshell Ca content (P < 0.05). Furthermore, egg yolks from the T1 and T2 groups contained higher levels of α-linolenic acid, and oleic acid than those of the CON group. Total AAs content in the egg yolks was markedly elevated in both T1 and T2 groups, particularly the glutamic acid and aspartic acid (P < 0.05). Twenty volatile compounds that differed significantly among the three groups were identified, including d-limonene and β-pinene. Metabolomic analyses revealed 326, 237, and 108 differential metabolites in plasma, liver, and cecal content, respectively, between the T1 and CON group. These metabolites were significantly enriched in the tryptophan metabolism (map00380) pathway in both plasma and cecal content. 16S rRNA sequencing indicated that cecal microbiome diversity and abundance were higher in T1 group compared with the CON group, although the differences were not statistically significant. Combined analysis showed seventy-five host metabolite-microbiota pairs were significantly correlated (P-adjust < 0.05). Collectively, L.a-SNK-6 supplementation modulated metabolites across multiple host tissues and the cecal microbiome, leading to improved egg quality, enhanced yolk nutrient composition, and alterations in yolk volatile compounds.},
}

@article {pmid41762973,
year = {2026},
author = {Vanderghinste, P and Bautil, A and Simmonds, SJ and Apajalahti, J and Bedford, MR and González-Ortiz, G and Courtin, CM},
title = {Extensive particle size reduction of wheat bran increases the broiler's caecal fermentative capacity, but not bran fermentability ex vivo.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106695},
doi = {10.1016/j.psj.2026.106695},
pmid = {41762973},
issn = {1525-3171},
abstract = {The inclusion of fibre-rich fractions such as wheat bran in broiler feed can increase the production of short-chain fatty acids (SCFA) in the broiler's gut, improving performance, gut health and immunity. Benefits of fine fibre additions (< 300 µm) on caecal fibre fermentation in broilers have been reported, but it is unclear if further reduction in bran particle size continues to stimulate caecal fermentation, and if the ideal particle size for such fermentation is driven by its effects in the gastrointestinal tract or by microbial size preference. To separate these effects, the caecal inocula of 198 Ross 308 male broilers (d 21 and d 35) which received a 0.5% dietary inclusion of 452 µm bran (WB452), 27 µm bran (WB27) or no bran (control) were combined with the same bran fractions in a 3 × 3 ex vivo fermentation simulation design (n = 8). Gas production, pH, SCFA, branched-chain fatty acid (BCFA) content and total bacteria count were measured to assess the effect of bran particle size on the fermentation of the added bran, the fermentative capacity of the bran-fed caecal inocula and their interaction. Both sizes of added bran increased SCFA content (P < 0.05) and lowered the pH (P < 0.05) and tended to increase SCFA-to-BCFA ratio (P < 0.10) and gas production (P < 0.10), while bran particle size had little effect on these parameters during the ex vivo fermentation. The size of the in vivo-fed bran altered the fermentative capacity of the caecal inocula, based on decreased total gas production (P = 0.010) and increased acetic acid content (P = 0.005) for the WB452-fed inoculum, in contrast to tendencies towards a higher total bacteria count (P = 0.075) and SCFA-to-BCFA ratio (P = 0.059) for the WB27-fed inoculum. This shows that bran size does not directly control microbial fermentation but mainly affects the fibre-fermenting capacity of the caecal inocula through its presence in vivo. The lack of an interaction effect between the bran additions and the bran-fed inocula indicates that bran size does not play a major role in priming the fibre-fermenting microbiome. These results highlight the importance of selecting fibre size in feed additions to stimulate broilers' caecal fibre-fermenting capacity.},
}

@article {pmid41762911,
year = {2026},
author = {Abdel Jaleel, GA and Ammar, NM and Shabaan, A and El Hotaby, W and Elshamy, AI and El-Gendy, ZA},
title = {Metabolite-rich Saccharomyces cerevisiae cell wall extract counter diabetic tissue damage via AMPK activation and microbiome modulation in rats.},
journal = {Tissue & cell},
volume = {101},
number = {},
pages = {103414},
doi = {10.1016/j.tice.2026.103414},
pmid = {41762911},
issn = {1532-3072},
abstract = {Saccharomyces cerevisiae cell wall extract (SCCWE) contains a variety of bioactive compounds, yet its antidiabetic action mechanisms remain unclear. The current work aimed to characterize the chemical components using GC-MS of SCCWE along with its antidiabetic, hepatoprotective, antioxidant, and microbiome-modulating properties in streptozotocin (STZ)-induced diabetic rats. The rats were treated with glibenclamide, SCCWE (25, 50, or 100 mg/kg), or non-diabetic normal rats as a control. Key regulators (P-AMPK, HMGR, SREBP-1c, and LXRα) as well as metabolic parameters, oxidative and inflammatory indicators, and histopathology and FTIR analysis were evaluated. Trehalose (16.03%), turanose (15.05%), glycerol (12.24%), and mannobiose (7.38%) were found to be the primary constituents by GC-MS profiling. STZ elevated fasting glucose 1.5-fold and reduced lactic acid bacteria 6.6-fold. SCCWE lowered glucose by 27.4-30.4% and restored lactic acid bacteria by 266.7-711.6%. Serum ALT, increased 2.1-fold in diabetic rats, decreased by 35.3-55.6% with SCCWE. Dyslipidemia improved markedly, with total lipids, cholesterol, and triglycerides reduced by up to 45.6%, 63.9%, and 46%. SCCWE decreased hepatic MDA by 56.5% and increased GSH up to 607.2%. It elevated P-AMPK while suppressing HMGR (18.9-154.6%), SREBP-1c (29.7-92.6%), and LXRα mRNA (21.3-87.6%). Histopathology and FTIR confirmed tissue and membrane restoration. SCCWE demonstrates potent antidiabetic and hepatoprotective activities, supporting its potential as a natural therapeutic for diabetes.},
}

@article {pmid41762838,
year = {2026},
author = {Li, D and Diao, Z and Shu, A and Gan, S and Zhang, W and Zhang, Y and Xiong, L and Wei, D and He, L and Shi, W and Sun, G and Yuan, F and Liu, Z and Gao, Z},
title = {Deinococcus sp. NH1 enhances cadmium tolerance in rice by modulating rhizosphere microbiome and plant metabolism.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141623},
doi = {10.1016/j.jhazmat.2026.141623},
pmid = {41762838},
issn = {1873-3336},
abstract = {Cadmium stress threatens rice safety and farmland management. To investigate the role of high‑cadmium‑tolerant Deinococcus in alleviating plant cadmium stress, this study identified a strain, Deinococcus sp. NH1, with highly cadmium-tolerant and growth-promoting potential, via 16S rRNA gene sequencing and whole-genome average nucleotide identity analysis. Under cadmium stress conditions, inoculation with NH1 significantly alleviated growth inhibition in rice, resulting in notable increases in plant height, fresh weight, and root density. In soil containing 10 mg/kg cadmium, NH1 inoculation downregulated originally elevated genes related to cadmium detoxification and stress response, while upregulating biosynthesis and energy metabolism genes. Cadmium reduced rhizobacterial diversity, but NH1 restored diversity and induced community restructuring, significantly enriching beneficial microorganisms, such as Massilia and Haliangium. At the metabolic level, NH1 treatment altered the rhizosphere metabolome, in which terpenoids, and shikimates and phenylpropanoids such as 5-O-methylembelin and linoleate that showed significant positive correlations with the enriched microorganisms may play key roles. In summary, NH1 enhances rice tolerance to cadmium stress by regulating host gene expression, restoring and reshaping the rhizosphere microbial community structure, and driving beneficial microbe‑metabolite interactions. This study offers new insights into plant-microbe interactions in heavy metal stress mitigation.},
}

@article {pmid41762502,
year = {2026},
author = {Lei, J and Wu, Z and Liu, Z and Yang, R and Cheng, L and Wang, J and Liu, Y and Chen, R},
title = {Predicting aerobic granular sludge structural instability: An intelligent early-warning framework integrating convolutional neural network and fluorescence fingerprint features.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129115},
doi = {10.1016/j.jenvman.2026.129115},
pmid = {41762502},
issn = {1095-8630},
abstract = {Aerobic granular sludge (AGS) was recognized as an innovative alternative superior to activated sludge processes, yet its development has been constrained by structural instability and the lack of early-warning methods for critical states. To address this limitation, an intelligent early-warning model (EPS-ResNet) based on multi-view convolutional neural networks was developed. This model achieved a 6±1-day advance prediction of AGS structural destabilization (accuracy:97.6%) by analyzing fluorescence characteristics in Excitation-Emission-Matrix Spectra (EEMs) of loosely/tightly bound extracellular polymeric substances (LB-EPS/TB-EPS). Through occlusion sensitivity analysis and fluorescence region segmentation, Region I (tyrosine-like proteins) of TB-EPS, Region IV (soluble microbial metabolites) of TB-EPS, and Region IV of LB-EPS were identified as the top three contributors to early-warning efficacy. Integrated microbiome analysis revealed that the superior early-warning performance of the model was primarily attributed to the capacity of key EEMs regions (I, IV, and V) of EPS to sensitively capture dynamic succession of dominant phyla and functional genera in AGS following shocks. Correlation analysis conducted through the Mantel test demonstrated that key dominant phyla responding to the model included Bacteroidota and Patescibacteria, while critical functional genera comprised Flavobacterium, Pseudazoarcus, Thauera, and Candidatus_Competibacter. An early-warning framework for abnormal states of AGS integrating scalability and mechanistic interpretation was developed in this study. This framework was demonstrated to be applicable not only for the early warning of AGS structural destabilization, but also extensible to the early detection of anomalies in biological treatment systems, thereby promoting the transformation of water treatment process operation and maintenance toward digitalization and intelligentization.},
}

@article {pmid41762333,
year = {2026},
author = {Pavan, JS and Deeksha, PM and Rajarushi, CN and Paschapur, AU and Rishika, KS and Ramakrishnan, B and Subramanian, S},
title = {Gut microbiota-mediated nitrogen recycling in the white Grub Holotrichia longipennis: A model for microbiome-targeted pest control.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41762333},
issn = {1573-0972},
}

@article {pmid41762294,
year = {2026},
author = {Joda, JF and Raji, RO and Nmadu, ME and Oyewole, OA},
title = {The Interactions of Emergent Contaminants (ECs) with Soil Microbiome.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {4},
pages = {},
pmid = {41762294},
issn = {1573-3017},
}

@article {pmid41762172,
year = {2026},
author = {Ghahari, AA and Nourizadeh, M and SalekShahabi, M and Davari, S and Mohammadzadeh Mounesyar, S},
title = {Psychobiotics and the microbiota-gut-brain axis: Emerging paradigms in mental health modulation.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP093301},
pmid = {41762172},
issn = {1469-445X},
abstract = {The global rise in mental health conditions has prompted interest in interventions that act beyond conventional psychopharmacology. Psychobiotics, broadly understood as live microorganisms or microbe-derived products that interact with the microbiota-gut-brain axis, have been suggested to exert neuroactive effects through neural, immune, endocrine and metabolic routes. This narrative review synthesizes recent preclinical, mechanistic and early clinical observations. Experimental studies show that selected strains can modulate cytokine signalling, influence stress-responsive systems such as the hypothalamic-pituitary-adrenal axis, and support synaptic plasticity via factors such as brain-derived neurotrophic factor. A limited number of human trials using well-characterized Lactobacillus and Bifidobacterium strains have reported improvements in affective and stress-related outcomes, but these effects are generally small to moderate, more apparent in adjunctive than stand-alone use, and dependent on strain, dose, population and intervention length (typically 4-12 weeks). Evidence on neurodevelopmental conditions (e.g., autism spectrum disorder, attention-deficit/hyperactivity disorder) remains preliminary, based on small and heterogeneous samples. Across studies, key constraints include methodological heterogeneity, incomplete strain-level reporting, and gaps in mechanistic resolution that make it difficult to link microbial shifts to psychiatric benefit. Emerging microbiome- and metabolomics-informed approaches may help identify likely responders and improve translational precision, but they are not yet ready for routine clinical application. Overall, psychobiotics should currently be viewed as a promising adjunct within integrative mental health care, warranting larger, standardized trials with clearly defined strains, doses and mechanistic endpoints.},
}

@article {pmid41762163,
year = {2026},
author = {Lu, Y and Nguyen, KN and Xia, J},
title = {Interpreting Microbiome Signatures with MicrobiomeNet.},
journal = {Current protocols},
volume = {6},
number = {3},
pages = {e70338},
pmid = {41762163},
issn = {2691-1299},
abstract = {MicrobiomeNet (https://microbiomenet.com) is a web-based platform developed to provide functional insights into microbiome signatures using genome-scale metabolic models (GEMs). It currently hosts 12,400 GEMs and around 6 million microbial signatures. Users can start by searching microbes, metabolites, genes, or enzymes, and perform common tasks such as to characterize the metabolic capacity for a given microbe, to explore known microbial associations, as well as to understand potential metabolic interactions. This book chapter provides practical, step-by-step instructions for navigating MicrobiomeNet to obtain functional insights into individual microbes or microbial association networks. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterizing the Metabolic Profile of a Microbe of Interest Basic Protocol 2: Elucidating Metabolic Interactions from Microbial Associations Basic Protocol 3: Analyzing Carbohydrate-Utilization Pathways to Explain Co-Responsive Taxa Basic Protocol 4: Identifying Novel Deoxycholic Acid-Producing Gut Microbes Basic Protocol 5: Assessing the Faecalibacterium prausnitzii-Coprococcus Relationship.},
}

@article {pmid41762159,
year = {2026},
author = {Zhang, Y and Liu, Q and Jing, L and Li, D},
title = {Suppressive microbiome protects against mulberry wilt by safeguarding host glycosylphosphatidylinositol-anchor biosynthesis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag060},
pmid = {41762159},
issn = {1365-2672},
abstract = {AIMS: Soil-borne pathogens pose a significant threat to global agriculture. While certain soils naturally suppress disease, the complex interplay between different microbial kingdoms and their metabolic functions in orchestrating this suppression remains poorly understood.

METHODS AND RESULTS: We integrated 16S/ITS/18S rRNA amplicon sequencing with non-targeted LC-MS/MS metabolomics to elucidate the multi-kingdom microbial drivers and metabolic profiles of rhizosphere soils from healthy (HS) and diseased (DS) mulberry (Morus alba L.) orchards. The HS orchard, under long-term organic fertilization, exhibited strong disease suppression (12% incidence), whereas the DS orchard, under chemical fertilization, was highly susceptible (85% incidence) to wilt disease. The HS soils harbored a more complex and stable microbial co-occurrence network. This community was significantly enriched in putative beneficial taxa, including the bacteria Stenotrophomonas and Pseudomonas, the fungus Mortierella, and the predatory protist Colpoda. In contrast, the pathogen Fusarium was enriched in DS soils. Functional profiling predicted that the HS microbiome possessed a higher potential for antibiotic biosynthesis and stress tolerance. Metabolomic analysis revealed a striking divergence in metabolic pathways. Diseased plants mounted a massive but ineffective defense, characterized by the accumulation of phytoalexins. We identified a significant downregulation of the glycosylphosphatidylinositol-anchor biosynthesis pathway in DS soils, a fundamental process for anchoring functional proteins to the plant cell surface.

CONCLUSIONS: Our findings reveal a novel pathogenic strategy of targeting host cell-surface architecture and the corresponding community-level defense mechanism.},
}

@article {pmid41761982,
year = {2026},
author = {Yan, L and Hu, J and Feng, Q and Sun, J and Huang, X and Xu, C},
title = {A Unique Perspective on Auto-reactive Antibody Production in Autoimmune Disease Induced by Microbiome.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {2},
pages = {45424},
doi = {10.31083/FBL45424},
pmid = {41761982},
issn = {2768-6698},
support = {2023-JC-QN-0855//Natural Science Basic Research Program of Shaanxi/ ; 2021JY-17//Shaanxi Provincial People's Hospital Science and Technology Talent Support Program Project/ ; },
abstract = {Activation of autoreactive lymphocytes leads to cellular and tissue damage, which results in the development of autoimmune diseases. External environmental changes, such as chronic microbial infections, can alter the immune homeostasis and disrupt the balance of autoreactive T and B cells. In this review, we first summarize immune tolerance mechanisms of T and B cells, and then describe the breakthroughs of immune tolerance in T and B cells, followed by related autoimmune diseases. Furthermore, we explore how microbial infections can induce the production of autoreactive antibodies via carrier effects when the balance of autoreactive T and B cells is disrupted. These kinds of antibodies can lead to autoimmune diseases through molecular mimicry mechanisms. Our perspective provides a theoretical framework and novel insights into the mechanism of autoreactive antibodies in the pathogenesis of autoimmune diseases associated with microbial infections. This analysis may offer novel directions for drug discovery of autoimmune diseases.},
}

@article {pmid41761881,
year = {2026},
author = {Jin, X and Luo, X and Shen, W and Lv, G and Jiang, X and Jin, C and Feng, B and Che, L and Xu, S and Lin, Y and Zhuo, Y and Wu, D and Hua, L},
title = {Nicotinamide Riboside Alleviates Heat Stress-Induced Intestinal Dysfunction by Enhancing Antioxidant Capacity, Restoring Immune Homeostasis, and Modulating Gut Microbiota in a Boar Model.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {5},
pages = {e70418},
doi = {10.1002/mnfr.70418},
pmid = {41761881},
issn = {1613-4133},
support = {2023YFD1300804/5//National Key R&D Program of China/ ; NCTIP XD/B04//Strategic Priority Research Program of the National Center of Technology Innovation for Pigs/ ; 32472948//National Natural Science Foundation of China/ ; U21A20255//National Natural Science Foundation of China/ ; 2023NSFSC1139//Sichuan Science and Technology Program/ ; CARS-35//earmarked fund for China Agriculture Research System/ ; },
abstract = {Heat stress (HS) induces adverse intestinal effects, including morphological damage, immune dysfunction, and microbial dysbiosis. Nicotinamide riboside (NR) supplementation has shown promise in protecting against intestinal injury. This study aimed to investigate the efficacy of NR in alleviating HS-induced intestinal damage in a porcine model. Eighteen boars were randomized into three groups (n = 6): control (CON, thermoneutral), heat stress (HS), and HS with NR supplementation (HS-NR). After an initial feeding phase, the HS and HS-NR groups were exposed to an HS environment (35 ± 1°C) for 2 weeks, while the CON group remained thermoneutral. Intestinal injury was assessed via histomorphology, biochemical parameters, transcriptomics, and microbiome sequencing. We found that NR supplementation significantly restored intestinal morphology and attenuated colonic oxidative stress compared to the HS group. Moreover, NR ameliorated HS-induced immune dysfunction and corrected gut microbial dysbiosis. These results suggest the therapeutic potential of NR as a nutritional intervention to mitigate HS-induced intestinal damage.},
}