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

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

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

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

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

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

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

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

PROSPERO: CRD42023433704.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid41969917,
year = {2026},
author = {Osuji, IE and Akanmu, AO and Babalola, OO},
title = {Leveraging Microbe-Rhizosphere Interactions in Organic Farming Systems: A Route to Sustainable Soybean Production.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {7},
number = {2},
pages = {e70147},
pmid = {41969917},
issn = {2575-6265},
abstract = {Soybean (Glycine max L.) is a major legume crop of global agricultural significance, and its yield is heavily dependent on the rhizospheric microbes. Conventional farming systems can enhance yields in the short term but often at the expense of soil health and biodiversity. Organic farming systems, by contrast, avoid the use of synthetic inputs and depend on microbial processes to achieve yield. This review aggregates peer-reviewed literature on organic soybean farming systems, drawing from a body of work that has characterized the diversity, composition, and functions of rhizospheric microbes in these systems. Organic amendments such as compost, manure, and biochar enhance the abundance of microbial communities in the rhizosphere of organic soybean crops, buffer soil pH, and improve soil structure. Organic soils have greater microbial biomass and functional activity than conventional soils, with increased populations of bacteria such as Bradyrhizobium, arbuscular mycorrhizal fungi, Trichoderma, Streptomyces, and phosphate-solubilizing bacteria. The rhizospheric microbes are responsible for processes such as nitrogen fixation, phosphorus acquisition, organic matter decomposition, and induced systemic resistance (ISR). Measures of soil health, such as microbial biomass, enzyme activity, respiration rates, and soil organic matter (SOM) content, all demonstrate that organic farming systems have greater ecological value than conventional systems. Organic soybean production systems foster distinct rhizosphere microbial assemblages that confer measurable functional benefits to the agroecosystem. Future research is required in microbiome engineering, biostimulant design for specific applications, biomarkers for monitoring changes in soil microbiology, and precision organic farming systems. This review demonstrates that microbe-rhizosphere interactions are a key factor to consider in the development of sustainable agricultural practices for soybean production.},
}

@article {pmid41970196,
year = {2026},
author = {Agache, I and Li, S and Zheng, Y and Gao, Y},
title = {Asthma endotypes and theratypes.},
journal = {Chinese medical journal pulmonary and critical care medicine},
volume = {4},
number = {1},
pages = {19-38},
pmid = {41970196},
issn = {2772-5588},
abstract = {The model of asthma as a single entity has now been replaced by a much more complex biological network of distinct and interrelating inflammatory and tissue driven pathways. Individual disease manifestations (phenotypes), pathogenetic pathways (endotypes) and response to therapy (theratypes) are discussed here in the context of current stratified management of asthma in the clinic based on biomarkers measured at the point-of-care. As the current classification criteria result in significant overlaps among phenotypes, endotypes and theratypes, this paper further describes the advantage of combining precision immunology, imaging and the digital biomarkers in an unbiased approach offered by machine learning. The new European Academy of Allergy and Clinical Immunology (EAACI) nomenclature for hypersensitivity reaction is detailed as a basis for the stratified asthma management with a special focus on tissue-driven mechanisms (type V asthma), metabolic/microbiome/epigenetic/neurogenic mechanisms (type VI asthma) and direct cellular activation (type VII asthma).},
}

@article {pmid41970284,
year = {2026},
author = {de Kreek, KA and Gols, R and de Zeeuw, JM and van Dam, I and Nijhof, R and Noordijk, BS and Dicke, M and Kloth, KJ},
title = {Caterpillar-induced plant-soil feedback affects resistance in wild and cultivated cabbage.},
journal = {Plant and soil},
volume = {520},
number = {2},
pages = {1721-1740},
pmid = {41970284},
issn = {0032-079X},
abstract = {BACKGROUND AND AIMS: Aboveground insect herbivory can change the plant rhizosphere and modulate the composition of the soil microbiome. However, it is unclear to what extent these changes in the rhizosphere affect plant resistance to above-ground herbivorous insects, and how these plant-soil feedback (PSF) mechanisms are shaped. Here, we investigated whether herbivore-induced changes in the rhizosphere increase resistance against caterpillars in cabbage, Brassica oleracea, and how intraspecific variation of the host plant, herbivory intensity, and soil type affect PSF outcomes.

METHODS: PSF experiments with rhizosphere-soil transfer were performed for a wild and cultivated B. oleracea, with different densities of the caterpillar Mamestra brassicae, and different soil types.

RESULTS: We found that caterpillar-induced soil conditioning affected the performance of M. brassicae feeding on the shoot, depending on both intraspecific variation of the host plant and the intensity and duration of herbivory. On wild cabbage, caterpillar-induced PSF positively affected plant resistance to M. brassicae, which needed more than two weeks to become detectable. In contrast, in cultivated cabbage, caterpillar-induced PSF had a neutral to negative effect on plant resistance and did not differ between soil types. The observed negative PSF effect was associated with downregulation of genes involved in jasmonic acid biosynthesis and downstream signalling.

CONCLUSION: Overall, we found that natural variation within one plant species can, depending on intensity and duration of herbivory, result in opposite PSF effects with consequences for jasmonic acid-mediated defences.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-026-08355-4.},
}

@article {pmid41970365,
year = {2026},
author = {Bradshaw, AJ and Poo, S and Malter, TE and Strasbaugh, RM and Bodner, B and Hincher, MR and Devan-Song, A and Tabima, JF},
title = {Characterization of a Core Fungal Community and Captivity-Induced Gut "Mycobiome" Change in Fowler's Toad (Anaxyrus fowleri).},
journal = {Ecology and evolution},
volume = {16},
number = {4},
pages = {e73430},
pmid = {41970365},
issn = {2045-7758},
abstract = {Amphibious animals, such as frogs, are found at the intersection of aquatic and terrestrial ecosystems. They may serve as keystone and sentinel species and play key roles in nutrient cycling and food webs. In recent decades, amphibians have experienced drastic population declines due to habitat loss, climate change, and disease. These declines have prompted investments in ex situ conservation and captive breeding programs, which aim to reduce extinction risk by creating assurance colonies and reintroducing individuals once threats are mitigated. A critical component of these programs is proper husbandry, which ensures the health and longevity of captive populations and their ability to produce offspring that can be reintroduced into the wild. The artificial environment in captivity can profoundly impact animal behavior and health, particularly in relation to diet and nutrition. Diet not only provides nutrients and energy but also shapes the host's gut microbial community, which in turn impacts digestive health. Complex microbial communities, collectively known as the microbiome, are characterized by a high diversity of prokaryotes, microscopic fungi, and viruses. The diet-associated microbiome is increasingly studied for its role in captive animal health and behavior, although research has focused more on bacteria than fungal communities, or the "mycobiome". Here, we investigated the core mycobiome using metabarcoding of fungal communities in 15 wild-caught Anaxyrus fowleri (Fowler's Toad), documenting shifts as toads transitioned from wild to captive settings. We identified a core set of fungal taxa and observed distinct changes in non-core fungi associated with dietary differences associated with captivity. The non-core mycobiome exhibited an ecological guild functional shift of the saprotrophic dominance relative to wild individuals, indicating large losses in both mycobiome diversity and functionality. These findings highlight the dynamic nature of the amphibian mycobiome and the dramatic impact captivity can have on microbial composition, providing a framework for understanding the role of the amphibian mycobiome in future conservation efforts.},
}

@article {pmid41970731,
year = {2026},
author = {Kishore, MM and Jeyaraman, M and Jeyaraman, N and Nallakumarasamy, A and Bharadwaj, S},
title = {Implications of Gut Microbiome in Fibromyalgia: A Scoping Review.},
journal = {Journal of orthopaedic case reports},
volume = {16},
number = {4},
pages = {420-425},
pmid = {41970731},
issn = {2250-0685},
abstract = {INTRODUCTION: Fibromyalgia (FM) is a chronic pain syndrome marked by widespread musculoskeletal pain, fatigue, sleep disturbances, and cognitive dysfunction. Despite extensive research, its pathophysiology remains unclear. Emerging evidence implicates the gut microbiome (GMB) in FM through mechanisms involving pain modulation, immune dysregulation, and neuroinflammation. This review explores the role of gut dysbiosis in FM pathogenesis, focusing on microbial alterations, immune interactions, intestinal permeability, and neurochemical pathways.

MATERIALS AND METHODS: A systematic search of PubMed, Scopus, and Web of Science was conducted to identify studies published in the last two decades examining the relationship between GMB and FM. Inclusion criteria encompassed original research, systematic reviews, and meta-analyses addressing microbial dysbiosis, immune modulation, and neurochemical alterations in FM. Studies focused solely on treatment interventions were excluded. A narrative synthesis approach was used to integrate findings and highlight mechanistic insights.

RESULTS: FM patients exhibit significant gut microbial dysbiosis, including reduced butyrate-producing bacteria and increased pro-inflammatory species. These alterations are associated with compromised intestinal barrier integrity, systemic immune activation, and elevated pro-inflammatory cytokines. Neurochemical disruptions include serotonin deficiency, gamma-aminobutyric acid/glutamate imbalance, and reduced short-chain fatty acids, contributing to central sensitization and neuroinflammation. Dysregulation of the gut-brain axis and microbial metabolite pathways further exacerbate FM symptoms.

CONCLUSION: GMB dysbiosis plays a pivotal role in FM pathogenesis through immune activation, intestinal permeability changes, and neurochemical modulation. Understanding these mechanisms may inform future research into microbiome-based biomarkers and therapeutic strategies. While treatment implications are beyond the scope of this review, the findings underscore the potential of targeting microbial pathways in FM management.},
}

@article {pmid41970986,
year = {2026},
author = {Soto, EK and Wagner, V and Engl, J and Mederer, M and Cibulkova, V and Piater, J and Schäfer, B and Dunzendorfer, E and Waschina, S and Kaser, S and Aden, K and Trajanoski, Z and Tilg, H and Effenberger, M},
title = {Escherichia-Shigella expansion and metabolite dysregulation in type 3c diabetes: linking microbiome alterations to exocrine pancreatic insufficiency.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1786756},
pmid = {41970986},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Exocrine Pancreatic Insufficiency/microbiology/metabolism ; Male ; Female ; Adult ; Middle Aged ; *Escherichia ; *Diabetes Mellitus, Type 1/microbiology/metabolism ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; },
abstract = {Emerging evidence supports a bidirectional gut-pancreas axis in which microbial dysbiosis, barrier dysfunction, and altered metabolite fluxes contribute to pancreatogenic diabetes (T3cDM). Whether gut microbial changes reflect systemic metabolic disturbances or primarily arise from exocrine pancreatic insufficiency (EPI) remains unclear. We profiled the gut microbiome of 48 outpatients with T3cDM, type 1 diabetes (T1DM), and healthy controls. Genus-level 16S rRNA data were analyzed using cross-validated LASSO logistic regression and patient-specific community metabolic models. T3cDM showed reduced α-diversity and distinct β-diversity compared with T1DM and controls. Key compositional shifts included enrichment of Enterobacteriaceae (notably Escherichia-Shigella) and Streptococcaceae in T3cDM. LASSO models discriminated T3cDM from T1DM (AUC 0.867; accuracy 0.818), highlighting Blautia, Escherichia-Shigella, Streptococcus, Clostridium, and Faecalibacterium as predictors. Metabolic modelling indicated elevated Escherichia-Shigella growth in T3cDM and disease-specific metabolite fluxes. Gut microbial shifts in T3cDM predominantly reflect EPI rather than systemic metabolic disturbances characteristic of T1DM, underscoring the central role of exocrine pancreatic dysfunction in shaping the gut microbiome and its metabolic activity.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Exocrine Pancreatic Insufficiency/microbiology/metabolism
Male
Female
Adult
Middle Aged
*Escherichia
*Diabetes Mellitus, Type 1/microbiology/metabolism
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Case-Control Studies

@article {pmid41971172,
year = {2026},
author = {Prasert, W and Akrimajirachoote, N and Pattarapanawan, M and Kovitvadhi, A and Phuengjayaem, S and Qin, H and Li, BZ and Soontorngun, N and Lansubsakul, N and Areerat, S and Kotatha, D},
title = {Enhancing the resistant starch content of cassava starch via heat-moisture treatment for application as a prebiotic in chicken feed.},
journal = {Veterinary and animal science},
volume = {32},
number = {},
pages = {100630},
pmid = {41971172},
issn = {2451-943X},
abstract = {This study aimed to increase the resistant starch (RS) content of cassava starch via heat-moisture treatment (HMT) and evaluate its prebiotic potential in chicken feed. The HMT involved autoclaving cassava starch at 20% moisture content and 121°C for 1 h (HMT-20), which yielded a high RS content (20.7%) in the cooked starch. In vitro fermentation with Limosilactobacillus reuteri TBRC291 demonstrated the promising prebiotic potential of cooked HMT-20, comparable to that of commercial fructo-oligosaccharides, as indicated by enhanced bacterial growth, reduced pH, and increased short-chain fatty acid (SCFA) production. A 1% concentration of cooked HMT-20 was identified as optimal for prebiotic use. In the in vivo assessment, chickens were given feed supplemented with 1% cooked HMT-20 (HMT-Feed), displaying no adverse effects on growth performance over 35 days and significantly reducing relative abdominal fat and heart weight while increasing breast weight. Meat from the HMT-Feed group also exhibited increased yellowness and reduced cooking loss. Histological analysis revealed an improved intestinal morphology, including a greater villus height, reduced crypt depth, and higher villus-to-crypt ratio. Additionally, the HMT-Feed group exhibited a lower cecal pH and higher SCFA levels (notably butyric acid). Deep gut microbiota profiling revealed enriched levels of lactic acid- and butyrate-producing bacteria, indicating improved gut health. The HMT-modified product demonstrates potential applicability as a value-added and sustainable feed additive in the poultry industry.},
}

@article {pmid41971184,
year = {2026},
author = {Ono, Y and Ota, H and Ogi, M and Fukushi, Y and Wada, S and Arase, H and Yoshino, O and Yamada, H},
title = {Uterine Endometrial Microbiome and Chronic Endometritis in Relation to Anti-β2-Glycoprotein I (β2GPI)/Human Leukocyte Antigen (HLA)-DR Autoantibodies in Women With Recurrent Implantation Failure and Recurrent Pregnancy Loss: A Cross-Sectional Study.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70049},
pmid = {41971184},
issn = {1445-5781},
abstract = {BACKGROUND: Anti-β2GPI/HLA-DR autoantibodies may be involved in recurrent implantation failure (RIF) and recurrent pregnancy loss (RPL). We examined their association with the endometrial microbiome and chronic endometritis (CE).

METHODS: In this cross-sectional study, 141 women (54 RIF, 87 RPL) were enrolled. Serum anti-β2GPI/HLA-DR positivity was defined using 99th/95th percentile cut-offs. Endometrial microbiome was assessed by 16S rRNA sequencing, focusing on reproductive-failure-related species (Gardnerella, Prevotella, Atopobium, Dialister, Anaerococcus, Ureaplasma, Mycoplasma). Microbiome and CE were compared by antibody status in RIF and RPL.

RESULTS: In RIF, antibody-positive women more frequently had Lactobacillus iners (99‰ and 95‰ cut-offs: 71.4% vs. 23.4%, p = 0.03; and 70.0% vs. 20.5%, p = 0.026) and reproductive-failure-related bacterial species (99‰: 100% vs. 51.1%, p = 0.016; 95‰: 90.0% vs. 52.3%, p = 0.032). In multivariable analysis with 95‰ cut-off, Lactobacillus iners (OR 13.1, p = 0.003) and reproductive-failure-related species (OR 9.64, p = 0.029) were independently associated with antibody positivity. In RPL, Anaerococcus was more frequent in antibody-positive women. CE frequency did not differ by antibody status in RIF or RPL.

CONCLUSION: Anti-β2GPI/HLA-DR antibody positivity was associated with endometrial dysbiosis and may serve as a biomarker of abnormal intrauterine environment in reproductive failure.},
}

@article {pmid41971315,
year = {2026},
author = {Cosma, BM and Abeel, T},
title = {A conserved bacterial signature characterizes plant microbiome responses to drought.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768028},
pmid = {41971315},
issn = {1664-302X},
abstract = {INTRODUCTION: Plant-associated microbes contribute to host resilience under stress, yet the extent to which microbial responses to drought generalize across hosts and environments remains unclear.

METHODS: Here, we performed a meta-analysis of 13 studies including more than 3,000 root and bulk soil samples from 52 plant hosts to identify bacterial taxa consistently affected by drought and link them to inoculation outcomes. Using a standardized processing workflow and differential abundance analysis, we derived a "drought signature" of taxa differentially abundant under water limitation across the endosphere, rhizosphere, and bulk soil.

RESULTS: The signature is dominated by Gram-positive Actinobacteria enriched under drought, including Kribella, and by Gram-negative taxa depleted under drought, such as Ramilbacter. Comparison with four independent inoculation experiments revealed limited overlap between drought and inoculation responses, with only Nitrospira depleted in both contexts.

DISCUSSION: Studies reporting improved plant performance under inoculation also exhibited stronger and more extensive microbial shifts, suggesting that the magnitude of community restructuring may be characteristic of successful inoculation outcomes. This work provides the fi rst genus-level meta-analysis of microbial responses under drought and inoculation, across hosts and experimental conditions, and delivers a unifi ed root and soil microbiome dataset.},
}

@article {pmid41971318,
year = {2026},
author = {Jin, L and Bian, X and Zhang, G and Zhu, J and Li, X and Yang, D},
title = {Combined polysaccharides from Angelica sinensis, Crataegus pinnatifida, Prunus persica, and Carthamus tinctorius attenuate cold exposure-induced bone loss by modulating the gut microbiota and fecal metabolites.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768890},
pmid = {41971318},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic cold stress is a significant risk factor for skeletal deterioration; however, effective therapeutic strategies targeting the underlying environmental-metabolic interactions remain unclear. This study investigated the osteoprotective potential of Mixed Polysaccharides (MPs) and elucidated the mediating role of the gut microbiome.

METHODS: Cold exposure-induced bone loss was established in rats. Fecal microbiota transplantation (FMT), 16S rRNA gene sequencing, and untargeted metabolomics was employed to illustrate the positive effect of MPs on the improvement of cold-exposed bone loss.

RESULTS: MPs treatment effectively reversed cold-induced trabecular microarchitecture deterioration and bone mass loss. In femoral tissue, MPs rebalanced skeletal turnover by upregulating osteogenic markers (Runx2, Osterix) and suppressing osteoclastogenic factors (TRAP, c-fos), concurrent with a marked reduction in the levels of pro-inflammatory cytokines TNF-α and IL-1β in femur. Furthermore, MPs restored intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Occludin), thereby mitigating the intestinal barrier impairment driven by cold stress. FMT experiments demonstrated that the osteoprotective effects of MPs are microbiota-dependent, as the transplantation of MPs-modulated microbiota recapitulated the bone-preserving and barrier-restoring phenotypes in recipient mice. Multi-omics integration identified that MPs selectively promoted the expansion of Lactobacillus intestinalis and the accumulation of cholylhistidine. Correlation analysis further revealed a strong link between the enrichment of these microbial and metabolic signatures, reduced pro-inflammatory cytokine levels, and improved bone formation.

CONCLUSION: Our findings indicate that MPs alleviate cold-stress-induced bone loss by remodeling the gut microbiota and metabolic profile, fortifying the intestinal barrier and decreasing pro-inflammatory cytokine.},
}

@article {pmid41971319,
year = {2026},
author = {Zhang, G and Altamimi, M and Shi, J and Lee, Y},
title = {Editorial: The interaction between food ingredients and gut microbiome on health and disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809622},
pmid = {41971319},
issn = {1664-302X},
}

@article {pmid41971320,
year = {2026},
author = {Wu, Y and Deng, L and He, X and Zhou, D and Ling, S and He, M and Wang, Q and Wang, C and Wang, M and Wu, H and Li, L and Li, D and Yun, L},
title = {Intestinal microbiome gone native: gut microbiome shift and resistome diversity in first homecoming giant panda family.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1737792},
pmid = {41971320},
issn = {1664-302X},
abstract = {INTRODUCTION: The world-famous giant pandas (Ailuropoda melanoleuca) often travel abroad for public exhibitions and international scientific cooperations. Previous research has reported alternations in the gut microbiome structure and enrichment of gut antibiotic-resistant genes (ARGs) in human international travelers, the latter of which is harmful to native residents and the environment. The microbiome and ARGs of these animal travelers, however, have not yet been investigated, even though they often interact with local keepers, visitors, and other pandas.

METHODS: In this study, we have clarified the dynamic microbiome composition and snapshot of ARGs (resistome) of the first panda family returning from overseas. Fecal samples were gathered for high-throughput sequencing for both amplicon and metagenomics sequencing, which were collected on the first day of their quarantine (Admission stage) and 3 days after the quarantine (Release stage). Feces from two native captive pandas were used as controls.

RESULTS AND DISCUSSION: The predominant Escherichia-Shigella proportion in the mother and father pandas decreased from 79.02 and 47.46% to 57.03 and 33.77%, while the Streptococcus abundance increased from 0.27 and 12.44% to 29.47 and 54.59%. The main genus of child pandas, Weissella, decreased from 45.24 to 0.02% after quarantine, and the Streptococcus ratio increased from 11.89 to 43.82%. Significant richness and bacterial diversities were found in these samples. The main ARG types are multidrug and polymyxin; the latter being an uncommon ARG in native pandas. Consequently, to protect local ecosystems from the introduction of novel ARGs, waste from translocated giant pandas should be managed under strict biosecurity protocols.},
}

@article {pmid41971323,
year = {2026},
author = {David, EM and Parthasarathi, T},
title = {Soil microbial processes shaping seed performance: linking soil microbiomes to sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797362},
pmid = {41971323},
issn = {1664-302X},
abstract = {Soil microorganisms are fundamental to soil sustainability, governing organic matter turnover, nutrient cycling, soil structure formation, and plant health regulation. In the context of accelerating soil degradation, climate change, and expanding agricultural salinization, understanding how soil microbial communities contribute to ecosystem resilience is crucial for sustainable soil management. Although rhizosphere and plant nutrition roles are well recognized, their influence across plant life cycles and generations remains insufficiently integrated. This Review synthesizes recent advances to propose the soil seed microbiome continuum as a unifying concept linking soil microbial processes to seed quality, early plant establishment, and crop stress tolerance under salinity stress. Unlike existing microbiome salinity reviews that predominantly focus on rhizosphere interactions or microbial inoculants under salt stress, this review advances an integrative soil seed continuum framework that connects soil ecological processes, microbial transmission, and seed associated microbiomes with a transgenerational context. We discuss how this ecosystem acts as a dynamic reservoir of beneficial and stress-adapted microorganisms that are selectively recruited by plants, transmitted through plant associated pathways, and ultimately incorporated into developing seeds. Under saline conditions, ecological filtering favors halotolerant microbial taxa that stabilize soil functions, and enhancing plant stress tolerance, with potential transgenerational benefits mediated through seed-associated microbiomes. The evidence from soil microbial ecology, plant microbe interactions, and emerging microbiome-enabled technologies, this review highlights the role of soil microorganisms as biological connectors between soil sustainability and crop performance. We further discuss implications for reduced chemical inputs, yield stability, nature-based restoration, and contributions to the United Nations Sustainable Development Goals. Positioning soil microorganisms within a soil seed continuum offers new perspectives for managing soil biodiversity and functionality, reinforcing their central role in sustainable agriculture and resilient soil ecosystems. This integrative perspective provides a strategic foundation for developing microbiome informed soil management approaches aimed at enhancing long term crop performance under increasing salinization and climate change.},
}

@article {pmid41971325,
year = {2026},
author = {Qi, L and Kang, H and Li, X and Wang, L and Lin, Y and Zhan, M and Zeng, F and Xiao, Z and Liu, X and Chen, Z and Liu, L},
title = {Multi-omics profiling implicates gut microbiota-sphingolipid interplay in the neuroprotective effects of semaglutide on diabetic cognitive impairment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705784},
pmid = {41971325},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome is a critical regulator of host health, but how it mediates the therapeutic effects of drugs targeting neurodegenerative diseases like diabetic cognitive impairment (DCI) is unclear. Here, we investigated whether the neuroprotective effects of the GLP-1 agonist semaglutide (SE) are linked to its modulation of the gut-brain axis.

METHODS: We used an integrative multi-omics approach in a mouse model of DCI. We combined fecal shotgun metagenomics and targeted bile acid profiling with cerebral proteomics and metabolomics to characterize the gut-brain crosstalk following a 12-week SE treatment. Animal behavior, neuronal survival and synaptic integrity were assessed to confirm therapeutic efficacy.

RESULTS: SE treatment reversed cognitive deficits, rescued hippocampal neuronal loss, and restored synaptic integrity in diabetic mice. At the ecosystem level, metagenomics revealed that SE treatment profoundly remodeled the gut microbiota, enhancing microbial α-diversity, enriched beneficial genera (Bacteroides, Barnesiella), and depleted the pro-inflammatory genus Desulfovibrio. This microbial shift was associated with normalized fecal and cerebral bile acid profiles. Mechanistically, our analysis implicated a dysregulated sphingolipid pathway in the DCI brain, characterized by the upregulation of the transporter ATP-binding cassette transporter A2 (ABCA2) and the enzymes sphingosine-1-phosphate phosphatase 1 (SGPP1) and ceramide synthase 2 (CERS2). SE treatment dynamically modulated this pathway: it downregulated ABCA2 in a potentially weight-independent manner and SGPP1 in a weight-dependent fashion, linked to the normalization of cerebral bile acid profiles. In contrast, CERS2, a robust marker of disease severity, was not altered by SE.

CONCLUSION: Our study uncovers a novel "gut microbiota-bile acid-sphingolipid" axis in DCI and suggests that SE acts via a dual mechanism. It drives a weight-dependent restoration of the gut-brain axis, normalizing microbial and bile acid profiles to regulate SGPP1, while also exerting weight-independent effects, potentially through direct modulation of targets like ABCA2. This work highlights the gut microbiome as a key component in the therapeutic action of SE and reveals the multifaceted nature of its neuroprotective effects.},
}

@article {pmid41971330,
year = {2026},
author = {Shuang, L and Ge, T and Hang, L and Wenjing, L and Jiang, X and Haoyu, H and Shuiming, X},
title = {Disease-induced changes in Panax ginseng phyllosphere fungal community assembly and functional adaptation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1740520},
pmid = {41971330},
issn = {1664-302X},
abstract = {INTRODUCTION: Phyllosphere microorganisms play essential roles in plant health and disease resistance, yet their responses to pathogen infections remain poorly understood. Panax ginseng is susceptible to multiple fungal diseases, which threaten its quality and yield. This study aimed to clarify the underlying disease resistance mechanisms of Panax ginseng by analyzing the phyllosphere fungal communities associated with fungal infections.

METHODS: Phyllosphere fungal communities of healthy Panax ginseng plants and those with three fungal infections (gray mold, damping-off and root rot) were compared to explore the disease resistance mechanisms related to fungal community changes.

RESULTS: Results revealed distinct niche differentiation: leaves were dominated by Basidiomycota (82.0%), while stems harbored more Ascomycota (94.2%), including pathogens like Monilinia laxa (35.73%). Fungal infection significantly reduced microbial alpha diversity, altered community structure (PERMANOVA, p = 0.001), and destabilized co-occurrence networks (modularity decreased from 0.8501 to 0.8116). Functional prediction indicated downregulation of key metabolic pathways (e.g., NAD/NADP interconversion, phospholipid biosynthesis). Disease stress induced an enrichment of potentially beneficial taxa (e.g., Rhodotorula) in leaves, indicative of a limited antagonistic response, while the overall community was ultimately dominated and disrupted by pathogens.

DISCUSSION: Elucidating these compositional shifts of phyllosphere fungal communities advances the understanding of plant-microbe-pathogen interactions and provides a critical theoretical groundwork for development of microbiome-driven early disease diagnosis, resistance breeding, and eco-friendly disease control strategies for Panax ginseng.},
}

@article {pmid41971337,
year = {2026},
author = {Alqaderi, H and Batorsky, R and Azar, G and Malik, MZ and Nizam, R and Altabtbaei, K and Devarajan, S and Ahmad, R and Michaud, DS and Zhao, N and Zavras, A and Al-Mulla, F},
title = {Comparative machine learning analysis of saliva and plaque microbiomes in Kuwaitis with type 1 diabetes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1735375},
pmid = {41971337},
issn = {1664-302X},
abstract = {BACKGROUND: Type 1 diabetes (T1D) is associated with microbial dysbiosis. While most research has focused on the gut microbiome, limited data addresses the role of the oral microbiome in T1D. The oral and gut microbiomes overlap substantially, and the oral cavity may influence gut microbial composition. Saliva and dental plaque represent two distinct oral niches with unique microbial communities, but it remains unclear which is better associated to systemic disease states like T1D. This study compares the performance of salivary and plaque microbiomes in classifying pediatric T1D status.

METHODS: Paired saliva and plaque samples were collected from 46 children (23 with T1D, 23 healthy controls). Microbial DNA was extracted and sequenced targeting the 16S rRNA gene. Data were processed using QIIME 2 for taxonomic classification and centered log-ratio transformation. Alpha diversity, microbial abundance, and clustering analyses were performed to compare the oral microbiome between T1D and control groups. Random forest classifiers were used to evaluate and compare the predictive accuracy of saliva- and plaque-based models, both with and without clinical metadata.

RESULTS: Saliva samples exhibited lower alpha diversity than plaque but had significantly higher bacterial load and total microbial abundance. Saliva-based models outperformed plaque-based models, achieving a classification accuracy of 94.2% with or without clinical metadata, compared to 73.3% accuracy for plaque-based models. ROC curve analysis further supported this difference, with saliva models reaching an AUC of approximately 0.94, versus 0.75 for plaque, indicating superior discriminative performance. UMAP clustering revealed more distinct separation of T1D and control groups in salivary profiles than in plaque. Feature importance analysis identified both unique and shared taxa predictive of T1D in each niche. Incorporating clinical and demographic metadata did not enhance model performance, underscoring the robustness and predictive strength of microbiome data alone.

CONCLUSION: The salivary microbiome is a more effective biospecimen than dental plaque for characterizing T1D-associated microbial profiles in children. It offers superior classification accuracy and greater sensitivity in distinguishing T1D status, supporting saliva's potential as a non-invasive, scalable medium for future microbiome-based monitoring.},
}

@article {pmid41971339,
year = {2026},
author = {Gao, Y and Zhang, J and Sun, L and Wang, K and Tang, X},
title = {Diversity and distribution of the microbiome in the bulbs and rhizosphere soil of Fritillaria thunbergii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1752283},
pmid = {41971339},
issn = {1664-302X},
abstract = {As global medical resources become increasingly scarce, the demand for medicinal plants continues to rise. The growth and metabolism of medicinal plants are closely linked to rhizosphere and endophytic microorganisms. The rhizosphere soil and internal tissues of plants form stable, nutrient-rich ecosystems largely dominated by microbial communities. However, how the rhizosphere and endophytic microbiomes of Fritillaria thunbergii vary across geographically distinct populations, and what ecological processes shape their assembly and functional potential remain largely unexplored. We hypothesized that distinct environmental selection pressures and spatial isolation would differentially shape the assembly of bacterial and fungal communities in bulb and rhizosphere niches, and that core and unique microbial taxa play pivotal roles in shaping ecological network structure. In this study, metabarcoding was employed to investigate the bacterial and fungal communities in the rhizosphere soil and bulbs of F. thunbergii across four populations in China, with the aim of elucidating the biogeographic patterns, assembly mechanisms, and ecological networks of the plant-associated microbiome. The results indicate that both bacterial and fungal communities exhibited significant differences in diversity and composition across the four populations, shaped jointly by geographic isolation and environmental selection. Only a few taxa displayed both cosmopolitan distributions and high abundance, whereas most communities were distinct among ecotypes. Co-occurrence network analysis revealed that core taxa exerted stronger ecological relevance within bacterial and fungal communities compared to other ecotypes, while unique taxa played more pivotal roles in cross-domain networks. Phylogenetic analyses further uncovered microdiverse clades shaped by environmental selection, which may enhance functional resilience and contribute to the overall biogeographic patterns observed. By elucidating the biogeographic patterns and assembly mechanisms of the F. thunbergii microbiome, the study provides a conceptual framework for understanding plant-microbe interactions in medicinal plants and offers insights for the sustainable utilization of microbial resources in traditional medicine.},
}

@article {pmid41971340,
year = {2026},
author = {Giner-Pérez, L and Felipo, V and Izquierdo-Altarejos, P and Llansola, M and Pérez Martínez, G},
title = {Hyperammonemia reduces the populations of beneficial lactobacilli and bifidobacteria, disrupting the metabolic balance of the gut microbiome in rats.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771709},
pmid = {41971340},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiome (GM) plays a critical role in metabolic and neurological health and is implicated in hepatic encephalopathy (HE). Chronic hyperammonemia (HA), a major contributor to cognitive and motor impairment in HE, may influence GM structure and function, yet its specific efects in GM remain unclear.

METHODS: Here, it was investigated how chronic HA alters the GM using a rat model fed an ammonia-enriched diet for 4 weeks. Fecal microbiota profiles obtained by 16S rRNA gene sequencing revealed marked taxonomic shifts in HA rats, with beta-diversity showing clear separation from controls.

RESULTS: Genera within the Lachnospiraceae family and Alistipes genus were enriched in HA rats, while lactic acid-producing and xylanolytic Firmicutes were reduced. Network analysis identified Alistipes as a central node in the HA microbiome. Predicted metabolic functions were significantly altered, showing negative associations between HA and pathways related to the pyruvate dehydrogenase complex, sucrose and urea degradation, and 4-aminobutyrate (GABA) degradation. Consistent with these predictions, fecal short-chain fatty acid (SCFA) analysis revealed reduced acetic and butyric acid, alongside increased valeric and isobutyric acid levels. The predicted GABA levels increasement by GM would activate GABA receptors in immune cells and would also contribute to peripheral inflammation and, eventually, neuroinflammation.

CONCLUSIONS: Together, these findings demonstrate that chronic HA reshapes GM composition, disrupts key metabolic pathways, and alters SCFA profiles, providing mechanistic insight into how HA- associated dysbiosis may contribute to the metabolic, immune, and neurological dysfunction characteristic of HE.},
}

@article {pmid41971342,
year = {2026},
author = {Martorell-Múgica, A and Gónzalez-Fernández, C and Greses, S},
title = {Indigenous microbiome as a key strategy for producing green chemicals.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798480},
pmid = {41971342},
issn = {1664-302X},
abstract = {INTRODUCTION: Reactors used for conventional anaerobic fermentation (C-AF) devoted to metabolite production are typically seeded with sludge collected from anaerobic digesters. This inoculum contains methanogens, which are the principal consumers of metabolites involved in biogas production. The use of the indigenous microbial community naturally present in the agroindustrial waste (AGW) was evaluated as an alternative inoculum to take advantage of its naturally scarce methanogenic abundance.

METHODS: Self-AF (lacking external inoculum) and C-AF were compared in terms of bioconversion yields and metabolite profiles. The effect of pH on community specialization and product distribution was assessed across the pH range naturally occurring during self-acidification.

RESULTS: Self-AF showed high bioconversion yields to metabolites (65.7 %) when compared to C-AF (58.7 %). Nevertheless, the inherent pH changes that the process suffered from self-acidification also resulted in metabolite profile oscillation. Whereas a pH of 4.5 maximized the lactic acid and ethanol production (13.9 and 11.7 g·L[-1], respectively) due to the lactic acid bacteria prevalence, when a pH of 6 was reached, the microbiome specialized in carboxylates production, leading to a concentration of 29.8 g·L[-1] in the steady state, with Clostridiales (51.8%) and Bifidobacteriaceae (21.4 %) as key bacteria.

CONCLUSION: This study demonstrated the feasibility of conducting AF in the absence of external inoculum. Moreover, the wide bacterial metabolisms present in the indigenous microbiome revealed its capability of maximizing product portfolio using self-AF.},
}

@article {pmid41971387,
year = {2026},
author = {Chen, J and Sun, T and Zhang, J and Huang, J and Chen, T and Weng, Y and Xiang, H and Dong, Z and Huang, Z and Cai, X and Liang, C and Zhang, M and Yu, W},
title = {Artificial intelligence-driven personalized dietary recommendations for gastric cancer high-risk populations: a narrative review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1802970},
pmid = {41971387},
issn = {2296-861X},
abstract = {This review summarizes the current applications of artificial intelligence (AI) in providing personalized dietary recommendations, and explores its potential applicability to populations at high risk for gastric cancer. Currently, there are no direct intervention trials for gastric cancer patients. However, evidence from metabolic diseases (like diabetes and obesity) shows that AI-driven dietary interventions could be beneficial. This approach may offer translatable benefits for cancer prevention. First, the paper elaborates on the severe incidence of gastric cancer and the limitations of traditional preventive measures, emphasizing the necessity of developing precise and efficient intervention strategies. Subsequently, it systematically outlines methods for identifying high-risk populations and risk stratification (including pathological basis, biomarkers, and genetic risks), as well as the close relationship between dietary patterns (protective and risky) and gastric cancer risk, with a particular focus on the interaction between diet and the gastric microbiome (especially Helicobacter pylori). The core section analyzes the technical principles of AI-driven personalized nutritional interventions (such as machine learning and deep learning) and their practical effects in improving chronic diseases like blood glucose control and obesity management, while looking forward to the potential of integrating AI with multi-omics data. In addition, the paper extends the discussion to the extended applications of AI in improving screening adherence, assisting endoscopic diagnosis, and clinical decision support systems. Finally, the paper points out current challenges such as technical interpretability, data privacy, population differences, and clinical validation, and proposes prospects for future research directions.},
}

@article {pmid41971531,
year = {2026},
author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B},
title = {Dynamic change patterns of the human gut microbiota-fluctuation, loss-acquisition, and turnover-and their underlying causes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag046},
pmid = {41971531},
issn = {2730-6151},
abstract = {The temporal dynamics of the gut microbiome are critical to human health, yet their patterns and underlying drivers remain poorly characterized at a monthly resolution and strain level. This knowledge gap limits the development of targeted microbiome interventions. Here, we integrate longitudinal analyses across three human cohorts-a cross-sectional cohort (n = 190), an intensive 52-month time series (n = 7), and a paired 6-month cohort (n = 43)-together with a humanized mouse model under antibiotic perturbation. Using shotgun metagenomics (516 samples), we resolve microbial dynamics at species and strain resolution. We identify three distinct modes of temporal variation: relative abundance fluctuations, species loss-acquisition events, and strain turnover. Strain turnover contributes substantially to the dynamic reservoir of functional genes, including those associated with virulence and antibiotic resistance. These dynamics are influenced by antibiotic exposure and microbial interspecies interactions. Our work provides a month-scale atlas of gut microbiome variation, revealing widespread transient colonization and strain-level plasticity, thereby offering a refined framework for understanding microbiome stability and personalized microbial ecology.},
}

@article {pmid41971550,
year = {2026},
author = {Suarez-Fernandez, M and García-Fernández, C and Ferreira, JJ and Campa, A},
title = {Farming system shapes rhizosphere microbiota and root gene expression in common bean.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1749874},
pmid = {41971550},
issn = {1664-462X},
abstract = {The rhizosphere is a dynamic interface where plant roots and microorganisms interact through the exchange of metabolites and signaling molecules. This study evaluated the impact of organic and conventional farming on the rhizosphere microbiota and root gene expression in common bean by integrating metabarcoding (16S rRNA and ITS) and RNA sequencing (RNA-seq) approaches. Bacterial alpha diversity was higher in the rhizosphere of plants grown under conventional than under the organic system (2961 vs. 1532 Amplicon Sequence Variants (ASVs) observed), whereas fungal alpha diversity was greater in the organic system (372 vs. 321 ASVs observed). The fungi-to-prokaryote ratio was approximately twofold higher in organic systems. Organic farming promoted Funneliformis, Metarhizium, Chitinophaga, and Rhizobium, while conventional farming favored Pirellula, Terrimonas, and Mortierella. Transcriptomic analysis identified 5511 differentially expressed genes (DEGs), of which 1085 showed |log2FC| ≥ 2, mainly upregulated under organic conditions. These genes were enriched in functions related to secondary metabolism, redox homeostasis, hormone signaling, nodulation, and nutrient transport. DEGs involved in the synthesis of root exudate metabolites, including fatty acids, indolic compounds, and organic acids, were also identified, highlighting their potential role in microbial recruitment. Downregulated genes were associated with cell cycle and kinase activity. Correlation analyses linked beneficial fungal taxa with the induction of genes related to plant growth, defense, and symbiosis. This work provides a basis for future studies aimed at identifying key genes involved in root development and plant-microbe interactions, potentially improving breeding programs for cultivar resilience and efficiency.},
}

@article {pmid41971606,
year = {2026},
author = {Zhu, S and Qiao, Y and He, W and Xiao, Y and Song, G and Liu, K and Fang, S},
title = {Multi-Strain Probiotics BLa80, LRa05, and BBr60 Modulate Inflammation, Bile Acids, and Gut Microbiota in Type 2 Diabetes: A Randomized Controlled Trial.},
journal = {Food science & nutrition},
volume = {14},
number = {4},
pages = {e71735},
pmid = {41971606},
issn = {2048-7177},
abstract = {To evaluate the effects of a multi-strain probiotic formula, Bifidobacterium animalis subsp. lactis BLa80, Lacticaseibacillus rhamnosus LRa05, and Bifidobacterium breve BBr60, on inflammation, metabolism, and the gut microbiota in patients with type 2 diabetes mellitus (T2DM). In a randomized, double-blind, placebo-controlled trial, 80 adults with T2DM received either the probiotic or a placebo in addition to standard hypoglycemic therapy for 12 weeks. We assessed inflammatory cytokines, glycemic indices, serum amino acids, bile acids (BAs), short-chain fatty acids (SCFAs), and gut microbiota composition. Compared with the placebo group, the probiotic intervention led to a significant reduction in the levels of IL-17 and TNF-α (p < 0.05), reduced serum concentrations of threonine, isoleucine, and arginine. Additionally, the BA profile was markedly altered, revealing 16 differential metabolites that were associated with pivotal metabolic pathways. SCFA analysis showed higher isobutyric and isovaleric acid after supplementation. The probiotic group also exhibited significant reductions in total glycated hemoglobin (GHb) and fasting plasma glucose (FPG, p < 0.05). Microbiome analyses indicated decreased alpha-diversity and distinct beta-diversity shifts, including increased Gemmatimonadota and reduced Clostridium abundance in the probiotic group. This multi-strain probiotic modulated inflammatory responses, metabolic profiles, including BA metabolism and SCFAs, and gut microbiota composition in T2DM, supporting its potential as an adjunct to metabolic management. Trial Registration: ClinicalTrials.gov identifier: NCT06440486.},
}

@article {pmid41971837,
year = {2026},
author = {Du, S and Lin, D and Zhang, TL and Chu, HY and Zhu, D},
title = {Earthworm gut's potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size.},
journal = {Fundamental research},
volume = {6},
number = {2},
pages = {837-846},
pmid = {41971837},
issn = {2667-3258},
abstract = {The earthworm microbiome significantly impacts global soil ecosystems. This study explores how earthworm gut eukaryome (fungi and protists) and functional genes respond to land use and climatic factors. Over 150 earthworm-soil sample pairs were collected from arable and forest ecosystems across China. High-throughput and shotgun metagenomic sequencing revealed lower fungal, protistan, and CAZyme gene diversities in the earthworm gut than in the soil (0.77-fold, 0.19-fold, and 0.74-fold compared to the soil, respectively), but higher proportions of parasitic protists (3.78-fold compared to the soil) and carbohydrate metabolism genes involved in glycosyl transfer (1.41-fold compared to the soil). Arable systems showed higher abundances of functional genes associated with carbon fixation, nitrification, phosphorus dissolution, and sulfite reduction compared to forest systems. This study highlights the associations between earthworm gut microeukaryotes and functional genes especially glycosyl transferases involved in carbohydrate biosynthesis. Furthermore, larger microbial genomes were found in the earthworm gut compared to the soil, which may harbor more functional genes involved in cellular processes, carbohydrate binding, and glycosyl transfer. These findings suggest that earthworm gut microeukaryotes may have a positive impact on their average genome sizes and carbohydrate metabolism within the carbon cycle. This study contributes to advancing our understanding of the functionality of microeukaryotes in the earthworm gut, especially for the carbon cycle.},
}

@article {pmid41971848,
year = {2026},
author = {Petersen, AE and Zafeiropoulou, K and Ghiboub, M and van Helsdingen, CPM and Konsten, JLM and Bouvy, ND and Stoot, JHMB and Tanis, PJ and de Jonge, WJ and Derikx, JPM},
title = {Preoperative Gut Microbiome in Patients With Colorectal Cancer: Potential for Fecal Biomarker-Based Recurrence Risk Prediction.},
journal = {JCO oncology advances},
volume = {},
number = {3},
pages = {},
pmid = {41971848},
issn = {2994-9750},
abstract = {PURPOSE: While gut microbiome dysbiosis is known to play a role in colorectal cancer (CRC) initiation and progression, its role in CRC recurrence remains unclear. This study investigates whether the gut microbiome is associated with CRC recurrence.

PATIENTS AND METHODS: In a prospective observational cohort, preoperative fecal samples from patients with stage I to III CRC undergoing surgical resection were analyzed using 16S rRNA gene sequencing. Alpha diversity and beta diversity were compared between patients with and without recurrence, and differential abundance analyses were conducted to identify bacterial genera associated with recurrence risk.

RESULTS: Among 294 patients, 61 (21%) patients developed recurrence during a median follow-up of 56 months, with a median time to recurrence of 19 months. Alpha diversity did not differ between groups, but beta diversity analysis revealed significantly distinct microbial clustering in patients with recurrence, particularly those with locoregional recurrence. Differential abundance analysis identified five bacterial genera associated with locoregional recurrence (Acidaminococcus, Alloprevotella, Butyrivibrio, Ruminococcaceae CAG-352, and Lachnospiraceae UCG-003), one with distant recurrence (Megamonas), and two with overall recurrence (Anaeroplasma, Porphyromonas). Stratifying patients into high- and low-abundance subgroups revealed that those with a high relative abundance of Porphyromonas had an increased risk of overall recurrence (hazard ratio, 2.80 [95% CI, 1.54 to 5.10]).

CONCLUSION: Patients with CRC who develop locoregional recurrence exhibit a distinct preoperative fecal microbial composition compared with those without recurrence. Our findings provide novel insights into the role of the intestinal microenvironment in recurrence and identify Porphyromonas as a potential fecal biomarker for overall recurrence risk.},
}

@article {pmid41971995,
year = {2026},
author = {Zhao, D and Gao, C and Zhu, D and Zheng, X and Sun, J and Liu, C and Chen, L and Shen, L and Wang, X and Zhang, Y},
title = {Gut microbiota-derived cholic acid ameliorates lung inflammation in bronchopulmonary dysplasia through modulation of macrophage function.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115398},
pmid = {41971995},
issn = {2589-0042},
abstract = {This study explores the impact of gut microbiota-derived metabolites on the pathogenesis of bronchopulmonary dysplasia (BPD), focusing on their roles in macrophage plasticity and inflammation. In a prospective nested case-control cohort of 30 infants with BPD and 33 preterm controls, 16S ribosomal RNA (16S rRNA) and mass spectrometry analyses identified seven differential gut bacterial genera, with depleted Streptococcus and enriched Klebsiella in patients with BPD, alongside reduced fecal and serum cholic acid levels. In chorioamnionitis-induced rat models of BPD, cholic acid supplementation alleviated lung inflammation by regulating macrophage migration and polarization. RNA-sequencing and in vitro experiments revealed that cholic acid acts by inhibiting hypoxia-inducible factor-1α (HIF-1α) expression and transcriptional activity, an effect that was abolished by HIF-1α silencing. These findings connect the gut microbiota to BPD, highlighting cholic acid as a key regulator of macrophage function through the HIF-1α pathway in mitigating inflammation and providing new clues for understanding and intervening in BPD.},
}

@article {pmid41972113,
year = {2026},
author = {Ramos, C and Hunter, K and Walton, GE and Whitham, A and Camp, N and Poveda, C and Gibson, GR and Hough, J and Magistro, D},
title = {Associations Between the Gut Microbiota and Physical Activity, Sedentary Behaviour and Physical Function in Community-Dwelling Older Adults.},
journal = {Journal of aging research},
volume = {2026},
number = {},
pages = {8981398},
pmid = {41972113},
issn = {2090-2204},
abstract = {Gut microbiota (GM) plays a crucial role in maintaining health through metabolic, endocrine and immune functions. With ageing, shifts in GM composition, characterised by increased pathogenic and decreased health-promoting bacteria, contribute to dysbiosis, which is linked to several age-related diseases. Given the global trend of increasing sedentary behaviour (SB) and declining physical activity (PA) among older adults, this study aims to explore the relationships between GM and two critical indicators of healthy ageing, movement behaviours and physical function. Cross-sectional study assesses the GM composition, PA levels and physical function of 101 healthy, community-dwelling older adults aged 65-85 years. Participants undertook anthropometric measures and functional tests, wore an accelerometer for 7 days and provided a faecal sample which was analysed using 16s rRNA sequencing. All the results were adjusted for key covariates such as diet, age and activity levels. Key findings include positive associations of Prevotella copri with moderate-to-vigorous PA, physical function and negative associations with SB, while Roseburia species were linked to better mobility and strength measures. Conversely, potentially pathogenic taxa like Bilophila wadsworthia and Eggerthella were negatively associated with PA and handgrip strength, underscoring their possible detrimental roles in muscle function and healthy ageing. This cross-sectional study highlights the associations between GM, PA, physical function and healthy ageing in older adults. These findings emphasise the potential for leveraging GM and PA interactions to develop nonpharmacological strategies for promoting healthy ageing, warranting further research through interventional and longitudinal studies.},
}

@article {pmid41972174,
year = {2026},
author = {Cui, L and Liu, P and Wu, K and Han, X and Peng, G},
title = {Targeting the JAK/STAT pathway in atopic dermatitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1757562},
pmid = {41972174},
issn = {1664-3224},
mesh = {Humans ; *Dermatitis, Atopic/drug therapy/metabolism/immunology/etiology ; *Janus Kinases/metabolism/antagonists & inhibitors ; *STAT Transcription Factors/metabolism/antagonists & inhibitors ; *Signal Transduction/drug effects ; *Janus Kinase Inhibitors/therapeutic use/pharmacology ; Animals ; Molecular Targeted Therapy ; },
abstract = {Atopic dermatitis (AD) is a chronic, inflammatory skin disorder characterized by immune dysregulation, skin barrier dysfunction, and pruritus. Central to its pathogenesis is the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway, which mediates cytokine responses-including interleukin (IL)-4, IL-13, IL-31, and thymic stromal lymphopoietin-that drive T-helper 2-skewed inflammation and epidermal barrier impairment. In recent years, the therapeutic landscape of AD has been transformed by the development of JAK inhibitors, offering both systemic and topical treatment options for patients unresponsive to conventional therapies. This narrative review provides a comprehensive overview of the JAK/STAT pathway's biological role in AD, including its regulation of immune responses and skin inflammation. We summarize current JAK inhibition therapies under clinical use or investigation, compare their efficacy and safety profiles, and examine unresolved controversies surrounding long-term outcomes and adverse effects. Furthermore, we explore future innovations in JAK/STAT research, including precision medicine approaches, third-generation allosteric inhibitors, microbiome-informed strategies, and advanced drug delivery technologies. Collectively, understanding and refining JAK/STAT-targeted therapy hold great promise for individualized, safe, and effective management of AD.},
}

Humans
*Dermatitis, Atopic/drug therapy/metabolism/immunology/etiology
*Janus Kinases/metabolism/antagonists & inhibitors
*STAT Transcription Factors/metabolism/antagonists & inhibitors
*Signal Transduction/drug effects
*Janus Kinase Inhibitors/therapeutic use/pharmacology
Animals
Molecular Targeted Therapy

@article {pmid41972361,
year = {2026},
author = {Engin, ED and Engin, AB and Engin, A},
title = {Immune Evasion of Helicobacter pylori and Extra-Gastric Cancer Risk.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70376},
pmid = {41972361},
issn = {1440-1746},
abstract = {Helicobacter pylori (H. pylori) is a group 1 gastric carcinogen that plays a significant role in extra-gastric digestive system cancers. H. pylori disrupts host cell homeostasis through expression of virulence factors leading to immune evasion as well as persistent gastric mucosal colonization. H. pylori infection has been shown to play a role in extra-gastric cancers such as, hepatocellular cancer, cholangiocarcinoma, colorectal, pancreatic, and esophageal cancers. H. pylori are highly heterogeneous bacterium, and different strains may carry different virulence factors, which varies across geographic regions. Intercellular communication via exosomes derived from H. pylori-infected cells, and the H. pylori-related gut microbiota dysbiosis leads to extra-gastric cancer development through the "microbiota-epigenetic-cancer regulatory axis" in epigenomic reprogrammed host. Because of the regional and social variabilities, studies have conflicting results concerning the effect of the mutual interactions between the virulence factors of H. pylori, host, and host's microbiota on the development of extra-gastric cancer. Consistently, a significant increase in kynurenine production from tryptophan via indoleamine-2,3-dioxygenase activity of gut microbiome suppresses host's immune response by activating the aryl hydrocarbon receptor in H. pylori seropositive patients. Immune suppression in extra-gastric digestive system cancer development preserves the tumor cells from immune attack and promotes tumor growth.},
}

@article {pmid41972428,
year = {2026},
author = {Wang, YF and Wang, YN and Lin, D and Xu, JY and Qi, FY and Cui, HL and Lu, HJ and Qiao, M and Topp, E and Zhu, D and Rillig, MC and Zhu, YG},
title = {Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm-Mediated Mechanisms.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18849},
doi = {10.1002/advs.202518849},
pmid = {41972428},
issn = {2198-3844},
support = {42307169//National Natural Science Foundation of China/ ; 42577136//National Natural Science Foundation of China/ ; U25A20803//National Natural Science Foundation of China/ ; 2023J02031//Fujian Provincial Natural Science Foundation of China/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; },
abstract = {The environmental accumulation of non-antibiotic pharmaceuticals is an emerging driver of antibiotic resistance. While individual compounds are known to shape the soil resistome, and contaminant diversity also plays a role, the impact of pharmaceutical diversity on the gut resistome of soil invertebrates remains unclear. Here, we combined metagenomics and metaproteomics to examine the collembolan gut and soil resistome across a gradient of pharmaceutical diversity under diurnal warming. Increasing pharmaceutical diversity at a constant total concentration significantly enriched antibiotic resistance genes (ARGs) in the gut microbiome, with no comparable effect in surrounding soils. This enrichment was mainly driven by multidrug resistance associated with efflux activity and biofilm-related processes, accompanied by increases in ARG-carrying taxa such as Gordonia and Ochrobactrum. Notably, Ochrobactrum encoded biofilm-related aryl polyene pathways. In vitro experiments confirmed that biofilm formation promotes resistance through coordinated cellular responses. Metaproteomic data indicated that Ochrobactrum initiates early biofilm formation by recruiting extracellular matrix producers such as Bacillus and Pseudomonas. Diurnal warming modulated these responses, indicating an interaction between chemical diversity and climate stress. These findings identify pharmaceutical diversity as an independent driver of ARG enrichment in host-associated microbiomes and establish chemical complexity as a key factor in assessing the ecological risks of pharmaceutical pollution.},
}

@article {pmid41972576,
year = {2026},
author = {Ma, R and Liu, Y and Wang, R and Li, S and Yang, Q and Chen, Y and Ren, J and Luo, Y and Xiang, Y and Luo, X},
title = {Polyethylene Microplastics Exert Dose-Dependent Effects on the Growth, Physiology, and Rhizosphere Microbiome of Persicaria capitata.},
journal = {Biology},
volume = {15},
number = {7},
pages = {},
pmid = {41972576},
issn = {2079-7737},
support = {2024YB002 and 2024BSKQ003//Fundamental Research Funds for the Guizhou Education University Scientific Research Fund Project/ ; 2024142234020, 2024142234044, 2024142230467//Innovation and Entrepreneurship Training Program for College Students of Guizhou Education University/ ; QKHJC MS〔2025〕079//Guizhou Provincial Basic Research Program (Natural Science) General Program/ ; },
abstract = {Microplastic pollution has become a major environmental challenge for terrestrial ecosystems; however, the mechanisms by which it affects the growth of medicinal plants and their rhizosphere microecology remain unclear. This study selected the important medicinal herb P. capitata as the research subject. A pot experiment was conducted to investigate the effects of different concentrations (0%, 1%, 4%, and 8% w/w) of polyethylene microplastics (PE-MPs) on its growth performance, physiological responses, and rhizosphere bacterial communities. The main findings are as follows: (1) PE-MPs exhibited a hormetic effect on the biomass of P. capitata. A low concentration (1%) slightly promoted total biomass (44.78 g) compared to the control (40.94 g), whereas higher concentrations caused significant inhibition. Total biomass decreased by 28.5% and 53.5% under the 4% and 8% treatments, respectively, indicating that the transition from stimulation to inhibition occurred between the 1% and 4% PE-MPs. (2) Chlorophyll a was more sensitive to stress, with its content significantly increasing under the 1% treatment but declining at higher concentrations. (3) Regarding the antioxidant system, POD activity was significantly inhibited at low and medium concentrations, while MDA content increased significantly only under the 8% treatment (by 72%). SOD and CAT showed no significant changes, indicating that POD and MDA were more sensitive indicators of oxidative damage. (4) PE-MPs significantly reduced rhizosphere bacterial community richness (Chao1 index), and the loss of microbial diversity was highly coupled with the decline in plant biomass and the exacerbation of oxidative damage. In conclusion, this study confirms a threshold effect in the toxicity of PE-MPs to P. capitata, with the transition from hormetic stimulation to toxic inhibition occurring between 1% and 4% (w/w). Furthermore, rhizosphere microecological imbalance is identified as a key indirect mechanism underlying phytotoxicity. These findings provide a new theoretical basis for understanding the potential impacts of microplastic pollution on medicinal plants and agroecosystems.},
}

@article {pmid41972590,
year = {2026},
author = {Suo, L and Bian, K and Tang, J and Li, F and Sun, K and Yang, C},
title = {Nasopharyngeal Bacterial-Fungal Dysbiosis in Respiratory-Diseased Endangered Forest Musk Deer (Moschus berezovskii).},
journal = {Biology},
volume = {15},
number = {7},
pages = {},
pmid = {41972590},
issn = {2079-7737},
support = {2024K-08; 2025k-26//Science and Technology Projects of Shaanxi Academy of Science/ ; 2025NC-YBXM-120//Shaanxi Key Research and Development Program/ ; },
abstract = {BACKGROUND: The nasopharyngeal microbiome is crucial for respiratory health in mammals, yet it remains poorly characterized in the endangered forest musk deer (Moschus berezovskii), particularly in the context of disease.

METHODS: We compared the bacterial (16S rRNA) and fungal (ITS2) communities in the nasopharynx of healthy (n = 6) and clinically diseased (n = 6) individuals.

RESULTS: Although alpha diversity did not differ significantly, beta diversity (PCoA) analysis revealed distinct bacterial (PERMANOVA, R[2] = 0.165, p = 0.014) and fungal (R[2] = 0.577, p = 0.003) community structures between groups. The diseased group exhibited a significant increase in the bacterial phylum Proteobacteria (70.97% vs. 46.27%), primarily driven by the genera Bibersteinia and Pseudomonas. Fungal communities in the diseased group were dominated by a higher relative abundance of Ascomycota and Basidiomycota, with significant enrichment of Wallemia and Aspergillus. LEfSe analysis identified Pseudomonas and multiple fungal taxa (e.g., Wallemia, Aspergillus) as biomarkers for the diseased group. PICRUSt2 prediction indicated enrichment of pathways related to carotenoid biosynthesis and sphingolipid metabolism in the diseased state, while FUNGuild analysis suggested a higher abundance of animal/plant pathogen-related fungi.

CONCLUSIONS: Symptomatic respiratory infections in forest musk deer are associated with significant dysbiosis of the nasopharyngeal microbiome, characterized by the marked enrichment of potential bacterial opportunists (e.g., Pseudomonas) and specific fungal taxa (e.g., Wallemia, Aspergillus), alongside distinct functional shifts in the microbiome. These findings provide the first integrated bacterial-fungal profile of the nasopharyngeal microbiome in this endangered species, and highlight potential microbial biomarkers associated with respiratory disease.},
}

@article {pmid41972685,
year = {2026},
author = {Andrzejczak, K and Kucharczyk, E and Sternak, A and Busłowicz, T and Ponikowska, M},
title = {Gut Dysbiosis and the Molecular Landscape of the Gut-Skin Axis: Comparative Insights and Therapeutic Implications for Atopic Dermatitis and Psoriasis.},
journal = {Cells},
volume = {15},
number = {7},
pages = {},
pmid = {41972685},
issn = {2073-4409},
mesh = {Humans ; *Dysbiosis/microbiology ; *Dermatitis, Atopic/microbiology/therapy/immunology ; *Gastrointestinal Microbiome ; *Psoriasis/microbiology/therapy/immunology ; *Skin/pathology/microbiology/immunology ; Animals ; },
abstract = {Chronic inflammatory skin diseases, including atopic dermatitis (AD) and psoriasis, are systemic immune-mediated disorders driven by dysregulated immune responses. The gut-skin axis is a bidirectional network linking intestinal microorganisms, their metabolites, and host immunity. It connects microbiome composition and function with systemic inflammation and cutaneous pathology, shaping disease-specific mechanisms such as Th2/IL-4/IL-13-mediated barrier dysfunction in AD and Th17/IL-23/IL-17-driven hyperproliferation in psoriasis. Microbiota-derived metabolites, including short-chain fatty acids, tryptophan-derived aryl hydrocarbon receptor ligands, and bile acid-dependent FXR/TGR5 signaling, modulate immune homeostasis and epithelial integrity. Gut dysbiosis, impaired metabolite production, and barrier dysfunction disrupt regulatory networks, amplifying inflammation. Microbiota-targeted interventions, including probiotics, synbiotics, postbiotics, and precision nutrition, may serve as adjunctive therapies, although further well-controlled clinical studies are needed. Integrating multi-omics, metabolomics, and functional microbial profiling, alongside investigations of the gut mycobiome and virome, will be critical to identify predictive biomarkers and optimize therapeutic strategies. These concepts remain mechanistically compelling but largely theoretical, requiring validation in longitudinal and interventional studies.},
}

Humans
*Dysbiosis/microbiology
*Dermatitis, Atopic/microbiology/therapy/immunology
*Gastrointestinal Microbiome
*Psoriasis/microbiology/therapy/immunology
*Skin/pathology/microbiology/immunology
Animals

@article {pmid41972755,
year = {2026},
author = {Langenfeld, K and Arts, P and Monahan, A and Criswell, A and Wigginton, KR and Duhaime, MB},
title = {Novel machine learning-based approach to identify viral biomarkers of human respiratory emissions from oral and nasal metagenomes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0011326},
doi = {10.1128/msphere.00113-26},
pmid = {41972755},
issn = {2379-5042},
abstract = {Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes, and prevalence was further increased to 77%-81% by combining two or three biomarkers. Real-time PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling.IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and, thus, exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.},
}

@article {pmid41973033,
year = {2026},
author = {Unlu, O and Chen, T and Yakar, N and Guney, Z and Paster, B and Carreras, I and Dedeoglu, A and Kantarci, A},
title = {Aging and periodontitis increase brain dissemination of oral bacteria.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70118},
pmid = {41973033},
issn = {1943-3670},
support = {RF1AG062496//National Institute for Health Research/ ; 2219-1059B192202291//Scientific and Technological Research Council of Turkey/ ; 2214/A-1059B142200465//Scientific and Technological Research Council of Turkey/ ; 2219-1059B192202848//Scientific and Technological Research Council of Turkey/ ; },
abstract = {BACKGROUND: The microbiome is a dynamic system that changes throughout life. Studies have revealed the relationship between periodontal disease and the oral microbiota; however, the impact of periodontal disease on the expression of senescence markers and on the inflammaging of the oral and systemic microbiome remains unclear. We hypothesized that aging increases the periodontitis-induced changes in the oral and systemic microbiome and is accompanied by an altered inflammatory response.

METHODS: Experimental periodontitis was induced in 18-month-old (old) and 8-month-old (young) C57BL/6 mice by placing ligatures around the second maxillary molars. Bone morphometric analyses were conducted to assess bone loss. Senescence- and inflammatory-related gene expression in the gingiva was measured by quantitative polymerase chain reaction (qPCR). Serum inflammatory markers were evaluated via immunoassay. Oral, brain, and gut microbial content were analyzed using next-generation sequencing.

RESULTS: Maxillary bone loss was significantly higher in the old mice with periodontal disease than in young mice. Senescence and inflammatory markers were higher in old mice than in young ones, and periodontitis increased their expression. The alpha diversity of the oral and brain microbial communities differed significantly between old and young mice. Treponema denticola, Fusobacterium nucleatum, Porphyromonas gingivalis, P. pasteri, and Prevotella nigrescens were only detected in the brains of old animals with periodontitis.

CONCLUSION: Periodontopathogens and oral commensals are either only found in the brains of old animals with periodontal disease or are more prevalent in the brains of old animals, suggesting that aging and periodontitis may contribute to the dissemination of oral bacteria to the brain.

PLAIN LANGUAGE SUMMARY: Aging may increase the periodontitis-induced changes in the oral and systemic microbiome, which an altered inflammatory response may accompany. Experimental periodontitis was created in old and young mouse models. Bone loss, senescence, and inflammatory gene expression and serum inflammatory markers were assessed in each model, and oral, brain, and gut microbial content was analyzed. Senescence and inflammatory markers were higher in old mice than in young ones, and periodontitis increased their expression. Our results suggested that aging and periodontitis may contribute to the dissemination of oral bacteria to the brain.},
}

@article {pmid41973043,
year = {2026},
author = {Hoff, CO and Heeke, S and Mitani, Y and de Sousa, LG and Siqueira, JM and Li, K and Bonini, F and Bell, D and Marques-Piubelli, ML and Lin, SY and Wargo, JA and El-Naggar, AK and McGrail, DJ and Ferrarotto, R},
title = {Axitinib plus Avelumab in Recurrent/Metastatic Adenoid Cystic Carcinoma: Biomarker Analysis and Updated Results of the Phase II Trial.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-25-4599},
pmid = {41973043},
issn = {1557-3265},
abstract = {PURPOSE: The phase II axitinib plus avelumab trial in recurrent/metastatic adenoid cystic carcinoma (ACC) demonstrated favorable response rates and progression-free survival (PFS), leading to its inclusion in NCCN guidelines as the first immunotherapy-based option for ACC. We sought to identify biomarkers predictive of clinical benefit from axitinib plus avelumab.

EXPERIMENTAL METHODS: Twenty-eight patients with ACC enrolled. Pre-treatment tumors underwent whole exome sequencing, transcriptome profiling, imaging mass cytometry, and tumor, oral rinse and stool microbiome characterization using 16s rRNA gene sequencing. Associations with PFS were assessed using Cox proportional hazards model, incorporating ACC subtype (ACC-I vs. ACC-II) as a covariate.

RESULTS: ACC comprises two proteogenomically distinct subtypes: aggressive, NOTCH1-activated ACC-I and more indolent ACC-II. Here, median PFS was 1.8 months for ACC-I versus 11.4 months for ACC-II (HR, 0.14; P<0.0001), representing the first demonstration of subtype-specific clinical trial outcomes in ACC. Clinical benefit was not associated with PD-L1 expression, tumor mutational burden, or recurrent genomic mutations. Instead, improved PFS correlated with the presence of intratumoral Escherichia and gut Bifidobacterium and Akkermansia. Transcriptomic profiling identified a 167-gene immune-enriched signature predictive of PFS benefit with axitinib plus avelumab. This signature also predicted benefit from ipilimumab plus nivolumab, but not from regorafenib monotherapy, suggesting its specificity for immunotherapy-based combinations.

CONCLUSIONS: Clinical trial outcomes with axitinib plus avelumab differ significantly by ACC subtype. Furthermore, the identified 167-gene immune-related signature predicts clinical benefit to immunotherapy-based combinations in ACC. These findings provide a framework for future biomarker-driven trial design and patient stratification strategies for this rare malignancy.},
}

@article {pmid41973071,
year = {2026},
author = {Liu, H and Bo, T and Li, J and Zhang, Y and Zhou, H},
title = {Comparative Analysis of Gut Microbiota Among Captive Waterbird Species: Effects of Diet and Environmental Factors.},
journal = {Veterinary medicine and science},
volume = {12},
number = {3},
pages = {e70865},
pmid = {41973071},
issn = {2053-1095},
support = {5242016//Natural Science Foundation of Beijing Municipality/ ; 32200381//National Natural Science Foundation of China for Youth/ ; 5242016//Beijing Natural Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diet/veterinary ; *Birds/microbiology ; Animals, Zoo/microbiology ; Feces/microbiology ; Lakes ; Species Specificity ; Geese/microbiology ; },
abstract = {The gut microbiota of avian species is influenced by a diverse array of factors, encompassing host genetics, environmental conditions, physiological states, dietary patterns and age, among others. With the advent of high-throughput sequencing technology, research into avian gut microbiota has gained momentum. The artificial lake within the zoo serves as a unique nexus between the natural and captive environments. Despite this, our understanding of the gut microbiota of waterbirds residing in such an artificial habitats remains limited. In this study, we focused on three distinct species of waterbird kept in the artificial lake and traditional enclosures. We used high-throughput sequencing technology to determine the faecal microbiome of 25 waterbirds from three species, including bar-headed goose (Anser indicus), ruddy shelduck (Tadorna ferruginea) and black-necked crane (Grus nigricollis). Our objective was to elucidate the composition and community structure of their gut microbiota, while exploring the nexus between dietary habits and gut microbiota. Our findings revealed that the dietary patterns and gut microbiota of ruddy shelducks and bar-headed geese exhibited similar traits. On the other hand, black-necked cranes, whose food primarily consists of fish and meat, possessed a gut microbiota optimized for the digestion of protein and fat. Notably, artificial lakes may support higher microbial diversity compared to cage feeding. The results underscore the significance of diet as the primary determinant of gut microbiota variation among the captive waterbird. This study provides implications for promoting the healthy growth and well-being of wild waterbird in captivity.},
}

Animals
*Gastrointestinal Microbiome
*Diet/veterinary
*Birds/microbiology
Animals, Zoo/microbiology
Feces/microbiology
Lakes
Species Specificity
Geese/microbiology

@article {pmid41973243,
year = {2026},
author = {Charaabi, K and Hamden, H and Fadhel, S and Tanfouri, N and Bouzenbila, S and Djobbi, W and Cherif, A and Msaad Guerfali, M},
title = {Probiotic Modulation of Gut Microbiota Enhances Immunity and Nutrition in SIT Ceratitis Capitata Sterile Males.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02754-x},
pmid = {41973243},
issn = {1432-184X},
}

@article {pmid41973268,
year = {2026},
author = {Ramadan, M and Hassan, EK and Abdalla, S and Ahmed, AAA and Azab, M and Ibrahim, KA and Amin, IA and Ali, ME and Alharbi, AE and Salah, M},
title = {Oral-gut microbiome dysbiosis in obese smokers reveals compartment-specific shifts.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02048-y},
pmid = {41973268},
issn = {2191-0855},
}

@article {pmid41973308,
year = {2026},
author = {Aydin, F and Çek, Ş},
title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.},
journal = {Veterinary research communications},
volume = {50},
number = {4},
pages = {},
pmid = {41973308},
issn = {1573-7446},
}

@article {pmid41973542,
year = {2026},
author = {Muurmann, AT and Rasmussen, JA and Limborg, MT and Gilbert, MTP and Bahrndorff, S},
title = {Functional gut microbiomes enhance performance in house fly larvae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0001126},
doi = {10.1128/aem.00011-26},
pmid = {41973542},
issn = {1098-5336},
abstract = {UNLABELLED: In a world with an increase in human population, food consumption, and the generation of organic waste, insects are emerging as a promising tool to convert organic waste material into human food or animal feed. The insect microbiome is known to play a key role in the degradation of organic substrates, but little is known about the metabolic potential of the microbiome of industrially reared fly larvae. We investigated the microbial composition and metabolic potential of the house fly (Musca domestica) larva gut microbiome from larvae grown on three different waste and by-product-based substrates. We found that bacteria associated with the larval gut were enriched for functions related to microbial stress mechanisms, indicating strong selection of the gut microbiome by house fly larvae. In addition, the gut microbiome of larvae reared on sludge-based substrate had higher diversity when weighting for rare species and a higher coverage of "carbohydrate transport and metabolism" genes compared to brewery by-product-based substrate. A positive correlation between coverage of "pyridoxal-P synthesis" and larval survival and substrate conversion efficiency suggests that microbial synthesis of vitamin B6 could enhance larval performance. Additionally, a negative correlation between coverage of the "Entner-Doudoroff pathway" and "homoprotocatechuate degradation" and substrate conversion indicates microbial competition for sugars and aromatic amino acids. Together, these results reveal how the host selects on gut microbiomes with metabolic potential that is optimized toward the conversion of substrates that may be ultimately valuable for commercial insect production.

IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.},
}

@article {pmid41973609,
year = {2026},
author = {Jalan-Sakrikar, N and Anwar, AA and Ali, A and Nasser-Ghodsi, N and Felzen, A and Huebert, RC and LaRusso, NF and O'Hara, SP},
title = {Cholangiocyte Biology in Primary Sclerosing Cholangitis and Other Cholangiopathies: Pathogenesis, Clinical Insights, and Experimental Tools.},
journal = {Physiological reviews},
volume = {},
number = {},
pages = {},
doi = {10.1152/physrev.00022.2025},
pmid = {41973609},
issn = {1522-1210},
support = {KL2 TR002379/TR/NCATS NIH HHS/United States ; //PSC Partners Seeking a Cure (PSC)/ ; //American Association for the Study of Liver Diseases (AASLD)/ ; DK117861//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK57993//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; DK57993//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; K2R Award//MC | Center for Clinical and Translational Science, Mayo Clinic (CCaTS)/ ; },
abstract = {Cholangiocytes are specialized epithelial cells that line the intrahepatic and extrahepatic biliary tree and play a critical role in bile modification, liver homeostasis, and response to injury. Cholangiocytes exhibit notable heterogeneity and plasticity, and their dysfunction is central to a spectrum of diseases targeting the bile ducts, collectively called cholangiopathies. These disorders include genetic, infectious, immune-mediated, and malignant diseases, with Primary Sclerosing Cholangitis (PSC) representing one of the most complex and enigmatic of these disorders. PSC is a progressive, fibro-inflammatory disease of the bile ducts that is closely linked to inflammatory bowel disease, carries a heightened risk of cancer, and lacks any approved therapies. This review explores the biology of cholangiocytes, including their development, functional plasticity, and roles in secretion, absorption, and cellular signaling. We provide a detailed examination of cholangiopathies, particularly PSC, a complex cholangiopathy characterized by a paradoxical state of cholangiocyte senescence and hyperproliferation. We describe how immune cell dysfunction, the gut microbiome, genetic predispositions, and environmental factors converge to mediate PSC pathogenesis. We revisit the foundational technologies that empowered early discoveries and shaped the field as we know it today. We also explore how newer techniques such as organoid cultures, single-cell transcriptomics, epigenomics, and spatialomics have transformed our modern understanding of biliary pathophysiology. Lastly, we provide an overview of existing rodent models of cholangiopathies and discuss their relevance to human disease. PSC remains therapeutically unaddressed, and thus ongoing multidisciplinary efforts are essential to developing targeted interventions. This review serves as a comprehensive resource for researchers and clinicians navigating the rapidly evolving landscape of cholangiocyte-centered liver disease research.},
}

@article {pmid41973723,
year = {2026},
author = {Denison, ER and Hillary, LS and Bolanos, HA and Anagu, HI and Emerson, JB},
title = {DNA Viral Size Fraction Metagenomics for Human Stool Samples.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {229},
pages = {},
doi = {10.3791/70187},
pmid = {41973723},
issn = {1940-087X},
mesh = {Humans ; *Feces/virology ; *Metagenomics/methods ; *DNA, Viral/genetics/isolation & purification/chemistry ; *DNA Viruses/genetics/isolation & purification ; },
abstract = {Understanding the healthy human virosphere (the viral component of the microbiome) requires accurate measurements of viral community composition across a diverse range of viral types. Building on prior experience with soil viral community ecology methods, here we demonstrate a series of laboratory approaches for enriching and extracting DNA from extracellular DNA viruses in human stool samples. A working primary protocol is presented, along with options for deviations at different steps. The general approach involves adding a liquid buffer (default: protein-enhanced phosphate buffered saline, PPBS) to facilitate removal of free viral particles from the stool matrix, centrifugation to separate the liquid fraction containing viral particles, filtration (default: 0.2 µm pore size) to remove most cells, concentration of viral particles (default: ultracentrifugation), removal of free nucleic acids with nucleases prior to virion lysis, and then DNA extraction for sequencing. Alternative techniques, including different buffers, filter sizes, and concentration methods, are also noted. Overall, multiple options for generating high-quality viromic DNA for sequencing are offered. Rather than tailoring the approach to specific equipment and resources, the protocol's flexibility should make it broadly applicable across labs with varying standard molecular biology equipment.},
}

Humans
*Feces/virology
*Metagenomics/methods
*DNA, Viral/genetics/isolation & purification/chemistry
*DNA Viruses/genetics/isolation & purification

@article {pmid41973868,
year = {2026},
author = {Zhang, X and Yu, C and Zhang, Z and Liu, M and Huang, X and Bai, D and Yang, R and Wang, P and Yang, C},
title = {The Nasal Microbiome in Inflammation and Disease: Bridging Mechanisms to Therapeutics.},
journal = {Annals of the New York Academy of Sciences},
volume = {1558},
number = {1},
pages = {e70258},
doi = {10.1111/nyas.70258},
pmid = {41973868},
issn = {1749-6632},
support = {82160211//National Natural Science Foundation of China/ ; 20252BAC250088//Jiangxi Provincial Nature Science Foundation/ ; },
mesh = {Humans ; *Microbiota/immunology ; *Inflammation/microbiology/immunology/therapy ; Probiotics/therapeutic use ; *Sinusitis/microbiology/immunology/therapy ; Dysbiosis/microbiology/immunology ; *Nasal Mucosa/microbiology/immunology ; Anti-Bacterial Agents/therapeutic use ; Animals ; Rhinitis, Allergic/microbiology/immunology/therapy ; },
abstract = {The nasal microbiome, an integral component of the upper respiratory tract's microecological system, plays a pivotal role in inflammatory diseases such as allergic rhinitis and chronic sinusitis, which affect a substantial population and markedly reduce quality of life. A healthy nasal flora and its metabolites are crucial for maintaining immune homeostasis and mucosal barrier integrity. This review comprehensively discusses the pathological mechanisms, immune interactions, and clinical intervention strategies involving the nasal microbiota in nasal inflammation. It has been shown that dysbiosis of the nasal flora disrupts immune function and compromises the epithelial barrier, thereby initiating and exacerbating a vicious cycle of inflammation. Furthermore, the formation of bacterial biofilms and the emergence of drug resistance contribute to persistent and recurrent symptoms. Regarding treatment, while antibiotics may offer short-term efficacy, they risk aggravating the microbial imbalance. In contrast, therapies including probiotics, novel immunomodulators, and traditional Chinese medicine demonstrate significant therapeutic potential by restoring microbial balance and modulating immune responses. This review synthesizes current research to provide new perspectives for understanding host-microbiome interactions and to guide future clinical treatments and drug development.},
}

Humans
*Microbiota/immunology
*Inflammation/microbiology/immunology/therapy
Probiotics/therapeutic use
*Sinusitis/microbiology/immunology/therapy
Dysbiosis/microbiology/immunology
*Nasal Mucosa/microbiology/immunology
Anti-Bacterial Agents/therapeutic use
Animals
Rhinitis, Allergic/microbiology/immunology/therapy

@article {pmid41973926,
year = {2026},
author = {Brittain, RSA and Bribiescas, RG and Jasienska, G},
title = {Industrialization increases the estrogen-recycling capacity of the gut microbiome.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {16},
pages = {e2523589123},
doi = {10.1073/pnas.2523589123},
pmid = {41973926},
issn = {1091-6490},
support = {2313905//National Science Foundation (NSF)/ ; },
mesh = {Humans ; *Estrogens/metabolism ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Feces/microbiology ; Adult ; *Gastrointestinal Tract/microbiology/metabolism ; Infant ; },
abstract = {Estrogens influence many aspects of human physiology and health, including fertility, growth, metabolic function, and susceptibility to disease. Up to 65% of circulating estrogens are excreted into the gut via bile, but only 10-15% are eliminated in feces, indicating substantial estrogen reabsorption [H. Adlercreutz and P. Järvenpää, J. Steroid Biochem. 17, 639-645 (1982); A. A. Sandberg and W. R. Slaunwhite, J. Clin. Investig. 36, 1266-1278 (1957)]. This estrogen recycling is enabled by the gut estrobolome, a subset of microbes that deconjugate conjugated estrogens in the gastrointestinal tract, facilitating their reabsorption into systemic circulation [C. S. Plottel and M. J. Blaser, Cell Host Microbe 10, 324-335 (2011)]. To date, it is not known if populations differ in this microbial function, and little is known about its determinants. Here we analyze estrobolomes using publicly available gut microbiome data from 24 populations spanning four continents and subsistence modes ranging from hunting and gathering to pastoralism, rural farming, and industrialized agriculture. We show that industrialized populations exhibit up to seven times greater estrogen-recycling capacity and nearly twofold higher estrobolome diversity compared with nonindustrial groups. We further find that formula-fed infants display two- to threefold higher recycling capacity and as much as eleven times greater estrobolome diversity than breastfed counterparts, revealing early-life divergence in microbial estrogen metabolism. By contrast, sex, age, and BMI are not associated with estrobolome characteristics. These findings demonstrate the crucial impact of industrialized lifestyles, including formula feeding, on the microbial capacity to influence systemic estrogen levels, with implications for life history, reproductive biology, and estrogen-associated diseases, including cancer.},
}

Humans
*Estrogens/metabolism
*Gastrointestinal Microbiome/physiology
Female
Male
Feces/microbiology
Adult
*Gastrointestinal Tract/microbiology/metabolism
Infant

@article {pmid41973972,
year = {2026},
author = {Asa'ad, F and Hasuike, A and Yoshida, K and Lira-Junior, R and Chaurasia, A and Giraldo-Osorno, PM and Garaicoa-Pazmino, C},
title = {Impact of OMICS Technologies in Our Understanding of the Pathogenesis of Peri-Implantitis.},
journal = {Clinical and experimental dental research},
volume = {12},
number = {2},
pages = {e70350},
pmid = {41973972},
issn = {2057-4347},
support = {HJSV2023038//Hjalmar Svensson Foundation/ ; },
mesh = {*Peri-Implantitis/genetics/immunology/etiology/metabolism ; Humans ; Proteomics/methods ; *Genomics/methods ; Metabolomics/methods ; Epigenomics ; Transcriptome ; Microbiota ; },
abstract = {OBJECTIVES: To evaluate the contribution of OMICS technologies to the understanding of peri-implantitis pathogenesis from a host immune perspective.

MATERIALS AND METHODS: A narrative review was conducted based on electronic searches of PubMed, MEDLINE, and Google Scholar up to October 2025, complemented by manual screening of reference lists. Search terms combined "peri-implantitis" with OMICS-related keywords, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, RNA sequencing, single-cell and spatial transcriptomics, multi-omics, and machine learning. Studies were selected based on clinical relevance and their contribution to understanding peri-implantitis pathogenesis from a host immune perspective.

RESULTS: Among the studies included, most focused on transcriptomic analyses, while fewer investigated genomics, epigenomics, proteomics, or metabolomics. Integration across OMICS layers highlights peri-implantitis as a multilayered host-microbiome molecular ecosystem. Genomic variants affecting metal ion binding, cytoskeletal organization, and cell adhesion may predispose tissues to heightened immune sensitivity. Epigenomic analyses revealed differential DNA methylation of immune-regulatory and signaling genes, linking environmental exposures, such as smoking, to altered host responses. Transcriptomic studies, including bulk, single-cell, and spatial approaches, demonstrated dysregulated immune signaling, pro-inflammatory fibroblast-neutrophil interactions, oxidative stress, and dysregulated tissue remodeling. Proteomic profiling of peri-implant crevicular fluid confirmed elevated neutrophil-derived antimicrobial proteins and inflammatory mediators, reflecting active host defense responses. Metabolomic studies identified disease-specific alterations in amino acids, organic acids, and polyamines, which correlate with pathogenic microbial taxa and modulate immune and tissue responses. Collectively, these findings reveal convergent pathways of immune dysregulation, extracellular matrix disruption, tissue remodeling, and host-microbiome crosstalk as central features of peri-implantitis.

CONCLUSIONS: OMICS analyses show that peri-implantitis is a complex host-microbiome molecular ecosystem. Integrated molecular insights provide a foundation for biomarker development, predictive diagnostics, and targeted interventions. However, future studies with larger cohorts and functional validation are needed to support clinical translation.},
}

*Peri-Implantitis/genetics/immunology/etiology/metabolism
Humans
Proteomics/methods
*Genomics/methods
Metabolomics/methods
Epigenomics
Transcriptome
Microbiota