@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

@article {pmid41974263,
year = {2026},
author = {Chen, R and Liu, L and Lin, Y and Yang, B and Wang, J},
title = {Chemotherapy-Induced Gastrointestinal Dysfunction: Mechanisms and Integrative Western-Chinese Medicine Strategies.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108191},
doi = {10.1016/j.phrs.2026.108191},
pmid = {41974263},
issn = {1096-1186},
abstract = {Chemotherapy-induced gastrointestinal dysfunction (CIGD) is a multifactorial clinical syndrome that substantially limits treatment tolerance, continuity, and quality of life in patients with cancer. Although targeted therapy and immunotherapy have expanded therapeutic options, chemotherapy remains a cornerstone of cancer treatment, and its gastrointestinal toxicities continue to pose major clinical challenges. Current evidence indicates that CIGD arises not from isolated lesions, but from interconnected pathological processes involving oxidative stress, mucosal barrier disruption, gut microbiota dysbiosis, immune amplification, and enteric nervous system (ENS) remodeling. In particular, microbiota-immune interactions and ENS-associated neuroimmune alterations may contribute to the persistence and amplification of tissue injury. Existing management strategies are still focused largely on symptom control and often do not adequately address the underlying biological drivers of dysfunction. In this review, we summarize the major mechanistic modules involved in CIGD and discuss a conceptual translational framework for mechanism-informed intervention. This framework includes: (1) targeted approaches aimed at interrupting key pathogenic loops, such as oxidative injury, microbial metabolite-related toxicity, and barrier dysfunction; (2) parameterizable integrative Western and Chinese medicine approaches, in which acupuncture and Chinese herbal formulae are considered as testable adjunctive modules alongside evidence-based supportive care; and (3) stratified management informed by interindividual variation in genetic background, drug metabolism, and microbiome features. On this basis, we further propose a working "niche medicine" framework that views CIGD as dysregulation of multicellular and molecular microenvironments across the gut ecosystem. This perspective may help connect mechanistic research with longitudinal monitoring, patient stratification, and multimodal intervention design, and may support a shift in CIGD management from predominantly symptomatic relief toward mechanism-guided restoration and recovery.},
}

@article {pmid41974411,
year = {2026},
author = {Ahmad, F and Sun, C and Muhammad, A and Shao, Y},
title = {Microplastics and pathogen risk across ecosystems: From biofilm to antimicrobial resistance and host susceptibility.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128128},
doi = {10.1016/j.envpol.2026.128128},
pmid = {41974411},
issn = {1873-6424},
abstract = {Microplastics (MPs) are ubiquitous in terrestrial and aquatic ecosystems, where they rapidly acquire organic coatings and biofilms (the plastisphere) and interact with co-occurring chemical pollutants. However, the conditions under which MPs become ecologically relevant in increasing disease risk remain underexplored. A key controversy is that microbial detection or enrichment on MPs is often treated as evidence of pathogen "vectoring," yet most studies do not quantify viability/infectivity, detachment, or delivered dose to hosts under environmentally realistic conditions. This review synthesizes evidence on MP-pathogen interactions and dispersal across ecosystems and reframes "MPs as vectors" through a vectorial-capacity lens that distinguishes association from transmission relevance and links MP-mediated risk to measurable dose delivery at host-relevant interfaces. Across ecosystems, evidence supports biofilm-driven persistence and enrichment of opportunistic taxa, but direct demonstrations of MP-mediated infection remain limited. We further highlight an unresolved issue, whether MPs confer unique transmission advantages compared with size-matched natural particulates that also sorb microbes and contaminants but are rarely used as comparators. We examine host susceptibility as a risk multiplier: MP exposure can compromise epithelial barriers via oxidative stress, modulate innate immunity, and disrupt microbiome-mediated colonization resistance. Plastisphere biofilms may also function as eco-evolutionary microhabitats that enrich antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), with plausible enhancement of horizontal gene transfer, although field-scale attribution is still scarce. Finally, we outline priorities for standardized evidence grading, comparator-based study designs, and quantitative metrics (loading, viability decay, detachment kinetics) to enable risk attribution and guide monitoring and mitigation.},
}

@article {pmid41974522,
year = {2026},
author = {Druzhinin, VG and Baranova, ED and Demenkov, PS and Matskova, LV and Larionov, AV and Zhivotovskiy, AS and Yuzhalin, AE},
title = {Bacterial effectors disrupt host DNA: Linking sputum microbiome profiles to chromosomal aberrations in leukocytes of lung cancer patients and healthy controls.},
journal = {Mutation research. Genetic toxicology and environmental mutagenesis},
volume = {911},
number = {},
pages = {503928},
doi = {10.1016/j.mrgentox.2026.503928},
pmid = {41974522},
issn = {1879-3592},
mesh = {Humans ; *Sputum/microbiology ; *Lung Neoplasms/genetics/microbiology/pathology ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; *Chromosome Aberrations ; *Leukocytes/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Case-Control Studies ; Aged ; Adult ; },
abstract = {BACKGROUND: Bacterial microbiome of the respiratory tract can influence the development of respiratory diseases, including lung cancer (LC). However, establishing a causal link between certain members of the respiratory microbiota and LC is challenging. This study aimed to analyze the sputum microbiome and its association with chromosome damage in leukocytes of LC patients and healthy controls.

METHODS: Sputum samples from 150 LC patients and 104 healthy donors were analyzed by 16S rRNA gene sequencing. Chromosomal aberrations (CA) were assessed cytogenetically in lymphocytes. Bioinformatics analyses examined correlations between sputum microbiome profiles and chromosome damage.

RESULTS: The sputum microbiomes of LC patients and healthy controls did not have significant indicators for the species richness index and the Faith's phylogenetic diversity, whereas the comparison index in LC patients was significantly lower than that of healthy controls. Bacterial community structures (beta diversity) were also similar in patients and controls. We showed higher abundance of Bacillus, Prevotella, Granulicatella and Bergeyella in LC patients' sputum. LC patients exhibited increased aberrant metaphases, as well as all major CA types, compared to healthy subjects. Positive associations between aberrant metaphases and bacteria from Fusobacteria phylum, genera Bacteroidetes, Leptotrichia, Lactobacillus, Macellibacteroides, Mycoplasma, Lachnoanaerobaculum, Bulleidea, and Dialister were found in LC patients. In healthy donors, CA only correlated with Anaerorhabdus and Peptococcus. Streptobacillus and Zhouia positively correlated with the proportion of aberrant metaphases in both LC patients and in healthy individuals.

CONCLUSIONS: Specific bacterial genera in sputum associate with chromosomal damage in host cells, suggesting possible genotoxic potential of these bacteria.},
}

Humans
*Sputum/microbiology
*Lung Neoplasms/genetics/microbiology/pathology
*Microbiota/genetics
Male
Female
Middle Aged
*Chromosome Aberrations
*Leukocytes/microbiology/pathology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
Case-Control Studies
Aged
Adult

@article {pmid41974712,
year = {2026},
author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y},
title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71718-z},
pmid = {41974712},
issn = {2041-1723},
support = {R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.},
}

@article {pmid41974724,
year = {2026},
author = {Lydon, EC and Deosthale, P and Glascock, A and Phan, HV and Osborne, CM and Leroue, MK and Allen, J and Mick, E and Wagner, BD and DeRisi, JL and Ambroggio, L and Mourani, PM and Langelier, CR},
title = {Host-microbiome archetypes differentiate infection from pathogen carriage in the human lower airway.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71863-5},
pmid = {41974724},
issn = {2041-1723},
support = {R01HL155418//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL124103//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI182308//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {Distinguishing lower respiratory tract infection (LRTI) from incidental pathogen carriage (IPC) is clinically challenging. The immunologic and microbial factors defining the states of LRTI and IPC are poorly understood. Here, we perform host-microbe metatranscriptomic profiling of tracheal aspirates from 326 mechanically ventilated children with clinically adjudicated LRTI (n = 207), IPC (n = 70), or non-infectious respiratory failure (n = 49). In the airway microbiome, LRTI shows reduced alpha diversity and taxonomic richness, while IPC displays greater bacterial abundance, enrichment in respiratory anaerobes, and increased metabolic activity. At the host level, patients with LRTI exhibit a distinct lower airway transcriptional signature of innate and adaptive immune activation compared to those with IPC, who have similar transcriptional profiles to uninfected controls. Mediation analyses suggest the airway microbiome influences the host response to pathogens. An integrated host-microbe metatranscriptomic classifier accurately discriminates LRTI from IPC and controls (AUC = 0.89, 95% confidence interval (CI) 0.85-0.92). The single gene FABP4, encoding a macrophage-associated lipid chaperone and recently described pneumonia biomarker, performs similarly when combined with alpha diversity; FABP4 protein alone achieves an AUC = 0.88 (95% CI 0.82-0.93). Together, our findings reveal distinct ecological and immunologic archetypes defining LRTI and IPC, and support data-driven, biology-informed LRTI diagnostics incorporating host and microbial features.},
}

@article {pmid41975031,
year = {2026},
author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE},
title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10048-8},
pmid = {41975031},
issn = {2399-3642},
support = {DairyBio//Dairy Australia/ ; },
abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.},
}

@article {pmid41961090,
year = {2026},
author = {Cao, Z and Chen, T and Xie, J and Xie, J},
title = {Artificial Intelligence in Functional Polysaccharides for Food Applications: Process Optimization, Structure-Function Decoding, and Rational Design.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c00806},
pmid = {41961090},
issn = {1520-5118},
abstract = {Functional polysaccharides are widely used as food ingredients but are hindered by extreme structural heterogeneity, poorly defined structure-function relationships, and inefficient trial-and-error production workflows. This review provides an integrative synthesis of how AI is reshaping functional polysaccharide research toward food-grade ingredients and formulations. We organize recent advances into a three-stage framework: (1) efficiency amplification, where machine-learning models improve extraction/fermentation optimization and enable rapid analysis when coupled with spectroscopic fingerprints; (2) mechanism-informed hypothesis generation, where deep Deep-QSAR, graph-based learning, and interpretable modeling begin to uncover quantitative links between structural motifs and functional properties, including microbiome-mediated effects relevant to health; and (3) design assistance, in which AI supports precision-guided polysaccharide engineering and formulation for targeted food functionalities. By bridging computational advances with experimental validation, this review provides a cohesive roadmap for polysaccharide discovery and discusses key translational barriers─data scarcity and standardization, model generalizability and interpretability, and regulatory acceptance─highlighting practical strategies for AI-guided polysaccharide discovery and application.},
}

@article {pmid41961102,
year = {2026},
author = {King, AC and Seiler, K and Swanson, K and Ciorba, MA and Alvarado, DM},
title = {IBD risk locus rs1077773 enhances aryl hydrocarbon receptor activity and modulates immune cell function in vitro.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {75},
number = {1},
pages = {},
pmid = {41961102},
issn = {1420-908X},
support = {R01-AI167285/DK/NIDDK NIH HHS/United States ; #648423//Crohn's and Colitis Foundation/ ; #UL1TR002345//Institute of Clinical and Translational Sciences/ ; },
mesh = {Humans ; *Receptors, Aryl Hydrocarbon/genetics ; Polymorphism, Single Nucleotide ; *Inflammatory Bowel Diseases/genetics/immunology ; *Basic Helix-Loop-Helix Proteins/genetics ; Cytochrome P-450 CYP1A1/genetics ; Genetic Predisposition to Disease ; Cytochrome P-450 CYP1B1/genetics ; Organoids ; Male ; Macrophages/immunology ; Female ; },
abstract = {INTRODUCTION: The inflammatory bowel diseases (IBD) Crohn's disease (CD) and ulcerative colitis (UC) are disorders that cause chronic inflammation of the gastrointestinal tract. Both genetic and environmental factors contribute to the pathogenesis of IBD. There are currently >200 known genetic susceptibility loci for the development of IBD. The physiological impact of the majority of these loci remain a gap in our knowledge. One such locus is the single nucleotide polymorphism rs1077773, located ~56 kbp downstream from the aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that is crucial to maintaining intestinal homeostasis. We hypothesized that rs1077773 enhances AHR activity to regulate mucosal immune response and maintain intestinal homeostasis.

METHODS: All study procedures and reagents were approved by the Washington University Institutional Review Board (#202011003). Patient biopsies were collected at Barnes Jewish Hospital and genotyped using the IBD Genetics Consortium custom GSA SNP chip (Broad Institute) followed by imputation using TopMed Imputation Server at University of Michigan. Patient derived organoids (PDOs; N=3 G/G, N=4 G/A, N=5 A/A) were derived and maintained in 3D culture and supplemented with 50% L-WRN conditioned medium with passage every 3-4 days as previously described. PDOs were treated with AHR agonist 6-Formylindolo[3,2-b]carbazole (FICZ) or vehicle for 48 h. Expression of AHR and its transcriptional targets Cytochrome P450 1A1 (CYP1A1) and CYP1B1 was assessed by RT-qPCR. Blood was collected from pediatric patients undergoing intestinal resection at St. Louis Children's Hospital and was genotyped with custom TaqMan SNP assay (N=3 G/G, N=5 G/A). Peripheral blood monocyte-derived macrophages (MDMΦs) were treated with lipopolysaccharide in the presence or absence of AHR ligands FICZ or indole-3-carboxaldehyde for 24 h. Cytokine levels in culture supernatant were measured via using the ProcartaPlex human cytokine, chemokine, and growth factor 45-plex (ThermoFisher) on a Luminex FLEXMAP3D instrument.

RESULTS: AHR expression was similar across genotypes and treatments. PDOs homozygous for rs1077773 demonstrate enhanced CYP1A1 expression in response to AHR activation. In MDMΦs, cytokine secretion was stimulated by LPS treatment and was abrogated by FICZ treatment. MDMΦs with rs1077773 alternate allele demonstrated significant reduction in secretion of 12 cytokines and chemokines.

CONCLUSIONS: This work demonstrates that rs1077773 enhances AHR activity and modulates epithelial and immune cell function in vitro. Further mechanistic understanding of this locus and its correlates could improve our understanding of the molecular mechanisms of IBD susceptibility and may lead to novel personalized therapeutic approaches in IBD.},
}

Humans
*Receptors, Aryl Hydrocarbon/genetics
Polymorphism, Single Nucleotide
*Inflammatory Bowel Diseases/genetics/immunology
*Basic Helix-Loop-Helix Proteins/genetics
Cytochrome P-450 CYP1A1/genetics
Genetic Predisposition to Disease
Cytochrome P-450 CYP1B1/genetics
Organoids
Male
Macrophages/immunology
Female

@article {pmid41961107,
year = {2026},
author = {Rai, SK and Gupta, S and Sarangi, PP},
title = {Metabolite sensing receptors in macrophage reprogramming: from inflammation to resolution.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {75},
number = {1},
pages = {},
pmid = {41961107},
issn = {1420-908X},
support = {MoE-STARS/STARS-2/2023-0939//Ministry of Education, Govt. of India/ ; },
mesh = {Humans ; *Macrophages/immunology/metabolism ; Animals ; *Inflammation/immunology/metabolism ; *Receptors, G-Protein-Coupled/metabolism/immunology ; },
abstract = {BACKGROUND: Macrophages are central to innate immunity, orchestrating both the inflammatory and resolution phases of host defense. Emerging evidence indicates that immunometabolic crosstalk critically dictates macrophage polarization and functions. Disruptions in cellular metabolism can impair these regulatory mechanisms, leading to dysfunctional immune responses associated with various disease pathologies. A key aspect of this regulation involves metabolite-sensing receptors that detect changes in intracellular metabolic intermediates and in extracellular metabolites derived from the diet, host tissues, and the microbiome.

METHODS: We have conducted a literature review of original research and review articles on metabolite-sensing receptors and their roles in immune cell function, drawn from central databases including PubMed and Google Scholar.

RESULTS AND CONCLUSION: A major class of extracellular metabolite-sensing receptors is G-protein-coupled receptors (GPCRs), which can directly or indirectly modulate macrophage activation, migration, cytokine production, and metabolic reprogramming. By fine-tuning macrophage-specific functions, metabolite-sensing receptors act as critical regulatory nodes in both inflammation and immune homeostasis, beyond their canonical role in sensing metabolic cues. This review provides a comprehensive overview of the metabolite-sensing receptor interactome, highlighting their central role in macrophage biology and underscoring their potential as therapeutic targets in inflammatory and metabolic diseases.},
}

Humans
*Macrophages/immunology/metabolism
Animals
*Inflammation/immunology/metabolism
*Receptors, G-Protein-Coupled/metabolism/immunology

@article {pmid41961381,
year = {2026},
author = {Low, A and Juang, YR and Ivan, FX and Ang, L and Ooi, LHS and Chan, SWJ and Mac Aogain, M and Jaggi, TK and Chotirmall, SH and Boucher, YF and Yii, ACA and Koh, MS and Lim, DWT and Lee, JWJ and Seow, WJ},
title = {Bacterial taxa associated with lung cancer cases in Southeast Asians: a pilot case-control study.},
journal = {Cellular oncology (Dordrecht, Netherlands)},
volume = {49},
number = {2},
pages = {},
pmid = {41961381},
issn = {2211-3436},
abstract = {PURPOSE: Lung cancer is the leading cause of cancer-related mortality worldwide, yet its underlying mechanisms remain unclear. Disruptions in the respiratory microbiome may promote inflammation and carcinogenesis. This study aimed to comprehensively compare genus-level sputum microbiota between lung cancer patients and healthy controls in a multiethnic Southeast Asian population.

METHODS: Sputum samples were collected from lung cancer patients across three Singapore hospitals. Socio-demographic data were obtained via questionnaire. We analyzed 16S rRNA amplicon sequences from 70 lung cancer patients and 47 healthy controls from a separate local cohort, using identical sequencing protocols to minimize batch effects. Alpha- and beta-diversity metrics, random forest models, and ANCOM-BC2 were used to identify microbial features associated with lung cancer and host characteristics.

RESULTS: Lung cancer cases showed significantly reduced genus richness compared to controls. Beta-diversity (Aitchison distance) differed by case-control status, sex, age, and smoking history. ANCOM-BC2 identified Lactobacillus as differentially enriched in cases. However, this enrichment did not pass the pseudo-count test among never-smokers. Further sex-stratified analysis revealed that the Lactobacillus enrichment was driven primarily by male cases. Conversely, [Eubacterium] nodatum group, Mogibacterium, and Campylobacter emerged as robust inverse signatures for lung cancer, with their depletion consistently supported across stratified and unstratified differential abundance analyses, random forest modeling, and Wilcoxon rank-sum tests. However, these findings may still be subjected to residual confounding by exogenous factors, such as medication use, which could not be adequately adjusted for between case-control groups.

CONCLUSION: This pilot case-control study, conducted in a multiethnic Southeast Asian population, identified distinct respiratory microbiota signatures associated with lung cancer using robust differential abundance and machine-learning methods, providing preliminary evidence for a potential role of the respiratory microbiome to lung carcinogenesis, warranting validation in larger, longitudinal studies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13402-026-01193-7.},
}

@article {pmid41961384,
year = {2026},
author = {Trivedi, A and Roy, S and More, M and Bose, D and Saha, P and Kumar, R and Sarkar, S and Skupsky, J and Tuteja, A and Sullivan, K and Klimas, N and Chatterjee, S},
title = {Spermidine Attenuates Neuroimmune Dysfunction in Gulf War Illness via Modulation of the Gut- Brain Axis.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {41961384},
issn = {1559-1182},
mesh = {Animals ; *Spermidine/pharmacology/therapeutic use ; *Persian Gulf Syndrome/drug therapy/immunology/microbiology/metabolism ; *Brain/drug effects/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; Male ; Receptors, Aryl Hydrocarbon/metabolism ; HMGB1 Protein/metabolism ; Receptor for Advanced Glycation End Products/metabolism ; *Brain-Gut Axis/drug effects ; },
abstract = {Gulf War illness (GWI) affects nearly one-third of US veterans deployed during the 1990-1991 Gulf War (GW) and is characterized by chronic fatigue, neuroinflammation, and gut dysbiosis. Through comprehensive fecal metabolomics sequencing, our lab previously reported the depletion of beneficial metabolites including spermidine in the preclinical GWI mouse model. Spermidine is an endogenously synthesized polyamine known for its anti-inflammatory and mucosal barrier protective effects in various pathological diseases. Given its established role in mitigating intestinal inflammation and maintaining homeostasis, this study investigated the therapeutic potential of spermidine in a persistent (22 weeks) GWI mouse model, with a specific focus on gut-brain axis regulation. Our results demonstrated that spermidine effectively restored both microbial richness and diversity by selectively enriching beneficial bacterial taxa and suppressing growth of opportunistic pathogens, which are otherwise dysregulated following exposure to GW chemicals. Spermidine treatment also improved gut epithelial barrier integrity and reduced epithelial release of high-mobility group box 1 (HMGB1) into systemic circulation. Recent studies on GWI have implicated a critical role of gut-derived damage-associated molecular patterns (DAMPs), particularly HMGB1 in mediating neuroinflammation. Our findings indicate that systemic levels of HMGB1 critically influence the extent of blood-brain barrier (BBB) disruption and subsequent microglial activation. Mechanistically, spermidine activated intestinal aryl hydrocarbon receptor (AhR)/nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) signaling, which played a role in limiting intestinal HMGB1 release and suppressing downstream receptor for advanced glycation end-product (RAGE)-mediated microglial activation in the brain. In vitro results indicate spermidine promoted AhR/Nrf2 nuclear translocation which reduced LPS-induced HMGB1 release from primary intestinal epithelial cells (IECs), effects abrogated by AhR inhibition. Additionally, we observed that HMGB1 directly induces microglial activation via RAGE receptors in immortalized microglial (IMG) cell lines in a dose-dependent manner. These results demonstrate that spermidine decreases neuroinflammation by modulating gut-brain axis pathophysiology associated with GWI. Together, this study demonstrates the therapeutic role of spermidine in ameliorating systemic and neurological disturbances in GWI.},
}

Animals
*Spermidine/pharmacology/therapeutic use
*Persian Gulf Syndrome/drug therapy/immunology/microbiology/metabolism
*Brain/drug effects/metabolism
*Gastrointestinal Microbiome/drug effects
Mice
Mice, Inbred C57BL
Male
Receptors, Aryl Hydrocarbon/metabolism
HMGB1 Protein/metabolism
Receptor for Advanced Glycation End Products/metabolism
*Brain-Gut Axis/drug effects

@article {pmid41961453,
year = {2026},
author = {Daly, L and Sullivan, ES and Fouhy, F and Watkins, C and Linaries, D and Power, D and O'Suilleabhain, C and O'Sullivan, A and O'Toole, P and Ross, P and Stanton, C and Ryan, A},
title = {The gut microbiota of hepato-pancreatico-biliary and gastric cancer patients is altered in composition and functionality.},
journal = {Irish journal of medical science},
volume = {},
number = {},
pages = {},
pmid = {41961453},
issn = {1863-4362},
support = {SFI/12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; },
}

@article {pmid41961543,
year = {2026},
author = {Shamabadi, A and Arabzadeh Bahri, R and Arab Bafrani, M and Karimi, H and Asadigandomani, H and Vahidi, H and Akhondzadeh, S},
title = {The gut-brain axis and inflammatory mediators in suicide and mental disorders with high suicide rates: a review of current evidence.},
journal = {Dialogues in clinical neuroscience},
volume = {28},
number = {1},
pages = {145-156},
doi = {10.1080/19585969.2026.2636468},
pmid = {41961543},
issn = {1958-5969},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mental Disorders/metabolism/immunology/microbiology/psychology ; *Suicide/psychology ; *Brain/metabolism/immunology ; *Brain-Gut Axis/physiology ; *Inflammation Mediators/metabolism ; *Inflammation/metabolism ; Animals ; },
abstract = {The interplay between gastrointestinal microbiota and mental disorders has recently been spotlighted. This review investigated discrete evidence suggesting associations between the gastrointestinal microbiome and inflammation with suicide. Fusicatenibavter, Hungatella, Veillonella, and Megasphaera have positive associations, but Clostridium, Butyricicoccus, Desulfovibrio piger, and Parabacteroides merdae have negative associations with suicidality. Additionally, lower species uniformity index, higher intestinal fatty acid binding protein secretion, lower zonulin secretion, higher interleukin-6 in cerebrospinal fluid, and laxative abuse are associated with suicidality. As nearly 90% of suicides occur in patients with mental disorders, the interaction between the gut microbiota and inflammation with these disorders together was also documented. Regarding this, major depressive disorder, psychosis and schizophrenia, generalised anxiety disorder, and substance use disorder were investigated. Bacteroidetes and Firmicutes show prominent changes in most cases. In addition, gut bacterial and non-bacterial microbiome alterations and subsequent dysbiosis may contribute to inflammation, in which cytokines affect microglial activity. Meanwhile, impaired intestinal homeostasis may influence these disorders through the vagus nerve, the hypothalamus-pituitary-adrenal axis, and the kynurenine pathway. Beyond these, direct effects of the gut microbiome on immunity are being hypothesised. In conclusion, the gut microbiota imbalance may influence the nervous system environment from non-inflammatory to inflammatory caused by pro-inflammatory cytokine influx into the brain. Consequently, microbiota imbalances may be associated with mental disorders. Specifically, limited evidence indicated possible links between microbiome alterations and suicide, highlighting the need for further research clarifying these associations and underpinning mechanisms. Other factors, including genetic vulnerability, environmental influences, and neurochemical pathways, should also be considered.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Mental Disorders/metabolism/immunology/microbiology/psychology
*Suicide/psychology
*Brain/metabolism/immunology
*Brain-Gut Axis/physiology
*Inflammation Mediators/metabolism
*Inflammation/metabolism
Animals

@article {pmid41961656,
year = {2026},
author = {Zhang, Y and Zhang, G},
title = {Causal relationship between gut microbiome, plasma metabolites, inflammation, and aortic stenosis: A multi-omics Mendelian randomization analysis.},
journal = {Medicine},
volume = {105},
number = {15},
pages = {e48238},
doi = {10.1097/MD.0000000000048238},
pmid = {41961656},
issn = {1536-5964},
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Aortic Valve Stenosis/genetics/blood/microbiology ; *Inflammation/blood/genetics ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; Biomarkers/blood ; Metabolomics ; Multiomics ; },
abstract = {As life expectancy increases and the population ages, aortic stenosis (AS) is the most common heart valve disease. Despite rapid improvements in interventional treatment options in recent years, morbidity and mortality from asymptomatic AS remain high. To date, there is no pharmacological therapy to prevent AS. In this study, we used multi-omics to systematically investigate potential causal association between the gut microbiome, human blood metabolites, inflammation and risk of AS, and search for potential biomarker for AS. Single-nucleotide polymorphisms associated with 207 gut microbiota, 1091 blood metabolites and the ratios of 309 metabolites, 731 immune cell phenotypes, 91 circulating inflammatory proteins, as exposures all were selected from recent large genome-wide association study and explored their causal association with AS using Mendelian randomization methods. We used the inverse variance weighted estimation method as the main method and other methods as supplementary methods. Mendelian randomization analysis has shown that 7 gut microbiota, 80 metabolites, 29 immune cells phenotypes, and 6 circulating inflammatory proteins are causally associated with AS. Co-localization analysis showed a significant correlation between 1-stearoyl-2-acryloyl-GPE levels and AS, with a P-value of .981 for posterior probability for hypothesis 4. In addition, metabolic pathway analysis revealed that the valine, leucine, and isoleucine biosynthesis (P = .0312) pathways were associated with AS. Four omics, including 207 gut microbiota, 1091 blood metabolites and the ratios of 309 metabolites, 731 immune cells, and 91 inflammatory proteins were used in this study to explain the causal relationship between multi-omics and AS.},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
*Aortic Valve Stenosis/genetics/blood/microbiology
*Inflammation/blood/genetics
Polymorphism, Single Nucleotide
Genome-Wide Association Study
Biomarkers/blood
Metabolomics
Multiomics

@article {pmid41961851,
year = {2026},
author = {Davey, SD and Forde-Thomas, JE and Hulme, BJ and Lees, K and Costain, AH and Evans, M and Rinaldi, G and Frame, L and Stojanovski, L and Simeons, FRC and Tavendale, A and MacLeod, AK and Pichon, R and Lee, YH and Polak, O and Chalmers, IW and Dankwa, B and Odhiambo, BK and Guimaraes, VH and Hegarty, M and Swain, MT and Aubrey, W and Caldwell, N and MacDonald, AS and Gilbert, IH and Baragaña, B and Read, KD and Hoffmann, KF},
title = {Use of a cytochrome P450 humanized mouse model to refine schistosomiasis drug discovery.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {15},
pages = {e2600197123},
doi = {10.1073/pnas.2600197123},
pmid = {41961851},
issn = {1091-6490},
support = {222153/Z/20/Z//Wellcome/ ; MR/W013568/1//UK Research and Innovation (UKRI)/ ; },
mesh = {Animals ; Mice ; *Cytochrome P-450 Enzyme System/metabolism/genetics ; Humans ; Disease Models, Animal ; Schistosoma mansoni/drug effects ; Praziquantel/pharmacology/therapeutic use ; *Drug Discovery/methods ; *Schistosomiasis mansoni/drug therapy/parasitology ; *Schistosomiasis/drug therapy/parasitology ; Anthelmintics/pharmacology ; Female ; Mice, Transgenic ; *Schistosomicides/pharmacology ; },
abstract = {Control of schistosomiasis, a neglected tropical disease caused by infection with Schistosoma spp., remains reliant on a single chemotherapy, praziquantel (PZQ). This strategy presents a risk to global health should PZQ-resistant schistosomes establish in endemic areas and justifies the search for new drugs. However, species-specific metabolic differences between humans and preclinical models hinder the optimization of next-generation anti-schistosomal therapeutics. Here, to bypass these species-specific limitations, we exploited a humanized mouse model, 8HUM, engineered to express the principal human Phase I cytochrome P450 enzymes (CYP1A1/2, CYP2C9, CYP2D6, CYP3A4/7) as well as the transcription factors constitutive androstane receptor and pregnane X receptor in place of 35 murine orthologs. We characterized Schistosoma mansoni development, immunopathology, hepatic transcriptomic responses, intestinal microbiome changes, and PZQ metabolism as well as PZQ efficacy in 8HUM vs. wild-type (WT) mice. 8HUM mice supported normal S. mansoni maturation, infection-associated microbiome dysbiosis, Th2-dominant immune responses, and characteristic hepatic pathology. PZQ intrinsic clearance in 8HUM hepatic microsomes mirrored human levels and was >10-fold lower than that found for WT microsomes. Oral dosing revealed human-like PZQ exposures of (R)-PZQ and 4OH-PZQ in 8HUM mice at 25 mg/kg bodyweight and >90% reductions in worm burdens at 100 mg/kg bodyweight (equivalent to that seen in WT mice administered PZQ at 400 mg/kg bodyweight). Our results revealed that 8HUM mice recapitulate key features of murine schistosomiasis while exhibiting human-relevant drug metabolism. These findings establish 8HUM as a refined translational platform for anti-schistosomal drug development, improving predictive accuracy and accelerating therapeutic discovery.},
}

Animals
Mice
*Cytochrome P-450 Enzyme System/metabolism/genetics
Humans
Disease Models, Animal
Schistosoma mansoni/drug effects
Praziquantel/pharmacology/therapeutic use
*Drug Discovery/methods
*Schistosomiasis mansoni/drug therapy/parasitology
*Schistosomiasis/drug therapy/parasitology
Anthelmintics/pharmacology
Female
Mice, Transgenic
*Schistosomicides/pharmacology

@article {pmid41961873,
year = {2026},
author = {Golpasand, S and Ghavi Hossein-Zadeh, N and Ghovvati, S},
title = {Genomic dissection of methane emission traits in cattle: A meta-GWAS and heritability analysis across populations.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0344752},
pmid = {41961873},
issn = {1932-6203},
mesh = {Animals ; Cattle/genetics ; *Methane/metabolism ; *Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; *Quantitative Trait, Heritable ; Genomics ; Quantitative Trait Loci ; },
abstract = {Enteric methane emissions from ruminants represent a significant contributor to agricultural greenhouse gases, necessitating precise genetic tools to guide mitigation strategies. This study aimed to identify genomic regions and estimate heritability parameters associated with methane-related traits in cattle through an integrated meta-analytical framework. The meta-analysis of the genome-wide association studies (meta-GWAS) was carried out with the METAL software, combining SNP level data extracted from published studies. Simultaneously, a distinct random effects meta-analysis of genomic and pedigree-based heritability estimates was performed using Comprehensive Meta-Analysis software. Functional analysis of the post-GWAS, including: Gene Ontology, KEGG, and network-based enrichment analysis, was also performed to describe the biological context of significant genes. The meta-GWAS identified 74 significant SNPs that were significant for the traits of methane, which are related to 113 candidate genes. Functional enrichment analyses revealed pathways related to metabolism, immune response, ion transport, and host-microbiome interactions. The KEGG metabolic pathway emerged as a highly enriched term, encompassing key genes such as: ALDH7A1, CYP51A1, P4HA2, and SHPK, which are involved in amino acid catabolism, lipid processing, and redox regulation functions critical to energy balance and digestive efficiency. Network analysis with Cytoscape has revealed TRPV3, TRPV1, ANK3, PKD2 and SHPK as network hub genes. Heritability meta-analysis indicated that methane production exhibited the moderate genomic (h2 = 0.296) and pedigree-based (h2 = 0.299) heritability estimations, and methane yield was also found to have moderate and high heritability. The findings highlight the potential for methane-related traits as viable targets for genetic selection. This research demonstrates the value of integrating functional genomics and quantitative genetic approaches to enhance understanding of the biological and heritable components of methane emissions, providing a robust foundation for an environmentally sustainable livestock breeding program.},
}

Animals
Cattle/genetics
*Methane/metabolism
*Genome-Wide Association Study
Polymorphism, Single Nucleotide
*Quantitative Trait, Heritable
Genomics
Quantitative Trait Loci

@article {pmid41961886,
year = {2026},
author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T},
title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0345919},
pmid = {41961886},
issn = {1932-6203},
mesh = {Humans ; *Metagenomics/methods ; Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; Neural Networks, Computer ; Multiomics ; },
abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.},
}

Humans
*Metagenomics/methods
Machine Learning
*Gastrointestinal Microbiome/genetics
*Microbiota
Inflammatory Bowel Diseases/microbiology
Neural Networks, Computer
Multiomics

@article {pmid41962053,
year = {2026},
author = {Westcott, RG and Rudzki, EN and Emerson, KJ and Woodley, SK and Kohl, KD},
title = {Exposure to Environmental Microbes Alters Responsiveness of Tadpole Gut Microbiome to Dietary Tannins.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70102},
pmid = {41962053},
issn = {1749-4877},
support = {1945956//National Science Foundation/ ; 2139321//National Science Foundation/ ; },
abstract = {Amphibian larvae consume variable diets in the wild, which can include tannin-rich plant material. Tannins are secondary metabolites that, when consumed, could have complex effects on herbivorous amphibian larvae, including altering their microbiome. Previous studies on the effects of dietary tannic acid on tadpoles were performed using laboratory water, largely devoid of natural microbes. Given that tadpoles acquire much of their gut microbiota from the aquatic environment, we sought to understand the effect of dietary tannins on tadpole size and the gut microbiome when animals were raised in natural pond water, supplying a diverse repertoire of microbes. We raised Green Frog (Lithobates clamitans) tadpoles in autoclaved (microbially depleted) or natural (microbially rich) pond water treatments for 4 weeks. Tadpoles were fed a control diet or a diet containing 2% tannic acid. Tadpoles raised in natural pond water had a greater body mass and length than those raised in autoclaved pond water, but dietary tannins had no effect on body size. Gut bacterial diversity was profiled using 16S rRNA sequencing. The gut microbiome from tadpoles raised in natural pond water was more diverse than that of tadpoles raised in autoclaved pond water. In general, dietary tannins caused a decrease in bacterial diversity and a net reduction in the relative abundance of potentially pathogenic bacterial genera in tadpoles raised in natural pond water but not autoclaved pond water. This study highlights the importance of replicating natural microbial contexts in captive experiments to better investigate biological interactions, such as plant-herbivore and host-microbe interactions.},
}

@article {pmid41962103,
year = {2026},
author = {Paczwa, J and Wu, C and Mulica, J and Siwasan, K and Fuentes, K and Razowska, D},
title = {The gut-brain axis and its role in obesity-induced homeostatic dysregulation.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {3},
pages = {597-604},
doi = {10.36740/WLek/218289},
pmid = {41962103},
issn = {0043-5147},
mesh = {Humans ; *Obesity/physiopathology/metabolism ; *Homeostasis ; *Gastrointestinal Microbiome/physiology ; *Brain/physiopathology/metabolism ; *Gastrointestinal Tract/physiopathology/metabolism ; *Brain-Gut Axis/physiology ; },
abstract = {OBJECTIVE: Aim: The gut-brain axis (GBA) plays a crucial role in maintaining systemic homeostasis through bidirectional communication between the central nervous system and the gastrointestinal tract. This review aims to summarize current evidence regarding the impact of obesity on GBA function and to discuss potential therapeutic strategies targeting this pathway.

PATIENTS AND METHODS: Materials and Methods: A narrative literature review was conducted using scientific publications indexed in databases including PubMed, ScienceDirect, and the European Journal of Endocrinology. Studies addressing obesity-related alterations in neural signaling, gut microbiota composition, and peptide hormone regulation (e.g., cholecystokinin, peptide YY, ghrelin) were analyzed. Particular attention was given to mechanisms involving dopaminergic reward circuits and emerging therapeutic targets such as ghrelin antagonists, gamma-aminobutyric acid modulators, and melanocortin-4 receptor agonists. Evidence indicates that obesity is associated with significant alterations in gut microbiota composition, vagal signaling, and neuroendocrine regulation of appetite and reward pathways. These changes contribute to dysregulation of nutrient absorption, inflammatory responses, and metabolic homeostasis. Both invasive and non-invasive interventions - including dietary modification, microbiome-targeted therapies, pharmacological agents, and neurostimulation techniques - show potential to modulate GBA signaling and restore physiological balance.

CONCLUSION: Conclusions: Understanding the complex relationship between obesity and the gut-brain axis may provide novel therapeutic targets for improving metabolic regulation and reducing obesity-related complications. Further clinical and translational studies are required to confirm the long-term effectiveness of GBAoriented interventions.},
}

Humans
*Obesity/physiopathology/metabolism
*Homeostasis
*Gastrointestinal Microbiome/physiology
*Brain/physiopathology/metabolism
*Gastrointestinal Tract/physiopathology/metabolism
*Brain-Gut Axis/physiology

@article {pmid41962111,
year = {2026},
author = {Sobiech, L and Wójcik, L and Jankowska, N and Turżańska, K},
title = {Periodontitis as a systemic inflammatory disorder - implications for cardiovascular and neurodegenerative diseases.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {3},
pages = {646-650},
doi = {10.36740/WLek/218274},
pmid = {41962111},
issn = {0043-5147},
mesh = {Humans ; *Cardiovascular Diseases/etiology ; *Neurodegenerative Diseases/etiology ; *Periodontitis/complications/microbiology ; *Inflammation/complications ; },
abstract = {OBJECTIVE: Aim: Periodontitis is a chronic inflammatory condition associated with oral microbiome dysbiosis and the dominance of Gram-negative bacteria such as Porphyromonas gingivalis. It is characterized by progressive destruction of the supporting tissues of the tooth, leading to loss of connective tissue attachment, resorption of the alveolar bone, and, consequently to tooth loosening and loss. If left untreated, it leads to recurrent bacteremia and persistent systemic inflammation. The aim of this study is to discuss the mechanisms linking periodontitis to cardiovascular and neurodegenerative diseases.

PATIENTS AND METHODS: Materials and Methods: A comprehensive literature review was conducted examining clinical studies, systematic reviews, and meta-analyses assessing the impact of periodontal disease on the development of cardiovascular and neurodegenerative diseases.

CONCLUSION: Conclusions: Chronic activation of the immune response, oxidative stress, and lipid metabolism disorders promote endothelial dysfunction and the progression of atherosclerosis, increasing the risk of cardiovascular events. At the same time, systemic inflammation can affect the permeability of the blood-brain barrier and exacerbate neuroinflammatory processes, promoting β-amyloid accumulation and the progression of Alzheimer's disease. Analysis of the literature indicates the significant, albeit complex, nature of these relationships, emphasizing the importance of prevention and treatment of periodontal disease as part of comprehensive patient care. The key in the approach to periodontal patients is an interdisciplinary perspective, integrating dentistry, cardiology, neurology, and geriatrics.},
}

Humans
*Cardiovascular Diseases/etiology
*Neurodegenerative Diseases/etiology
*Periodontitis/complications/microbiology
*Inflammation/complications

@article {pmid41962296,
year = {2026},
author = {Wang, Y and Yu, K and Meng, L and Gong, S and Yu, X and Huang, X and Huang, W},
title = {Host proteins and symbiotic bacteria mediate the thermal response differences of the two color phenotypes of Porites lutea to extreme marine heatwaves in Weizhou Island.},
journal = {Marine pollution bulletin},
volume = {229},
number = {},
pages = {119723},
doi = {10.1016/j.marpolbul.2026.119723},
pmid = {41962296},
issn = {1879-3363},
abstract = {Extreme marine heatwaves driven by global warming are the major threat to coral reefs, causing mass coral bleaching and mortality. Color polymorphism is a key coral phenotypic trait, but the mechanisms underlying thermal adaptability differences among color phenotypes remain unclear. This study investigated two Porites lutea phenotypes (green and brown) from Weizhou Island, integrating field surveys, proteomics, and symbiotic microbial community analyses to explore their thermal response differences and molecular mechanisms. Field monitoring during the 2020 marine heatwave revealed a 46% bleaching rate in brown P. lutea, whereas green P. lutea exhibited no bleaching, demonstrating the latter's superior thermal tolerance. Proteomics revealed that green coral hosts maintained thermal adaptability by regulating proteins related to heat shock response, antioxidant defense, and green fluorescent protein (GFP), with GFP expression significantly upregulated by 7.2-fold compared to the brown phenotype. Additionally, the two phenotypes differed in symbiotic bacterial relative abundance: the green P. lutea was dominated by Proteobacteria and Chloroflexi (aiding nitrogen fixation and photosynthesis), while the brown P. lutea was enriched with Thermus and Prosthecochloris (enhancing antioxidant capacity and thermal resistance). No significant differences were found in the community structure or density of Symbiodiniaceae. In conclusion, differential host protein expression and functional complementarity of symbiotic bacteria jointly mediate thermal adaptation differentiation between the two P. lutea phenotypes. This study reveals color phenotypic differentiation as an effective coral survival strategy against environmental stresses, enhancing adaptive potential under future climate change and providing theoretical and technical support for coral reef ecological early warning and restoration under global warming.},
}

@article {pmid41962521,
year = {2026},
author = {Yamada, S and Morine, Y and Ikemoto, T and Saito, Y and Teraoku, H and Miyazaki, K and Shimada, M},
title = {Effect of TU-100 on Colorectal Liver Metastasis in Mouse Model of MASH.},
journal = {The Journal of surgical research},
volume = {322},
number = {},
pages = {10-16},
doi = {10.1016/j.jss.2026.03.073},
pmid = {41962521},
issn = {1095-8673},
abstract = {INTRODUCTION: The incidence of metabolic dysfunction-associated steatohepatitis (MASH) is rapidly increasing, and colorectal liver metastasis (CLM) has been reported to be enhanced in MASH. We previously reported that the herbal medicine Daikenchuto (TU-100) regulates the intestinal microbiome and MASH in a mouse model. This study was performed to examine the effect of TU-100 on CLM using a Western diet (WD)-fed mouse model.

METHODS: Six-week-old male C57BL/6J mice were used. Mice in the WD group were fed a WD, and TU-100 was administered to mice in the WD+TU-100 group. Splenic injection of MC38 colon cancer cells was performed at 16 wk, and mice were sacrificed 2 wk after splenic injection to assess steatosis, fibrosis, and hepatic mRNA expression.

RESULTS: The degree of steatosis was significantly reduced in the WD+TU-100 group compared with the WD group (P < 0.05). The maximum tumor diameter was significantly smaller in the WD+TU-100 group than in the WD group (P < 0.05). Hepatic mRNA expression of serum amyloid A1 and tissue inhibitor of matrix metalloproteinases 1 was significantly suppressed in the WD+TU-100 group compared with the WD group (P < 0.05).

CONCLUSIONS: TU-100 improved hepatic steatosis in an MASH mouse model and suppressed CLM. Suppression of hepatic serum amyloid A1 and tissue inhibitor of matrix metalloproteinases 1 expression may contribute to these effects.},
}

@article {pmid41962594,
year = {2026},
author = {Ott, A and Gül, AZ and Löber, U and Birkner, T and Popova, E and Winter, C and Hadar, R},
title = {Exposure to a High-Fat Diet Compromises Gut Health, Behavior, and HPA Axis Function, with Partial Reversal When Limited to Adolescence.},
journal = {Brain research bulletin},
volume = {},
number = {},
pages = {111883},
doi = {10.1016/j.brainresbull.2026.111883},
pmid = {41962594},
issn = {1873-2747},
abstract = {High-fat diet (HFD) consumption contributes to obesity, yet its impact on females of (pre)reproductive age and the effects of dietary modification after adolescence remain underexplored. This study examined how continuous HFD exposure or an adolescent switch from HFD to a standard diet (SD) shapes the gut microbiome, behavior, neurochemistry, metabolism, and key components of the hypothalamic-pituitary-adrenal (HPA) axis in female rats. Because HPA-axis alterations can occur across generations after HFD exposure, we examined reproductive-tissue HPA-axis components as potential mechanisms of transmission. Females received SD, HFD, or HFD followed by SD after majority of adolescence (postnatal day 60). HFD exposure impaired HPA-axis regulation and switching to SD during adolescence did not prevent persistent dysfunction into adulthood. However, reproductive HPA-axis components remained unaltered. Diet also strongly influenced the microbiome: while HFD disrupted microbial composition in adolescence, switching to SD partially restored it by adulthood. Behavioral and metabolic effects, including increased adiposity and anxiety-like behavior, emerged only with prolonged HFD exposure. Brain neurotransmitter concentrations remained largely unaffected. Overall, dietary history across adolescence and early adulthood shaped long-term HPA-axis function, microbiome composition, and behavioral outcomes. The absence of reproductive HPA-axis alterations suggests it is not a major mediator of maternal HFD-induced intergenerational effects. Persistent HPA-axis dysfunction despite dietary switching indicates limited reversibility, whereas the microbiome showed the greatest adaptive capacity. In contrast, lasting behavioral and metabolic consequences of HFD require continued exposure to adulthood.},
}

@article {pmid41962630,
year = {2026},
author = {Venezia, M and Russo, M and Colomba, P and Zizzo, C and Vinci, M and Marsana, EM and D'Errico, A and Giacalone, I and Duro, G and Moschetti, M},
title = {Epigenetic Modulation of the Gut-Muscle Axis in Pompe Disease: Microbiota Fingerprints to Cellular and Molecular Pathomechanisms.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102364},
doi = {10.1016/j.molmet.2026.102364},
pmid = {41962630},
issn = {2212-8778},
abstract = {Inter-organ cross-talk is increasingly recognised as a fundamental determinant in the pathogenesis of neurodegenerative and neuromuscular disorders, modulating neuroinflammation, protein misfolding, and cellular dysfunction through systemic mediators such as cytokines, adipokines, and growth factors. In neuromuscular diseases, particularly Pompe disease, muscle degeneration is tightly linked to impaired autophagy and chronic inflammation. Recent evidence highlights the gut microbiota as a key regulator of innate and adaptive immune responses, exerting direct effects on skeletal muscle and supporting the existence of a gut-muscle axis. Dysbiosis has been proposed to influence myopathy progression, suggesting that modulation of the intestinal ecosystem may hold therapeutic relevance. Consequently, interventions employing probiotics, prebiotics, and targeted nutritional compounds have emerged as promising strategies to modulate immune activity, attenuate inflammation, and enhance autophagic efficiency, thereby contributing to the restoration of intestinal eubiosis and complementing enzyme replacement therapy.In parallel, epigenetic mechanisms are gaining prominence as additional modulators of pathogenic pathways, with the potential to influence microbiome composition and function. Collectively, these insights position the gut-muscle axis as a central regulatory node in Pompe disease and a compelling target for personalised nutritional and nutraceutical approaches. This review aims to provide a comprehensive examination of the gut-muscle axis and its implications in Pompe disease. Understanding how nutrient-induced changes in microbial gene expression may be harnessed to develop novel, synergistic therapeutic strategies could ultimately improve clinical outcomes and enhance the quality of life of affected individuals.},
}

@article {pmid41962883,
year = {2026},
author = {Li, D and Du, H and Xu, J and Zhang, C and Hou, N},
title = {Bisphenol A-mediated root exudates of ryegrass as potential activators of functional succession in the rhizosphere microorganisms: Mechanistic insights into microbial community assembly and biodegradation.},
journal = {Environmental research},
volume = {300},
number = {},
pages = {124466},
doi = {10.1016/j.envres.2026.124466},
pmid = {41962883},
issn = {1096-0953},
abstract = {The toxic threat of bisphenol A (BPA) pollution to plant growth has drawn increasing attention. Although the plant's inherent repair mechanisms and the regulation of rhizosphere microecological processes hold promise as green remediation strategies, the specific mechanisms by which plants actively modulate rhizosphere metabolites at this critical interface to directionally enhance microbial remediation capacity under BPA stress remain to be further elucidated. Here, during the reclamation process of ryegrass exposed to a BPA concentration of 50 mg kg[-1], the contents of key rhizosphere metabolites (abscisic acid, xanthine, trehalose) in the rhizosphere soil solution significantly increased from 95 ± 12.4 to 201.7 ± 19.1 mg L[-1]. Multi-omics analysis revealed that BPA stress induced the phased accumulation of three key metabolites. From days 0-30, abscisic acid peaked (114.6 ± 11.1 mg L[-1]), coinciding with the upregulation of microbial genes related to cell membrane biosynthesis (slp, lolC) by 1.3-3.8 folds. During days 30-60, xanthine peaked (201.7 ± 19.1 mg L[-1]), corresponding to the highest BPA degradation percentages (62.5 ± 4.2%) and upregulation of TCA cycle-related genes (CS, aco, mdh) by 2.2-4.6 folds. From days 60-90, trehalose accumulation peaked (159.4 ± 19.5 mg L[-1]), alongside stabilized BPA degradation and upregulation of glycolytic pathway genes (ATH1, NTH1, HK) by 2.2-4.6 folds. A structural equation model further demonstrated that these metabolites directly and indirectly influence microbial community function, with abscisic acid, xanthine, trehalose strongly affecting microbial structure and functional gene. This study provides inspiration for the development of technologies related to phytoremediation and root exudates to reduce pollutant in agriculture.},
}

@article {pmid41963036,
year = {2026},
author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y},
title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105055},
doi = {10.1016/j.fm.2026.105055},
pmid = {41963036},
issn = {1095-9998},
mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Phylogeny ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Seeds/microbiology ; Microbiota ; Metagenome ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; },
abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.},
}

*Oryza/microbiology/genetics
*Bacteria/genetics/drug effects/classification/isolation & purification
Phylogeny
Metagenomics
Anti-Bacterial Agents/pharmacology
Soil Microbiology
Seeds/microbiology
Microbiota
Metagenome
*Genes, Bacterial
*Drug Resistance, Microbial/genetics

@article {pmid41963048,
year = {2026},
author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M},
title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105075},
doi = {10.1016/j.fm.2026.105075},
pmid = {41963048},
issn = {1095-9998},
mesh = {Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Animals ; Swine ; Food Storage ; *Meat Products/microbiology/analysis ; Cooking ; *Microbiota ; Food Microbiology ; Food Handling ; },
abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.},
}

Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
Animals
Swine
Food Storage
*Meat Products/microbiology/analysis
Cooking
*Microbiota
Food Microbiology
Food Handling

@article {pmid41963066,
year = {2026},
author = {Yan, R and Watson, SC and Wei, X and Kovac, J},
title = {Psychrotolerant spoilage bacteria enhanced Campylobacter jejuni culturability on refrigerated chicken meat.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105051},
doi = {10.1016/j.fm.2026.105051},
pmid = {41963066},
issn = {1095-9998},
mesh = {Animals ; *Campylobacter jejuni/growth & development/genetics/isolation & purification/physiology ; Chickens/microbiology ; *Meat/microbiology ; Refrigeration ; Microbial Viability ; Microbiota ; Food Packaging ; Food Microbiology ; *Bacteria/isolation & purification/genetics/classification/growth & development ; Food Storage ; },
abstract = {Campylobacter jejuni is a leading cause of bacterial foodborne illness, with poultry as a major transmission vehicle. The bacterium can enter a viable but non-culturable (VBNC) state, which complicates detection using culture-based methods. While cold and oxidative stress are known VBNC inducers, the role of poultry-associated microbiota in influencing C. jejuni culturability and viability during refrigeration is poorly understood. This study characterized the effect of retail chicken microbiota on C. jejuni over 10 days of cold storage in aerobic and vacuum conditions. We profiled microbiota from chicken breasts in aerobic, modified atmosphere, and vacuum packaging, and from whole chicken under aerobic packaging conditions. Microbiota composition varied with packaging, with Pseudomonas, Brochothrix, and Acinetobacter dominating in aerobic, and Lactococcus and Leuconostoc in vacuum conditions. These genera were isolated and assessed for growth and biofilm formation at 4 °C. Psychrotolerant isolates were whole genome sequenced and used to evaluate their effect on C. jejuni viability and culturability on chicken breast. Three microbiome treatments, including T1 (Pseudomonas, Brochothrix, Acinetobacter), T2 (Lactococcus, Leuconostoc), and T3 (T1 + T2), were co-inoculated with C. jejuni and stored at 4 °C. Viability was assessed by viability qPCR and culturability by plating on Campy Cefex and mCCDA agars. Campy Cefex recovered significantly more (0.74 log10) C. jejuni than mCCDA on day 10 but underestimated viable cell concentration by 2.87 log10. All microbiome treatments improved culturability by > 1 log under aerobic conditions, but not vacuum, highlighting the need to further explore the interactions between non-pathogens and Campylobacter in meat stored aerobically. Microbiome effects on viability were modest and variable. Overall, culture-based methods underestimated C. jejuni viability, underscoring the need for complementary molecular quantification in food safety assessments.},
}

Animals
*Campylobacter jejuni/growth & development/genetics/isolation & purification/physiology
Chickens/microbiology
*Meat/microbiology
Refrigeration
Microbial Viability
Microbiota
Food Packaging
Food Microbiology
*Bacteria/isolation & purification/genetics/classification/growth & development
Food Storage

@article {pmid41963103,
year = {2026},
author = {García-García, B and de Oro, LM and Dorado-Rico, MJ and Martín, L},
title = {Biological protection of grapevine pruning wounds: Training system design and mycobiome dynamics.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70804},
pmid = {41963103},
issn = {1526-4998},
support = {//Junta de Extremadura/ ; //European Regional Development Fund/ ; //Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/ ; //Agencia Estatal de Investigación/ ; },
abstract = {BACKGROUND: Grapevine trunk diseases (GTD) lead to progressive vine decline and are a major threat to viticulture sustainability worldwide. GTD can involve multiple fungal species, with Phaeomoniella chlamydospora being one of the most prevalent pathogens. Pruning wounds are the primary entry point for wood-inhabiting fungi. This study assesses the effectiveness of the biological control agent (BCA) Trichoderma atroviride strain SC1 in preventing natural GTD pathogen infections across three vineyard training systems.

RESULTS: Trichoderma recovery was significantly lowest (48.1%) in the double-cordon training system (V3) and consistently higher (71.9%) in the head/spur system (V1). The treatment reduced GTD infection by 3.75%, and disease control declined markedly 1 year after application (61.1%) compared with ≤90 days post-treatment (92.6%). The controlled assay including culture-dependent and culture-independent approaches (high-throughput sequencing and quantitative polymerase chain reaction) revealed distinct detection patterns: culture methods favoured fast-growing fungi such as Trichoderma, whereas molecular tools enabled the detection of slower-growing taxa like P. chlamydospora. T. atroviride colonised wood up to 1-2 cm from the application point, whereas P. chlamydospora spread up to 5 cm. Overall, the pathogen had a stronger impact on wood mycobiome than the BCA, supporting the compatibility of Trichoderma with the resident grapevine microbiome.

CONCLUSION: These findings provide new insights into the integration of BCAs within vineyard GTD management strategies and contribute to the broader transition towards sustainable viticulture and integrated pest management. © 2026 Society of Chemical Industry.},
}

@article {pmid41963512,
year = {2026},
author = {Matoba, R and Iijima, H and Sakamoto, Y and Kawabata, R and Ishiguro, A and Akamaru, Y and Kito, Y and Aizawa, M and Matsuyama, J and Takahashi, M and Makiyama, A and Suzuki, T and Tsuda, M and Yasui, H and Hihara, J and Okuda, H and Kawada, J and Yoshioka, T and Kawakami, H and Eguchi Nakajima, T and Muro, K and Ichikawa, W and Fujii, M and Sunakawa, Y},
title = {Metabolic and functional pathways of gut microbiota in patients with gastric cancer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47830-x},
pmid = {41963512},
issn = {2045-2322},
abstract = {We analysed the differences in bacterial composition between 475 Japanese patients with advanced gastric cancer (median age, 70 years; median BMI 20.0) and 106 healthy individuals using a comprehensive metagenome shotgun analysis. Among the patients with advanced gastric cancer, 71% were male, 37% had relapsed, and 55.5% previously underwent gastrectomy. Bifidobacterium, Anaerostipes, and Parabacteroides were predominant in healthy individuals, whereas Streptococcus, Lactobacillus, and Odoribacter were predominant in patients with advanced gastric cancer. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that butanoate and pyruvate metabolism was enriched in healthy individuals, whereas factors, such as ABC transporters and ribosomes, were enriched in patients with advanced gastric cancer. Cluster analysis broadly classified patients with advanced gastric cancer and healthy individuals into two clusters; however, clustering using pathway data more clearly classified patients with advanced gastric cancer and healthy individuals than clustering using flora analysis. Moreover, healthy individuals showed higher bacterial flora diversity than those with advanced gastric cancer. Although the dataset we used was limited and may be difficult to generalise, we identified some molecular characteristics and functional pathways of the microbial genera within the intestines of patients with advanced gastric cancer.},
}

@article {pmid41963777,
year = {2026},
author = {Rosenbaum, W and Rubio Garcia, M and Löfgren-Burström, A and Larsson, P and Edin, S and Bronnec, V and Palmqvist, R},
title = {Full-length 16S rRNA nanopore sequencing enables species resolution of Fusobacterium associated with colorectal cancer.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2656004},
doi = {10.1080/19490976.2026.2656004},
pmid = {41963777},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Fusobacterium/genetics/classification/isolation & purification ; *Nanopore Sequencing/methods ; *Fusobacterium Infections/microbiology ; DNA, Bacterial/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome ; },
abstract = {Recent studies have revealed that the long-recognized link between the historically defined Fusobacterium nucleatum group and colorectal cancer is largely driven by Fusobacterium animalis. This species, along with two others (Fusobacterium polymorphum and Fusobacterium vincentii), was recently reclassified as distinct from F. nucleatum, highlighting functional divergence within this group. Due to their close genetic relatedness, traditional partial 16S rRNA gene sequencing lacks the resolution to reliably distinguish these species. Nevertheless, accurate species-level identification remains essential in cancer-associated microbiome research. Here, we demonstrate that full-length 16S rRNA sequencing using Oxford Nanopore Technology, combined with a novel custom demultiplexing software, enables robust species-level discrimination within the Fusobacterium genus. Our approach accurately classified clinically relevant Fusobacterium species and recovered their expected proportions from whole cells, DNA mixtures, and clinical CRC specimens. This method provides high-resolution profiling to elucidate species-specific roles of Fusobacterium in colorectal cancer.},
}

*Colorectal Neoplasms/microbiology
Humans
*RNA, Ribosomal, 16S/genetics
*Fusobacterium/genetics/classification/isolation & purification
*Nanopore Sequencing/methods
*Fusobacterium Infections/microbiology
DNA, Bacterial/genetics
Phylogeny
Sequence Analysis, DNA/methods
Gastrointestinal Microbiome

@article {pmid41963929,
year = {2026},
author = {Liu, M and Zhou, M and Zhang, J and Chen, C},
title = {Unraveling the relationship between the vaginal microbiome and return to estrus in post-weaning sows.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05467-y},
pmid = {41963929},
issn = {1746-6148},
support = {2022YFA1304204//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: Return to estrus in post-weaning sows has a significant impact on reproduction performance. Changes in sex hormone levels influence the composition of the vaginal microbiota in sows. However, the relationship between return to estrus and the vaginal microbiota in post-weaning sows remains poorly understood.

RESULTS: In this study, we characterized the vaginal microbiota of 74 Landrace × Yorkshire post-weaning sows including 40 normal-return and 34 non-return sows by sequencing the V3-V4 region of the 16 S rRNA gene. The results revealed significant differences in both the composition and predicted functional capacities of the vaginal microbiota between normal-return and non-return sows. Non-return sows were characterized by reduced abundances of Clostridium sensu stricto 1, Lactobacillus, and Christensenellaceae R-7 group, and increased abundances of Facklamia and Weissella. Furthermore, the predicted functional pathways of Clostridium acetobutylicum acidogenic fermentation and pyruvate fermentation to butanoate were significantly enriched in normal-return sows. Significant differences were also observed in the co-occurrence networks of the vaginal microbiota between normal and non-return sows, revealing distinct microbial interaction patterns between normal return and non-return sows. A random forest analysis identified several vaginal bacterial taxa that showed high discriminatory capacity between normal and non-return sows (AUC = 0.907), including Rikenellaceae RC9 gut group and Christensenellaceae R-7 group that were strongly associated with return to estrus in post-weaning sows.

CONCLUSIONS: We observed significant differences in the composition and predicted functional capacities of the vaginal microbiota between normal-return and non-return sows, and identified several bacterial taxa associated with return to estrus of weaned sows. These findings enhance our understanding of the relationship between the vaginal microbiota and return to estrus in post-weaning sows and provide a foundation for future mechanistic and interventional studies.},
}

@article {pmid41964025,
year = {2026},
author = {Yoshioka, H and Debeljak, P and Prado, S and Fuji, Y and Ichihashi, Y and Iwata, H},
title = {Interpretable multi-omics machine learning reveals drought-driven shifts in plant-microbe interactions.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00883-x},
pmid = {41964025},
issn = {2524-6372},
support = {JP23KJ0506//Japan Society for the Promotion of Science/ ; JPMJCR16O2//Japan Science and Technology Agency/ ; },
abstract = {BACKGROUND: Plant-microbe interactions in the rhizosphere are central to plant growth, nutrient acquisition, and stress resilience. Although multi-omics approaches enable comprehensive profiling of different biological layers, integrating these data to understand the mechanisms underlying plant-microbe symbiosis, particularly under drought stress, remains a challenge.

RESULTS: Genomic, metabolomic, and microbiome data from 198 soybean accessions grown under both control and drought conditions were integrated to identify environment-specific predictive features of the plant phenotypes. We compared best linear unbiased prediction (BLUP), genome-wide association study (GWAS), and a nonlinear machine learning model to evaluate their ability to detect informative features. The machine learning models provided flexible variable selection and outperformed linear models in capturing nonlinear dependencies. Model interpretation using SHapley Additive exPlanations (SHAP) indicated that the isoflavone derivative, daidzin, and the drought-tolerant Candidatus Nitrosocosmicus, were major contributors to phenotypic variation, specifically under drought stress. SHAP-based interaction networks indicated cross-omics links, including connections between daidzin, gamma-aminobutyric acid (GABA), and Paenibacillus.

CONCLUSION: The proposed interpretable machine learning approach for plant phenotype prediction identified multi-omics biomarkers and interactions, providing insights into plant adaptation to drought stress through environment-dependent rhizosphere networks and symbiotic associations.},
}

@article {pmid41964088,
year = {2026},
author = {Krysmann, A and Woolsey, I and da Silva Duarte, V and Kranjec, C and Porcellato, D and Boysen, P},
title = {Bacteria-dependent modulation of immune responses in the bovine udder.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-026-01754-6},
pmid = {41964088},
issn = {1297-9716},
support = {314733//Norges Forskningsråd/ ; },
abstract = {Subclinical mastitis remains difficult to characterize due to the complex interplay between pathogens, local microbiota, and host immune responses. The aim of this study was to investigate how different bacterial species detected in the hindmilk influenced bovine udder immune response and its regulation. Quarter-level hind milk samples were collected from 24 healthy Norwegian Red cows before drying off and through a next full lactation period. Somatic cell populations, cytokines and host-proteome were assessed and combined with the presence of different pathogens. Quarters harboring Staphylococcus aureus and Streptococcus spp. showed significantly elevated somatic cell counts and inflammation associated patterns of somatic cell populations, while those with minor pathogens exhibited lower counts, particularly fewer granulocytes. Cytokines profiling revealed suppressed levels of IFN-γ, IL-10 and TNF-α in the presence of Staphylococcus chromogenes in contrast to the intensive inflammatory activity associated with S. aureus. Weighted gene co-expression network analysis of the host proteome identified two modules of proteins that were negatively correlated with increasing somatic cells count and several modules with strong positive correlation with the SCC. At protein level, we detected 67 proteins differentially expressed based on the pathogen present in the hindmilk. Of these, 19 were linked to immune system functions such as TLR2 and lactoferrin. Our study provides insights into host response in bovine mastitis and reveals a notable lack of interaction between S. chromogenes and the host body compared to an intense immune response in the presence of other pathogens such as S. aureus.},
}

@article {pmid41964093,
year = {2026},
author = {Wang, Q and Duan, C and Dai, H and Lv, D and Shi, Z and Joshi, N and Gierus, M and Zhu, W and Hao, L and Cheng, Y},
title = {Phytosterols improve feed efficiency in yaks by enriching rumen Succiniclasticum.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00562-9},
pmid = {41964093},
issn = {2524-4671},
support = {2024-ZJ-905//Qinghai Provincial Natural Science Fund for Distinguished Young Scholars/ ; 2022YFD1302103//National Key Research and Development Program of China/ ; 2025KTST04//Qinghai University Research Ability Enhancement Project/ ; 2025, L.Z.H.//Qinghai University Graduate Supervisor Innovation Team/ ; QHKLYC-GDCXCY-2024-071//Leading talent of "Kunlun Talents High-level Innovation and Entrepreneurial Talents" in Qinghai Province/ ; },
abstract = {BACKGROUND: Yaks are important livestock species on the Qinghai-Tibet Plateau (QTP), but their productivity is constrained by the harsh alpine environment and the seasonal scarcity of forage resources. Improving feed efficiency has become the key to the sustainable development of Plateau Yak breeding industry. Phytosterols have shown a good application prospect in ruminant feed efficiency improvement, but the impact on yaks is not clear. This study explored the effects of dietary phytosterols supplementation on growth performance, nutrient digestibility, rumen microbial community structure and metabolic function of yaks fed in a barn.

RESULTS: Twenty-eight 1.5-year-old male yaks (137.10 ± 8.70 kg) were randomly divided into two groups after 28 days of pre feeding period: the control group (Con, n = 14) was fed with basic diet, and the experimental group (PS, n = 14) was added with 200 mg/kg phytosterols in concentrate. The formal test period was 60 days. Compared with Con group, PS group significantly increased average daily gain (P = 0.001), apparent digestibility of crude protein (P = 0.036) and neutral detergent fiber (P = 0.006), and reduced feed conversion rate (P = 0.002). The rumen fermentation mode of PS group changed, the proportion of propionate increased significantly (P = 0.001), while the proportion of acetate (P = 0.006), acetate to propionate ratio (P = 0.001) and lactate (P = 0.035) concentration decreased significantly. Phytosterols significantly changed the structure of rumen microbial community and significantly increased the copy number of rumen bacteria (P < 0.05). Metatranscriptomic analysis showed that PS group significantly increased the relative abundance of key bacteria, including Succiniclasticum, Faecalibacterium, Ruminococcus, Butyrivibrio, and Alistipes (P < 0.05). Microbial co-occurrence network analysis revealed that the number of edges, average degree and modular index of microbial community structure network in PS group increased. Rumen function analysis showed that glycolysis / gluconeogenesis and propionate metabolism were significantly enhanced in PS group (P < 0.05), and the expression of key enzymes such as hexokinase and fumarate hydratase were significantly enhanced (P < 0.05). Metabolomic analysis revealed that phosphoenolpyruvic acid, fumarate and methylmalonyl-CoA were significantly accumulated in the rumen of PS group (P < 0.05). Pathway analysis showed that the pathway impact value of propionate metabolism and glycolysis / gluconeogenesis was greater than 0.1.

CONCLUSIONS: Phytosterols (200 mg/kg of concentrate) can effectively improve the feed efficiency of yaks by regulating the structure and function of rumen microorganisms and altering the fermentation patterns.},
}

@article {pmid41964098,
year = {2026},
author = {de Medeiros, MC and Fontaine, S and Danella, E and Hillman, E and Schmidt, TM and Furgal, A and Wellik, DM and Inohara, N and Núñez, G and Li, G and Chen, GY and D'Silva, NJ},
title = {Loss of salivary agglutinin induces changes in the salivary microbiome and accelerates development of oral cancer.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02337-5},
pmid = {41964098},
issn = {2049-2618},
support = {CA250214/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: Salivary agglutinin, also known as deleted in malignant brain tumors 1 (DMBT1), is an anti-microbial protein. DMBT1 is low in saliva from patients with oral squamous cell carcinoma (OSCC) and dramatically increases after treatment, with accompanying microbial changes. While this suggests an association between DMBT1 suppression and changes in the oral microbiota, causation has not been established. DMBT1 is also a tumor suppressor protein; its loss promotes OSCC progression, but its role in OSCC development is unknown. In this study, OSCC development was investigated in a murine carcinogen model that simulates human OSCC. Microbiota were standardized between Dmbt1 knockout (Dmbt1[-/-]) and wild-type (Dmbt1[+/+]) mice via interbreeding and co-housing. Saliva was collected at baseline and at 4, 8, 12, 16, and 22 weeks post-carcinogen initiation (stopped at 16 weeks). Tongues were harvested at week 22 for histopathology, and the salivary microbiome was profiled by 16S rRNA sequencing. Microbial diversity metrics and conditional dependence networks assessed community structure, while longitudinal patterns were analyzed using a locally sparse varying coefficient mixed model and functional principal component analysis (fPCA).

RESULTS: Despite microbiota standardization, Dmbt1[-/-] and Dmbt1[+/+] displayed differences in microbiome composition based on β-diversity metrics. At endpoint, carcinogen-treated Dmbt1[-/-] showed higher OSCC prevalence and more aggressive invasion than Dmbt1[+/+]. Several OTUs, including those from Lachnospiraceae, Sphingomonas, Carnobacteriaceae, and Candidatus Saccharibacteria families, demonstrated differential abundance patterns over time, either genotype-specific, diagnosis-specific, or both. Notably, Sphingomonas and Lachnospiraceae exhibited time-dependent abundance differences in mice that developed OSCC. fPCA identified taxa with abundance trajectories that were different between OSCC and precancer and genotype specific.

CONCLUSIONS: Thus, DMBT1 shapes salivary microbiota composition and protects against OSCC development. Dynamic, genotype-specific microbial shifts during carcinogenesis underscore the complex interplay between the oral microbiota and cancer progression. Video Abstract.},
}

@article {pmid41964141,
year = {2026},
author = {Durham, SH and McAllister, AK and Chahine, EB},
title = {Gepotidacin for the Treatment of Uncomplicated Urogenital Gonorrhea.},
journal = {The Annals of pharmacotherapy},
volume = {},
number = {},
pages = {10600280261435593},
doi = {10.1177/10600280261435593},
pmid = {41964141},
issn = {1542-6270},
abstract = {OBJECTIVE: To review the efficacy and safety of gepotidacin for the treatment of uncomplicated urogenital gonorrhea (uUGG).

DATA SOURCES: A literature search of PubMed and Google Scholar (January 2010 to January 2026) was conducted using the terms gepotidacin and GSK2140944. Additional sources included conference abstracts, the manufacturer's website, and prescribing information.

Relevant English-language studies evaluating the efficacy and safety of gepotidacin for uUGG were included.

DATA SYNTHESIS: Gepotidacin is a first-in-class triazaacenaphthylene antibiotic with a novel mechanism of action and potent activity against Neisseria gonorrhoeae. In the phase 3 EAGLE-1 trial, gepotidacin demonstrated noninferiority to ceftriaxone plus azithromycin for uUGG treatment. It was generally well tolerated, with gastrointestinal adverse effects most commonly reported. Gepotidacin is administered as 3000 mg orally every 12 hours for 2 doses and is approved for adults and pediatric patients aged ≥12 years weighing ≥45 kg with limited or no alternative treatment options. Administration with food is recommended to reduce gastrointestinal adverse effects.Relevance to Patient Care and Clinical Practice in Comparison to Existing Drugs:Gepotidacin provides a new 2-dose oral option for uUGG treatment. Compared with ceftriaxone, the current drug of choice, oral administration may improve convenience and access. Similar to cefixime and zoliflodacin, its oral formulation may facilitate treatment while potentially reducing microbiome disruption compared with ceftriaxone.

CONCLUSIONS: Gepotidacin is a promising oral antibiotic with a novel mechanism of action and demonstrated efficacy for uUGG treatment.},
}

@article {pmid41964374,
year = {2026},
author = {Mustafa, AM},
title = {Commentary on oral microbiota analysis in HPV-infected individuals: considerations for future research.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-2},
doi = {10.1080/17460913.2026.2656108},
pmid = {41964374},
issn = {1746-0921},
}

@article {pmid41964509,
year = {2026},
author = {Chen, Z and Zhu, P and Kong, D and Luo, L and Yu, X and Liu, G},
title = {Decoding the genetic mechanism of heterosis in rice: insights from multi-omics and systems approaches.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcag010},
pmid = {41964509},
issn = {1095-8290},
support = {23015821200//Project for Demonstration and Industrialization of Water-Saving and Drought-Resistant Rice in Hainan/ ; //Qinghe Program/ ; //Shanghai Agrobiological Gene Center/ ; },
abstract = {Heterosis, or hybrid vigour, describes the superior growth, yield and adaptability of F1 hybrids from genetically diverse parents and is vital for global food security. Although widely applied for over a century, its molecular basis remains unresolved. Classical hypotheses, including dominance, overdominance and epistasis, serve as theoretical frameworks to explain this complex phenomenon. Recent progress in genomics and multi-omics technologies has deepened our understanding, but genome-level insights alone are insufficient to fully account for hybrid performance. This review synthesizes current advances in elucidating the genetic architecture and regulatory mechanisms underlying heterosis in rice. It emphasizes key genetic loci, the integration of high-throughput omics data, and insights gained from structural variation and plant-microbiome interactions. By integrating diverse omics layers through classical genetic frameworks, the field is moving towards a more comprehensive model of heterosis. These advances offer new strategies for molecular design breeding in rice and point to future directions for enhancing the utilization of heterosis in crop improvement.},
}

@article {pmid41964565,
year = {2026},
author = {Valentine, YA and Duff, AF and Bailey, MT and Pyter, LM},
title = {A systematic assessment of the short- and long-term effects of commonly used breast cancer chemotherapeutics on the gut microbiome‒blood‒brain axis of female mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655149},
doi = {10.1080/19490976.2026.2655149},
pmid = {41964565},
issn = {1949-0984},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Breast Neoplasms/drug therapy/microbiology ; Cyclophosphamide/adverse effects ; *Antineoplastic Agents/adverse effects/therapeutic use ; Cisplatin/adverse effects ; *Brain/drug effects/metabolism ; Doxorubicin/adverse effects ; Paclitaxel/adverse effects ; Bacteria/classification/genetics/drug effects/isolation & purification ; },
abstract = {Chemotherapy affects over 300,000 U.S. breast cancer patients, which disrupts the gut microbiome and induces gut inflammation-an effect hypothesized to drive gastrointestinal side effects (e.g., diarrhea, vomiting) experienced by 50%-80% of patients. Preclinical studies have found causal links amongst chemotherapy-induced gut microbiome disruption, systemic inflammation, and brain-mediated side effects. Therefore, the gut microbiome represents a therapeutic target to attenuate chemotherapy side effects. Because clinical populations are administered multiple chemotherapeutics in combination, a comprehensive understanding of which treatments disrupt the gut microbiome‒blood‒brain axis is lacking. Here, translationally-relevant regimens of four commonly used breast cancer chemotherapies (paclitaxel, cyclophosphamide, cisplatin, and doxorubicin) were given to adult female C57BL/6 mice, and inflammatory, metabolomics and/or bacteriome outcomes were measured in the gut, gut contents, blood, and brain tissues, along with a fatigue and anxiety-like behavioral assessment. Many inter-chemotherapy differences were observed but notable findings include prolonged circulation and central proinflammatory signals by paclitaxel and sustained disruption of the gut microbiome by cisplatin. In contrast, cyclophosphamide and doxorubicin modestly disrupted the gut microbiome‒blood‒brain axis. Taken together, this study systematically identified that paclitaxel and cisplatin most robustly disrupted the gut microbiome‒blood‒brain axis, suggesting that those treated with these drugs may benefit the most from gut-targeted interventions for associated side effects.},
}

Animals
Female
*Gastrointestinal Microbiome/drug effects
Mice
Mice, Inbred C57BL
*Breast Neoplasms/drug therapy/microbiology
Cyclophosphamide/adverse effects
*Antineoplastic Agents/adverse effects/therapeutic use
Cisplatin/adverse effects
*Brain/drug effects/metabolism
Doxorubicin/adverse effects
Paclitaxel/adverse effects
Bacteria/classification/genetics/drug effects/isolation & purification