@article {pmid41497123,
year = {2026},
author = {Mehmood, MS and Hajj, F},
title = {Noninvasive early detection of colorectal cancer through gut microbiome-derived biomarkers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {997-998},
pmid = {41497123},
issn = {2049-0801},
abstract = {Colorectal cancer (CRC) remains a major global burden, with 1.9 million new cases and 935000 deaths reported in 2024. Despite available screening tools, nearly 45% of cases are still diagnosed at advanced stages, where the 5-year survival rate falls below 14%, compared to >90% in early detection. The limitations of colonoscopy its invasiveness, cost, and poor compliance (<40% globally) demand innovative, noninvasive diagnostic solutions. Gut microbiome profiling has recently emerged as a transformative approach, with specific bacterial signatures such as Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus anaerobius showing AUC values between 0.85 and 0.93 for early CRC identification. Integrating metagenomic and metabolomic data enhances diagnostic accuracy to 89% sensitivity and 91% specificity. Moreover, altered microbial metabolites including decreased short-chain fatty acids and elevated secondary bile acids correlate with a 2.3- to 3.1-fold higher risk of carcinogenesis. Novel CRISPR-Cas13a-based assays further allow sub-attomolar detection of microbial RNA transcripts, underscoring a new frontier in microbiome-driven cancer diagnostics. Collectively, gut microbiome-derived biomarkers represent a noninvasive, mechanistically grounded, and highly sensitive platform for early CRC detection with significant translational potential.},
}

@article {pmid41497081,
year = {2026},
author = {Mazandarani, M and Lashkarbolouk, N and Ejtahed, HS and Qorbani, M},
title = {Effect of probiotics and synbiotics on antimicrobial resistance in frequent infections: a systematic review of clinical trials.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {698-717},
pmid = {41497081},
issn = {2049-0801},
abstract = {BACKGROUND: Antibiotic resistance and recurrent infections, driven by increased antibiotic use, represent a global health problem. This study aims to evaluate the effect of probiotics and synbiotics consumption on antibiotic resistance in common infections.

METHODS: A systematic search was performed on international electronic databases (PubMed/Medline, Scopus, and Web of Science) using predefined keywords to identify relevant clinical trials published prior to 1 March 2025. Study quality was assessed, and the PRISMA 2020 guideline was followed.

RESULTS: In our systematic review, 47 studies were included. Twenty studies reported positive effects on antibiotic resistance, eradication rates, and recurrence, particularly in gastrointestinal infections. In contrast, 10 studies reported no effect, and 2 indicated a negative effect of these interventions on infection recurrence and antibiotic resistance. In three studies focusing on children, probiotics significantly lowered the risk of urinary tract infection (UTI) recurrence and antibiotic resistance. However, an adult study found that probiotics had minimal effect on UTI recurrence. Four studies examined the effect of probiotics on respiratory infections in both children and adults, showing improvements in antibiotic resistance outcomes. Three studies involving preterm infants found that probiotics could modify their gut microbiome composition, with two studies confirming this effect.

CONCLUSION: Our study indicates that incorporating probiotics and synbiotics into common infection therapy could improve antibiotic resistance, eradicate rates, minimize side effects, and boost treatment compliance. However, concerns remain regarding the potential transfer of antibiotic resistance genes via probiotics.},
}

@article {pmid41497069,
year = {2026},
author = {Mehmood, MS and Danaf, N},
title = {Microbial metabolites regulating PD-L1 and checkpoint pathways: translational implications.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {953-954},
doi = {10.1097/MS9.0000000000004267},
pmid = {41497069},
issn = {2049-0801},
abstract = {Recent advances in microbiome research reveal that microbial metabolites directly regulate programmed death ligand-1 (PD-L1) expression and influence checkpoint immunotherapy outcomes. Multi-cohort analyses of over 1300 patients show that elevated short-chain fatty acids, indole derivatives, and secondary bile acids modulate PD-L1 and T-cell activity through histone deacetylase inhibition, STAT3 phosphorylation, and aryl hydrocarbon receptor signaling. High fecal butyrate correlates with a 2.4-fold higher response rate and 6.3-month improvement in progression-free survival during PD-1 blockade. Conversely, dysbiosis-associated metabolites, including lipopolysaccharide and succinate, induce PD-L1 hyperexpression and immune resistance. Metabolomic profiling now achieves AUCs of 0.82-0.89 in predicting immunotherapy response, outperforming tumor mutational burden and PD-L1 IHC. These findings establish microbial metabolites as active immunoregulatory mediators, offering new translational strategies for microbiome-informed immunotherapy personalization and biomarker integration in oncology.},
}

@article {pmid41497008,
year = {2026},
author = {Mehmood, MS and Masood, M and Danaf, N},
title = {Engineered food-borne probiotics delivering checkpoint-inhibitor modulators.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {27-28},
pmid = {41497008},
issn = {2049-0801},
abstract = {Engineered food-borne probiotics represent an emerging food-oncomicrobiology strategy that unites synthetic biology, nutrition, and cancer immunotherapy. Preclinical models demonstrate potent antitumor effects: Lactococcus lactis secreting soluble CD80-reduced tumor growth by 64%; Escherichia coli Nissle 1917 producing PD-L1 nanobodies achieved complete regression in 50% of treated mice with a two-fold rise in CD8[+]IFNγ[+]TNFα[+] T-cell infiltration; and Lactobacillus plantarum delivering IL-2 enhanced NK-cell activity 2.5-fold and extended survival by 30%. Clinical meta-analyses reveal that gut-microbiome diversity increases checkpoint-inhibitor response by 40% and median progression-free survival by 12 months. A phase I trial in Non-Small Cell Lung Cancer (NSCLC) showed reduced immune-related colitis (from 14% to 6%) and higher response rates (36% vs 21%) with probiotic co-therapy. Remaining challenges in colonization and biosafety, together with advances in controllable genetic circuits, make edible biologics a promising, low-toxicity immunotherapeutic platform.},
}

@article {pmid41496990,
year = {2026},
author = {Saif, P and Tausif, M and Fatima, M and Imtiaz, A and Hassan, M},
title = {CRISPR-targeted microbiome modulation in rare Henoch-Schonlein purpura IgA nephropathy-gastritis: insights into the gut-kidney axis.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {1090-1091},
pmid = {41496990},
issn = {2049-0801},
}

@article {pmid41496973,
year = {2026},
author = {Mehmood, MS and Abid, M and Danaf, N},
title = {Microbiome-selective DNA Pol IIIC inhibitors in oncology infection management.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {1070-1071},
pmid = {41496973},
issn = {2049-0801},
abstract = {Oncology patients experience high rates of bacterial infection due to chemotherapy-associated mucosal injury and immunosuppression, with up to 60% developing infectious complications and 20-30% of hematopoietic transplant recipients requiring hospitalization. Broad-spectrum antibiotics, although essential, frequently induce gut microbiome dysbiosis, which is associated with recurrent infection and reduced immune checkpoint inhibitor (ICI) effectiveness. Meta-analyses indicate that antibiotic exposure near ICI initiation leads to a 30-50% decrease in overall survival and a 25-40% reduction in progression-free survival. DNA polymerase IIIC inhibitor antibiotics, including ibezapolstat, have demonstrated 88-96% clinical cure rates in Clostridioides difficile infection while preserving gut microbial diversity and limiting expansion of antimicrobial-resistant organisms. Recent conference data suggest these microbiome-sparing effects may be class-wide. This targeted antimicrobial mechanism offers a potential strategy to maintain immune function, reduce recurrent infection, and support anticancer treatment response in immunocompromised patients.},
}

@article {pmid41496941,
year = {2026},
author = {Mehmood, MS and Iqbal, I and Hajj, F},
title = {CRISPR-Cas13a diagnostics for circulating microbial transcripts in pancreatic cancer.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {1038-1039},
pmid = {41496941},
issn = {2049-0801},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is the seventh leading cause of global cancer deaths, with a 5-year survival rate below 11% and over 80% of cases diagnosed at advanced, unresectable stages. Current biomarkers such as CA19-9 show suboptimal diagnostic accuracy (sensitivity 65-75%; specificity 70-80%), necessitating more precise and minimally invasive diagnostic tools. Recent advances in CRISPR-Cas13a technology, an RNA-guided, RNA-targeting system with attomolar sensitivity and >95% diagnostic accuracy, enable rapid detection of circulating RNA molecules. Concurrently, microbial transcriptomic studies have revealed distinct bacterial RNA fragments in plasma of PDAC patients, including Fusobacterium and Enterobacter small RNAs, detected in up to 68% of advanced and 41% of early-stage cases. Integrating Cas13a platforms with microbial RNA biomarkers could revolutionize liquid biopsy diagnostics by providing a fast (<30 min), low-cost ( }

@article {pmid41496931,
year = {2026},
author = {Mehmood, MS and Danaf, N},
title = {Helicobacter pylori persists in pancreatic ductal adenocarcinoma despite eradication therapy.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {955-956},
pmid = {41496931},
issn = {2049-0801},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with global 5-year survival below 12%. Recent molecular analyses have revealed that Helicobacter pylori may persist within the pancreatic ductal microenvironment despite successful gastric eradication. In a 2024 multicenter study, H. pylori DNA was detected in 41.6% of PDAC tissues, including patients with documented eradication. Metagenomic sequencing identified H. pylori 16S rRNA reads comprising up to 2.5% of total microbial DNA, supporting selective intrapancreatic survival. Mechanistically, CagA/VacA-mediated STAT3 and NF-κB activation drives cytokine release, oxidative stress, and mismatch repair suppression, enhancing oncogenic inflammation and genomic instability. Chronic colonization increased pancreatic intraepithelial neoplasia by more than 60% in murine models, underscoring its pathogenic potential. These findings suggest that H. pylori persistence represents a novel microbial co-factor in PDAC, warranting further exploration as a diagnostic biomarker and therapeutic target.},
}

@article {pmid41496502,
year = {2026},
author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO},
title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611543},
doi = {10.1080/19490976.2025.2611543},
pmid = {41496502},
issn = {1949-0984},
mesh = {Humans ; *Immunoglobulin A/metabolism ; Animals ; Phylogeny ; *Campylobacter jejuni/physiology ; *Campylobacter Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Mice ; *Clostridiales/enzymology/genetics/classification ; Neutrophils/immunology/microbiology ; *Bacterial Proteins/genetics/metabolism ; China ; Phagocytosis ; Epithelial Cells/microbiology ; Serine Endopeptidases ; },
abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.},
}

Humans
*Immunoglobulin A/metabolism
Animals
Phylogeny
*Campylobacter jejuni/physiology
*Campylobacter Infections/microbiology/immunology
*Gastrointestinal Microbiome
Mice
*Clostridiales/enzymology/genetics/classification
Neutrophils/immunology/microbiology
*Bacterial Proteins/genetics/metabolism
China
Phagocytosis
Epithelial Cells/microbiology
Serine Endopeptidases

@article {pmid41496455,
year = {2026},
author = {Ramesh, A and Subbarayan, R and Shrestha, R and Adtani, PN},
title = {Exploring Fecal Microbiota Transplantation: Potential Benefits, Associated Risks, and Challenges in Cancer Treatment.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {9},
number = {1},
pages = {e70455},
doi = {10.1002/cnr2.70455},
pmid = {41496455},
issn = {2573-8348},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods/adverse effects ; *Neoplasms/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Tumor Microenvironment/immunology ; Immunotherapy/methods ; Animals ; Risk Assessment ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has emerged as a groundbreaking strategy for modulating the gut microbiome and improving cancer treatment outcomes. This review synthesizes the current evidence on the role of FMT in oncology, focusing on its potential to enhance the efficacy of immunotherapy, restore microbiome homeostasis, and mitigate cancer-associated complications.

RECENT FINDINGS: Preclinical and clinical studies have demonstrated that FMT can reprogram the tumor microenvironment, augment immune checkpoint inhibitor responses, and reduce chemotherapy-induced toxicity. However, risks such as pathogen transmission, immune dysregulation, and unintended microbial shifts necessitate rigorous donor screening and a personalized approach. Challenges in standardization, regulatory frameworks, and mechanistic understanding further complicate their clinical translation. Emerging innovations, including precision microbial consortia, synthetic biology, and biomarker-driven strategies, have the potential to address these limitations.

CONCLUSION: While FMT holds transformative potential in cancer care, its integration into oncological practice requires robust clinical validation, long-term safety assessments, and interdisciplinary collaboration to harness its full therapeutic potential.},
}

Humans
*Fecal Microbiota Transplantation/methods/adverse effects
*Neoplasms/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Tumor Microenvironment/immunology
Immunotherapy/methods
Animals
Risk Assessment

@article {pmid41496451,
year = {2026},
author = {Wang, P and Jiang, F and Xue, Z and Bu, F and Zhu, W and Zhang, Y and Wen, T and Li, Y and Zhang, P and Cai, Y and Niu, C and Li, S and Zhou, Y and Cheng, X},
title = {The Medicago SPX1/3-PHR2 Network Relays Phosphate Signaling to Orchestrate Root Nodulation-dependent Nitrogen Acquisition by Controlling Flavonoid Biosynthesis.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101695},
doi = {10.1016/j.xplc.2026.101695},
pmid = {41496451},
issn = {2590-3462},
abstract = {The formation of symbiotic associations with rhizospheric microbes is an important strategy for sessile plants to acquire nitrogen and phosphorus from the soil. Root exudate plays a key role in shaping the rhizosphere microbiome. Depending on their needs for nitrogen or phosphorus, plants can adjust the composition of root exudate to attract the appropriate microbes. Flavonoids, a group of secondary metabolites, have been well studied for their role in shaping the root microbiome, particularly in mediating root nodule symbiosis in legumes. However, the mechanism by which plants regulate the absorption of microbe-mediated nitrogen and phosphorus remains unclear. Here, we show that the Medicago truncatula phosphate starvation response regulatory network SPX1/3-PHR2 controls flavonoid biosynthesis to recruit nitrogen-fixing microbes for nitrogen acquisition. Nitrogen-fixing microbes, including rhizobia, were fewer recruited in the rhizosphere of the spx1spx3 double mutant. This was caused by lower flavonoid levels in the root exudate compared to wild-type plants R108. Further results indicate that the control of flavonoid biosynthesis is exerted via PHR2, the interacting transcription factor of SPX1/3. Under phosphate-limiting conditions, PHR2 suppresses the expression of flavonoid biosynthetic genes to reduce root nodule symbiosis levels. Under phosphate-sufficient conditions, the interaction between SPX1/3 and PHR2 releases this suppression, thereby promoting root nodule symbiosis. We further showed that PHR2 can bind to the promoter regions of flavonoid biosynthetic genes in yeast. We propose that the SPX1/3-PHR2 network can modulate root nodule-dependent nitrogen acquisition in response to phosphate levels. Thus, the SPX1/3-PHR2 module contributes to maintaining a balance in microbe-mediated nitrogen and phosphorus acquisition for optimal plant growth.},
}

@article {pmid41496347,
year = {2026},
author = {Saghafi, S and Yaghoubi, MA and Safarpour, H and Raeisi, H and Mousavi, Z},
title = {Protecting the endocrine axis in immuno-oncology: GLP-1 receptor agonists as host-directed modulators in colorectal cancer.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {194},
number = {},
pages = {118948},
doi = {10.1016/j.biopha.2025.118948},
pmid = {41496347},
issn = {1950-6007},
abstract = {Immune checkpoint inhibitors (ICIs) have transformed colorectal cancer (CRC), particularly in microsatellite instability-high (MSI-H) and mismatch repair-deficient (dMMR) tumors, delivering durable responses and long-term survival. Yet this success is shadowed by immune-related adverse events (irAEs). Among them, endocrine toxicities including thyroiditis, hypophysitis, adrenalitis, and insulin-deficient diabetes are relatively frequent, irreversible, and frequently life-long. Survivors who might otherwise be considered cured remain tethered to chronic hormone replacement, underscoring a striking gap in immuno-oncology: management is reactive, supportive, and devoid of preventive strategies. Concurrently, glucagon-like peptide-1 receptor agonists (GLP-1RAs), introduced for type 2 diabetes (T2D) and obesity, are emerging as systemic modulators of inflammation, immunometabolism, and the gut microbiome. These three axes converge on mechanisms central to endocrine irAEs. Preclinical and epidemiologic data suggest that GLP-1RAs may also be associated with reduced cancer incidence and alterations in tumor-associated immune responses, raising the possibility of dual utility: mitigating endocrine autoimmunity while preserving or even augmenting anti-tumor efficacy. At the same time, their appetite-suppressing and weight-reducing effects highlight the countervailing risk of exacerbating cancer cachexia, demanding careful integration with nutritional and exercise strategies. Here, we synthesize current understanding of ICI-induced endocrine injury, delineate the immunobiology of GLP-1RAs, and develop a unified mechanistic framework linking these domains in CRC. We propose a translational roadmap spanning retrospective pharmacoepidemiology, biomarker-driven stratification, and prospective clinical trials. More broadly, GLP-1RAs exemplify host-directed therapies that may help shift the therapeutic focus of immuno-oncology toward preserving survivorship and endocrine health as integral endpoints of cancer care.},
}

@article {pmid41496313,
year = {2026},
author = {Sun, L and Sun, X and Qiao, C and Lu, Y and Li, Q and Wang, Q and Gao, H},
title = {Precision medicine in Crohn's disease: Navigating the path from biomarker discovery to clinical implementation.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {},
number = {},
pages = {},
pmid = {41496313},
issn = {1998-4049},
abstract = {Crohn's disease (CD) is a highly heterogeneous inflammatory bowel disorder. Despite an expanding therapeutic arsenal, treatment selection remains largely empirical, often leading to delayed effective control and suboptimal outcomes. Precision medicine, which tailors therapy to individual patient characteristics, offers a promising alternative. Advances in biomarker discovery are enabling more personalized approaches. Research has moved beyond conventional markers to high-dimensional data from genomics, proteomics, and microbiome studies. Over 200 genetic susceptibility loci have been identified, and dysbiosis is recognized as a key modulator of disease and treatment response. Integrating these multi-omics data is crucial for building predictive models, a task increasingly aided by artificial intelligence and machine learning. However, translating these discoveries into clinical practice faces significant hurdles. These include insufficient validation across diverse populations, methodological heterogeneity, and a lack of real-world evidence. Biomarker performance may vary significantly across genetically diverse patient cohorts, raising concerns that precision medicine tools validated only in homogeneous populations could inadvertently propagate health disparities. It is also important to consider regional contexts, such as the Middle East and Saudi Arabia, where rising IBD incidence due to urbanization and unique genetic architectures may affect biomarker performance and therapy response. This review synthesizes recent progress, outlines the major barriers to implementation, and discusses future directions, such as leveraging digital health technologies and international collaborations, to accelerate the adoption of precision medicine and improve outcomes for CD patients.},
}

@article {pmid41496250,
year = {2026},
author = {Anyango, OV and Aool, OW and Lukindu, M and Nakayiki, T and Lutwama, J and Kayondo, JK and Phillips, CD and Lutomiah, J and Mutisya, J and Brelsfoard, CL and Onyango, MG},
title = {Molecular detection of medically important rickettsiae, including Rickettsia prowazekii in Rhipicephalus appendiculatus and Hyalomma rufipes: A microbiome perspective.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {1},
pages = {102596},
doi = {10.1016/j.ttbdis.2025.102596},
pmid = {41496250},
issn = {1877-9603},
abstract = {The East African region hosts more than 50 % of Africa livestock and 9 % of global cattle, creating an ideal environment for ticks to thrive and transmit pathogens. Little is known of the full spectrum of tick-associated bacterial pathogens that circulate in the vast pastoralist-intense regions of East Africa, the range of the pathogens and their genetic relationships. To define this, we need to first delineate the microbial composition of the medically and veterinary important East African tick species. This study focused on the likely vectors of Orthonairovirus haemorrhagiae in Kenya and Uganda, specifically H. rufipes and R. appendiculatus. To characterize the bacterial microbiome associated with these two tick species, the V3-V4 hypervariable region of the 16S rRNA gene was sequenced from a total of 25 R. appendiculatus and 24 H rufipes specimens using the Illumina MiSeq platform. Microbial abundance and diversity were subsequently analysed to assess the composition and structure of their bacterial communities. We observed a richer and balanced bacterial microbiome profile among the H. rufipes compared to that of the R. appendiculatus, which was mainly dominated by Coxiella-like endosymbionts. Furthermore, a few bacterial taxa were unique to each sampling site, while several were common across all sampling sites. This study identified several medically important Rickettsia species, including R. aeschlimannii, R. conorii, and, for the first time, R. prowazekii, the causative agent of epidemic typhus, in H. rufipes sampled from Northeast Kenya. Furthermore, our findings demonstrate that R. africae exhibits a broad tick host tropism. Our present findings provide insights into the microbial community of medically important tick species of East Africa. The observation of a significant level of Coxiella-like endosymbionts in R. appendiculatus warrants an investigation into their transmissibility and impacts on the transmission of other pathogens. The identification of R. prowazekii in H. rufipes suggest that R. prowazekii is broadening its host tropism in Kenya.},
}

@article {pmid41496086,
year = {2026},
author = {Gao, Y and Yu, X},
title = {Acupuncture treatment for insomnia based on the microbiome-gut-brain axis theory: A review.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46967},
pmid = {41496086},
issn = {1536-5964},
mesh = {Humans ; *Sleep Initiation and Maintenance Disorders/therapy/microbiology ; *Acupuncture Therapy/methods ; *Gastrointestinal Microbiome/physiology ; Brain ; *Brain-Gut Axis/physiology ; },
abstract = {Insomnia, a prevalent sleep disorder, significantly impacts patient social function and quality of life, creating a substantial burden on individuals. This underscores the need for effective treatments. Acupuncture, an essential part of complementary and alternative medicine, has received increasing attention for its therapeutic effect on insomnia, although its mechanism is still not fully understood. In recent years, some studies have focused on the microbiome-gut-brain axis, a promising area of study that may shed light on how acupuncture alleviates insomnia. This review explores the possible mechanisms by which acupuncture therapy improves insomnia through the microbiome-gut-brain axis. These mechanisms include adjusting the types and diversity of intestinal microbiome and altering short-chain fatty acid levels, inhibiting inflammatory responses, improving the tight connection of the intestinal mucosal barrier, controlling the release and production of brain-gut peptides, and regulating the pathways associated with the hypothalamic-pituitary-adrenal axis and the vagus nerve. The findings aim to provide a more objective basis for the use of acupuncture and moxibustion in treating insomnia.},
}

Humans
*Sleep Initiation and Maintenance Disorders/therapy/microbiology
*Acupuncture Therapy/methods
*Gastrointestinal Microbiome/physiology
Brain
*Brain-Gut Axis/physiology

@article {pmid41496083,
year = {2026},
author = {Wang, X and Qin, W},
title = {Effect of gut microbiome and blood metabolites on colorectal cancer: A bidirectional Mendelian randomization and mediation analysis based on STROBE-MR guidelines.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46936},
pmid = {41496083},
issn = {1536-5964},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Colorectal Neoplasms/blood/genetics/microbiology ; Mendelian Randomization Analysis/methods ; Genome-Wide Association Study ; Mediation Analysis ; },
abstract = {Previous studies have shown that gut microbiome as well as blood metabolites are involved in the development of colorectal cancer (CRC). Therefore, this study attempted to discover the causal effects of gut microbiome and blood metabolites on CRC. Using genetic data from published genome-wide association studies, the 2-sample Mendelian randomization (MR) and 2-step MR analyses were applied to evaluate the causal connections between gut microbiome (exposure) and CRC (outcome) with blood metabolites as the mediators, as well as between blood metabolites (exposure) and CRC (outcome) with gut microbiome as the mediators. Moreover, a reverse MR analysis was done to measure the impact of CRC on gut microbiome and blood metabolites. The inverse variance weighted method was primarily utilized to analyze causal effects, with the robustness of the findings further assessed by sensitivity analyses. The 2-sample MR analyses illustrated that 14 gut microbes, 23 gut bacterial pathways, and 96 blood metabolites exerted an evidence of causal effect on CRC. However, there were no causal relationships between CRC and gut microbes and blood metabolites. Additionally, mediation analyses revealed that 5 gut microbiome (three gut microbes and 2 gut bacterial pathway abundance) influenced CRC through 4 blood metabolites, and 9 blood metabolites influenced CRC through 7 gut microbiome (four gut microbes and 3 gut bacterial pathways). Sensitivity analyses indicated that all results were reliable. Our study further highlights the complex relationship among gut microbiome, blood metabolites, and CRC and provides insights into clinical interventions for CRC.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
*Colorectal Neoplasms/blood/genetics/microbiology
Mendelian Randomization Analysis/methods
Genome-Wide Association Study
Mediation Analysis

@article {pmid41496069,
year = {2026},
author = {Zhao, Y and Wang, H and Lu, Y and Lou, D},
title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46594},
pmid = {41496069},
issn = {1536-5964},
support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTDã€"2025〕046//The Program for High level Innovative Talents in the Guizhou Province/ ; },
mesh = {Humans ; *Asthma/microbiology/immunology ; *Bibliometrics ; *Gastrointestinal Microbiome ; Child ; Dysbiosis ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.

METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.

RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.

CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.},
}

Humans
*Asthma/microbiology/immunology
*Bibliometrics
*Gastrointestinal Microbiome
Child
Dysbiosis
*Biomedical Research/trends

@article {pmid41496014,
year = {2026},
author = {Yan, Y and Hu, M and Liu, C and Liu, Q and Xiong, T and Su, K},
title = {Unveiling the causal relationships between gut microbiota, circulating metabolic biomarkers, and benign prostate hyperplasia: A Mendelian randomization study.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46466},
pmid = {41496014},
issn = {1536-5964},
mesh = {Male ; Humans ; *Prostatic Hyperplasia/microbiology/blood/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Mendelian Randomization Analysis ; Biomarkers/blood ; *Dysbiosis/microbiology/complications ; Genome-Wide Association Study ; Risk Factors ; },
abstract = {The complex roles of gut microbiome (GM) dysbiosis and circulating metabolites in benign prostatic hyperplasia (BPH) pathogenesis have been widely hypothesized but lacked causal evidence. Critically, no Mendelian randomization (MR) study has established whether GM and metabolites exert direct causal effects or act through mediating pathways in BPH development. Using genome-wide association studies data, we conducted comprehensive 2-sample and mediation MR analyses. Causal effects were estimated via inverse-variance weighted methods with sensitivity analyses. Six bacterial phyla/genera showed significant causal links to BPH, including Actinobacteria (genus Bifidobacterium), Bacteroidetes (genus Bacteroides), Firmicutes (genera Blautia, Holdemania), and Proteobacteria (genus Comamonas). Additionally, 2 circulating metabolites - the mean diameter of low-density lipoprotein (LDL) particles and the free cholesterol to total lipids ratio in small very LDL - were significantly associated with BPH. However, no mediation effect was found for any circulating metabolites on BPH. In summary, our 2-sample and mediation MR analysis revealed 18 GM and 2 circulating metabolites significantly linked to BPH, highlighting their potential as risk factors. While no mediation effects for circulating metabolites were detected, these findings enhance our understanding of preventive strategies for BPH, emphasizing the intricate relationship between GM dysbiosis, circulating lipid metabolites, and disease onset.},
}

Male
Humans
*Prostatic Hyperplasia/microbiology/blood/genetics
*Gastrointestinal Microbiome/physiology/genetics
Mendelian Randomization Analysis
Biomarkers/blood
*Dysbiosis/microbiology/complications
Genome-Wide Association Study
Risk Factors

@article {pmid41495909,
year = {2026},
author = {Derollez, E and Roson-Calero, N and Rouzé, P and Dedieu-Berne, A and Ballesté-Delpierre, C and Fraikin, N and Iorga, BI and Huang, TD and Bigot, S and Vila, J and Bogaerts, P and Lesterlin, C},
title = {Specific killing and resensitization of pathogenic Escherichia coli strains carrying blaCTX-M-15 β-lactamase using targeted-antibacterial-plasmids (TAPs).},
journal = {Nucleic acids research},
volume = {54},
number = {1},
pages = {},
pmid = {41495909},
issn = {1362-4962},
support = {//Joint Programming Initiative on Antimicrobial Resistance/ ; JPIAMR2021-194//JPIAMR/ ; FRM-EQU202103012587//Foundation for Medical Research/ ; ANR-20-PAMR-0010//French Priority Research Program/ ; //Agence Nationale de la Recherches/ ; },
mesh = {*beta-Lactamases/genetics/metabolism ; *Escherichia coli/genetics/drug effects/enzymology ; *Plasmids/genetics ; CRISPR-Cas Systems ; Humans ; Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli Infections/microbiology ; },
abstract = {Targeted-Antibacterial-Plasmids (TAPs) offer a precise approach to combat multidrug-resistant bacteria by selectively removing resistant strains while preserving commensals. Here, we assess TAPs that deliver CRISPR/Cas systems via conjugation to kill or resensitize extended-spectrum β-lactamase (ESBL)-producing Escherichia coli carrying the blaCTX-M-15 gene. We systematically tested multiple variables in the TAP approach, including two commensal E. coli donors, three distinct helper plasmids encoding the transfer machineries, and six recipient strains harbouring the resistance gene either chromosomally or on a plasmid. Cas9-based TAPs induced double-stranded breaks in chromosomal blaCTX-M-15 genes, resulting in immediate bacterial death. When the target gene was plasmid-borne, Cas9 cleavage triggered plasmid loss and partial toxin-antitoxin-mediated killing. In contrast, dCas9-based TAPs inhibited blaCTX-M-15 expression without affecting cell viability, thereby restoring third-generation cephalosporin susceptibility. In mixed-culture experiments, TAPs specifically eliminated only blaCTX-M-15-carrying E. coli while sparing other non-targeted bacterial species. Conjugation assays in human faeces demonstrated substantial suppression of cefotaxime-resistant (CtxR) E. coli by both Cas9- and dCas9-based TAPs, underscoring their efficacy in complex microbial environments. These findings highlight TAPs' decolonization promise, paving the way for future microbiome-editing interventions against multidrug-resistant carriage or infection.},
}

*beta-Lactamases/genetics/metabolism
*Escherichia coli/genetics/drug effects/enzymology
*Plasmids/genetics
CRISPR-Cas Systems
Humans
Anti-Bacterial Agents/pharmacology
Conjugation, Genetic
Drug Resistance, Multiple, Bacterial/genetics
Escherichia coli Infections/microbiology

@article {pmid41495831,
year = {2026},
author = {Éliás, AJ and Földvári-Nagy, KC and Al-Gharati, YZ and Veres, DS and Schnabel, T and Teutsch, B and Erőss, B and Hegyi, P and Lenti, K and Földvári-Nagy, L},
title = {Effect of probiotic supplementation on the gut microbiota diversity in healthy populations: a systematic review and meta-analysis of randomised controlled trials.},
journal = {BMC medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12916-025-04602-0},
pmid = {41495831},
issn = {1741-7015},
abstract = {BACKGROUND: Probiotics are widely used dietary supplements promoted to positively influence gut health and microbiota diversity, making them popular among healthy individuals. One of the purported benefits of probiotics is their ability to enhance gut microbiota diversity, a feature associated with improved resilience and overall health. However, evidence supporting this claim remains inconclusive. We aimed to investigate whether probiotics significantly modify gut microbiota diversity in healthy populations through a systematic review and meta-analysis.

METHODS: A systematic search of MEDLINE, Embase, and Cochrane databases was conducted on 12/04/2024, following the search strategy registered in PROSPERO (CRD42022286137). Out of 9217 identified articles, 47 met the inclusion criteria of the current review, and 22 studies with data from 1068 individual subjects were eligible for meta-analysis of changes in gut microbiota diversity assessed by diversity indices. A random-effects model was employed to estimate the means of median differences (MedD) with 95% confidence intervals (CI) due to the expected heterogeneity.

RESULTS: The quantitative synthesis revealed no statistically significant effects of probiotics on Shannon diversity (MedD = - 0.08, 95% CI [- 0.16 to 0.01]), observed operational taxonomic units (MedD = 2.19, 95% CI [- 2.20 to 6.57]), Chao1 (MedD = - 3.19, 95% CI [- 27.28 to 20.89]), or Simpson's index of diversity (MedD = - 0.01, 95% CI [- 0.02 to 0.00]) indices compared to unsupplemented controls. Subgroup and sensitivity analyses suggest that the probiotic taxonomic family, the risk of bias, or the duration of intervention did not change our findings. Insufficient data prevented us from meta-analysing other diversity indices; however, most of the included studies reported no difference in other reported α- and ß-diversity indices between the probiotic and control groups.

CONCLUSIONS: Our results indicate that probiotic supplementation does not produce statistically significant changes in gut microbiota diversity in healthy individuals. This study highlights the need for further research to determine whether specific probiotic strains or formulations may influence diversity in targeted subgroups or under specific conditions.},
}

@article {pmid41495822,
year = {2026},
author = {Xie, S and Zhi, Y and Badehnoosh, B},
title = {Microbial modulators of the epigenome: probiotic regulation of MiRNAs and LncRNAs in health and disease and preventive medicine.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {4},
pmid = {41495822},
issn = {1757-4749},
abstract = {Current improvements in microbiome research have illuminated the serious function of probiotics in modulating host gene expression through epigenetic mechanisms, particularly via the regulation of non-coding RNAs (ncRNAs) such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). These regulatory RNAs are essential mediators of gene silencing, chromatin remodeling, and cellular signaling pathways implicated in immunity, inflammation, cancer, and neurodegenerative diseases. This review comprehensively examines current evidence on how specific probiotic strains influence miRNA and lncRNA expression, leading to beneficial outcomes in various pathological and physiological conditions. We explore the underlying molecular mechanisms by which probiotic-derived metabolites, like extracellular vesicles and short-chain fatty acids, interrelate with host transcriptional machinery and ncRNA biogenesis. Special emphasis is placed on disease models including inflammatory bowel disease, colorectal cancer, metabolic syndrome and Alzheimer's disease, highlighting the beneficial possible of targeting the gut microbiota-ncRNA axis. Moreover, we discuss the prospects for personalized microbiome-based interventions, challenges in clinical translation, and future directions for leveraging probiotic-ncRNA interactions in precision medicine. The integration of probiotics into epigenetic therapy represents a promising, non-invasive strategy for modulating gene expression and restoring homeostasis in complex diseases.},
}

@article {pmid41495581,
year = {2026},
author = {Cheng, Y and Yang, Y and Guo, Y and Shi, Y and Feng, J and Jiang, X and Yang, Z and Zhu, H and Liu, X},
title = {Exploring the pathogenesis of NAFLD: a study of the correlation of gut microbes and metabolites in humanized mouse gut microbiota.},
journal = {Journal of molecular medicine (Berlin, Germany)},
volume = {104},
number = {1},
pages = {24},
pmid = {41495581},
issn = {1432-1440},
support = {2022YFF0710600//Key Technologies Research and Development Program/ ; },
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism/pathology/etiology ; *Gastrointestinal Microbiome ; Humans ; Mice ; Disease Models, Animal ; Male ; Liver/pathology ; Female ; Feces/microbiology ; *Metabolome ; },
abstract = {There is mounting scientific evidence indicating a robust association between gut microbiota and nonalcoholic fatty liver disease (NAFLD). Exposure to commensal microbiota in germ-free mice has a significant impact on the regulatory mechanisms of gut genes, in contrast to those conventionally raised. In this study, we have successfully inoculated the gut microbiota from healthy individuals and NAFLD patients into germ-free mice, with the objective of developing a humanized mouse model that accurately replicates the gut microenvironment of NAFLD patients. Changes in blood composition and liver pathology in these mice were systematically measured. Furthermore, we have conducted a detailed analysis of the variations in fecal microbiota and differential metabolites in the blood composition. Our findings indicate a high degree of similarity in disease characteristics between mice colonized with microbiota and humans suffering from NAFLD. Notably, we have observed a strong correlation between alterations in serum differential metabolites and gut microbiota in these mice. KEY MESSAGES: A humanized NFALD mouse model was established based on sterile mice. In microbiota-colonized mice and humans with NAFLD, disease characteristics showed a high degree of similarity. There was a strong association between changes in serum differential metabolites and gut microbiota in mice colonized by intestinal microbiota.},
}

Animals
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism/pathology/etiology
*Gastrointestinal Microbiome
Humans
Mice
Disease Models, Animal
Male
Liver/pathology
Female
Feces/microbiology
*Metabolome

@article {pmid41495500,
year = {2026},
author = {Huang, JS and Zhang, ZY and Zhong, QH and Guo, FL and Wu, JY and Chen, S and Lin, WW and Lin, JB},
title = {ASO Visual Abstract: Tumor-Intrinsic Microbiome-Based Subtyping of Esophageal Cancer as Predictive Biomarkers for Postoperative Survival.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
doi = {10.1245/s10434-025-19013-x},
pmid = {41495500},
issn = {1534-4681},
}

@article {pmid41495419,
year = {2026},
author = {Bang, YH and Choi, JH and Park, K and Lee, B and Han, KY and Pyo, DH and Cho, YB and Kim, TY and Park, KJ and Ryoo, SB and Kang, SB and Yu, CS and Lee, J and Lee, KY and Kim, KT and Lee, JY and Chu, HBK and Shah, N and Gupta, S and Sonpatki, P and Kim, YJ and Park, WY},
title = {Colorectal microenvironment determines the prognosis of colorectal cancer.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {41495419},
issn = {2092-6413},
support = {NRF2017M3A9A7050803//National Research Foundation of Korea (NRF)/ ; 2022R1C1C1012415//National Research Foundation of Korea (NRF)/ ; 2021R1A4A3031875//Ajou University/ ; },
abstract = {Here we aimed to evaluate the feasibility of distinguishing colorectal microenvironments that support cancer cell growth from those that do not. We hypothesized that patients whose non-tumor-bearing tissue (NBT) obtained from the furthest margins of resected cancer specimens resembled the tumor had a poorer prognosis. Patients with colorectal cancer were divided into groups with tumor-supportive (TSM) or healthy microenvironments using bulk RNA sequencing data from 273 paired NBT and tumor samples. Patients in the TSM group exhibited significantly poorer 5-year recurrence-free survival and overall survival compared with those in the healthy microenvironment group. Pathway and 16S rRNA sequencing analyses revealed that NBT and tumors from the TSM group shared a microbiome composition, along with decreased pathway activity related to microvilli maintenance and flavonoid or vitamin metabolic processes. Single-cell RNA sequencing uncovered upregulated interactions between IL1B[high] neutrophils and OLFM4[+] epithelial cells in NBTs from the TSM group, as well as organized microniches in TSM tumors, featuring interactions between EMP1[high] epithelial cells, IL1B[high] neutrophils and GZMK[high] CD8[+] T cells. Collectively, the colorectal microenvironment can serve as a prognostic biomarker to effectively predict cancer invasiveness and tumor-promoting inflammation. Maintaining a healthy colorectal mucosal microenvironment, potentially through dietary intervention, is crucial.},
}

@article {pmid41495254,
year = {2026},
author = {Kukreja, B and Jeon, S and Cao, W and Rusu, B and Harrison, CF and Ghazisaeidi, S and Tahmasian, N and Feng, MY and Chan, R and Loan, A and Johnston, WB and Padhy, S and Rakoff-Nahoum, S and Wang, J and Yim, YS and Kalish, BT},
title = {Spatial transcriptomics of the developing mouse brain immune landscape reveals effects of maternal immune activation and microbiome depletion.},
journal = {Nature neuroscience},
volume = {},
number = {},
pages = {},
pmid = {41495254},
issn = {1546-1726},
abstract = {Immune molecules and their cognate receptors are developmentally regulated in brain and dynamically expressed in the context of neurodevelopmental disorders. Despite the importance of immune molecules to brain wiring, a comprehensive map of the neuroimmune landscape is lacking in developing brain. Here we employed multiplexed in situ spatial transcriptomics to measure the expression of major immune ligands and receptors in developing mouse brain during mid and late gestation. Given the importance of maternal environment in shaping fetal neurodevelopment, we determined how embryonic neuroimmune landscape was altered after maternal immune activation (MIA) and maternal microbiome depletion. Our study revealed notable sex-specific patterns in gene expression and spatial architecture within developing brain. We observed changes in the CXCL12/CXCR7 chemokine network after MIA and microbiome depletion, suggesting a potential common mechanism underlying neural progenitor abnormalities. This resource underscores how the maternal environment programs precise regulation of immune molecules in developing brain, highlighting sex-specific vulnerability.},
}

@article {pmid41495071,
year = {2026},
author = {Suryavanshi, M and Mukherjee, SD and Miller, AW},
title = {Predicting probiotic success: lessons from Oxalobacter and oxalate metabolism.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00896-3},
pmid = {41495071},
issn = {2055-5008},
support = {R01KD121689//NIH NIDDK/ ; },
abstract = {The gut microbiota influences host metabolism, immunity, and organ physiology, making it an attractive therapeutic target. However, clinical probiotic trials often produce inconsistent results, reflecting context-dependent effects shaped by metabolic, ecological, dietary, and host-specific factors. We critically synthesized the literature on hyperoxaluria, a condition of elevated urinary oxalate associated with kidney stones and chronic kidney disease, as a mechanistically tractable model for probiotic development. We examined evidence from clinical studies, microbiome analyses, and mechanistic experiments to identify factors influencing efficacy, with a focus on Oxalobacter formigenes, a specialist oxalate-degrading anaerobe. Across trials, probiotic success depended less on dose, strain identity, or persistence, and more on the ecological context - particularly the baseline abundance of oxalate-degrading genes (oxc, frc) in the native microbiota. Efficacy was highest when these metabolic niches were vacant. Diet, delivery format, and broader microbial community structure also shaped outcomes. A taxon-centric approach is insufficient for predicting probiotic efficacy. We propose a three-phase framework for rational design: (1) case-control microbiome studies to identify metabolically relevant deficits; (2) mechanistic in vivo and in vitro validation to establish causality; and (3) complex systems modeling to predict context-specific responses. This metabolism-first, ecology-grounded strategy is generalizable to other microbiota-linked conditions and supports precision microbial therapeutics.},
}

@article {pmid41495007,
year = {2026},
author = {Khan, A and Mushtaq, M and Shah, M and Khan, RU and Alonaizan, R and Naz, S and Abudabos, A and Israr, M},
title = {Synergistic Effects of Garlic Extract and Mannan-Oligosaccharide Prebiotic Supplementation on Growth Performance, Carcass Quality, Immunity, Gut Morphology and Microbiome in Broiler Chickens.},
journal = {Veterinary medicine and science},
volume = {12},
number = {1},
pages = {e70751},
pmid = {41495007},
issn = {2053-1095},
mesh = {Animals ; *Chickens/growth & development/microbiology/immunology/anatomy & histology/physiology ; *Prebiotics/administration & dosage/analysis ; *Garlic/chemistry ; *Mannans/administration & dosage/pharmacology/metabolism ; *Plant Extracts/administration & dosage/pharmacology/metabolism ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/administration & dosage/pharmacology ; Diet/veterinary ; Drug Synergism ; Male ; },
abstract = {This study evaluated the effects of dietary supplementation with garlic extract, mannan oligosaccharide (MOS) and their combinations on growth performance, immunity, gut morphology and microbiota in broilers. A total of 250 Hubbard chicks were allocated into five groups: control (basal diet), garlic extract, MOS, Combo-I (half doses of both) and Combo-II (full doses of both). The trial lasted 42 days under standard management conditions. Results demonstrated that Combo-I consistently improved body weight gain and feed conversion ratio (FCR) during the starter, grower and finisher phases (p < 0.05), highlighting a synergistic effect of the combined supplements. Carcass weight was significantly enhanced in Combo-II (p = 0.03), although dressing percentage and organ weights were not affected (p > 0.05). Immunological parameters were strongly influenced by supplementation. Combo-I induced the highest antibody titres against Newcastle disease and infectious bursal disease (p < 0.05), with Combo-II ranking second, whereas single additives showed moderate improvements compared to the control. Similarly, serum immunoglobulin concentrations (IgM, IgA and IgG) were greatest in Combo-I, confirming enhanced humoral immunity. Gut morphology was significantly improved in the combination groups, particularly Combo-I, which showed increased villus height, wider villi, reduced crypt depth, and the highest villus:crypt ratio (p < 0.05), reflecting superior absorptive potential. Although differences in ileal microbiota were not statistically significant, both combination treatments reduced Escherichia coli and Salmonella counts while promoting Lactobacillus spp. populations. In conclusion, the combined use of garlic extract and MOS, especially at half doses (Combo-I), optimally improved growth, immune response, gut architecture and microbial balance, offering a synergistic strategy for enhancing broiler performance.},
}

Animals
*Chickens/growth & development/microbiology/immunology/anatomy & histology/physiology
*Prebiotics/administration & dosage/analysis
*Garlic/chemistry
*Mannans/administration & dosage/pharmacology/metabolism
*Plant Extracts/administration & dosage/pharmacology/metabolism
Dietary Supplements/analysis
Animal Feed/analysis
*Gastrointestinal Microbiome/drug effects
*Oligosaccharides/administration & dosage/pharmacology
Diet/veterinary
Drug Synergism
Male

@article {pmid41494844,
year = {2026},
author = {Nguyen, P and Rehan, S},
title = {Integrating behaviour and microbiomes into considerations of bee health.},
journal = {Genome},
volume = {69},
number = {},
pages = {1-11},
doi = {10.1139/gen-2025-0047},
pmid = {41494844},
issn = {1480-3321},
mesh = {Bees/microbiology/physiology ; Animals ; *Microbiota ; Pollination ; *Behavior, Animal ; Symbiosis ; },
abstract = {Relationships between individuals play an important role in their behaviour and health, ranging from interactions between individuals to symbioses with microorganisms. Defining bee health may benefit from examining these relationships at different levels of biological organization, suggesting that bee genetics could be influencing microbial communities or that the social microbiome may be a unique way of characterizing pollinator health. Here, we review research in bee behaviour and microbiomes to examine different perspectives influencing health and how factors such as an individual's physiology, genetics, behaviour, social role, and environment can interact with its microbiota. As the role of the microbiome is explored across wild bee species and sociality, examining these factors together rather than in isolation provides a more comprehensive understanding of microbial communities and their impact on their bee hosts. Considering increasing environmental threats to bees, holistic perspectives can inform conservation efforts and actionable methods to support pollinators in altered environments.},
}

Bees/microbiology/physiology
Animals
*Microbiota
Pollination
*Behavior, Animal
Symbiosis

@article {pmid41494802,
year = {2026},
author = {Mayorga, L and Noguera Segura, A and Campderros, L and Pons-Tarin, M and Soler, Z and Vega-Abellaneda, S and Serrano-Gomez, G and Herrera-deGuise, C and Robles-Alonso, V and Borruel, N and Manichanh, C},
title = {Distinct microbial mediators link diet to inflammation in Crohn's disease and ulcerative colitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337480},
pmid = {41494802},
issn = {1468-3288},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) arises from complex interactions among diet, host and gut microbiome. Although diet influences intestinal inflammation, the microbial and metabolic pathways involved, and their differences between Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD remain unclear.

OBJECTIVE: To investigate how the gut microbiome mediates the effects of habitual diet on inflammatory activity in IBD.

DESIGN: This longitudinal study included 198 adults (100 healthy controls, 49 CD, 49 UC), participants completed a validated food frequency questionnaire. Dietary quality was evaluated using established indices (Alternative Mediterranean Diet, Healthy Eating Index-2015, Índice de Alimentación Saludable, Mean Adequacy Ratio, Plant-Based Dietary Indexes, Healthy Food Diversity). Participants also provided two stool samples (baseline and 6 months). Shotgun metagenomics (n=366) enabled taxonomic and functional profiling. Causal mediation analyses were used to identify microbial features mediating the effect of diet on inflammation.

RESULTS: IBD patients exhibited lower dietary diversity, fibre intake and nutritional adequacy compared with controls. Microbiome diversity was lowest in CD, intermediate in UC and correlated positively with higher intake of fibre, fruit, vegetables and nuts, and negative with processed foods and sugary beverages. Causal mediation analyses revealed that in CD, coffee, whole wheat bread and healthier diets lowered the Harvey-Bradshaw index through specific bacterial species and metabolites. In UC, Mediterranean-like diets, fruits and coffee reduced C reactive protein via greater microbial richness, reduced dysbiosis and short-chain fatty acid-related functions.

CONCLUSION: Diet quality influences inflammation in IBD through distinct microbiome pathways: specific taxa and metabolites mediate effects in CD, whereas microbial richness and global composition drive protection in UC.},
}

@article {pmid41494643,
year = {2026},
author = {Takahashi, H and Harada, N and Hayamizu, Y and Dungubat, E and Nakazawa, M and Kitakaze, T and Sugimoto, K and Inui, H and Yoshihara, E and Takahashi, Y and Yamaji, R},
title = {Testosterone deficiency synergistically exacerbates fructose-induced hepatic steatosis through gut microbiota and pyruvate in mice.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpendo.00518.2025},
pmid = {41494643},
issn = {1522-1555},
support = {22H02289 and 25K01971//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; #2022-006//Thomas J. Beatson Jr. foundation Grant/ ; R01DK136888//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; 5-CDA-2022-1178-A-N//JDRF/United States ; },
abstract = {Hepatic steatosis is the initial stage of metabolic dysfunction-associated steatotic liver disease (MASLD) and is highly prevalent among middle-aged men. Low testosterone levels and dietary fructose intake are independent risk factors for MASLD, although these can occur simultaneously. This study investigated the combined effects of testosterone deficiency and fructose intake on hepatic steatosis and gut microbiota involvement. Male mice were castrated or sham-operated at 8 weeks of age and administered fructose water with or without antibiotics for 8 weeks after being divided into six groups: Sham/Control, Sham/Fructose, Sham/Fructose+Antibiotics, Castration/Control, Castration/Fructose, and Castration/Fructose+Antibiotics. The castrated groups had lower body weights than the sham-operated groups, whereas castration did not affect portal and circulating fructose concentration. Although castration alone did not affect hepatic lipid accumulation, it synergistically promoted fructose-induced triglyceride accumulation, which was alleviated by antibiotic treatment. The expression of lipogenesis-related genes (Srebp-1c), fatty acid transporters (Cd36), and fructose metabolism-related genes (Aldob, Khk-A, and Khk-C) was upregulated by the combination of castration and fructose intake, but antibiotic administration did not suppress this effect. Castration, fructose intake, and their combination influenced β-diversity, but not α-diversity of gut microbiota composition. Cecal pyruvate concentrations were increased by the combination of castration and fructose intake and were suppressed by antibiotics. PICRUSt2 and MaAslin2 analyses supported pyruvate accumulation mediated by alterations in the gut microbiota. Furthermore, pyruvate promoted triglyceride accumulation in primary hepatocytes in the presence of fructose. Our results indicated that testosterone deficiency synergistically exacerbates fructose-induced hepatic steatosis, which is partly mediated by gut-derived pyruvate.},
}

@article {pmid41494563,
year = {2026},
author = {Zhao, C and Zhang, W and Zhang, S and Zhang, L and Han, F and Lei, J and Li, Y and Zhou, W},
title = {Co-regulation of substrate flux and biomass density for enhanced ammonia assimilation under saline conditions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133947},
doi = {10.1016/j.biortech.2026.133947},
pmid = {41494563},
issn = {1873-2976},
abstract = {Drawing inspiration from the self-regulating carbon-nitrogen cycling of saline ecosystems, this study investigates how substrate flux and biomass density co-regulate the structure and function of marine sediment-derived halophilic heterotrophic ammonia assimilation (HAA) microbiome cultivated in saline ammonia-containing wastewater with a COD/N radio of 20 under volumetric exchange ratios (VER) of 75 %, 50 %, and 25 % and mixed liquor suspended solids (MLSS) increasing from 5 to 15 g/L. The combined variation in VER and MLSS generated a gradient in food-to-microorganism radio (F/M). With increasing in biomass, COD removal efficiencies peaked at 94.4-99.3 % at 15 g MLSS/L, whereas ammonia removal efficiencies reached at 90.3-96.8 % at 12.5 g MLSS/L before declining. A VER of 25 % reduced sludge activity, while a VER of 75 % impaired floc settleability. The directed HAA community shifted in substrate flux and biomass density, centering on dominant genera such as Halomonas and Marinobacter, ultimately forming a stable microbiome.},
}

@article {pmid41494226,
year = {2025},
author = {Xiao, Y and Long, J and Liu, L and Wang, Z and Wang, W and Huang, P},
title = {Water extract of Ampelopsis grossedentata improves reproductive performance in laying hens by regulating gut microbiota and PI3K/AKT signaling pathway.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106368},
doi = {10.1016/j.psj.2025.106368},
pmid = {41494226},
issn = {1525-3171},
abstract = {Reproductive function plays a central role in health but declines with aging. Recent studies have focused on natural flavonoids to mitigate reproductive aging, with the water extract of Ampelopsis grossedentata (WEA) showing promise due to its antioxidant, antitumor, antibacterial, and anti-inflammatory properties. However, the specific bioactive constituents and mechanisms of WEA in alleviating reproductive aging remain unclear. This experiment analyzed the active flavonoid components in WEA and predicted the molecular mechanism by which WEA alleviates reproductive system aging through network pharmacology. Furthermore, based on the predicted molecular mechanisms, the effects of WEA on laying hens' production performance, reproductive function, and intestinal health were explored. A total of 288 laying hens (55 weeks old) were assigned to four groups: control and three WEA doses (50, 150, 250 mg/kg). During the experiment, production performance indicators such as egg weight were recorded daily. After the 8-week period, biological samples were collected for analysis. Network pharmacology identified dihydromyricetin, myricetin, and (-)-epicatechin as key active components, primarily affecting the PI3K/AKT signaling pathway. WEA significantly improved egg quality, immune parameters, reproductive organ morphology, intestinal morphology, and serum sex hormone levels, and reduced inflammatory factor levels. WEA improved ovarian apoptosis by regulating the PI3K/AKT/mTOR pathway and alleviated oviduct inflammation by inhibiting the NF-κB pathway. WEA enhanced intestinal anti-inflammatory and antioxidant functions by regulating NF-κB and Nrf2 pathways and increased short-chain fatty acids in the hindgut. WEA altered the intestinal microbiome, particularly reducing the relative abundance of Methylobacterium-Methylorubrum in the foregut and Bacteroides in the hindgut. Correlation analysis revealed that WEA may alleviate oxidative and inflammatory responses by regulating intestinal microbiota, further impacting the PI3K/AKT cascade. In conclusion, WEA improves antioxidant, anti-inflammatory, and reproductive functions in laying hens by regulating the PI3K/AKT pathway and may alleviate oxidative and inflammatory responses by modulating microbiota. This study provides insights into the mechanism of WEA in improving reproductive performance and intestinal regulation.},
}

@article {pmid41493848,
year = {2026},
author = {Kawaguchi, Y and Terui, K and Fumita, T and Shibata, R and Yoshizawa, H and Ogasawara, S and Kondo, T and Ozawa, Y and Inaba, Y and Hishiki, T},
title = {Cholestasis-reducing effects of bezafibrate on survivors of biliary atresia with native livers: A prospective phase II trial.},
journal = {Hepatology communications},
volume = {10},
number = {1},
pages = {},
pmid = {41493848},
issn = {2471-254X},
mesh = {Humans ; Male ; Female ; *Bezafibrate/therapeutic use/administration & dosage ; *Biliary Atresia/complications/surgery ; *Cholestasis/drug therapy/etiology ; Prospective Studies ; Adult ; *Hypolipidemic Agents/therapeutic use/administration & dosage ; Young Adult ; Adolescent ; Alkaline Phosphatase/blood ; Liver ; Treatment Outcome ; Survivors ; gamma-Glutamyltransferase/blood ; },
abstract = {BACKGROUND: Long-term survivors of biliary atresia (BA) require liver transplantation owing to cholestasis-associated complications. Bezafibrate (BZF), an antihyperlipidemic agent, can improve cholestasis-induced liver damage. Herein, we evaluated the cholestasis-reducing effect of BZF on survivors of BA with native livers, a condition that has not been previously assessed in any study.

METHODS: In this single-center, single-arm, open-label, uncontrolled, prospective phase II trial, patients were enrolled from a central registry system at the Chiba University Data Center. Postoperative patients (n=10) aged older than 18 years (median age, 29 y) with BA and increased serum ALP levels were enrolled between July 2021 and March 2022. Patients with high total bilirubin or alanine aminotransferase levels, recent changes in BA medication, cholangitis within 3 months, renal dysfunction, or liver transplantation were excluded. Participants were administered 400 mg BZF orally in 2 daily doses for 12 weeks and subsequently underwent a 12-week observation. Other drugs were continued. The primary endpoint was the change in ALP levels after 12 weeks of oral BZF administration. The secondary and exploratory endpoints were changes in gamma-glutamyl transpeptidase and triglyceride levels, fecal microbiota, and bile acids.

RESULTS: The mean change in the ALP level was -67 U/L (±20 U/L; p=0.0042). Changes in ALP and gamma-glutamyl transpeptidase levels differed between week 0 and week 6. Adverse events occurred in 5 patients. BZF administration increased the number of Fusicatenibacter without affecting microbiome diversity or bacterial phylum abundance while decreasing lithocholic acid levels and increasing chenodeoxycholic acid levels.

CONCLUSIONS: BZF decreased cholestasis markers in survivors of BA with native livers, indicating its potential as an alternative to delayed liver transplantation for this population.},
}

Humans
Male
Female
*Bezafibrate/therapeutic use/administration & dosage
*Biliary Atresia/complications/surgery
*Cholestasis/drug therapy/etiology
Prospective Studies
Adult
*Hypolipidemic Agents/therapeutic use/administration & dosage
Young Adult
Adolescent
Alkaline Phosphatase/blood
Liver
Treatment Outcome
Survivors
gamma-Glutamyltransferase/blood

@article {pmid41493605,
year = {2026},
author = {Ben-Dahan, O and Gutvirtz, G and Wainstock, T and Sheiner, E},
title = {Exposure to maternal vaginal flora during labor and long-term infectious morbidity of the offspring.},
journal = {Archives of gynecology and obstetrics},
volume = {313},
number = {1},
pages = {15},
pmid = {41493605},
issn = {1432-0711},
mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology ; Adult ; *Labor, Obstetric ; *Cesarean Section/adverse effects/statistics & numerical data ; *Microbiota ; Cohort Studies ; Hospitalization/statistics & numerical data ; Delivery, Obstetric ; Proportional Hazards Models ; Young Adult ; Kaplan-Meier Estimate ; Incidence ; Infant, Newborn ; },
abstract = {PURPOSE: Cesarean delivery (CD) has been linked to increased long-term infectious morbidity in offspring, potentially due to limited exposure to the maternal vaginal microbiome, which may influence immune development. We hypothesized that the degree of exposure to vaginal microbiota during labor would be associated with differences in long-term infectious morbidity.

METHODS: We conducted a population-based cohort study including 348,332 singleton deliveries. Offspring were classified into four groups: vaginal delivery (VD, reference), CD for non-progressive labor in the first stage (NPL1), CD for non-progressive labor in the second stage (NPL2), and elective (pre-labor) CD. Infectious-related hospitalizations up to age 18 were assessed. Kaplan-Meier curves compared cumulative incidence between the groups and a Cox proportional hazards model adjusted for various potential confounders.

RESULTS: Of the cohort, 89.2% were VD, 1.4% NPL1, 0.6% NPL2, and 8.8% elective CD. Infectious-related hospitalization rates were higher for NPL1 and elective CD (26.2% each) compared to NPL2 (24.3%) and VD (23.8%) (p < 0.001). Kaplan-Meier analysis demonstrated a dose-response pattern, with the lowest cumulative incidence in VD, followed by NPL2, NPL1, and highest in elective CD (log-rank p < 0.001). In adjusted analysis, NPL1 (aHR 1.10) and elective CD (aHR 1.13) were associated with increased long-term infectious morbidity, whereas NPL2 was not significantly different from VD.

CONCLUSION: Reduced exposure to vaginal microbiota, as in elective CD and NPL1, is associated with increased long-term infectious morbidity in offspring, while exposure during the second stage of labor (NPL2) may confer immunological benefits.},
}

Humans
Female
Pregnancy
*Vagina/microbiology
Adult
*Labor, Obstetric
*Cesarean Section/adverse effects/statistics & numerical data
*Microbiota
Cohort Studies
Hospitalization/statistics & numerical data
Delivery, Obstetric
Proportional Hazards Models
Young Adult
Kaplan-Meier Estimate
Incidence
Infant, Newborn

@article {pmid41493557,
year = {2026},
author = {Talha, M and Faisal, M and Mujtaba, A and Amjad, A and Abbas, N and Shamim, L and Mahin, FE and Hassan, M and Hassan, MD and Awaisi, MAR},
title = {Virophages: mechanisms, ecological Roles, and therapeutic potential in combating giant virus infections.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {96},
pmid = {41493557},
issn = {1432-072X},
mesh = {Humans ; *Virophages/physiology/genetics ; *Giant Viruses/physiology/genetics ; Virus Replication ; *DNA Virus Infections/therapy/virology ; Animals ; },
abstract = {Virophages, identified when scientists discovered Sputnik, a double-stranded DNA (dsDNA) viruses that form a unique group of viral entities that can parasitize giant viruses. They rely on these giant viruses for replication and inhibiting them from spreading inside eukaryotic hosts. This review seeks to bring together current knowledge on dsDNA virophages. It details how they work, explains their roles in the host, giant virus, and virophage system, and evaluates their potential as new antiviral treatments. Mechanistically, virophages disrupt the giant by replication through competitive resource depletion inside the viral factory. It modifies viral gene expression, and disrupts progeny formation, thus supporting the survivability of the host cell. In addition to these intracellular effects, virophages participate in ecological processes, such as controlling microbial communities and facilitating nutrient recycling. The therapeutic potential of virophages is hypothesized in the context of diseases where the giant viruses have been detected (e.g., hospital-acquired pneumonia), though causal roles remain debated. Furthermore, their possible use as genetic vectors is being fully investigated. However, there are several challenges to overcome before clinical translation is possible: restricted host range, risks of immune activation, and difficulties in scalable production. Future research should focus on the discovery of new virophage species, their mechanism of actions, and bioengineering strategies to improve their antiviral characteristics.},
}

Humans
*Virophages/physiology/genetics
*Giant Viruses/physiology/genetics
Virus Replication
*DNA Virus Infections/therapy/virology
Animals

@article {pmid41493496,
year = {2026},
author = {Barton, XW and S Tobe, S and Fontaine, JB and Oskam, CL},
title = {A framework for optimising arthropod DNA quality and quantity for modern sequencing tools using hard ticks (Ixodidae).},
journal = {Parasitology research},
volume = {125},
number = {1},
pages = {5},
pmid = {41493496},
issn = {1432-1955},
mesh = {Animals ; *DNA/isolation & purification/genetics ; *Specimen Handling/methods ; *Sequence Analysis, DNA/methods ; *Amblyomma/genetics ; *Ixodidae/genetics ; },
abstract = {Advanced sequencing technologies require strict standards for DNA input and integrity. This study addresses the challenge of extracting high-quality, endogenous DNA from smaller arthropods with mixed DNA sources (arthropod, host, and microbiome), using Amblyomma triguttatum as a model organism. We evaluated three tissue types (Whole, Bisected, and Legs), three disruption methods (Undisrupted, Sliced, and liquid nitrogen bead Homogenisation), and two extraction kits (Qiagen DNeasy Blood & Tissue and MagAttract HMW) to optimise DNA yield, quality, and composition. The Qiagen MagAttract High Molecular Weight Kit significantly increased the proportion of large DNA fragments (20-48.5 kbp) by 11-fold compared to the Qiagen DNeasy Blood & Tissue Kit. Aggressive homogenisation methods produced the highest proportion of short fragments (97%, 1-10 kbp). Whole-Homogenised specimens yielded the highest DNA concentration (198 ng µL[-1]), whereas Bisected-Undisrupted specimens achieved 146 ng µL[-1] with a greater proportion of large fragments (3.15%). Bacterial DNA content remained consistent across treatments. Our findings highlight the importance of selecting appropriate extraction methods to ensure optimal DNA quality for advanced sequencing applications. These results provide useful guidelines for optimising DNA extractions from smaller-bodied arthropods (~ 10-20 mg) and establish a framework for future studies to consider DNA quantity, quality, and composition.},
}

Animals
*DNA/isolation & purification/genetics
*Specimen Handling/methods
*Sequence Analysis, DNA/methods
*Amblyomma/genetics
*Ixodidae/genetics

@article {pmid41493385,
year = {2026},
author = {Xu, Y and Wang, X and Chen, M and Xiong, J and Cheng, G},
title = {Gut microbiome as a predictor for positive youth development transition from childhood to early adolescence: a cohort study.},
journal = {Journal of child psychology and psychiatry, and allied disciplines},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpp.70109},
pmid = {41493385},
issn = {1469-7610},
support = {82304135//National Natural Science Foundation of China/ ; U25A20154//National Natural Science Foundation of China/ ; 2024NSFSC1806//the Department of Science and Technology of Sichuan Province/ ; 2025ZNSFSC0641//the Department of Science and Technology of Sichuan Province/ ; 2023M742451//the China Postdoctoral Science Foundation/ ; },
abstract = {BACKGROUND: The gut microbiome is increasingly implicated in childhood mental health and may influence positive youth development (PYD). This study aims to characterize PYD transition patterns from childhood to adolescence and explore the predictive value of the gut microbiome.

METHODS: This cohort study used two waves of data from the Chinese Adolescent Cohort study, including children aged 8-11 years at Wave 1, from Sichuan, Guizhou, and Chongqing provinces. PYD was assessed at both time points, and latent transition analysis identified changes over the 3-year follow-up period. Baseline stool samples were analyzed using 16 s rRNA sequencing. A light gradient boosting machine model was developed to link gut microbiota with PYD transition type in a training set (70%, n = 461), and validated with multinominal logistic analysis within a test set (30%, n = 200). Linear regression models were performed to assess dietary modifications on the gut microbiome.

RESULTS: Three PYD transition profiles were identified: downgraded (declining to a lower pattern), promoted (advancing to a higher pattern), and stable development type (remaining in the same pattern). Fifteen microbial genera were identified as predictors of PYD transitions, and children with higher abundance of these taxa were more likely to transition to a stable or promoted profile rather than a downgraded profile (odds ratio ranging from 2.03 to 5.45). This predictive model demonstrated excellent performance, with an area under the curve of 0.91 (95% CI: 0.89, 0.93). The microbiome-PYD transition association was more pronounced in children in earlier stages of puberty. Furthermore, a diet high in fruits, vegetables, and soybeans was positively linked with PYD stable or promoted transition type.

CONCLUSIONS: The gut microbiome presents predictive value in PYD transition from childhood to adolescence. Targeting these microbial taxa may inform future health promotion programs to optimize child development, particularly during the critical pubertal transition.},
}

@article {pmid41493379,
year = {2026},
author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA},
title = {A mathematical framework to correct for compositionality in microbiome data sets.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0112625},
doi = {10.1128/aem.01126-25},
pmid = {41493379},
issn = {1098-5336},
abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.},
}

@article {pmid41493185,
year = {2026},
author = {Zhang, X and Zhan, T and Liu, Q and Xing, M and Yu, W and Chen, B and Peng, Y},
title = {BbCFEM7 plays an important role in the pathogenicity and gut microbial community formation in the co-infection of Beauveria bassiana with Metarhizium rileyi.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0245725},
doi = {10.1128/spectrum.02457-25},
pmid = {41493185},
issn = {2165-0497},
abstract = {UNLABELLED: This study investigated the effects of the BbCFEM7 gene in Beauveria bassiana on host pathogenicity and the gut microbial community during co-infection with Metarhizium rileyi in Spodoptera litura. Our results showed that BbCFEM7 significantly enhanced the virulence of B. bassiana and significantly reduced the host LT50 in the 1:0, 9:1, and 1:1 (Bb:Mr) groups. Sequencing of the gut microbial diversity showed that the presence of BbCFEM7 significantly altered the structure of the host gut microbial community, particularly in the 9:1 group. The presence of BbCFEM7 increased the relative abundance of Enterococcus and decreased that of Thomasclavelia. Furthermore, BbCFEM7 was found to play a pivotal role in enhancing B. bassiana's tolerance to chemical stress and promoting its rapid colonization of the host's hemolymph, thereby giving it an advantage over M. rileyi. These results suggest that BbCFEM7 plays an important role not only in fungal pathogenicity but also in indirectly influencing host health by regulating gut microbial communities. This study provides a new perspective on the interactions between entomopathogenic fungi, hosts, and gut microorganisms and establishes a theoretical basis for optimizing the application of entomopathogenic fungi in pest control.

IMPORTANCE: This study investigates the role of BbCFEM7 in B. bassiana during co-infection with M. rileyi in S. litura. It reveals that BbCFEM7 significantly enhances fungal pathogenicity, shortens the time taken for the host to die, and alters gut microbial communities. These findings provide novel insights into the interactions between entomopathogenic fungi, hosts, and gut microbes, offering a theoretical basis for optimizing the application of entomopathogenic fungi in pest control, while also contributing to our understanding of the insect microbiome and immunology.},
}

@article {pmid41493072,
year = {2026},
author = {Martinsen, T and Brennan, L},
title = {Key evidence for personalised nutrition: a review of randomised controlled trials.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo02969d},
pmid = {41493072},
issn = {2042-650X},
abstract = {The field of personalised nutrition is growing and is based on the concept that delivering personalised dietary advice will be more effective than generic healthy eating guidelines for individuals to improve their diet and metabolic health. While there is substantial interest in the field, there is also a need to examine the evidence base. The objective of this review was to examine existing literature on the efficacy of personalised nutrition approaches and to identify research gaps and future needs. A literature search was conducted in PubMed for randomised controlled trials published between 2000 and 2025. Studies investigating the effects of personalised nutrition were included, and relevant papers were identified through the reference lists of existing papers. In total, 24 papers were included, with 12 studies investigating personalised nutrition based on current diet, phenotype, and metabolic biomarkers, five studies examining the effects of genotype-based personalised nutrition, and seven studies exploring approaches based on gut microbiome and machine learning algorithms. Overall, evidence from the included studies indicates that personalised nutrition approaches consistently improved dietary quality and led to significant improvements in metabolic markers, including HbA1c, triglycerides, and insulin sensitivity. However, few studies showed significant between-group differences in weight loss, and most studies did not find significant differences in blood pressure. While the results are promising, there are key challenges and research gaps that remain. Some approaches demonstrated potential for targeted improvements, but further high-quality research is needed to confirm their effectiveness and long-term impact. Future research should prioritise longer-term studies, better stratification of responders and non-responders, and cost-effectiveness evaluations to determine where and for whom personalised nutrition adds the most value.},
}

@article {pmid41493000,
year = {2026},
author = {Shah, S and Ilyas, M and Refaie, A and Yang, FL},
title = {Microbial Chemical Sensing of Microplastic-Derived Compounds in Insect Gut Ecosystems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12962},
pmid = {41493000},
issn = {1520-5851},
abstract = {Microplastic (MP) pollution threatens terrestrial and aquatic ecosystems worldwide. Insects, essential for pollination, decomposition, and nutrient cycling, ingest MPs through feeding and contact. Despite growing evidence of MP-caused gut microbe imbalance, how insect gut microbiomes detect and react to MP leachates, mainly organic additives like phthalates and bisphenol A, is still unclear, limiting our understanding of adaptive resilience against toxicity. This perspective reviews microbial sensing pathways, including two-component systems, ligand-responsive transcriptional regulators, and quorum sensing, which differentiate responses to soluble leachates from inert polymers and orchestrate either enzymatic biodegradation in plastivorous species like Tenebrio molitor or detrimental shifts toward oxidative stress, immune activation via Toll and Imd pathways, and epithelial disruption. These host-microbiota feedbacks influence metabolic homeostasis, vector competence, and ecological processes including trophic transfer and biodiversity. By linking these molecular interactions to ecological processes, we propose the utilization of insect-associated symbionts in bioremediation, guided by omics-based approaches, to develop targeted interventions that mitigate plastic pollution while maintaining ecosystem functionality.},
}

@article {pmid41492861,
year = {2026},
author = {Koshida, T and Nittono, H and Takei, H and Murakoshi, M and Yamashiro, Y and Suzuki, Y and Gohda, T},
title = {A Comprehensive Analysis of Serum and Urine Bile Acid Profiles in Chronic Kidney Disease: An Exploratory Study of Clinical Associations.},
journal = {Nephrology (Carlton, Vic.)},
volume = {31},
number = {1},
pages = {e70156},
doi = {10.1111/nep.70156},
pmid = {41492861},
issn = {1440-1797},
support = {JP24K19136]//JSPS KAKENHI/ ; },
mesh = {Humans ; Male ; Female ; *Bile Acids and Salts/urine/blood ; Cross-Sectional Studies ; Middle Aged ; *Renal Insufficiency, Chronic/blood/urine/physiopathology/diagnosis ; Aged ; Glomerular Filtration Rate ; Biomarkers/urine/blood ; Adult ; Gastrointestinal Microbiome ; Case-Control Studies ; },
abstract = {AIM: Dysbiosis contributes to systemic inflammation and the accumulation of uremic toxins, leading to end-stage kidney disease. However, the role of bile acids (BAs), key metabolic products of the gut microbiota, in the pathophysiology of chronic kidney disease (CKD) remains incompletely understood. Profiling BA metabolism may provide valuable insights into CKD pathophysiology and help in identifying novel therapeutic targets.

METHODS: This cross-sectional study recruited 29 patients with advanced CKD and 30 sex- and age-matched individuals with normal renal function (NRF). Serum and urine BA profiles were compared between the two groups.

RESULTS: Total BA levels in serum did not differ significantly between the CKD and NRF groups. However, patients with CKD exhibited lower serum levels of unconjugated BAs and significantly higher levels of sulfate-conjugated BAs than those with NRF. In contrast, urinary total BA levels and most BA subgroups were significantly lower in patients with CKD. Additionally, the serum levels of ursodeoxycholic, chenodeoxycholic acid and sulfated-conjugated BAs were associated with a decline in the estimated glomerular filtration rate, even after adjusting for demographic factors and diabetes status.

CONCLUSION: This study provides a comprehensive analysis of serum and urinary BAs in patients with advanced CKD. Our findings highlight the association between specific BAs and CKD, suggesting a distinct pathophysiological role of BA metabolism in CKD progression.},
}

Humans
Male
Female
*Bile Acids and Salts/urine/blood
Cross-Sectional Studies
Middle Aged
*Renal Insufficiency, Chronic/blood/urine/physiopathology/diagnosis
Aged
Glomerular Filtration Rate
Biomarkers/urine/blood
Adult
Gastrointestinal Microbiome
Case-Control Studies

@article {pmid41492732,
year = {2026},
author = {Luo, J and Wu, Y and Ahsan, H and Olopade, CO and Pinto, JM and Aschebrook-Kilfoy, B},
title = {The Role of the Oral Microbiome in Circulating Metabolic Biomarkers and the Influence of Air Pollution.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70197},
pmid = {41492732},
issn = {1601-0825},
support = {//NIEHS/ ; /NH/NIH HHS/United States ; },
abstract = {AIMS: The oral microbiome is at the frontline for environmental exposure and plays an important role in human metabolism. This study explores the relationship between PM2.5 exposure, the oral microbiome, and metabolic biomarkers including ghrelin, resistin, and insulin.

METHODS: Data from 473 adult participants (97.7% Black; median age: 53.6) were analyzed. PM2.5 exposure was retrospectively assigned based on residential addresses, metabolic biomarkers were measured from blood samples, and oral microbiome profiles were obtained from saliva samples. Multivariate linear regression, weighted quantile sum regression, and high-dimensional mediation analysis were employed to estimate microbiome-biomarker associations, the association of the oral microbiome mixture, and mediation effects for PM2.5 exposure.

RESULTS: A total of 20 oral microbiome taxa were significantly associated with at least one biomarker, with genus Atopobium linked to all three. Insulin demonstrated the strongest sensitivity to the oral microbiome influence. Genera in phyla Actinomycetota and Bacillota played key roles in the relationship between the oral microbiome and metabolic biomarkers. Mediation analysis revealed that the oral microbiome mediated 16.5% and 11.1% of PM2.5's associations with resistin and insulin, respectively.

CONCLUSION: This study suggests potential mechanisms regarding how the oral microbiome influences metabolic biomarkers and mediates the metabolic effects of PM2.5 exposure.},
}

@article {pmid41492650,
year = {2026},
author = {Wu, Y and Chen, W and Ye, X and Hao, X and Wen, Y and Wu, J and Li, D and Xu, L},
title = {Targeted C3G delivery by engineered milk exosomes for effective therapy in microplastics-induced colitis.},
journal = {Materials today. Bio},
volume = {36},
number = {},
pages = {102639},
pmid = {41492650},
issn = {2590-0064},
abstract = {Microplastic polystyrene (PS) ingestion through the food chain induces chronic colitis, with no effective intervention strategy, posing a public health concern globally. Cyanidin-3-O-glucoside (C3G), an anthocyanin abundant in red bayberry, can alleviate colitis while has limited therapeutic efficacy due to its low colonic bioavailability after oral administration. Targeted delivery strategies may enhance colonic C3G concentration and improve its therapeutic efficacy. Exosomes are engineerable nanoparticles with excellent biocompatibility and unique biological activities. In this study, the mucosal addressin cell adhesion molecule 1 (MAdCAM-1, F6) antibody, which specifically binds to colonic inflammatory MAdCAM-1 marker, was conjugated to the raw milk derived-exosome surface to form C3G@Exo-F6, aiming to enhance colonic C3G targeting. In vitro, C3G@Exo-F6 exhibited significantly enhanced stability in simulated digests and was more efficiently taken up by colon cells. In a PS-induced in vivo chronic colitis mice model, C3G@Exo-F6 demonstrated superior efficiency compared to C3G only by inhibiting inflammatory responses, restoring gut barriers integrity and modulating the gut microbiota. Mechanically, 16S rRNA sequencing and untargeted metabolomics demonstrated that C3G@Exo-F6 significantly increased the Lactobacillus abundance and subsequently upregulated the metabolic L-Proline level. Molecular docking identified that L-Proline binds effectively to nuclear receptor subfamily 1 group D member 1 (NR1D1) protein, inhibiting the expression of inflammatory TLR-4/COX-2 pathway. Additionally, Exo-F6 carries exhibited similar therapeutic effects, indicating that exosomes derived from raw milk possess collaborative anti-inflammatory activities. Collectively, these findings emphasize the potential of C3G@Exo-F6 for targeted treatment of chronic colitis, providing a food-derived therapeutic approach for microplastics-induced colonic inflammation.},
}

@article {pmid41492481,
year = {2026},
author = {Joshi, A and Cornu, A and Luxner, J and Zarfel, G and Braun, C and Nicolas, JF and Gallo, RL and Vocanson, M and Wolf, P and Patra, V},
title = {Atopic Dermatitis-like mouse model using early inoculation of patient-derived S. aureus together with MC903.},
journal = {JID innovations : skin science from molecules to population health},
volume = {6},
number = {2},
pages = {100436},
pmid = {41492481},
issn = {2667-0267},
abstract = {Staphylococcus aureus (S. aureus) worsens atopic dermatitis (AD), but how individual strains differ in pathogenicity remains unclear. Mouse models that mimic AD and allow direct manipulation of S. aureus in early stages of disease are limited. Moreover, these models rarely incorporate clinical S. aureus strains isolated from patients with AD. In this study, we investigated the inflammatory potential of clinical S. aureus and S. epidermidis isolates from patients with AD in a mouse model. Clinical S. aureus strains showed significant variability in their ability to elicit inflammation. The inflammation was associated with differences in virulence factor expression and, to a lesser extent, with genomic variation. In contrast, S. epidermidis strains (taken from the same lesional skin sites of patients) induced only mild but consistent inflammation, with less variability at the strain level. Next, we examined the impact of a pathogenic clinical S. aureus strains in the presence of an MC903-induced type 2 immune environment. Under these conditions, S. aureus enhanced colonization; increased inflammation; and promoted type 1, type 2, and type 17/22 immune responses. These responses were less evident with either treatment alone. Our findings suggest that clinical S. aureus strains from patients with AD differ in their capacity to modulate skin inflammation, particularly within a type 2-skewed environment. These results highlight the potential value of incorporating clinically relevant S. aureus isolates into early-stage in vivo models to better understand AD immunopathology and to inform microbiome-targeted therapeutic strategies.},
}

@article {pmid41492371,
year = {2026},
author = {Li, N and Dong, Z and Zhang, S and Ma, J and Liu, S},
title = {Pathogenesis of various pulmonary diseases by tuning immune response: insight from host-microbial crosstalk.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100531},
pmid = {41492371},
issn = {2666-5174},
abstract = {Growing research has highlighted the participation of lung microbiota in various pathological processes. Despite its low bacterial biomass compared with other organs, the resident flora of the healthy lung is essential for immune system development, immune tolerance fostering, and defense against foreign substance incursion. The host-microbial crosstalk, typically mediated by microbial metabolites, pattern recognition receptors, and immune cells, exerts bidirectional regulatory effects on the pulmonary immune microenvironment. Specifically, the lung microbiota modulates the activation status or tolerance of mucosal immune cell populations to maintain immune balance; conversely, perturbations to the lung's homeostatic microbiome, arising from dysbiosis, immune dysfunction, or pathogenic invasion, drive lung disease by inciting chronic inflammation and tissue remodeling via direct and immune mediated damage. Although the importance of host-microbial interactions in lung health is well recognized, the mechanisms of the relationship between changes in microbiota composition and immune dysregulation in different diseases have not been fully elucidated. Therefore, we summarize the latest research progress on the involvement of the lung microbiota in pulmonary disease development, focusing on the interaction mechanisms among microorganisms, immune homeostasis, and lung diseases. The aim of this review is to expand our mechanistic understanding of the lung microbiota-mediated regulation of immune cell function. Insights from various disciplines into lung microbiota could pave the way for innovative ideas and technologies aimed at preventing and treating respiratory illnesses.},
}

@article {pmid41492366,
year = {2026},
author = {Su, K and Yan, Y and Huang, J and Chen, Y and Shang, X and Wang, X and Liu, Y and Lai, Z and Song, F and Zhang, Z and Wu, P and Wu, K and Liang, XJ},
title = {Mitochondrial-targeted injectable hydrogel for periodontitis therapy via oral immunity and flora regulation.},
journal = {Bioactive materials},
volume = {58},
number = {},
pages = {348-369},
pmid = {41492366},
issn = {2452-199X},
abstract = {The therapy of chronic periodontitis poses a perennial challenge due to its intricate etiology, specific bacterial involvement, and the presence of an inflammatory immune microenvironment. The misuse of antibiotics not only triggers bacterial resistance but also disrupts the balance of oral microbiota, exacerbating the host's inflammatory response. Herein, a novel integrated synergistic hydrogel delivery platform (named GM/OHA-GZN&M) was designed to facilitate rapid, non-invasive, and antibiotic-free periodontitis treatment. This injectable hydrogel delivery platform fulfils three distinct roles: as a subgingival plaque disruptor, immune microenvironment remodeler, and microbiome modulator. As a subgingival plaque disruptor, GM/OHA-GZN&M hydrogel effectively disrupted bacterial membrane homeostasis, depolarized it, and induced the leakage of materials in the membrane. As an immune microenvironment remodeler, it effectively mediates the targeted clearance of mitochondrial reactive oxygen species (mtROS) through polyphenols, restores mitochondrial function, and disrupts the free radical cycle of inflammation. As a microbiome modulator, it effectively suppressed pathogenic bacterial overgrowth, restored oral gingival microbiota balance in rats, and created a favorable subgingival microenvironment for periodontitis treatment. In in vivo experiments, the GM/OHA-GZN&M hydrogel was used to treat a periodontitis model established by silk thread ligation in rats. Histological, microbiological, and biochemical analyses demonstrated that the hydrogel could significantly suppress inflammation and effectively promote alveolar bone regeneration through immunomodulation. To sum up, this study presents a supports therapeutic potential approach for managing periodontitis.},
}

@article {pmid41492364,
year = {2025},
author = {Solly, EF and Jaeger, ACH and Barthel, M and Six, J and Mueller, RC and Hartmann, M},
title = {Soil water limitation intensity alters nitrogen cycling at the plant-soil interface in Scots pine mesocosms.},
journal = {Plant and soil},
volume = {516},
number = {1},
pages = {705-723},
pmid = {41492364},
issn = {0032-079X},
abstract = {BACKGROUND AND AIM: More intense episodes of drought are expected to affect terrestrial nitrogen (N) cycling by altering N transformation rates, the functioning of soil microorganisms, and plant N uptake. However, there is limited empirical evidence of how progressive water loss affects N cycling at the plant-soil interface.

METHODS: We adopted [15]N tracing techniques and metagenomic analyzes of microbial genes involved in N cycling to assess how different levels of soil water availability influenced the fate of N derived from decomposing litter in mesocosms with Scots pine saplings.

RESULTS: With increasing water limitation, the release of N from decomposing litter into the soil declined rapidly. However, moderate levels of water limitation barely affected the microbial metagenome associated with N cycling and the uptake of N by the saplings. Comparatively, severe levels of water limitation impaired plant N uptake, and increased the prevalence of microbial N-cycling genes potentially involved in mechanisms that protect against water stress. Genes associated with the uptake and release of N during mineralization and nitrification declined under low soil water contents.

CONCLUSIONS: When soil water becomes largely unavailable, the cycling of N at the plant-soil interface is slowed down, and microbial and plant tolerance mechanisms may prevail over N uptake and microbial decomposition.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07758-z.},
}

@article {pmid41492235,
year = {2026},
author = {Zou, Q and Tan, M and Li, D and Fu, Z and Wang, Y},
title = {Effects of Neutral Electrolytic Water on Growth, Carcass, and Gut Microbiota of Arbor Acres Plus (AA+) Broilers.},
journal = {Animal science journal = Nihon chikusan Gakkaiho},
volume = {97},
number = {1},
pages = {e70141},
doi = {10.1111/asj.70141},
pmid = {41492235},
issn = {1740-0929},
support = {S202210160027//National College Students' Innovation and Entrepreneurship Training Program/ ; 2023py06//Research on the Effects of Compound Water Treatment Agents on Waterline Microecological Flora and Growth Performance of Broilers/ ; 2023py01//Effect and Correlation Analysis of Electrolyzed Water on Growth Performance and Cecal Microflora of Broiler Chickens/ ; },
mesh = {Animals ; *Chickens/growth & development/microbiology ; *Gastrointestinal Microbiome/drug effects ; Cecum/microbiology ; *Water/pharmacology/administration & dosage ; *Bone Development/drug effects ; Lactobacillus/isolation & purification ; Weight Gain/drug effects ; Male ; Housing, Animal ; *Animal Nutritional Physiological Phenomena ; Eating ; *Diet/veterinary ; Electrolysis ; },
abstract = {The purpose of this study was to examine the influence of neutral electrolytic water (NEW) on the growth performance, slaughter performance, bone development, and cecum microbiome of Arbor Acres Plus (AA+) broilers. A total of 120 broilers were raised in an environmentally controlled room with four rows of battery cages, each equipped with a water line housing 30 broilers. Two lines supplied normal water (CK), and the other two supplied NEW (TRT), with 10 broilers per cage (six replicates per group) over a 42-day trial. Results showed that broilers in the TRT group had significantly higher average daily gain (ADG) (p < 0.05) and lower feed consumption-to-gain ratio (F/G) (p < 0.05) at 22-42 and 1-42 days compared with the CK group. NEW consumption had no significant impact on slaughter performance or bone development (p > 0.05). The TRT group increased cecal flora diversity and abundance, with Lactobacillus as the dominant genus at the genus level. Correlation analysis revealed Oscillospira abundance was significantly positively correlated with F/G (R > 0.6, p < 0.05). Lactobacillus abundance was significantly positively correlated with ADG and average daily feed intake (ADFI) (R > 0.6, p < 0.05) and significantly negatively correlated with F/G (R < -0.6, p < 0.05). In summary, NEW improved growth performance, enhanced cecal flora diversity, and increased Lactobacillus abundance in AA+ broilers.},
}

Animals
*Chickens/growth & development/microbiology
*Gastrointestinal Microbiome/drug effects
Cecum/microbiology
*Water/pharmacology/administration & dosage
*Bone Development/drug effects
Lactobacillus/isolation & purification
Weight Gain/drug effects
Male
Housing, Animal
*Animal Nutritional Physiological Phenomena
Eating
*Diet/veterinary
Electrolysis

@article {pmid41492068,
year = {2026},
author = {Grant, ET and Monzel, E and Desai, MS},
title = {Navigating the duality of Akkermansia muciniphila.},
journal = {Nature microbiology},
volume = {11},
number = {1},
pages = {20-30},
pmid = {41492068},
issn = {2058-5276},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Probiotics ; *Akkermansia/physiology ; Mucins/metabolism ; Intestinal Mucosa/microbiology/metabolism ; Animals ; *Verrucomicrobia/physiology ; Polysaccharides/metabolism ; },
abstract = {Akkermansia muciniphila is a prominent member of the intestinal microbiota that has the unique ability to subsist on the mucin O-glycans that form a protective barrier between the host and the gut microbiome. Numerous studies highlight its positive role in metabolic regulation and mucosal barrier maintenance, leading to propositions that A. muciniphila could be used as a next-generation probiotic. However, other work indicates that the effects of A. muciniphila vary depending on nutrition, host genetics and the interaction with surrounding microbes. Furthermore, strain-specific differences in the ability to modulate intestinal barrier function and antimicrobial resistance profiles remain underexplored. Here, by focusing on potential sources of this variation, we provide a nuanced discussion on the complex role of A. muciniphila in human health. With A. muciniphila as an example, we argue that a microbe's specific environment must be considered to enable critical evaluation of next-generation probiotics.},
}

Humans
*Gastrointestinal Microbiome/physiology
Probiotics
*Akkermansia/physiology
Mucins/metabolism
Intestinal Mucosa/microbiology/metabolism
Animals
*Verrucomicrobia/physiology
Polysaccharides/metabolism

@article {pmid41492042,
year = {2026},
author = {Mikkonen, RS and McClung, H and Giersch, G and Van Cutsem, J and Wright, H and O'Leary, TJ and Greeves, JP},
title = {Menstrual Health in Servicewomen: The Menstrual Cycle, Menstrual Disturbances, and Occupational Consequences.},
journal = {Sports medicine - open},
volume = {12},
number = {1},
pages = {2},
pmid = {41492042},
issn = {2199-1170},
abstract = {BACKGROUND: Most women serving in the military do so during their reproductive life and enter service at a young gynecological age. This review provides an overview of the menstrual cycle and summarizes the evidence for menstrual cycle disturbances in the military and how these disturbances to the menstrual cycle impact health and performance in the military.

MAIN TEXT: Servicewomen often manage the practical challenges of menstruation and symptoms of the menstrual cycle or menstrual disturbances/dysfunction in an austere environment with no formalized support and/or education, and with unknown stigma and risks. Menstrual health in the military context implies that those who experience a menstrual cycle can access timely information, diagnosis, and support/treatment to achieve "a state of complete physical, mental, and social well-being and not merely the absence of disease or infirmity, in relation to the menstrual cycle." Herein we describe how menstrual health is impacted in a multistressor environment, including nutrition (energy balance and energy availability, micronutrients, and microbiome), physical activity, and recovery (occupational tasks, sleep, psychological stress, environment), and how menstrual disturbances can affect occupational performance and the lived experience of the female workforce.

CONCLUSIONS: We call for action of militaries worldwide to protect the health of Servicewomen to maximize their potential. Low representation, relatively recent full integration of women into the military workforce, and the exclusion of women from military research have led to policies developed from evidence on men, with the potential to impact the health and performance of Servicewomen.},
}

@article {pmid41492005,
year = {2026},
author = {Miyamoto, K and Sujino, T},
title = {Microbiota-derived D-amino acids in intestinal homeostasis and inflammatory bowel disease.},
journal = {Inflammation and regeneration},
volume = {},
number = {},
pages = {},
doi = {10.1186/s41232-025-00403-3},
pmid = {41492005},
issn = {1880-9693},
abstract = {Inflammatory bowel disease (IBD) encompasses chronic, relapsing inflammatory disorders of the gastrointestinal tract, which are driven by intricate interactions between the host immune system and intestinal microbiota. Recent studies have revealed that microbiota-derived D-amino acids (D-AAs), once considered biologically inert, play critical roles in maintaining mucosal homeostasis and modulating immune responses. These metabolites, which are increasingly classified as postbiotics, directly influence epithelial barrier integrity, immune cell activity, and microbial ecology. In this review, we summarize the current insights into the biosynthesis, bacterial functions, and immunological implications of D-AAs in the gut, with a particular focus on their involvement in IBD pathogenesis. Specific D-AAs, such as D-alanine, contribute to bacterial cell wall integrity and quorum sensing and interact with host immune cells, alter microbial communities, and regulate mucosal barrier function. Evidence from both human studies and murine models highlights how disrupted D-AAs' metabolism through dysbiosis or impaired host sensing via enzymes such as D-amino acid oxidase (DAO) exacerbates inflammation. Finally, we discuss the translational potential of D-AAs as non-invasive biomarkers and therapeutic targets in IBD, emphasizing the need for integrative multi-omics approaches that connect microbial metabolism with host immune regulation and disease outcomes.},
}

@article {pmid41491874,
year = {2026},
author = {Thassakorn, P and Fungbun, N and Sukon, P and Phuektes, P},
title = {Characterization and comparative analysis of urinary bacterial microbiome profiling in healthy cats and cats with feline idiopathic cystitis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34196-9},
pmid = {41491874},
issn = {2045-2322},
support = {KKU Vet. Res. VM025/2565//Faculty of Veterinary Medicine, Khon Kaen University/ ; KKU Vet. Res. VM025/2565//Faculty of Veterinary Medicine, Khon Kaen University/ ; KKU Vet. Res. VM025/2565//Faculty of Veterinary Medicine, Khon Kaen University/ ; KKU Vet. Res. VM025/2565//Faculty of Veterinary Medicine, Khon Kaen University/ ; },
abstract = {Over the past decade, the make up of urinary microbiota and its association with disease has garnered substantial attention. However, the urinary microbiota patterns in healthy cats remain unclear, as do the potential dysbiosis conditions in cats with feline idiopathic cystitis (FIC). We hypothesized that urinary microbiota differ by age and sex in healthy cats, and vary between healthy cats and those with FIC. Using 16S rRNA gene sequencing, we analyzed the urinary microbiota of 25 healthy cats and 15 cats with FIC. Our results indicate that the feline urinary microbiota is primarily composed of Proteobacteria. While no significant differences in bacterial abundance were found between sexes in healthy cats, some taxa showed variations by age. Cats with FIC demonstrated microbiota disruption, characterized by an increase in Firmicutes and Bacilli, along with a decrease in Proteobacteria, particularly a reduction in the Pseudomonas genus, compared to healthy cats. These results demonstrate the presence of a bacterial microbiome in the urine of cats and suggest a potential association between altered microbiota and FIC. Multi-omics approaches could provide further insights into the core urobiome and its role in feline urinary tract disease.},
}

@article {pmid41491791,
year = {2026},
author = {Seo, J and Araneta, RP and Lee, JH and Montecillo, JA and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Yoon, HY and Kim, MJ and Kim, JM and Lee, YH and Lee, NY and Park, NJ and Han, HS and Seo, I and Chong, GO},
title = {Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {2},
pmid = {41491791},
issn = {1471-2180},
support = {RS-2023-KH135444//Ministry of Health and Welfare/ ; },
abstract = {BACKGROUND: Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy.

RESULTS: Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20 °C, and -80 °C), revealed no significant impact on microbial composition. Additionally, the NEBNext® Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes.

CONCLUSIONS: These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04523-1.},
}

@article {pmid41491699,
year = {2026},
author = {Wang, R and Zhang, W and He, Z and Zhou, Y and Chen, C and Song, K and Shang, Q and Wu, Y and Gu, P and Shu, D and Zhao, L},
title = {Core microbiota recruited by healthy grapevines enhance resistance against root rot disease.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-025-03905-y},
pmid = {41491699},
issn = {1474-760X},
support = {2023BCF01026//Key Research and Development Program of Ningxia/ ; 2025NC-YBXM-068//Key Research and Development Projects of Shaanxi Province/ ; 32372501//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Root rot disease caused by fungal pathogens of wine grapevines poses a serious threat to their growth and results in a substantial economic impact on grape industry. The rhizosphere microbiome recruited to plants is critical for mitigating soil-borne pathogens. However, how beneficial microbes influence disease resistance remains unclear.

RESULTS: We investigate the composition and gene functions of microorganisms in wine grapevines with root rot disease and healthy controls by amplicon and metagenomic sequencing. We use culturomics and in vivo experiments to verify the pathogen and beneficial strains to improve plant health. We find that root rot disease in grapevines significantly affects rhizosphere microbiome diversity and composition. The microbial interkingdom network indicates that the disease destabilizes the bacteria-fungi co-occurrence network. We find that plants recruit the potentially beneficial bacteria Pseudomonas, Bacillus and Streptomyces in healthy rhizosphere soil. By culturomics, we confirm that Fusarium solani is the main pathogen causing root rot disease. We further observe that these three key beneficial bacteria from the co-occurrence networks enhance the resistance of grapevines to pathogens. Furthermore, metagenomic analysis reveals that beneficial bacterial strains suppress pathogens by enriching potential functional genes in pathways involved in disease resistance.

CONCLUSIONS: Our findings highlight the critical role of disease resistance pathways of potentially beneficial microorganisms in fighting disease and supporting plant health, offering new insight for the exploration of beneficial microbial resources and providing a basis for the development of biological control of grape root rot disease.},
}

@article {pmid41491653,
year = {2026},
author = {Mihori, S and Nichols, FC and Jellison, ER and Blesso, CN and Graziano, V and Rathinam, V and Clark, RB},
title = {Harnessing the microbiome to regulate myeloid TREM2 expression and innate immune responses.},
journal = {ImmunoHorizons},
volume = {10},
number = {1},
pages = {},
pmid = {41491653},
issn = {2573-7732},
support = {300714//UConn Health AEF/ ; },
mesh = {Animals ; *Membrane Glycoproteins/metabolism/genetics ; *Immunity, Innate ; *Receptors, Immunologic/genetics/metabolism ; Mice ; *Gastrointestinal Microbiome/immunology ; Mice, Inbred C57BL ; *Macrophages, Peritoneal/immunology/metabolism ; NF-kappa B/metabolism ; Inflammation/immunology ; Monocytes/immunology ; *Microbiota/immunology ; Signal Transduction ; },
abstract = {The composition of the gastrointestinal microbiome is correlated with numerous immune-mediated systemic diseases, but underlying mechanisms remain unclear. In murine studies, we recently identified microbiome Bacteroidota-derived bacterial molecules, serine-glycine lipodipeptides (S/G lipids), as mediators of microbiome-systemic innate immune system crosstalk. By altering microbiome production of S/G lipids, we documented that proinflammatory responses of splenic monocytes could be regulated. Transcriptomic analysis revealed that this regulation occurred by modulating the mRNA levels of inhibitors of the TLR/NF-κB pathways such as Trem2. The present murine study had 2 goals: (1) to determine if our approach allows for modulation of activated innate immune cells, that is, macrophages rather than splenic monocytes, in a site of inflammation and (2) to document that our approach regulates cellular expression of the disease-relevant TLR/NF-κB pathway inhibitor, TREM2, at the protein level. We now report that decreasing microbiome-derived S/G lipid levels enhances proinflammatory responses and decreases expression of TREM2 in activated peritoneal macrophages (PMs). Furthermore, after lowering microbiome S/G lipid production, administering S/G lipids normalizes both PM proinflammatory responses and TREM2 expression. The harnessing of the microbiome and S/G lipids to modulate proinflammatory responses and TREM2 expression in activated innate immune cells suggests the therapeutic potential of this approach in inflammatory diseases such as Alzheimer's disease, atherosclerosis, autoimmunity and liver disease.},
}

Animals
*Membrane Glycoproteins/metabolism/genetics
*Immunity, Innate
*Receptors, Immunologic/genetics/metabolism
Mice
*Gastrointestinal Microbiome/immunology
Mice, Inbred C57BL
*Macrophages, Peritoneal/immunology/metabolism
NF-kappa B/metabolism
Inflammation/immunology
Monocytes/immunology
*Microbiota/immunology
Signal Transduction

@article {pmid41491581,
year = {2026},
author = {Chen, T and Yu, S and Li, K and Huang, K and Shi, W and Chen, H and Hong, Q and Zhang, Y and Wang, J and Yu, Z and Wang, J},
title = {Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02283-8},
pmid = {41491581},
issn = {2049-2618},
support = {2023YFD1300901//the Ministry of Science and Technology of the People's Republic of China/ ; D21C170001//the Natural Science Foundation of Zhejiang Province/ ; 31622056//the National Natural Science Foundation of China/ ; 226-2025-00026//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The transition from milk to solid feed during weaning often imposes metabolic stress on young ruminants due to energy deficits. Previous studies suggest that ruminal microbiota transplantation from adults to juveniles can alleviate weaning stress, but the underlying mechanisms remain poorly defined.

RESULTS: In this study, 48 Hu lambs were randomly assigned to two groups (n = 24 each): an inoculated group (Inoc) that received lyophilized ruminal microbiota and a control group (Ctrl) that received no inoculation. We evaluated rumen fermentation characteristics, blood metabolites, hepatic glycogen levels, expression of hepatic gluconeogenic genes, and shifts in the rumen microbiome at three key time points-the end of weaning, 1 and 2 weeks post-weaning. Oral inoculation significantly elevated rumen propionate concentration, upregulated the gene expression of hepatic pyruvate carboxylase (EC 6.4.1.1) and glucose-6-phosphatase (EC 3.1.3.9), and increased hepatic glucose production. Microbiome analysis revealed increased colonization by lactic acid-producing bacteria (e.g., Olsenella and Sharpea) and propionate producers, such as Megasphaera elsdenii, alongside enriched families associated with propionate production, including Prevotellaceae, Succinivibrionaceae, and Erysipelotrichaceae. Genome-resolved metagenomics further demonstrated an increased abundance of metagenome-assembled genomes (MAGs) carrying polysaccharide utilization loci (PULs) and genes involved in lactate-to-propionate conversion. Notably, the inoculation promoted co-occurrence of functionally complementary MAGs-such as s_Megasphaera elsdenii (MAG98), s_Bilifractor sp902797025 (MAG125), s_Prevotella sp002391185 (MAG342), and s_Prevotella sp900540375 (MAG298)-that carry a wide repertoire of genes involved in polysaccharide degradation and lactate-to-propionate fermentation. In vitro co-culture experiments with Megasphaera elsdenii and Bilifractor porci confirmed their synergistic role in promoting propionate production.

CONCLUSIONS: This study demonstrates that oral inoculation of pre-weaned lambs with starter feed-adapted adult rumen microbiota facilitates the establishment of a microbial consortium capable of enhanced lactate and propionate production, thereby enhancing hepatic gluconeogenesis and energy homeostasis, which ultimately mitigates weaning stress. This approach may offer a promising strategy to facilitate dietary transition and enhance metabolic resilience in young ruminants during weaning by modulating rumen microbial composition toward a propionate-producing community. Video Abstract.},
}

@article {pmid41491300,
year = {2026},
author = {Helm, ET and Burrough, ER and Gabler, NK and Leite, FL},
title = {Lawsonia intracellularis infection induces changes in microbial community function and composition associated with reduced pig growth and feed efficiency.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {1},
pmid = {41491300},
issn = {2524-4671},
abstract = {BACKGROUND: Lawsonia intracellularis and its resulting disease remains a troubling pathogen for pork producers worldwide. In the current experiment, we aimed to characterize the microbiome of pigs challenged with L. intracellularis through peak disease impact to better understand microbial community function and how microbial changes may contribute to disease and resulting decreased growth. Twenty-four L. intracellularis negative barrows were assigned to either L. intracellularis negative (NC) or L. intracellularis challenged (PC) treatment groups (n = 12 pigs/treatment). On days post-inoculation (dpi) 0, PC pigs were inoculated with L. intracellularis. Feed disappearance was monitored daily, body weights and fecal samples were collected weekly. At dpi 21, pigs were euthanized for sample collection and macroscopic lesion scoring.

RESULTS: Pigs challenged with L. intracellularis had sustained reductions in growth performance and feed intake throughout the 21-day period (P < 0.001). This was accompanied by changes to fecal microbial communities, particularly increased abundance of Chlamydia suis in challenged pigs at dpi 7, 14, and 21. Changes to microbial communities were also accompanied by differences in microbial metabolism, marked most notably by signatures of lesser amino acid biosynthesis and greater nucleotide synthesis in challenged pigs.

CONCLUSIONS: In summary, L. intracellularis challenge produced reductions in growth and feed intake. This was accompanied by sustained changes to fecal microbial communities, particularly sustained increased abundance of C. suis in challenged pigs. Changes to microbial communities were also accompanied by differences in microbial metabolism which likely play a role disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00501-0.},
}

@article {pmid41491103,
year = {2026},
author = {Bryant, JA and Vulić, M and Walsh, EA and Allen, EG and Beauchemin, NJ and Chafee, ME and Diao, L and Fenn, K and Ford, KA and Hasson, BR and Litcofsky, KD and Lombardo, MJ and Martinez, A and O'Brien, EJ and Straub, TJ and Sykes, SM and Marshall, LF and Winkler, JA and McGovern, BH and Ford, CB and Wortman, JR and Henn, MR},
title = {The impact of an oral purified microbiome therapeutic on the gastrointestinal microbiome.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41491103},
issn = {1546-170X},
abstract = {VOWST (VOWST oral spores, VOS; fecal microbiota spores, live-brpk, formerly SER-109) is an FDA-approved, orally administered consortium of purified Firmicutes spores developed to prevent recurrent Clostridioides difficile infection (CDI). Although 86.7% (26/30) of patients with recurrent CDI did not experience a subsequent recurrence over 8 weeks in an open-label phase 1b study, a subsequent double-blind phase 2 study (NCT02437487) did not demonstrate a significant benefit over placebo (rate of recurrence at 8 weeks in SER-109 versus placebo: 44.1% versus 53.3%). These discordant outcomes were hypothesized to be due to suboptimal dosing. This hypothesis was addressed in a pivotal phase 3 trial (NCT03183128) using an approximately tenfold higher dose. In phase 3, only 12% of VOS-treated patients versus 40% of placebo patients recurred by week 8 (relative risk 0.32, P < 0.001). Here in this follow-up post hoc analysis, across-trial comparisons confirmed that the higher, efficacious phase 3 dose is associated with improved pharmacokinetics, assessed by VOS engraftment (patients with available samples: phase 1b: 28, phase 2: 79, phase 3: 170). In-depth phase 3 analyses revealed that VOS significantly altered microbial composition, significantly enriching the diversity and abundance of Firmicutes species and reducing the prevalence and abundance of C. difficile and opportunistic pathogens (for example, Enterobacteriaceae species). Consistent with these taxonomic changes, significant changes in key bioactive metabolites were observed, including depletion of conjugated and deconjugated primary bile acids, enrichment of secondary bile acids and increases in short-chain and medium-chain fatty acids. In vitro, VOS batches produced these C. difficile-inhibiting metabolites. These findings on the pharmacology of VOS underscore the importance of rapidly restoring key protective functions of the microbiome in patients with recurrent CDI to achieve durable prevention of recurrence, as observed in the phase 3 study; they also highlight the need to include the microbiome in the clinical management of CDI. ClinicalTrials.gov registrations: NCT02437487 and NCT03183128 .},
}

@article {pmid41491008,
year = {2026},
author = {Ajene, IJ and Tanga, CM and Akutse, KS and Karanu, SW and Khamis, FM},
title = {Multi-omics comparison of two emerging storage pests (Necrobia rufipes and Tribolium castaneum) of dried black soldier fly larvae product.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34902-7},
pmid = {41491008},
issn = {2045-2322},
support = {ProteinAfrica: LS/2020/154//Australian Centre for International Agricultural Research/ ; WAVE-IN: 2021 FOD 030//Rockefeller Foundation/ ; G-2204-02144//IKEA Foundation/ ; NESTLER Project: 101060762 and INNOECOFOOD project: 101136739//European Commission/ ; },
abstract = {The black soldier fly (BSF) larvae is a rich and promising source of alternative protein that continues to increasingly gain global traction as a functional ingredient for sustainable livestock and fish production. The key setback to postharvest processing of stored BSF larvae (BSFL) products is the significant damage caused by two notable storage pests (Tribolium castaneum and Necrobia rufipes). Here, we present a comparative analysis of the complete mitochondrial genomes and gut microbiome profiles of T. castaneum and N. rufipes. The study mitogenomes were similar in size and structure to other coleopteran mitogenomes. The gut microbiome profiles of the two pests showed a high abundance of bacteria in the Proteobacteria and Firmicutes phyla. However, T. castaneum had 78% more phyla represented within its microbiome than N. rufipes. The most abundant genera in T. castaneum were Staphylococcus and Streptococcus, while in N. rufipes, the dominant genera were Klebsiella and Synechococcus. We also identified the presence of potentially clinically harmful microbial genera (Stenotrophomonas maltophilia) in the gut of T. castaneum and N. rufipes in relatively high abundance. These results provide insight into potential harmful associations in the gut of the storage pest, picked from contaminated, poorly processed BSFL products.},
}

@article {pmid41490763,
year = {2026},
author = {Mazur, M and Pooranachandran, N and Zawisza, M and Baran, Z and Michalik, A and Adamek, M and Marcinkowska, M and Surachetpong, W and Prajsnar, TK and Rakus, K and Pijanowski, L and Chadzinska, M},
title = {The role of the circadian clock gene cry1 in the regulation of the antiviral response in zebrafish (Danio rerio) larvae.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111098},
doi = {10.1016/j.fsi.2026.111098},
pmid = {41490763},
issn = {1095-9947},
abstract = {All living organisms are influenced by the circadian clock. This mechanism generates rhythms that affect organismal processes involved in cellular activity, behavior and immunity. In the present study we investigated the function of the circadian clock genes: cry1a and cry1b in zebrafish larvae, focusing on their roles in early development, behavior, microbiota composition, and antiviral immune response. Using Clustered Regularly Interspaced Short Palindromic Repeats - CRISPR-associated protein 9 (CRISPR-Cas9) gene editing, we generated zebrafish lines with targeted mutations in cry1a and cry1b genes and found that cry1 genes are not essential for larval survival or development. However, both mutations led to significant behavioral changes, with mutant larvae exhibiting increased locomotor activity compared to their wild type (WT) counterparts. Microbiome analysis revealed that cry1a mutation, in particular, resulted in a higher abundance of Proteobacteria in the larval microbiota. When challenged with Tilapia lake virus (TiLV), both cry1a and cry1b mutants displayed increased viral loads and reduced survival rates, indicating a compromised antiviral response. Specifically, cry1a mutants had lower initial expression of tlr22, while cry1b mutants showed reduced gene expression of antiviral Mxa at later stages post-infection, both contributing to decreased resistance against TiLV. Overall, the findings demonstrate that while cry1a and cry1b mutations do not significantly affect an early development, both genes play important roles in regulating behavior, shaping the microbiome, and modulating innate antiviral immunity in zebrafish larvae. The study highlights the multifaceted functions of circadian clock genes in vertebrate physiology and immunity.},
}

@article {pmid41490313,
year = {2025},
author = {Mahnoor, and Ullah, R and Sonyia, and Khan, R and Bahadar, A and Elbatel, I and Khan, I and Alnahari, AA and Haider, A and Jamal, SB and Khan, R},
title = {A modified targeted culturing approach provided a snapshot into interdependencies and resistome among core anaerobic bacteria of the healthy human gut.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0318225},
doi = {10.1128/spectrum.03182-25},
pmid = {41490313},
issn = {2165-0497},
abstract = {The core anaerobic component of the human microbiome plays a critical role in preserving the overall structure and function of the microbiome. However, how these core strains interact with each other and with other gut microbes is largely unknown. We employed a modified culturomics approach to selectively culture these core genera from the human gut and provided a snapshot into their ecological interactions, clinically relevant resistome, and whole genome sequence (WGS)-based insights into their observed phenotypes. This strategy successfully isolated representatives of the targeted 21 core genera, with some isolates reported for the first time. Cross-interactions and resistome-based profiling revealed important insights. Out of the 440 interaction assessments, a significant proportion exhibited either cooperative or competitive effects on other core genera. Interestingly, Bacteroides thetaiotaomicron displayed dual roles, inhibiting potential pathogens while enhancing the growth of beneficial probiotic strains. Moreover, resistome profiling revealed variable resistance and susceptibility toward various antibiotics. WGS analysis revealed the ability of the selected organism to produce metabolites consistent with the observed phenotype. Our unique culturomics approach successfully isolated key anaerobic genera and revealed their complex interdependencies and clinically relevant resistance. Furthermore, our approach lays the foundation for exploring larger-scale microbial community dynamics in terms of interdependencies and for assessing how clinically significant antibiotics impact the key microbiome, something that may be important when making therapy decisions. In summary, our research improves our knowledge of the interactions present among core gut microorganisms and hints at possible mechanisms responsible for sustaining gut microbial homeostasis and rehabilitation. IMPORTANCE This study presents a unique strategy for the targeted isolation and characterization of key interaction dynamics as well as the resistome of core anaerobic bacteria in the healthy human gut. By utilizing this targeted single, optimized core anaerobe-specific growth medium approach, we were able to culture a major proportion of the core anaerobic gut species, where some of those were cultured for the first time. Through the combinatorial approach of cross-interaction, antimicrobial resistance profiling, and whole genome sequencing (WGS) resolved functional insights, we uncovered interesting insights into interdependencies and competition among these core strains as well as their ecological flexibilities. Moreover, we observed that some strains, such as Bacteroides thetaiotaomicron and Bifidobacterium angulatum, are capable of either inhibiting or promoting the growth of certain strains, depending on the pairing. Such findings go against the traditional binary view of microbes as being purely commensal or pathogenic and suggest that microbial behavior is highly context-dependent. Furthermore, WGS analysis provided useful insights into the potential genomic basis of the observed phenotype. Taken together, our findings provide valuable data and enhance our current understanding of how core anaerobes interact with each other, survive, and adapt within the gut environment. Moreover, our work also lays the critical basis for a more rational design of synthetic microbial communities as well as precision-based microbiome aimed at targeted gut health rehabilitation, both with accuracy and sensitivity.},
}

@article {pmid41490089,
year = {2026},
author = {Hobbs, A and Ochoa-Rojas, D and Humphrey, CE and Kyndt, JA and Moore, TC},
title = {Soil microbiome perturbation impedes growth of Bouteloua curtipendula and increases relative abundance of soil microbial pathogens.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0312218},
pmid = {41490089},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Microbiota ; *Poaceae/growth & development/microbiology ; Soil/chemistry ; Bacteria/genetics ; },
abstract = {Bouteloua curtipendula (sideoats grama) is a valuable prairie grass for livestock forage, supporting food webs of herbivorous insects, reducing soil erosion, and limiting weed infiltration in urban grasslands. Efficient establishment of B. curtipendula in prairie restorations and urban plantings could drastically improve long-term functionality of the space. Soil microbial communities have been linked to plant germination, growth, and drought tolerance in many plant species, however little is known about the factors contributing to B. curtipendula germination and early growth. In this study, we used sterilized soil to examine the impact of soil microbes on B. curtipendula growth under greenhouse conditions. We found Bouteloua curtipendula emergence and growth to be impaired in sterilized soil compared to not-sterilized soil. Using high throughput sequencing of the soil, we found that B. curtipendula grown in sterilized soil induced a greater proportion of plant pathogens and fewer nitrifying bacteria as compared to when grown in not-sterilized soil. For example, there was a significantly higher proportion of Acidovorax, Cellvibrio, and Xanthomonas which are known to contain plant pathogens, while plant-growth promoting bacteria, like Rhodopseudomonas, were significantly higher in the not-sterile soil conditions. We found that soil sterilization and growth of B. curtipendula changed the relative abundance of metabolic subsystem genes in the soil, however, by seven weeks after seeding, B. curtipendula transformed the bacterial community of sterile soil such that it was indiscernible from not-sterile soil. In contrast, fungal communities in sterilized soil were still different from not-sterilized soil seven weeks post-seeding. It appears that the bacteria are involved in the initial establishment of beneficial conditions that set the stage for a robust fungal and plant seedling development.},
}

*Soil Microbiology
*Microbiota
*Poaceae/growth & development/microbiology
Soil/chemistry
Bacteria/genetics

@article {pmid41489381,
year = {2026},
author = {Zhou, Y and Ying, G and Shen, W and Cui, Y and Xiang, B and Jiang, M and Bao, J and Jin, Q},
title = {Variation in microbiome and metabolites is associated with advantageous effects of cholestyramine on primary biliary cholangitis with pruritus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0074725},
doi = {10.1128/spectrum.00747-25},
pmid = {41489381},
issn = {2165-0497},
abstract = {Emerging evidence implicates bile acid-intestinal microbiota interactions in the pathogenesis of pruritus associated with primary biliary cholangitis (PBC). Cholestyramine, a bile acid sequestrant, is clinically recommended for pruritus alleviation. This study investigates its regulatory effects on gut microbiome composition and metabolite profiles. A prospective cohort of 54 pruritic PBC patients and 25 asymptomatic controls underwent longitudinal multi-omics profiling. Fecal 16S rRNA sequencing and untargeted metabolomics were performed pre-/post-4-week cholestyramine intervention (4 g twice daily). Serum autotaxin, as a biomarker for pruritus assessment, and liver function tests were completed simultaneously. Four important findings were listed as follows. (i) Pruritus phenotype characteristics: Pruritic patients exhibited elevated cholestasis indices (total bilirubin, alkaline phosphatase [ALP], and gamma-glutamyl transferase), higher ATX levels, and increased Gp210 antibody positivity compared to controls (all P < 0.01). Cholestyramine significantly reduced 5-D pruritus scores, ATX levels, and cholestasis markers (P < 0.01). (ii) Microbial dysbiosis: Gut microbiota diversity (Shannon/Simpson indices) was markedly decreased in pruritic patients, with taxonomic enrichment of Romboutsia, Stenotrophomonas, and Achromobacter, whereas Lachnospiraceae and Bacteroidaceae predominated in controls. (iii) Metabolomic perturbations: Metabolomic analysis identified diminished medium-chain fatty acids and indole derivatives (e.g., norharman) in pruritic patients. (iv) Therapeutic efficacy: Microbial-metabolite-clinical correlations revealed the pivotal role of the Romboutsia-norharman-ATX/ALP axis in the pathogenesis of pruritic PBC. Post-treatment, cholestyramine restored microbial diversity, normalized metabolite levels, and attenuated pruritus. Enterobacteriaceae/long-chain fatty acids have been identified as a significant marker for predicting the efficiency of the response to cholestyramine.IMPORTANCEPruritus in primary biliary cholangitis arises from synergistic cholestasis and gut microbiome-metabolite dysregulation. Cholestyramine mitigates symptoms by modulating the microbiome-metabolite-host axis, highlighting its therapeutic potential through microbiota remodeling and metabolic homeostasis restoration.},
}

@article {pmid41489355,
year = {2026},
author = {Cheong, KL and Chen, W and Li, J and Zhong, HJ and Wang, D and Zhong, S},
title = {Nature-inspired oligosaccharides: plant and algal routes to human milk functionality.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/10408398.2025.2609753},
pmid = {41489355},
issn = {1549-7852},
abstract = {Human milk oligosaccharides (HMO) shape early-life health by guiding microbiome assembly, fortifying the mucosal barrier, calibrating immune responses by enhancing secretory IgA at mucosal surfaces, blocking pathogen adhesion, and influencing the microbiota-gut-brain axis. Direct deployment of structurally diverse HMO at population scale remains constrained by manufacturing complexity and cost. This review examines "nature-inspired" oligosaccharides derived from plant and marine algal as affordable, scalable HMO mimetics, mapping chemistry to biology across five functional domains: microbiota architecture & metabolism, inhibition of pathogen adhesion via glycan decoy mechanisms, immune education, mucosal barrier enhancement and gut-brain regulation. We synthesize and critically appraise evidence on plant-derived fructo-, xylo-, and mannan-oligosaccharides, as well as on red-algal agaro-oligosaccharides and brown-algal fuco-oligosaccharides. Although these glycans do not fully replicate individual HMO structures, they can exhibit convergent mechanisms: selective fueling of saccharolytic consortia to produce functional metabolites (SCFAs), multivalent fucose-rich decoying of viral/bacterial adhesins, dendritic-cell/T- and B-cell tuning, epithelial junction and mucus programs, and neuroactive/metabolite signaling along the gut-brain axis. Framed as functional mimicry rather than strict structural emulation, plant and marine oligosaccharides emerge as promising "glycobiotics" to deliver HMO-like benefits across the lifespan, with opportunities for precision, personalized, and sustainable formulations guided by multi-omics and glycoinformatics.},
}

@article {pmid41489339,
year = {2026},
author = {Romero-Alfano, I and Julia López, A and Piña, B and Gómez-Canela, C and Barata, C},
title = {From Gut to Brain: Glyphosate and Triclosan Impair Microbiome Composition, Neuroactive Metabolites, and Cognitive and Ecological Fitness in Daphnia magna.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15302},
pmid = {41489339},
issn = {1520-5851},
abstract = {Gut microbiome dysbiosis is a major off-target effect of many pharmaceuticals, personal care products (PPCP), and plant protection products (PPP). This study aims to characterize these effects for two compounds, glyphosate (a PPP) and triclosan (a PPCP), in Daphnia magna juveniles and to trace the downstream consequences for gut- and brain-associated metabolite levels, reproductive performance, and behavior. Both compounds altered levels of neurotransmitters and related metabolites in both head and gut at the ppb-ppt dose range, promoting anxiogenic behavior and inhibiting reproductive traits in a concentration-related manner. These effects occurred concomitantly with alterations in the gut microbiome, analyzed by 16S rDNA sequencing. Correlation analyses between the observed metabolic, reproductive, and behavioral effects and the changes in the metabolic pathway prediction for the treated gut microbiomes revealed an enrichment in pathways related to the biosynthesis of vitamins, of essential fatty acids, and production of short chain fatty acids, which are known to affect systemic serotonin levels. The results suggest a direct link between gut microbiome dysbiosis and cognitive and reproduction effects in D. magna, with implications for the environmental and human health hazard assessment of these and other substances with broad antimicrobial spectra.},
}

@article {pmid41489138,
year = {2026},
author = {Reed, FE and DeFilipp, Z},
title = {Innovative approaches in acute graft-versus-host disease: emerging therapeutics and novel clinical trial design.},
journal = {Leukemia & lymphoma},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/10428194.2025.2610407},
pmid = {41489138},
issn = {1029-2403},
abstract = {Acute graft-versus host disease (aGVHD) is a major early complication of allogeneic hematopoietic cell transplantation and is associated with substantial morbidity and mortality, particularly in severe cases. The use of corticosteroids as first-line therapy remains standard of care, despite limited efficacy in high-risk cases and associated toxicities. Ruxolitinib has emerged as the treatment of choice for patients who fail corticosteroids, but there remains a need for novel treatment strategies. In this review, we examine the evolving therapeutic landscape of aGVHD and summarize emerging approaches including small molecule inhibitors, biologics, and cellular- and microbiome-modulating therapies. We explore how improved understanding of aGVHD pathophysiology continues to inform new interventions while also addressing the operational and conceptual challenges that constrain clinical trial design and regulatory progress. Finally, we discuss new innovations in biomarker-driven strategies and adaptive clinical trial designs that may facilitate future therapeutic development and advance outcomes for patients with aGVHD.},
}

@article {pmid41489025,
year = {2026},
author = {Pace, R and Monti, MM and Cuomo, S and Affinito, A and Ruocco, M},
title = {Machine Learning Approaches to Assess Soil Microbiome Dynamics and Bio-Sustainability.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70719},
pmid = {41489025},
issn = {1399-3054},
mesh = {*Soil Microbiology ; *Machine Learning ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fungi/genetics ; Soil/chemistry ; Agriculture ; Principal Component Analysis ; },
abstract = {Understanding soil microbiota dynamics is essential for enhancing bio-sustainability in agriculture, yet the complexity of microbial communities hampers the prediction of their functional roles. Artificial intelligence (AI) and machine learning (ML) offer powerful tools to analyse high-dimensional microbiome data generated by high-throughput sequencing. Here, we apply unsupervised AI-based algorithms to uncover microbial patterns that are not immediately recognisable but are crucial for characterising the biological status of agricultural soils. Soil samples were collected from a site in Northern Italy managed under four strategies: conventional farming without organic matter (C), with organic matter (C + O), with beneficial microorganisms but without organic matter (M), and with both beneficial microorganisms and organic matter (M + O). Metagenomic amplicon sequencing of the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer (ITS) region was used to profile bacterial and fungal communities. Principal component analysis (PCA), k-means clustering, and t-distributed stochastic neighbour embedding (t-SNE) revealed coherent temporal trajectories in both datasets, with sampling time and crop presence emerging as dominant drivers of community assembly and only subtle compositional shifts attributable to treatments. Fungal communities exhibited higher plasticity and a stronger response to management than bacterial communities, which converged towards a stable oligotrophic core. Our findings highlight the complementary roles of fungal and bacterial guilds and show that unsupervised ML-based workflows provide an effective framework to disentangle temporal and treatment effects in complex microbiome datasets. This exploratory study lays the groundwork for future predictive models aimed at identifying microbial indicators of soil biological status and supporting bio-sustainable agronomic decisions.},
}

*Soil Microbiology
*Machine Learning
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
Fungi/genetics
Soil/chemistry
Agriculture
Principal Component Analysis

@article {pmid41488894,
year = {2025},
author = {Lin, B and Zhu, Z and Yang, X and Li, Z and Zhou, H and Luo, M and Guan, J and Zou, Y and Chen, H and Zhuang, Z and Meng, S and Li, W and Yang, Q and Dai, D},
title = {Protocol for the efficacy and safety of fecal microbiota transplantation in children with autism spectrum disorder: a prospective single-center, single-arm interventional study.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1660773},
pmid = {41488894},
issn = {2296-2360},
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a neurodevelopmental condition affecting 0.7% of children globally, with 90% experiencing comorbid gastrointestinal (GI) symptoms. Fecal microbiota transplantation (FMT) may modulate ASD symptoms via the microbiota-gut-brain axis (MGBA).

METHODS: This open-label single-arm trial enrolls 30 children (2-12 years) with moderate-to-severe ASD, defined as a Childhood Autism Rating Scale (CARS) score of ≥36. Participants receive 3 nasojejunal FMTs (5 mL/kg) over 5 days. The primary outcomes are GI symptom improvement, assessed using the Gastrointestinal Symptom Rating Scale (GSRS), and ASD severity, assessed using the CARS. Secondary outcomes include social responsiveness (Social Responsiveness Scale, SRS), aberrant behaviors (Aberrant Behavior Checklist, ABC), and gut microbiota changes assessed by metagenomic next-generation sequencing (mNGS).

ETHICS AND DISSEMINATION: Ethical approval obtained from Shenzhen Children's Hospital Ethics Committee. Results will be disseminated via peer-reviewed publications and conference presentations.Clinical Trial Registration: https://www.chictr.org.cn/showproj.html?proj=229136, identifier ChiCTR2400083998. Registered on 2024-05-08. Registered title: "Efficacy and safety of fecal microbiota transplantation in treatment of autism spectrum disorder: a prospective single-center intervention study".},
}

@article {pmid41488762,
year = {2025},
author = {Zhao, Y and Hu, X and Li, C and Huang, J and Guo, K and Pan, Q and Yu, Z},
title = {Comprehensive Analysis of Vaginal and Gut Microbiome Alterations in Endometriosis Patients.},
journal = {International journal of women's health},
volume = {17},
number = {},
pages = {5775-5786},
pmid = {41488762},
issn = {1179-1411},
abstract = {PURPOSE: Endometriosis (EMS) is a chronic gynecological disorder with unclear pathogenesis. While the vaginal and gut microbiomes are known to influence EMS, few studies have analyzed both microbiomes integrally. This study aims to characterize the vaginal and gut microbiome profiles in EMS patients and evaluate their diagnostic potential.

PATIENTS AND METHODS: We conducted metagenomic sequencing on 22 paired vaginal and fecal samples from EMS patients and controls. Microbial composition, diversity, and metabolic pathways were analyzed. Machine learning models were employed to assess the predictive performance of microbiome features in EMS diagnosis.

RESULTS: EMS patients exhibited pronounced shifts in the vaginal microbiome, characterized by reduced Lactobacillus and increased Bifidobacterium and Gardnerella, which correlated with elevated luteinizing hormone (LH) and follicle-stimulating hormone (FSH) levels. The gut microbiome displayed decreased diversity, with a depletion of beneficial taxa such as Ruminococcus and Prevotella, alongside an enrichment of Dialister. Metabolic pathways in both microbial communities were significantly altered. Machine learning analyses demonstrated that gut microbiome features outperformed both vaginal microbiome and hormonal indices in predicting EMS, highlighting their strong diagnostic potential.

CONCLUSION: This study underscores the pivotal role of the gut microbiota in EMS and elucidates the complex interplay between microbial dysbiosis and disease pathogenesis. Our findings indicate that gut microbiome signatures may serve as superior diagnostic biomarkers for EMS, thereby paving the way for microbiome-based diagnostic and therapeutic strategies.},
}

@article {pmid41488660,
year = {2025},
author = {Wilburn, AN and Korkmaz, RÜ and McAlees, JW and Hargis, JM and Shirdel, S and Lingel, I and Watanabe-Chailland, M and Romick-Rosendale, L and Schmudde, I and Bridges, JP and Chougnet, CA and Deshmukh, H and Zacharias, WJ and Köhl, J and Konig, P and Laumonnier, Y and Rothenberg, M and Haslam, DB and Lewkowich, IP},
title = {Maternal antibiotic exposure-mediated alterations in basal, and allergen-induced lung function are associated with altered recruitment of eosinophils to the developing lung.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1715675},
pmid = {41488660},
issn = {1664-3224},
mesh = {Animals ; *Eosinophils/immunology/drug effects ; Female ; Mice ; *Lung/immunology/drug effects/embryology/growth & development ; *Anti-Bacterial Agents/adverse effects ; Allergens/immunology ; *Prenatal Exposure Delayed Effects/immunology ; *Maternal Exposure/adverse effects ; Pregnancy ; Asthma/immunology ; Dysbiosis/chemically induced/immunology ; Mice, Knockout ; Mice, Inbred C57BL ; },
abstract = {INTRODUCTION: Early-life dysbiosis is associated with increased risk of asthma development but the underlying mechanisms remain unclear. Although eosinophils have been reported in the developing lung, their contributions to alveolar morphogenesis and lung mechanics have not been functionally interrogated.

METHODS: Maternal exposure to antibiotics (ABX) was used to induce early-life offspring dysbiosis, and the effects on lung function and development was assessed. Similar measurements were made in mice lacking eosinophils due to genetic modification, or administration of IL-5 blocking agents.

RESULTS: ABX exposure between Embryonic Day 15 (E15) and post-natal day 28 (PN28), increased allergen-induced, and baseline airway hyperreactivity (AHR). Similar observations were made when maternal ABX exposure was limited to PN10 to PN20. Complete characterization of baseline lung mechanics demonstrated downward-shifted pulmonary PV loops, increased small airway resistance, decreased compliance, and reduced inspiratory capacity at weaning and 14 months of age. Consistent with observation of small airway dysfunction, offspring of ABX-exposed dams demonstrated significantly smaller alveoli at multiple stages of lung development. Examination of recruitment to developing lungs demonstrated an exaggerated recruitment of eosinophils at key developmental periods (PN14) in offspring of ABX-exposed dams. Mice with fewer eosinophils (through genetic knockout, or treatment with anti-IL-5) display altered patterns of lung mechanics opposite to that seen in offspring of ABX-exposed dams.

DISCUSSION: These data underscore an underappreciated role of eosinophils in homeostatic lung development and suggest that early life modulation of pulmonary eosinophil activity has long-term effects on susceptibility to the development of chronic lung diseases such as asthma.},
}

Animals
*Eosinophils/immunology/drug effects
Female
Mice
*Lung/immunology/drug effects/embryology/growth & development
*Anti-Bacterial Agents/adverse effects
Allergens/immunology
*Prenatal Exposure Delayed Effects/immunology
*Maternal Exposure/adverse effects
Pregnancy
Asthma/immunology
Dysbiosis/chemically induced/immunology
Mice, Knockout
Mice, Inbred C57BL

@article {pmid41436819,
year = {2025},
author = {Lim, JK and Kim, JA and Lee, N and Oh, C and Woo, S},
title = {Comparison of microbial assemblages associated with the stalked barnacle Neolepas marisindica from two adjacent hydrothermal vent fields on the Central Indian Ridge.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {597},
pmid = {41436819},
issn = {2045-2322},
support = {PEA0314//Korea Institute of Ocean Science and Technology/ ; 20170411//Ministry of Ocean and Fisheries, Korea/ ; },
abstract = {Neolepas marisindica, a stalked barnacle endemic to the Central Indian Ridge (CIR), hosts microbial communities that remain poorly characterized. In this study, we performed 16S rRNA amplicon sequencing to characterize the microbiome associated with N. marisindica collected from two geographically adjacent hydrothermal vent fields along the Central Indian Ridge (CIR): Solitaire (Site A) and Onnuri (Site D). We further used PICRUSt2 to infer the functional potential of these microbial communities and to assess whether differences in in situ geochemical conditions between the two vents shape microbiome composition and metabolic capacity. Both sites harbored microbiota dominated by Proteobacteria, yet displayed distinct taxonomic and functional differences. Site D was enriched in methanotrophic genera (Methylobacter, Methylomicrobium), while Site A was dominated by sulfur-oxidizing taxa such as Thiotrichaceae. Although alpha diversity was higher at Site D, the difference was not statistically significant. Beta diversity analysis showed clear clustering by site. Functional prediction using PICRUSt2 revealed elevated pathways for oxidative phosphorylation, lipid metabolism, and secondary metabolite biosynthesis in Site D samples, suggesting adaptation to methane-rich conditions. LEfSe analysis supported these site-specific functional patterns. Overall, this study reveals both a shared microbial core and localized differences in microbiome structure and function in N. marisindica, underscoring the influence of geochemical variation on host-associated microbiota in deep-sea hydrothermal ecosystems.},
}

@article {pmid41327018,
year = {2025},
author = {Gajjar, K and Patel, S and Chaudhary, M and Agrawal, D and Maniyar, R and Chaudhary, D and Patel, CK and Joshi, C and Joshi, M and Dharajiya, D},
title = {Metagenomic insights reveal the impact of natural farming on soil nutrients, enzyme activities, microbial communities, and yield in turmeric cultivation.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {28},
pmid = {41327018},
issn = {1471-2229},
support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; },
abstract = {BACKGROUND: Turmeric (Curcuma longa L.) is a key spice, medicinal and industrially important crop that is increasingly being cultivated under sustainable practices such as natural farming system (NFS). This study compares NFS and conventional/chemical farming system (CFS) in terms of soil physicochemical properties, enzyme activities, microbial diversity, and yield parameters, providing a comprehensive understanding of their ecological and agronomic impacts.

RESULTS: Field experiments evaluated nine NFS treatments alongside CFS for high throughput amplicon (16S rRNA and ITS) metagenomics, soil physicochemical properties, enzyme activities, and yield parameters. NFS treatments with ≥ 5 t/ha mulching and 4 t/ha Ghanjeevamrit (i.e. NFS-T6 and NFS-T9) significantly enhanced soil organic carbon (~ 0.25%), nitrogen (~ 239.9 kg/ha), and phosphorus (~ 38.16 kg/ha), alongside elevated enzyme activities like alkaline phosphatase (ALP; ~112.11 µg PNP/g/hr) and protease (PR; ~16.22 µg Tyrosine/g/hr). These treatments also exhibited significantly higher microbial richness and evenness (Shannon index: ~5.09; Simpson index: ~0.981). NFS enriched beneficial bacterial (e.g., Priestia, unclassified Acidobacteria, etc.) and saprophytic fungal genera (e.g., Humicola, Mortierella, etc.), enhancing soil nutrient cycling and soil health. Conversely, CFS enriched chemical-resilient and pathogenic taxa (e.g., Alternaria, Curvularia, etc.). NFS-T5 (40.66 t/ha) and NFS-T9 (40.47 t/ha) yielded over twice the fresh rhizome compared to CFS. NFS treatments recorded higher net returns and Benefit-Cost Ratios (BCRs) of 7.51 to 10.57. Microbial profiling of natural farming (NF) inputs (Beejamrit, Jeevamrit, and Ghanjeevamrit) showed distinct bacterial and fungal communities influencing soil microbiome structure. Co-occurrence network analysis of NF soils revealed that microbial taxa introduced via NF inputs had limited integration into native soil communities, indicating selective incorporation governed by competitive ecological interactions.

CONCLUSIONS: Natural farming practices significantly enhanced soil fertility, microbial community structure, enzymatic activity (ALP and PR), and turmeric productivity with superior BCRs. These findings provide scientific evidence supporting natural farming as a viable and sustainable agricultural approach, contributing to improved soil health and crop performance in turmeric cultivation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07781-3.},
}

@article {pmid41488481,
year = {2025},
author = {Xie, Z and Chen, Z and Ma, G},
title = {Dynamic changes in the pregnancy microbiome and their role in preterm birth.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1683610},
pmid = {41488481},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Premature Birth/microbiology/etiology ; *Microbiota ; Vagina/microbiology ; Dysbiosis/microbiology/complications ; Gastrointestinal Microbiome ; Probiotics ; Mouth/microbiology ; Pregnancy Outcome ; },
abstract = {Preterm birth (PTB) remains a leading cause of neonatal morbidity and mortality worldwide, posing significant challenges to maternal and child health. Recent advances have highlighted the critical role of the maternal microbiome-encompassing vaginal, gut, and oral microbial communities-n influencing pregnancy outcomes. This review comprehensively summarizes the dynamic changes of the pregnancy microbiome and elucidates its association with PTB. During healthy pregnancy, the vaginal microbiome is dominated by Lactobacillus with low diversity, while dysbiosis with fewer Lactobacilli and more anaerobes increases PTB risk. The gut microbiome also shifts, with reduced beneficial bacteria and more pro-inflammatory species linked to adverse outcomes. Changes in the oral microbiome and periodontal disease can promote systemic inflammation contributing to PTB. Microbial imbalance may trigger PTB through inflammation, immune changes, and microbial spread to the uterus. Targeting the microbiome via probiotics shows promise, but more clinical studies are needed. This review highlights the pregnancy microbiome as a key biomarker and intervention target to reduce PTB.},
}

Humans
Female
Pregnancy
*Premature Birth/microbiology/etiology
*Microbiota
Vagina/microbiology
Dysbiosis/microbiology/complications
Gastrointestinal Microbiome
Probiotics
Mouth/microbiology
Pregnancy Outcome

@article {pmid41488368,
year = {2025},
author = {Wang, Q and Chen, J and Chen, H and Liang, D and Zhou, H and Chen, J and Gui, Y and Yao, F and Chen, Y and Zeng, X and Ma, Y and Zhou, D and Fu, H},
title = {Indole-3-propionic acid exacerbates cisplatin-induced chronic kidney disease through the AHR/NF-κB signaling pathway.},
journal = {iScience},
volume = {28},
number = {12},
pages = {114149},
pmid = {41488368},
issn = {2589-0042},
abstract = {Cisplatin is a commonly used chemotherapy agent for treating various solid tumors, but its clinical application is limited by nephrotoxicity. While the potential for cisplatin to cause chronic kidney disease (CKD) following repeated administration has been underexplored, effective therapeutic strategies for cisplatin-induced CKD are lacking. We found that cisplatin-induced CKD is characterized by renal dysfunction and inflammation, along with intestinal barrier impairment. 16S rRNA and metabolomics revealed that cisplatin disrupts the gut microbiome and raises levels of tryptophan metabolites-indole-3-propionic acid (IPA). Notably, oral administration of IPA reproduced similar harmful effects in cisplatin-induced CKD. Integrated analyses of the microbiome, metabolomics, Raman spectroscopy, and DESI-MSI indicated that IPA supplementation exacerbates the production of uremic toxins linked to tryptophan metabolism and promotes the growth of pathogenic bacteria. Our findings demonstrates that IPA exacerbates renal inflammation and fibrosis by regulating AHR/NF-κB signaling pathways, altering intestinal microbiome composition, and disrupting tryptophan metabolism.},
}

@article {pmid41488316,
year = {2025},
author = {Seo, K and Min, JY and Min, KB and Oh, KH and Ryoo, SW and Son, SY and Lee, JH},
title = {Change of oral microbiome diversity by smoking across different age groups.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1714229},
pmid = {41488316},
issn = {1664-302X},
abstract = {INTRODUCTION: The oral microbiome, a complex ecosystem linked to both oral and systemic diseases, undergoes compositional and functional changes with aging. Tobacco exposure is a known disruptor of microbial homeostasis, yet its effect on microbial diversity remains inconsistent. Whether agingmodifies the relationship between smoking and the oral microbiome remains unclear. This study aimed to evaluate (1) the association between serum cotinine and oral microbial diversity, (2) whether this association varies by age, and (3) taxonomic shifts that may explain smoking-related dysbiosis.

METHOD: We analyzed data from 4,387 adults aged 30-69 years in the U.S. National Health and Nutrition Examination Survey 2009-2012. Serumcotinine, an objective biomarker of nicotine exposure, was used as the primary exposure. Oral microbiome diversity was assessed via 16S rRNA gene sequencing of oral rinse samples. Microbial profiles were analyzed using observed amplicon sequence variants and Bray-Curtis. Alpha diversity declined progressively with age, with the most pronounced reduction among current smokers.

RESULTS: Serum cotinine was inversely associated with alpha diversity, particularly in current smokers aged 60-69 years (adjusted β = -0.1081, p = 0.0002). Beta diversity differed significantly by smoking status (PERMANOVA p < 0.0001). Analysis identified 29 genera were associated with serum cotinine: Haemophilus, Neisseria, and Gemella decreased with higher exposure, while Atopobium and Lactobacillus increased. Tobacco exposure is associated with reduced oral microbial diversity, particularly in older adults.

DISCUSSION: This highlights the synergistic impact of aging and smoking on the oral microbiome and underscores the need for age-specific prevention strategies. Prospective studies are warranted to confirm causality and assess the reversibility of smoking-induced dysbiosis.},
}

@article {pmid41488298,
year = {2025},
author = {Adams, S and Lakamp, A and Aluthge, N and Laible, E and Loy, JD and Spangler, ML and Fernando, SC},
title = {Investigating the establishment of the rumen and oral bacterial communities in beef cattle and assessing the applicability of using the oral bacterial community composition as a proxy for rumen bacterial community structure in cattle.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1667498},
pmid = {41488298},
issn = {1664-302X},
abstract = {INTRODUCTION: Studies have investigated the rumen microbiome composition and functions to improve ruminant agriculture and its environmental impacts. Yet, sample collection for rumen microbiome analysis can be difficult and invasive, hindering the ability to sample large animal populations. Studies have proposed using oral swabs as an alternative to rumen sample collection. Here, we investigated the potential of using the oral bacterial community as a proxy for the rumen bacterial community during the cattle production cycle.

METHODS: We investigated the development of the bovine rumen and oral bacterial communities using longitudinal sampling and the applicability of using the oral to predict host phenotypes. To this end, we utilized 16S rRNA gene sequencing to characterize and compare the rumen and oral bacterial community composition over multiple time points using amplicon sequence variants (ASVs) in a beef cattle population of 166 animals. Additionally, host phenotype of weaning weight was predicted using the Bayesian ridge regression model to evaluate the applicability of using the oral bacterial community for phenotype prediction.

RESULTS: Our results identified the rumen and oral bacterial communities to have different trajectories of assembly. The proportion of Proteobacteria and Actinobacteriota was higher (p < 0.0001) in the oral samples. Whereas rumen samples had greater abundance of members of the phyla Bacteroidota, Firmicutes, Verrucomicrobiota, Fibrobacterota, and Spirochaetota. The investigation of the oral and rumen bacterial community establishment demonstrated considerable dynamism, where diet and age-related factors to contribute toward bacterial colonization through introduction of new species and the proliferation of early colonizers. Finally, a Bayesian ridge regression model was developed to estimate weaning weight using the centered and scaled log-transformed relative abundance of ASVs. The proportion of variation explained in weaning weight by the oral and rumen bacterial communities were 30 and 37%, respectively.

DISCUSSION: Results from this study suggest that oral and rumen bacterial communities are distinctive, and the oral bacterial community may not serve as a good proxy for the rumen bacterial community even in adult animals with a well-established microbiome. However, the oral bacterial community may serve as a proxy for phenotypic traits of interest in beef cattle.},
}

@article {pmid41488297,
year = {2025},
author = {Tye, KD and Ran, X and Liu, X},
title = {Moderate physical activity during late pregnancy enhances gut microbial network stability in pregnant women.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1731350},
pmid = {41488297},
issn = {1664-302X},
abstract = {AIM: This study aimed to investigate the impact of moderate physical activity during late pregnancy on the overall structure and stability of the maternal gut microbiota, with particular emphasis on microbial network interactions and their potential implications for mucosal immune resilience.

METHODS: A prospective cohort study was initiated at 32 weeks of gestation, during which physical activity was assessed, and fecal samples were subsequently collected at full-term admission for delivery. Fecal samples were collected and analyzed using 16S rDNA sequencing, and daily physical activity levels were recorded. Participants were categorized into two groups based on the duration of moderate-intensity physical activity: T1 (≥30 min/day, 18 women) and T2 (<30 min/day, 5 women). Bioinformatics analyses were used to compare gut microbiota composition, diversity, and network interactions between the groups, and to assess correlations between microbial abundance and physical activity levels.

RESULTS: Firmicutes, Bacteroidetes, Actinomycetes, and Proteobacteria were the dominant phyla in both groups. Alpha diversity and principal coordinate analysis (PCoA) showed no significant differences in overall diversity. However, LEfSe analysis revealed an enrichment of Christensenellaceae and Prevotella stercorea in the T2 group. The gut microbial network in the T1 group was more complex and stable, with predominantly positive microbial correlations. Spearman analysis indicated significant associations between physical activity levels and specific gut microbes: sedentary behavior correlated negatively with Romboutsia (p = 0.033, R = -0.445) and was positively correlated with Senegalimassilia (p = 0.043, R = 0.443), light-intensity activity correlated negatively with Phascolarctobacterium (p = 0.015, R = -0.500), and moderate-intensity activity correlated positively with Parasutterella (p = 0.040, R = 0.432).

CONCLUSION: Moderate physical activity during late pregnancy promotes a more stable and functionally interactive gut microbiota network. Such microbial resilience may strengthen mucosal immune regulation and reduce infection susceptibility during gestation. These findings highlight the potential of physical activity as a non-pharmacological strategy to modulate the maternal gut microbiome for improved host defense and health outcomes.},
}

@article {pmid41488292,
year = {2025},
author = {Zaki, R and Bourne, E and Storino, A and Nadeau, J},
title = {Microbial communities of selected regions of the Deep Springs Lake aquifer system.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689006},
pmid = {41488292},
issn = {1664-302X},
abstract = {Deep Springs Lake is a small, isolated, highly alkaline soda lake in Inyo County of Eastern California, USA. It is a seasonally filled salt lake or playa, and is part of a closed aquifer system. Such closed systems are globally rare, occurring only in arid zones where annual evaporation is greater than annual rainfall. Deep Springs Lake's hydrology and geology have been well studied, and it is home to a unique toad species, but its microbiome remains unexplored. Here we perform 16S, 18S, and ITS amplicon sequencing of the lake water, dried salt crust at the edges the lake, and nearby feeder springs to investigate the community composition of prokaryotes, eukaryotes, and fungi. Bacterial communities in the lake water consist predominantly of Pseudomonadota and Bacteroidota. Nearby springs and salt crust contain different genera of Pseudomonadota than the lake water but similar Bacteroidota, along with an abundant population of Chlorobiota. Noticeably rare in the lake itself but abundant in the biofilms and crust are populations of photosynthetic Cyanobacteria. Archaea are found only in the lake water, largely Halobacterota. Fungi are mostly Ascomycota, with some Chytridiomycota and Rozellomycota; chytrid fungi show no evidence of pathogens related to amphibian die-offs. Eukaryotes in the lake water consist mostly of flagellates, notably the photosynthetic Dunaliella, and brine shrimp (Artemia). In order to compare these sites with source waters elsewhere in the watershed, we also perform 16S amplicon sequencing of three feeder springs found at higher elevations remote from the lake. The Pseudomonadota found in the remote sites differ from those in the lake at the genus level or higher. Some of the genera of Bacteroidota found in the lake are also seen in the remote springs, while most are unique to the springs. Taxonomy and Bayesian source/sink analysis show that the microbiome of Deep Springs Lake derives very little input from the remote feeder springs, but contains extremophiles similar to those of soda lakes worldwide. Further investigation of the lake and its surrounding springs may lead to the identification of new species of bacteria, fungi, and eukaryotes and allow comparisons with other closed aquifer systems.},
}

@article {pmid41488241,
year = {2025},
author = {Uğur, K},
title = {The influence of endocrine disruptors on the gut microbiota.},
journal = {Turkish journal of medical sciences},
volume = {55},
number = {7},
pages = {1635-1640},
pmid = {41488241},
issn = {1303-6165},
mesh = {Humans ; *Endocrine Disruptors/adverse effects/pharmacology ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {Endocrine disruptors (EDs) are closely associated with the second brain, the microbiota-derived enteric nervous system, commonly referred to as the gut microbiota. The microbiota plays a crucial role in human health and the development of diseases. In today's industrialized world, the presence of EDs in air, water, and soil leads to primary human exposure through dermal contact and ingestion. The impact of these EDs on the microbiota remains unclear. EDs that disrupt the balance of the gut microbiota may contribute to a range of disorders, including metabolic (obesity, diabetes mellitus), cardiovascular (vascular stenosis, cerebrovascular disease), reproductive (infertility, ovarian and testicular tumors), neurological (dysfunction of the amygdala, cortex, and cerebellum), and behavioral disorders (dementia, depression, anxiety, and schizophrenia). This review examines the effects of commonly encountered environmental EDs on the gut microbiota and summarizes the most recent findings on this topic. The concept of the microbiota-derived enteric nervous system and the modulation of the hormonal system through interactions between microorganisms and environmental chemicals have prompted specialists in endocrinology and metabolism to reconsider patient management and treatment strategies. This necessitates a comprehensive evaluation of treatment options that incorporate microbiome data. The information presented in this review will help illuminate future research directions and serve as a valuable resource for subsequent studies.},
}

Humans
*Endocrine Disruptors/adverse effects/pharmacology
*Gastrointestinal Microbiome/drug effects

@article {pmid41488081,
year = {2025},
author = {Li, Y and Chen, D and Feng, Y and Li, Q and Mao, W and Yu, P and Zhang, Y},
title = {A pilot study of cervicovaginal microbiome patterns associated with embryo implantation outcomes in endometriosis-associated infertility.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1642770},
pmid = {41488081},
issn = {2296-858X},
abstract = {BACKGROUND: The cervicovaginal microbiome-spanning from the vagina to endometrium-remains undercharacterized in endometriosis-associated infertility. Objective: To determine whether combined vaginal and cervical microbial profiles predict frozen embryo transfer (FET) outcomes.

METHODS: In 22 endometriosis patients undergoing FET, paired vaginal and cervical samples were collected on transfer day. 16S rDNA sequencing quantified microbial composition; alpha/beta diversity, PCoA, LEfSe, and PICRUSt analyses identified taxonomic and functional signatures linked to implantation success. Conduct a differential analysis of microorganisms in different body parts through DMI.

RESULTS: Microbial profiles associated with successful pregnancies featured a higher relative abundance of Lactobacillus and Bifidobacterium, whereas Gardnerella, Streptococcus, and Atopobium were more enriched in failures. Cervical alpha diversity was significantly lower in successful transfers. LEfSe highlighted differential taxa including Peptostreptococcales in successes and Pseudomonadaceae in failures. Functional inference predicted dysregulated metabolic pathways in failure-associated communities. Furthermore, the cervical microbiota exhibited higher DMI, indicating greater individual specificity.

CONCLUSIONS: Our pilot findings suggest that a continuous cervicovaginal microbial ecosystem presents distinct taxonomic and functional patterns associated with FET success in endometriosis. Specifically, cervical microbiota profiling emerges as a promising, minimally invasive approach worthy of further investigation to potentially personalize ART strategies.},
}

@article {pmid41488054,
year = {2025},
author = {Diao, X and Zhang, H and Wang, S and Zhang, Q and Wang, Z},
title = {Bridging ancient wisdom and modern technology: an AI and multi-omics framework for three causes tailored treatment in personalized medicine.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1732340},
pmid = {41488054},
issn = {2296-889X},
abstract = {The 'one-size-fits-all' therapeutic model is inadequate to address individual patient variability, creating an urgent need for an integrative framework for precision medicine. The 'Three Causes Tailored Treatment' (TCTT) principle from traditional Chinese medicine offers a time-tested, holistic blueprint that simultaneously considers the individual, temporal, and environmental dimensions of health. Here, we argue that the synergy of artificial intelligence (AI) and multi-omics technologies is the key to transforming this ancient wisdom into a modern, quantitative clinical paradigm. We demonstrate how multi-omics data provides the foundational layers to quantify the TCTT principle-for instance, using integrated omics (e.g., genomics, proteomics, microbiome) to establish the individual's molecular baseline ("Who"); chronomics to capture temporal fluxes ("When"); and the exposome to decipher the internalized environmental imprint ("Where")-while AI-powered multimodal integration models their complex interactions. By synthesizing evidence across the disease continuum, this review provides a translational roadmap for building dynamic clinical decision-support systems, thereby charting a course toward truly personalized, time-sensitive, and context-aware healthcare.},
}

@article {pmid41487796,
year = {2025},
author = {Waqas, M and Sarwar, I},
title = {Efficacy of Probiotic Supplementation in the Management of Psoriasis: A Systematic Review.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98265},
pmid = {41487796},
issn = {2168-8184},
abstract = {Psoriasis is a chronic immune-mediated skin disease that is increasingly associated with alterations in gut microbiota through the gut-skin axis. This systematic review assessed the efficacy of probiotic supplementation in managing psoriasis. A comprehensive search was performed across PubMed, Scopus, and the Cochrane Library for studies published between 2010 and 2025. After screening 688 unique records and removing duplicates and incomplete entries, 10 studies were found relevant, and eight with accessible full texts were included for qualitative synthesis. Across included randomized controlled and observational studies, probiotic or synbiotic supplementation either alone or as an adjunct to topical or systemic therapy was associated with reductions in Psoriasis Area and Severity Index (PASI) and Dermatology Life Quality Index (DLQI) scores. Several included studies also reported improvements in inflammatory biomarkers and gut microbiota composition, which were narratively presented in this review. Due to heterogeneity in study designs and interventions, findings were synthesized narratively. Multistrain formulations containing Lactobacillus, Bifidobacterium, or Lactiplantibacillus plantarum consistently demonstrated clinical benefits, whereas single-strain products yielded variable outcomes. All interventions were well tolerated, with only mild gastrointestinal discomfort noted in a small minority of participants. The available evidence suggests that probiotic supplementation may reduce disease severity, improve quality of life, and support immune and barrier function in individuals with psoriasis. The therapeutic effect appears strain-dependent and more pronounced in mild-to-moderate disease. Larger, well-controlled trials with standardized probiotic strains, defined dosages, and longer follow-up are needed to clarify the long-term clinical value of probiotics as adjunctive therapy in psoriasis management.},
}

@article {pmid41487676,
year = {2025},
author = {Yang, R and He, S and Wang, J and Yang, J and Su, R and Zhao, W},
title = {Inhibitory effects and amino acid metabolism regulations of active polyphenol from foxtail millet bran on chronic colitis in mice.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1714755},
pmid = {41487676},
issn = {2296-861X},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is frequently associated with metabolic imbalances. Polyphenols have demonstrated efficacy in alleviating colitis by restoring the metabolic disorders. Our previous studies revealed that bound polyphenols extracted from millet bran could alleviate acute colitis and colitis-associated colorectal cancer (CRC) via restoring the gut microbiome and that the low molecular weight (MW) (<200 Da) portion of bound polyphenol (BPLP) constituted the primary active component, comprising six phenolic acids.

METHODS: To further evaluate the effects of BPLP on inflammation, a dextran sodium sulfateb(DSS)-induced experimental colitis model was constructed, and BPLP was gavaged on mice. The effects of BPLP on colitis were assessed by detecting the weight, mouse status, gut barrier integrity, and inflammatory cytokine secretion. Additionally, non-targeted metabolomics was used to identify altered metabolites.

RESULTS AND DISCUSSION: BPLP administration restored body weight and colon length, protected epithelial structure from DSS-induced damage, and relieved chronic colitis. In colons, BPLP reduced the levels of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β), enhanced the secretion of the anti-inflammatory cytokine IL-10, and upregulated the expression of tight junction proteins. Nontarget metabolomic results showed that BPLP alleviated colitis by modulating amino acid metabolism pathways, including valine/leucine/isoleucine biosynthesis,phenylalanine/tyrosine/tryptophan biosynthesis, and phenylalanine metabolism. Furthermore, alterations in specific amino acids, such as valine and beta-alanine, were consistent with profiles observed in clinical IBD patients. Collectively, these results indicate that BPLP effectively alleviates chronic colitis in mice and regulates inflammation-related amino acid metabolism in vivo.},
}

@article {pmid41487523,
year = {2025},
author = {Gómez-Cebrián, N and Trull, MC and Gras-Colomer, E and Edo Solsona, MD and Poveda Andrés, JL and Puchades-Carrasco, L},
title = {Systemic metabolic reprogramming and microbial dysbiosis in Fabry disease: Multi-omics mechanisms and implications for drug development.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1702682},
pmid = {41487523},
issn = {1663-9812},
abstract = {Current treatments, including enzyme replacement and pharmacological chaperones, have improved disease outcomes but often fail to fully prevent progression or alleviate persistent symptoms, underscoring the need for novel therapeutic strategies. Recent systems biology and multi-omics approaches have revealed consistent and previously underappreciated alterations in systemic metabolism and the gut microbiota in FD. Here, we synthesize evidence from metabolomic, lipidomic, transcriptomic, and metagenomic studies in patients and experimental models, highlighting disturbances in redox balance, mitochondrial function, energy metabolism, and microbiota-derived metabolites such as short-chain fatty acids and tryptophan catabolites. These findings point to new mechanisms underlying gastrointestinal, inflammatory, and metabolic complications in FD, with direct implications for biomarker discovery and drug development. We further discuss the challenges of integrating multi-omics data into clinical research, the value of mechanistic studies in disease models, and the potential for translating omics-derived insights into precision diagnostics and targeted therapies. By framing FD as a systemic disorder of metabolic and microbial dysregulation, this review outlines a roadmap for mechanism-based interventions that extend beyond canonical glycosphingolipid targets.},
}

@article {pmid41487351,
year = {2025},
author = {Xie, Y and Dai, D and Zeng, H and Tian, Y and Zou, C and Meng, Y and Wu, Z and Li, J},
title = {Endophyte community shifts in Rubus chingii during fruit ripening are associated with key metabolites.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1727436},
pmid = {41487351},
issn = {1664-462X},
abstract = {INTRODUCTION: The fruit of Rubus chingii Hu is a prized traditional medicine and functional food, with its quality predominantly determined by its secondary metabolites. While the metabolic dynamics during fruit ripening are documented, the role of the endophytic microbiome, a key regulator of plant physiology, remains entirely unexplored.

METHODS: An integrated approach, combining 16S/ITS amplicon sequencing with spectroscopic and chromatographic analyses, were employed to investigate the correlation between the endophytic microbiome and the metabolome across four distinct ripening stages of R. chingii fruit.

RESULTS: Significant stage-dependent shifts in the community structure of both bacterial and fungal endophytes were revealed in this study. Notably, Spearman correlation analysis identified specific microbial taxa, including the bacterial genera Geodermatophilus and Brevundimonas, and the fungal yeasts Metschnikowia and Starmerella, that were significantly positively correlated with the accumulation of key secondary metabolites (ellagic acid, flavonoids, and phenolic acids). Concurrently, the content of these beneficial metabolites and the fruit's antioxidant capacity decreased markedly as ripening progressed.

DISCUSSION: This study provides the first evidence of a structured succession in the endophytic microbiome of R. chingii fruit and its close association with the dynamics of medically relevant metabolites. The findings propose that the ripening process is a tripartite interplay between host development, microbial succession, and metabolic reprogramming. The identified keystone taxa represent promising targets for future microbiome-based strategies to manipulate fruit quality, offering novel insights into the role of the microbiome in medicinal plant biology and its potential application in sustainable agriculture.},
}

@article {pmid41487047,
year = {2026},
author = {Xie, W and Wang, X and Liu, Y and Cai, L and Song, B and Zhang, S and Shao, Y and Wang, W and Xue, X and Li, J and Cui, W and Jiang, Y and Wang, X and Tang, L},
title = {Gut Microbiota-Derived Ursodeoxycholic Acid Mediates the Resistance to Colonic Inflammation in Pigs.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08687},
pmid = {41487047},
issn = {1520-5118},
abstract = {Microbes in the gut are crucial for host health, yet their role in disease resistance remains unclear. Using fecal microbiota transplantation from disease-resistant Min pigs to Duroc × Landrace × Yorkshire (DLY) pigs, combined with 16S rRNA sequencing and metabolomics, we investigated this relationship. The transferred microbiota alleviated lipopolysaccharide-induced intestinal inflammation and barrier damage in the DLY piglets. Key bacterial genera and bile acid metabolites have been identified, with in vitro evidence showing that the gut microbiome can convert bile acids to secondary forms, primarily ursodeoxycholic acid (UDCA). Subsequent mechanistic validation in a mouse model demonstrated that UDCA acts via the gut-liver axis on the farnesoid X receptor, inhibiting PI3K/AKT/NF-κB pathways and reducing inflammatory responses, thereby preserving tissue structure in the liver and colon. These findings establish a causal link between gut microbiota and disease resistance, indicating that targeting microbial bile acid metabolism may restore intestinal and hepatic health.},
}

@article {pmid41486934,
year = {2025},
author = {Yun, M and Son, D and Kim, N and Lee, SH and Cho, E and Lim, S},
title = {Synergistic anti-obesity effects of Bifidobacterium breve BR3 and Lactiplantibacillus plantarum LP3 via coordinated regulation of lipid metabolism and gut microbiota.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {12},
pages = {e2511001},
doi = {10.71150/jm.2511001},
pmid = {41486934},
issn = {1976-3794},
support = {KE2503-1//Ministry of Science and ICT/ ; RS-2023-00218423//Ministry of SMEs and Startups/ ; },
mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Obesity/metabolism/therapy/microbiology ; *Lipid Metabolism/drug effects ; Mice, Inbred C57BL ; Mice ; Male ; Diet, High-Fat/adverse effects ; *Bifidobacterium breve/physiology ; *Anti-Obesity Agents/pharmacology/administration & dosage ; Adipose Tissue/metabolism ; Liver/metabolism ; },
abstract = {The global rise in obesity and its associated metabolic complications underscores the urgent need for safe and effective interventions. This study investigated the anti-obesity efficacy of a probiotic mixture containing Bifidobacterium breve BR3 and Lactiplantibacillus plantarum LP3 in C57BL/6 mice with high-fat diet (HFD)-induced obesity. After obesity was established by feeding a 60% kcal HFD, the probiotic mixture was administered orally for 4 weeks. Compared with the control group, mice receiving the L. plantarum LP3 and B. breve BR3 mixture exhibited significant reductions in body weight and total fat mass, as assessed by Dual-energy X-ray Absorptiometry (DXA) and Echo Magnetic Resonance Imaging (EchoMRI). The probiotic treatment also lowered serum Aspartate Aminotransferase (AST), Alanine Aminotransferase (ALT), and glucose levels, and attenuated lipid accumulation in both hepatic and epididymal adipose tissues. Transcriptomic profiling revealed upregulation of lipolytic genes (Sirt1, Pparα) and downregulation of lipogenic genes (Srebp1c, Fas), suggesting that the probiotic mixture promotes lipid catabolism while suppressing lipid synthesis. Additionally, serum adipokine levels were favorably modulated, indicating improved metabolic homeostasis. Gut microbiota analysis demonstrated an increased relative abundance of beneficial genera, including Akkermansia and Bacteroides, highlighting a microbiome-mediated contribution to the observed metabolic benefits. Overall, our findings indicate that the combined administration of Lactiplantibacillus plantarum LP3 and Bifidobacterium breve BR3 exerts multi-faceted anti-obesity effects by enhancing lipolysis, regulating lipid metabolism, and restoring a healthy gut microbial balance. This probiotic mixture represents a promising therapeutic approach for managing obesity and related metabolic disorders.},
}

Animals
*Probiotics/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
*Obesity/metabolism/therapy/microbiology
*Lipid Metabolism/drug effects
Mice, Inbred C57BL
Mice
Male
Diet, High-Fat/adverse effects
*Bifidobacterium breve/physiology
*Anti-Obesity Agents/pharmacology/administration & dosage
Adipose Tissue/metabolism
Liver/metabolism

@article {pmid41486930,
year = {2025},
author = {Gan, X and Wen, Y and Chen, S and Ke, F and Liu, S and Wang, Z and Zhang, C and Wang, X and Wang, Q and Gao, X},
title = {Multi-omic profiling reveals the impact of keratinase kerZJ on mouse gut homeostasis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {12},
pages = {e2509011},
doi = {10.71150/jm.2509011},
pmid = {41486930},
issn = {1976-3794},
support = {2024NSFSC2097//Science and Technology Program of Sichuan province/ ; SKLSIM-F-202458//Open Fund of State Key Laboratory of Neurology and Oncology Drug Development/ ; 2024NSFSC2097//Science and Technology Program of Sichuan province/ ; SKLSIM-F-202458//Open Fund of State Key Laboratory of Neurology and Oncology Drug Development/ ; 2024LZXNYDJ054//Science and Technology Strategic Cooperation Program of Luzhou Municipal Peoples Government and Southwest Medical University/ ; 2023XYXNYD06//Strategic Cooperation program of Xuyong County Peoples Hospital and Southwest Medical University/ ; DZFHXM202318//Phoenix Project of Dazhou/ ; },
mesh = {Animals ; Mice ; *Homeostasis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Peptide Hydrolases/metabolism/pharmacology/administration & dosage ; Proteomics ; Intestinal Mucosa/drug effects/microbiology/metabolism ; Male ; Mice, Inbred C57BL ; Fatty Acids, Volatile/metabolism ; Immunity, Mucosal/drug effects ; Multiomics ; },
abstract = {Keratinase kerZJ is a multifunctional protease with potential as a feed additive and functional ingredient. Here we performed an integrated multi‑omics evaluation of its biosafety and impact on gut homeostasis in mice. Our findings confirm that kerZJ is well-tolerated, with no evidence of systemic toxicity or intestinal epithelial damage. Integrated transcriptomic and proteomic analyses revealed that kerZJ reinforces intestinal barrier integrity by upregulating extracellular matrix components, including collagen IV, and modulates mucosal immunity by enhancing B-cell activation and antimicrobial peptide defenses without inducing inflammation. Furthermore, kerZJ administration led to a significant upregulation of digestive enzymes and a dose-dependent increase in short-chain fatty acids production. Microbiome analysis showed that while high-dose kerZJ altered community composition, it enriched for beneficial taxa like Lactobacillaceae and did not induce dysbiosis. These results demonstrate that kerZJ safely enhances gut barrier function, promotes a favorable immune and metabolic environment, and fosters a resilient gut ecosystem, supporting its development as a safe feed additive and nutraceutical component.},
}

Animals
Mice
*Homeostasis/drug effects
*Gastrointestinal Microbiome/drug effects
*Peptide Hydrolases/metabolism/pharmacology/administration & dosage
Proteomics
Intestinal Mucosa/drug effects/microbiology/metabolism
Male
Mice, Inbred C57BL
Fatty Acids, Volatile/metabolism
Immunity, Mucosal/drug effects
Multiomics

@article {pmid41486857,
year = {2026},
author = {Xin, L and Chen, Y and Guan, D and Huang, L and Lv, Y and Rong, W and Li, X},
title = {Integrated Analysis of Midgut Transcriptome and Microbiome Reveals That Manganese-Induced Dysbiosis Drives Metabolic Disruption and Developmental Toxicity in Bombyx mori.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70223},
doi = {10.1111/1462-2920.70223},
pmid = {41486857},
issn = {1462-2920},
support = {Heke ZY230301//Local Science and Technology Development Fund project guided by the Central Government/ ; 23-026-08//2023 Annual Operation Subsidy Project of the Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; 2020XJZC002//Research Project of Hechi University/ ; 2023GXCSSC04//Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; },
mesh = {Animals ; *Bombyx/microbiology/growth & development/drug effects/metabolism ; *Manganese/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Transcriptome/drug effects ; Larva/drug effects/growth & development/microbiology ; *Dysbiosis/chemically induced ; Bacteria/genetics/classification/drug effects/isolation & purification ; },
abstract = {Manganese (Mn) contamination poses a significant environmental threat, yet the mechanisms underlying its toxicity remain poorly characterised. Here, we used an integrative multi-omics approach to elucidate how dietary Mn disrupts the gut-microbiome axis in the silkworm, Bombyx mori. High-dose Mn exposure triggered severe, dose-dependent growth retardation, reducing larval weight by 55.1%. This was concurrent with profound gut microbiome dysbiosis, evidenced by reduced bacterial diversity, community homogenisation and a sharp decline in beneficial genera such as Delftia, alongside the complete elimination of key commensals like Bifidobacterium. Host midgut transcriptomics revealed 1255 differentially expressed genes, with significant upregulation of detoxification and stress pathways and marked suppression of genes involved in nutrient metabolism. Critically, integrative analysis demonstrated a strong correlation between microbiome disruption and host metabolic gene expression, suggesting that Mn toxicity operates by disrupting the gut microbiome-host metabolic axis. Our findings provide crucial mechanistic insights into heavy metal ecotoxicology and highlight the vulnerability of beneficial insect-microbe symbioses to environmental contamination, with important implications for sustainable agriculture in metal-polluted regions.},
}

Animals
*Bombyx/microbiology/growth & development/drug effects/metabolism
*Manganese/toxicity
*Gastrointestinal Microbiome/drug effects
*Transcriptome/drug effects
Larva/drug effects/growth & development/microbiology
*Dysbiosis/chemically induced
Bacteria/genetics/classification/drug effects/isolation & purification

@article {pmid41486530,
year = {2025},
author = {Zabolotnyi, D and Serezhko, Y and Zabolotna, D and Maliarenko, Y and Voroshylova, N and Verevka, S},
title = {ON THE POSSIBLE MECHANISMS OF MICROBIOME INVOLVEMENT IN INDUCTION OF MALIGNANCY.},
journal = {Experimental oncology},
volume = {47},
number = {3},
pages = {389-392},
doi = {10.15407/exp-oncology.2025.03.389},
pmid = {41486530},
issn = {2312-8852},
mesh = {Humans ; *Neoplasms/microbiology/etiology/pathology ; *Microbiota ; *Biofilms/growth & development ; Animals ; },
abstract = {The сlose coexistence of organisms of different biological species is one of the leading principles of the organization of living matter. The interaction of microbial biofilms with adjacent tissues of the host deserves special attention. The article raises controversial issues related to the possible malignant effect of microbial biofilms.},
}

Humans
*Neoplasms/microbiology/etiology/pathology
*Microbiota
*Biofilms/growth & development
Animals

@article {pmid41486484,
year = {2025},
author = {Boogari, M and Mohebbi, M and Hadidi, N},
title = {Genetically Engineered Probiotics: Design, Therapeutics, and Clinical Translation.},
journal = {Iranian biomedical journal},
volume = {29},
number = {6},
pages = {374-383},
doi = {10.61882/ibj.5197},
pmid = {41486484},
issn = {2008-823X},
abstract = {Genetically engineered probiotics aim to address transient colonization and the intra- and inter-subject variability that limit conventional probiotics. These strains utilizes CRISPR/Cas editing, programmable gene circuits, and biosensors in chassis such as E. coli Nissle 1917 and L. lactis. This narrative review summarizes the current engineering toolkits and standards (e.g., SEVA), chassis selection criteria, biocontainment strategies, and translational requirements under CMC/GMP frameworks and discusses regulatory considerations for clinical translation. Representative examples include IL-10-secreting L. lactis and phenylalanine-metabolizing strains for PKU (SYNB1618/SYNB1934), which illustrate pharmacodynamic target engagement and short-term preclinical safety. We outline clinical advancements in predefined pharmacodynamics, durability of function, monitoring shedding and HGT, and genomic-microbiome-informed patient stratification. Systems modeling approaches (GEM/ABM) are discussed as tools to guide rational design. GEPs offer programmable "sense-and-respond" therapeutics, with successful clinical adoption depending on durable efficacy, long-term safety, and clearly defined regulatory pathways.},
}

@article {pmid41486395,
year = {2026},
author = {Hajjar, R and Mars, RAT and Kashyap, PC},
title = {Harnessing the microbiome for cancer therapy.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41486395},
issn = {1740-1534},
abstract = {The microbiome is increasingly recognized as a key player in cancer pathogenesis and treatment response, acting through both local and systemic mechanisms. Microbial communities and their metabolites can directly influence drug metabolism, shape the immune landscape, and alter transcriptional and epigenetic programmes in the gut, systemically and in the tumour microenvironment. Emerging data support the potential of microbiome-targeted interventions (such as faecal microbiota transplantation, diet, prebiotics and probiotics) as adjuncts to conventional cancer therapies, with the goal of enhancing efficacy and reducing toxicity. This Review highlights the promise of the microbiome as a prognostic and predictive biomarker, a modifiable factor in cancer care and prevention, and a therapeutic target. We also discuss major knowledge gaps, limitations in current study designs, and the need for mechanism-guided, personalized strategies to advance clinical translation.},
}

@article {pmid41486317,
year = {2026},
author = {Arya, AS and Mythili, A},
title = {Gut microbiota centered approaches for breast cancer intervention leveraging probiotics and postbiotics.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-025-04344-8},
pmid = {41486317},
issn = {2730-6011},
}

@article {pmid41486169,
year = {2026},
author = {Pei, X and Zhang, N and Deng, X and Li, R and Wang, Y and Wang, Y and Huang, W and Yue, Y and Geisen, S and Gao, Z and Guo, S and Tian, D and Shen, Q and Kowalchuk, GA and Li, R},
title = {Biofertilizer induces soil disease suppression by activating pathogen suppressive protist taxa.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00897-2},
pmid = {41486169},
issn = {2055-5008},
support = {42307171//the National Natural Science Foundation of China/ ; 42277294//the National Natural Science Foundation of China/ ; 2023M731724//the Postdoctoral Science Foundation of China/ ; KTTQ2025018//the Fundamental Research Funds for the Central Universities/ ; CX(22)2043//the Agricultural Science and Technology independent innovation fund project of Jiangsu Province/ ; 2060302//the key project at central government level: the ability establishment of sustainable use for valuable Chinese medicine resources/ ; },
abstract = {Given the increasing demand for sustainable agricultural solutions utilizing the microbiome, particularly the use of biofertilizer (BF), it is essential to understand the mode of action and the role of predatory protists, along with their interactions with biocontrol strains and resident community members. We therefore examined these interactions through a long-term field experiment and a series of greenhouse and pot experiments. In field and greenhouse studies, we observed that Bacillus significantly stimulated the growth of Cercomonas, a genus of predatory protists, in the soil. In turn, these protists promoted the growth of Bacillus, leading to increased detection of polyketide synthase (PKS) genes and the inhibition of bacterial wilt pathogen Ralstonia solanacearum. We here reveal a positive feedback loop between the biocontrol agent Bacillus and predatory protists, which explains the biofertilizer-induced reduction of plant pathogens. These findings highlight the significance of synergistic interactions between functional microbes and predatory protists in suppressing soil-borne diseases. Moreover, it underscores the potential of incorporating predator-prey interactions into agricultural practices to foster more sustainable ecosystem development.},
}

@article {pmid41486167,
year = {2026},
author = {Chen, Y and Fang, Y and Lyu, Z and Tian, Y and Niu, S and Li, YR and Yang, L},
title = {Microbiome modulation of tumorigenesis and immune responses.},
journal = {Journal of biomedical science},
volume = {33},
number = {1},
pages = {4},
pmid = {41486167},
issn = {1423-0127},
support = {UCLA MIMG M. John Pickett Post-Doctoral Fellow Award//University of California, Los Angeles/ ; UCLA BSCRC Innovation Award//University of California, Los Angeles/ ; },
mesh = {Humans ; *Carcinogenesis/immunology ; *Neoplasms/immunology/microbiology/therapy ; *Microbiota/immunology ; Gastrointestinal Microbiome ; Immunotherapy ; },
abstract = {The microbiome has emerged as a critical, context-dependent regulator of tumorigenesis and anticancer immunity, capable of either promoting cancer progression or protecting against malignancy. This dual role is mediated by multiple interconnected mechanisms-including chronic inflammation, modulation of immune responses, and alterations in host metabolic signaling. These microbiome-cancer interactions vary across organs, influencing malignancies in the colon, breast, lung, and beyond. Clinically, the microbiome significantly affects patient responses to cancer therapies, particularly immunotherapies such as immune checkpoint blockade (ICB) and chimeric antigen receptor (CAR)-T cell therapy. Although emerging therapeutic strategies aimed at modulating the microbiome have shown promising early results, challenges remain, including individual microbiome variability and the dynamic interplay between the immune system and microbial communities. Nevertheless, harnessing the microbiome holds significant potential to transform precision oncology, offering personalized cancer prevention and treatment strategies tailored to each patient's unique microbial ecosystem.},
}

Humans
*Carcinogenesis/immunology
*Neoplasms/immunology/microbiology/therapy
*Microbiota/immunology
Gastrointestinal Microbiome
Immunotherapy

@article {pmid41486026,
year = {2025},
author = {Nguyen, VH and Pereira, LR and Shannon, OM and Stephan, BC and Siervo, M},
title = {Dietary patterns and endothelium dysfunction: a literature review.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104484},
doi = {10.1016/j.numecd.2025.104484},
pmid = {41486026},
issn = {1590-3729},
abstract = {The integrity of the vascular endothelium is fundamental to regulating cardio-metabolic and neurological functions. Endothelial dysfunction (ED) is a key driver of atherosclerosis and is strongly linked to the pathogenesis of heart disease, peripheral arterial disease, and stroke. This review describes the relationship between dietary patterns and endothelial health, focusing on observational and experimental studies that investigate the protective effects of healthy dietary patterns in the maintenance of endothelial integrity and prevention of ED. Plant-based diets, including Mediterranean and Dietary Approaches to Stop Hypertension (DASH) dietary patterns, have been linked to improvement of endothelial function through multiple mechanisms such as increased nitric oxide bioavailability, reduced oxidative stress and inflammation, and fostering a healthy gut microbiome. Traditional Japanese, Nordic, and Palaeolithic dietary patterns also show potential cardiovascular benefits through improved vascular biomarkers and significant anti-inflammatory effects, though evidence on effects on endothelial function remains less established. The consequences of poor endothelial health extend to all systems, and the brain is one of the organs crucially affected by ED. ED has been increasingly recognised as a critical contributor to cognitive decline, dementia, and stroke, largely accounted and explained by mechanisms impairing cerebral blood flow, neuronal metabolism, neuro-vascular coupling and compromised integrity of the blood-brain barrier. This review highlights the importance of maintaining endothelial health as a protective strategy for cognitive function and reduction of dementia risk. Adherence to dietary patterns with protective effects on endothelial integrity may represent an effective strategy to promote lifelong health for both the heart and brain.},
}

@article {pmid41486021,
year = {2025},
author = {Yao, CC and Tai, WC and Liang, CM and Tsai, MC and Tsai, YC and Wu, CK and Huang, PY and Chen, CH and Kuo, YH and Chuah, SK and Lian, WS and Chiu, YC and Kuo, CM and Wu, KL},
title = {Alternation of the oral, gastric and stool microbiome in patients with reflux esophagitis and Barrett's esophagus.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2025.12.007},
pmid = {41486021},
issn = {1995-9133},
abstract = {BACKGROUND: The imbalance of human microbiota has been associated with various inflammatory disease. Compared to intestinal flora, the esophageal microbiome has been understudied,and it remains unclear whether dysbiosis is related to reflux esophagitis (RE) and Barrett's esophagus (BE).This study aimed to synthesize findings on microbial composition changes across different regions of the gastrointestinal tract and their relationship with chronic esophageal reflux diseases.

METHODS: We recruited 29 RE patients (10 Grade A; 10 Grade B; 9 Grade C), 9 BE patients, and 10 healthy volunteers to study microbial composition in saliva, gastric juice, and stool using 16S rRNA gene pyrosequencing and analyzed serum inflammatory cytokines using ELISA.

RESULTS: Microbiota alpha diversity exhibited no significant changes between groups. In terms of taxonomy, RE and BE patients had more gram-negative anaerobic bacteria in salivary microbiota. Notably, increased Tannerellaceae abundance correlated with elevated serum IL-6 levels, which have been linked to chronic inflammation. Helicobacter was more abundant in gastric fluid of controls. Stool analysis revealed BE patients had higher abundance of phylum Bacteroidetes, and the genus Prevotella, while Fusobacterium was more prevalent in controls.

CONCLUSIONS: The increased abundance of Tannerellaceae in saliva was correlated with elevated serum IL-6 levels and may be a contributing factor in chronic esophageal reflux disease. BE patients had a higher abundance of Prevotella, a gram-negative bacterium, which may be linked to early stage esophageal inflammation in chronic reflux disease. Conversely, the increased abundance of Helicobacter in gastric juice may serve as a protective factor.},
}

@article {pmid41485840,
year = {2026},
author = {Jurgiel, J and Gromowski, T and Król, J and Bomba-Opoń, D and Kościółek, T and Wielgoś, M},
title = {The impact of maternal microbial transfer on the infant gut microbiome after cesarean delivery: a systematic review.},
journal = {American journal of obstetrics and gynecology},
volume = {233},
number = {6S},
pages = {S541.e1-S541.e16},
doi = {10.1016/j.ajog.2025.09.001},
pmid = {41485840},
issn = {1097-6868},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cesarean Section ; Female ; Infant, Newborn ; Pregnancy ; *Fecal Microbiota Transplantation ; Vagina/microbiology ; Bacteroides ; Lactobacillus ; Bifidobacterium ; },
abstract = {OBJECTIVE: To systematically review the results of maternal microbial transfer in shaping microbial diversity, improving neonatal development, and evaluating the microbial transfer procedure's adverse events.

DATA SOURCES: A comprehensive search was conducted on April 25, 2024, using PubMed/MEDLINE, Academic Search Ultimate, and ClinicalTrials.gov for studies published in English from 2000 to 2023. The following keywords were used: "vaginal seeding," "microbiota," "maternal fecal microbiota transplantation," "maternal microbial transfer," and "bacterial baptism."

STUDY ELIGIBILITY CRITERIA: The review included English-language, peer-reviewed randomized controlled trials and nonrandomized interventional studies investigating maternal microbial transfer in neonates born via elective cesarean delivery.

Data were extracted and analyzed for key outcomes, including severe adverse effects, alpha diversity, beta diversity, and the abundance of key taxa such as Bacteroides spp., Bifidobacterium spp., and Lactobacillus spp.

RESULTS: A total of 10 studies, including 4 randomized controlled trials and 6 nonrandomized interventional studies with 1450 participants, were included in this qualitative review. The findings regarding changes in alpha diversity (a measure of microbial richness within individual samples) were inconclusive, while several studies indicated a potential increase in beta diversity (reflecting differences in microbial composition between samples) associated with the procedure. Bacteroides spp., Bifidobacterium spp., and Lactobacillus spp. were the most frequently assessed taxa, with some studies suggesting beneficial changes in their abundance. Developmental outcomes, such as anthropometric measures and allergy risks, showed limited evidence of benefit, with one study reporting preliminary findings of improved neurodevelopmental scores. No significant increase in severe adverse effects was observed in any of the included studies.

CONCLUSION: The efficacy of maternal microbial transfer in restoring neonatal microbiota and promoting health outcomes remains uncertain, with neonatal outcomes addressed in only 3 of the included studies-one on allergy and one on neurodevelopment. However, while no serious adverse effects have been consistently reported, data on safety remain limited.},
}

Humans
*Gastrointestinal Microbiome
*Cesarean Section
Female
Infant, Newborn
Pregnancy
*Fecal Microbiota Transplantation
Vagina/microbiology
Bacteroides
Lactobacillus
Bifidobacterium

@article {pmid41485837,
year = {2026},
author = {Sanchez-Ramos, L and Preis, R and Romero, R},
title = {Prophylactic antibiotics to prevent postcesarean infection: which antimicrobial, when, how, and why?.},
journal = {American journal of obstetrics and gynecology},
volume = {233},
number = {6S},
pages = {S483-S503},
doi = {10.1016/j.ajog.2025.09.044},
pmid = {41485837},
issn = {1097-6868},
mesh = {Humans ; Female ; *Antibiotic Prophylaxis/methods ; *Surgical Wound Infection/prevention & control ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; *Cesarean Section/adverse effects ; Cefazolin/therapeutic use ; Pregnancy ; Clindamycin/therapeutic use ; Endometritis/prevention & control ; Azithromycin/therapeutic use ; Gentamicins/therapeutic use ; },
abstract = {Before the introduction of routine antibiotic administration, the rate of postcesarean infection exceeded 30% to 50%. Since the 1970s, postpartum infection occurs in approximately 1% to 2% of patients after vaginal birth and in 5% to 20% following cesarean delivery. Evidence from randomized clinical trials and systematic reviews has demonstrated that the administration of a single dose of antibiotics within 60 minutes before skin incision significantly reduces maternal infection-related morbidity without adverse neonatal outcomes. These results have informed clinical guidelines of professional organizations. Antibiotic selection is empiric and primarily guided by knowledge of the microbiology of intra-amniotic and puerperal infection. Cefazolin is the standard prophylactic agent due to its broad-spectrum activity, favorable pharmacokinetics, and established safety. However, its lack of activity against organisms such as Ureaplasma species has motivated investigation of adjunctive azithromycin, particularly in high-risk or unscheduled cesarean deliveries, where randomized trials and meta-analyses show additional benefit in reducing wound infections and endometritis. For patients with severe beta-lactam allergies, clindamycin and gentamicin are commonly used, although use of these agents is associated with higher rates of surgical site infection, increased antimicrobial resistance, and risks such as nephrotoxicity and necrotizing enterocolitis due to Clostridioides difficile infection. Special considerations include obesity, which doubles the risk of surgical site infection and alters antibiotic pharmacokinetics, prompting recommendations for a 3-gram cefazolin dose in patients ≥120 kg. Prolonged operative time and excessive blood loss also warrant intraoperative redosing to maintain therapeutic levels. In addition, emerging evidence suggests that adjunctive postcesarean antibiotic administration (eg, cephalexin with metronidazole) may reduce wound complications in obese women, although professional guidelines remain in evolution. In summary, judicious use of antibiotic prophylaxis is essential to reduce cesarean-related infections and optimize maternal outcomes, while continued research seeks to refine strategies that mitigate unintended neonatal consequences.},
}

Humans
Female
*Antibiotic Prophylaxis/methods
*Surgical Wound Infection/prevention & control
*Anti-Bacterial Agents/therapeutic use/administration & dosage
*Cesarean Section/adverse effects
Cefazolin/therapeutic use
Pregnancy
Clindamycin/therapeutic use
Endometritis/prevention & control
Azithromycin/therapeutic use
Gentamicins/therapeutic use