@article {pmid40492798,
year = {2025},
author = {Manjarres, Z and Plumb, AN and Sadler, KE},
title = {Bug in the Syndrome: Using the Gut Microbiome to Diagnose Complex Regional Pain Syndrome.},
journal = {Anesthesiology},
volume = {143},
number = {1},
pages = {20-21},
pmid = {40492798},
issn = {1528-1175},
}

@article {pmid40492779,
year = {2025},
author = {N S, S and Maske, VB and Punchappady Devasya, R and Rekadwad, BN},
title = {Draft genome sequence of an antibiotic-resistant Heyndrickxia oleronia strain UL23-01-03 isolated from the Arabian Sea coast, Dakshina Kannada, India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0049425},
doi = {10.1128/mra.00494-25},
pmid = {40492779},
issn = {2576-098X},
abstract = {Here, we present the draft genome of antibiotic-resistant Heyndrickxia oleronia UL23-01-03 isolated from the Arabian Sea coast, Mangalore, India. The draft genome consists of 53 contigs totaling 5,003,978 bp, with a guanine-cytosine content of 34.8% and an OrthoANI of 97.37% compared to the reference strain.},
}

@article {pmid40492748,
year = {2025},
author = {LaGrutta, A and Arnold, D and Coetzee, O},
title = {Boosting Testosterone Naturally in Hashimoto's: A Case Report on Trans-Geranylgeraniol Supplementation.},
journal = {Alternative therapies in health and medicine},
volume = {},
number = {},
pages = {},
pmid = {40492748},
issn = {1078-6791},
abstract = {UNLABELLED: This case report details an integrative nutrition approach for a 27-year-old male diagnosed with Hashimoto's thyroiditis, suboptimal testosterone levels, and gut dysbiosis. Initially diagnosed in 2020, the patient presented with persistent thyroid autoimmunity and vitamin D insufficiency, but maintained stable androgen levels until 2023. Early interventions focused on foundational strategies, including anti-inflammatory dietary modifications, removal of gluten and dairy, and repletion of key nutrients such as vitamin D3/K2. Gut-directed therapies were added to support microbial diversity and intestinal barrier function, using digestive enzymes and increased intake of polyphenol-rich foods. Thyroid biomarkers showed steady improvement with these interventions. However, in 2023, the patient began to experience declining testosterone levels, accompanied by decreased muscle mass and athletic performance. To address this, a targeted supplementation protocol was introduced: 600 mg/day (two 300 mg capsules) of trans-geranylgeraniol (Annatto-GG™ 300) for nine weeks. Over the nine weeks, this intervention resulted in a clinically meaningful increase in total testosterone, accompanied by notable improvements in strength and physical performance. This case highlights the critical interplay between immune function, endocrine balance, and gastrointestinal health, illustrating the efficacy of a multifaceted, non-pharmacological approach in optimizing hormonal regulation and metabolic resilience. The findings emphasize the necessity of a systems-based, integrative framework in addressing complex, interrelated physiological imbalances.

KEYWORDS: case report, testosterone, low testosterone and thyroid function, autoimmune disease, Hashimoto's thyroiditis, TRT, mevalonate pathway, Leydig cell function, infammation, trans-geranylgeraniol, vitamin D, microbiome, gut-thyroid.},
}

@article {pmid40492742,
year = {2025},
author = {Edwin, NR and Duff, A and Deveautour, C and Brennan, F and Abram, F and O'Sullivan, O},
title = {Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0105924},
doi = {10.1128/msystems.01059-24},
pmid = {40492742},
issn = {2379-5077},
abstract = {Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.},
}

@article {pmid40492703,
year = {2025},
author = {Alam, I and Marasco, R and Momin, AA and Aalismail, N and Laiolo, E and Martin, C and Sanz-Sáez, I and Foix, BB and Sá, EL and Kamau, A and Guzmán-Vega, FJ and Jamil, T and Acinas, SG and Gasol, JM and Gojobori, T and Agusti, S and Daffonchio, D and Arold, ST and Duarte, CM},
title = {Widespread distribution of bacteria containing PETases with a functional motif across global oceans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf121},
pmid = {40492703},
issn = {1751-7370},
abstract = {Accumulating evidence indicates that microorganisms respond to the ubiquitous plastic pollution by evolving plastic-degrading enzymes. However, the functional diversity of these enzymes and their distribution across the ocean, including the deep sea, remain poorly understood. By integrating bioinformatics and artificial intelligence-based structure prediction, we developed a structure- and function-informed algorithm to computationally distinguish functional polyethylene terephthalate-degrading enzymes (PETases) from variants lacking PETase activity (pseudo-PETase), either due to alternative substrate specificity or pseudogene origin. Through in vitro functional screening and in vivo microcosm experiments, we verified that this algorithm identified a high-confidence, searchable sequence motif for functional PETases capable of degrading PET. Metagenomic analysis of 415 ocean samples revealed 23 PETase variants, detected in nearly 80% of the samples. These PETases mainly occur between 1000 and 2000 m deep and at the surface in regions with high plastic pollution. Metatranscriptomic analysis further identified PETase variants that were actively transcribed by marine microorganisms. In contrast to their terrestrial counterparts-where PETases are taxonomically diverse-those in marine ecosystems were predominantly encoded and transcribed by members of the Pseudomonadales order. Our study underscores the widespread distribution of PETase-containing bacteria across carbon-limited marine ecosystems, identifying and distinguishing the PETase motif that underpins the functionality of these specialised cutinases.},
}

@article {pmid40492462,
year = {2025},
author = {Zheng, Z and Liu, X and Zhang, Y and Zhang, H and Chen, S and Zhu, J},
title = {Research trends and hotspots on gut microbiota in rheumatoid arthritis: a bibliometric analysis from 2004 to 2024.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/3899sf},
pmid = {40492462},
issn = {0392-856X},
abstract = {OBJECTIVES: Rheumatoid arthritis (RA) is an autoimmune condition linked to alterations in the gut microbiota. This study aims to conduct a comprehensive analysis of the literature on gut microbiota and RA over the past 21 years through bibliometric methods, thereby identifying emerging trends and hotspots, and providing insights for the precision treatment of RA.

METHODS: The authors analysed articles on gut microbiota in RA published from 2004 to 2024 based on the Web of Science Core Collection database. Bibliometric methods employed tools such as CiteSpace, VOSviewer, and COOC to conduct visual analyses of countries, institutions, references, and keywords.

RESULTS: 1,267 articles from 80 countries led by China and the United States were included. A notable increase in annual publications reflects the growing interest in this field. Simultaneously, contributions and cooperation of institutions in the field are discussed. Furthermore, co-citation and keyword analysis revealed four research hotspots: 1. specific gut microbiota like Prevotella copri modulating immune responses in RA; 2. dietary interventions regulating gut microbiota as therapeutic approaches for RA; 3. high-throughput sequencing technologies enabling microbiome analysis for diagnostic RA; and 4. probiotics and plant-derived bioactive compounds serving as promising adjunctive therapies for RA management.

CONCLUSIONS: The relationship between RA and gut microbiota has been extensively studied. The hotspot of future research may be to further study the pathological mechanism of gut microbiota in RA and how to improve the symptoms of RA patients through dietary therapy and adjustment of the homeostasis of gut microbiota.},
}

@article {pmid40492389,
year = {2025},
author = {Shen, H and Ma, X and Zhang, L and Li, H and Zheng, J and Wu, S and Zuo, K and Yin, Y and Wang, J and Tan, B},
title = {Targeted Intervention Strategies for Maternal-Offspring Transmission of Christensenellaceae in Pigs via a Deep Learning Model.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e03411},
doi = {10.1002/advs.202503411},
pmid = {40492389},
issn = {2198-3844},
support = {2021YFD1300401//National Key R&D Program/ ; U24A20445//National Natural Science Foundation of China/ ; U20A2054//National Natural Science Foundation of China/ ; U22A20510//National Natural Science Foundation of China/ ; 2024JJ1004//Natural Science Foundation of Hunan Province/ ; 2024RC3188//Natural Science Foundation of Hunan Province/ ; },
abstract = {Understanding the mechanisms of maternal microbial transmission is crucial for early gut microbiota development and long-term health outcomes in offspring. However, early maternal microbial interventions remain a challenge due to the complexity of accurately identifying transmitted taxa. Here, the maternal-offspring microbial transmission model (MOMTM), a deep learning framework specifically designed to map maternal microbiota transmission dynamics across pig breeds and developmental stages, is introduced. Using MOMTM, key transmitted taxa, such as the Christensenellaceae R-7 are successfully predicted, which show high transmission centrality during early development periods. Additionally, it is demonstrated that galacto-oligosaccharide intervention in sows promotes a Christensenellaceae R-7-dominated enterotype and improves fiber digestibility in offspring. Further analysis reveals that Christensenellaceae, particularly Christensenella minuta, have enhanced adhesion and mucin utilization capabilities, facilitating its gut colonization. These findings highlight MOMTM's potential as a novel approach for microbiota-targeted health interventions in early life, offering insights into strategies that promote gut health and development from birth.},
}

@article {pmid40492293,
year = {2025},
author = {O'Hare, MA and Rust, C and Malan-Müller, S and Pirovano, W and Lowry, CA and Ramaboli, M and van den Heuvel, LL and Seedat, S and , and Hemmings, SMJ},
title = {Preliminary Insights Into the Relationship Between the Gut Microbiome and Host Genome in Posttraumatic Stress Disorder.},
journal = {Genes, brain, and behavior},
volume = {24},
number = {3},
pages = {e70025},
doi = {10.1111/gbb.70025},
pmid = {40492293},
issn = {1601-183X},
support = {//South African Medical Research Council Genomics of Brain Disorders Unit/ ; //Stellenbosch University Postgraduate Scholarship Programme/ ; 847635//Una4Career/ ; PID2021-126468OA-I00//Knowledge Generation Grant from the Ministry of Science and Innovation (Spain)/ ; PNSD 2022I033//Ministry of Health (Spain) Research Grant/ ; 138430//National Research Foundation of South Africa/ ; //South African Medical Research Council: Self-Initiated Research Grant/ ; 024.004.012//NWO Gravitation: BRAINSCAPES - a roadmap from neurogenetics to neurobiology, grant no./ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Stress Disorders, Post-Traumatic/genetics/microbiology ; Male ; Female ; Adult ; Genome-Wide Association Study ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Polymorphism, Single Nucleotide ; },
abstract = {Posttraumatic stress disorder (PTSD) may develop following trauma exposure; however, not all trauma-exposed individuals develop PTSD, suggesting the presence of susceptibility and resilience factors. The gut microbiome and host genome, which are interconnected, have been implicated in the aetiology of PTSD. However, their interaction has yet to be investigated in a South African population. Using genome-wide genotype data and 16S rRNA (V4) gene amplicon sequencing data from 53 trauma-exposed controls and 74 PTSD cases, we observed no significant association between the host genome and summed abundance of Mitsuokella, Odoribacter, Catenibacterium and Olsenella, previously reported as associated with PTSD status in this cohort. However, PROM2 rs2278067 T-allele was significantly positively associated with the summed relative abundance of these genera, but only in individuals with PTSD and not trauma-exposed controls (p < 0.014). Polygenic risk scores generated using genome-wide association study summary statistics from the PGC-PTSD Overall Freeze 2 were not predictive of gut microbial composition in this cohort. These preliminary results suggest a potential role for the interaction between genetic variation and gut microbial composition in the context of PTSD, underscoring the need for further investigation.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Stress Disorders, Post-Traumatic/genetics/microbiology
Male
Female
Adult
Genome-Wide Association Study
Middle Aged
RNA, Ribosomal, 16S/genetics
Polymorphism, Single Nucleotide

@article {pmid40492114,
year = {2025},
author = {Zhang, Y and Fan, J and Zhao, J and Zhu, H and Xia, Y and Xu, H},
title = {A telomere-associated molecular landscape reveals immunological, microbial, and therapeutic heterogeneity in colorectal cancer.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1615533},
pmid = {40492114},
issn = {2296-889X},
abstract = {BACKGROUND: Colorectal cancer (CRC) ranks among the most prevalent malignancies of the gastrointestinal tract and remains a leading cause of cancer-related mortality worldwide. Although telomere biology has been increasingly implicated in immune modulation and tumor progression, its clinical significance in CRC remains poorly understood.

METHODS: We developed a telomere score, termed TELscore, by integrating transcriptomic and intratumoral microbiome profiles from publicly available colorectal cancer (CRC) cohorts. To comprehensively characterize TELscore subgroups, we performed pathway enrichment analysis, tumor immune microenvironment (TIME) profiling, and microbiome niche assessment. Whole-slide histopathological images (WSIs) and immunohistochemical (IHC) staining were utilized to visualize immune features, including tertiary lymphoid structures (TLSs), across subgroups. Patients were stratified into high and low TELscore categories, and the predictive robustness was validated across multiple independent training and validation cohorts. Chemotherapeutic drug sensitivity was evaluated using pharmacogenomic data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. Furthermore, the predictive capacity of TELscore for immunotherapy response was independently assessed in an external cohort. Finally, single-cell RNA sequencing (scRNA-seq) analysis was conducted to further dissect the cellular landscape and immunological heterogeneity within the TME.

RESULTS: TELscore stratified patients into two biologically and clinically distinct subgroups. The high TELscore group, which exhibited significantly shorter DFS, showed marked enrichment of tumorigenic pathways such as EMT, along with a distinctly immunosuppressive TME. This was reflected by elevated ESTIMATE/TIDE scores and corroborated by CIBERSORT, which revealed increased infiltration of M0 macrophages and upregulation of immunosuppressive signatures. In contrast, the low TELscore group was enriched for cell cycle related pathways, including E2F targets and the G2/M checkpoint, and demonstrated higher infiltration of pro-inflammatory M1 macrophages. 16S rRNA sequencing further revealed a divergent intratumoral microbiome between subgroups, the high TELscore group harbored significantly greater relative abundance of Selenomonas and Lachnoclostridium, two pathogenic genera previously associated with colorectal tumorigenesis. Complementary histopathological assessment via WSI demonstrated a marked absence of intraTLSs in high TELscore tumors. From a therapeutic standpoint, high TELscore tumors exhibited reduced sensitivity to standard chemotherapeutic agents-including Fluorouracil, Irinotecan, Oxaliplatin, and Docetaxel-as reflected by elevated IC50 values. Conversely, these tumors demonstrated increased susceptibility to MAPK pathway inhibitors, such as Selumetinib and Trametinib. Notably, TELscore also served as a robust predictor of immunotherapy response, which was validated in the IMvigor210 cohort. Finally, scRNA analysis highlighted profound cellular and functional divergence between TELscore subgroups. We identified intensified intercellular communication between inflammatory macrophages and fibroblasts, reinforcing the presence of an immunosuppressive niche.

CONCLUSION: TELscore is a robust stratification tool that captures the interplay between tumor biology, immune characteristics, and microbial ecology in colorectal cancer. By identifying clinically relevant subtypes with distinct therapeutic vulnerabilities, TELscore offers a powerful framework to advance personalized treatment and precision oncology.},
}

@article {pmid40492113,
year = {2025},
author = {Nuñez-Selles, AJ and Nuñez-Musa, RA and Guillen-Marmolejos, RA},
title = {Linking oxidative stress biomarkers to disease progression and antioxidant therapy in hypertension and diabetes mellitus.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1611842},
pmid = {40492113},
issn = {2296-889X},
abstract = {Oxidative stress (OS) is increasingly recognized as a key factor linking hypertension (HTN) and diabetes mellitus (DM). This review summarizes recent evidence regarding the dual role of OS as both an instigator and an amplifier of cardiometabolic dysfunction. In HTN, reactive oxygen species (ROS) produced by NADPH oxidases (NOXs) and mitochondrial dysfunction contribute to endothelial impairment and vascular remodeling. In DM, hyperglycemia-induced ROS production worsens beta-cell failure and insulin resistance through pathways such as the AGE-RAGE signaling, protein kinase C (PKC) activation, and the polyol pathway. Clinically validated biomarkers of OS, such as F2-isoprostanes (which indicate lipid peroxidation), 8-OHdG (which indicates DNA damage), and the activities of redox enzymes like superoxide dismutase (SOD) and glutathione peroxidase (GPx), show strong correlations with disease progression and end-organ complications. Despite promising preclinical results, the application of antioxidant therapies in clinical settings has faced challenges due to inconsistent outcomes, highlighting the need for targeted approaches. Emerging strategies include: 1. Mitochondria-targeted antioxidants to enhance vascular function in resistant HTN; 2. Nrf2 activators to restore redox balance in early diabetes; and 3. Specific inhibitors of NOX isoforms. We emphasize three transformative areas of research: (i) the interaction between the microbiome and ROS, where modifying gut microbiota can reduce systemic OS; (ii) the use of nanotechnology to deliver antioxidants directly to pancreatic islets or atherosclerotic plaques; and (iii) phenotype-specific diagnosis and therapy guided by redox biomarkers and genetic profiling (for example, KEAP1/NRF2 polymorphisms). Integrating these advances with lifestyle modifications, such as following a Mediterranean diet and exercising regularly, may provide additional benefits. This review outlines a mechanistic framework for targeting OS in the comorbidity of HTN and DM while identifying critical knowledge gaps, particularly regarding the timing of antioxidant signaling and the development of personalized redox medicine, which may serve as a reference for researchers and clinicians working in this area.},
}

@article {pmid40492077,
year = {2025},
author = {Ahrens, AP and Lynch, K and Hyöty, H and Lloyd, RE and Petrosino, J and Triplett, EW and Agardh, D},
title = {Temporal dynamics of the gut microbiome preceding celiac disease in genetically at-risk children.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.29.25328357},
pmid = {40492077},
abstract = {Longitudinal study of the microbial dysbiosis preceding celiac disease (CD) is needed, particularly in the first several years of life. Within the Environmental Determinants of Diabetes in the Young (TEDDY) multi-national prospective cohort study, a case-cohort study of 306 CD cases (i.e., seroconverting by 48 months of age), with controls matched 2:1 by site, gender, and time of birth, was assessed. Temporal microbiome case-control dynamics were modelled by 16S rRNA analysis of monthly sequential stool samples taken from age three months up to age four (or until the development of CD). Significant differences were identified across time, including key taxa that break down gluten and influence inflammation, all before the development of autoantibodies. Key bacterial associations with environmental factors such as diet were assessed using detailed longitudinal nutrient intake and diary data, along with genetic variants conferring high CD risk.},
}

@article {pmid40491929,
year = {2025},
author = {Hao, J and Jie, Y and Lu, Z and Ye, T and Meng, J and Liu, C and Yan, J and Zheng, Y and Dong, Z and Gu, Z},
title = {Integrated transcriptomic and microbiomic analyses reveal mechanisms of Decapod iridescent virus 1 resistance in Macrobrachium rosenbergii.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1611481},
pmid = {40491929},
issn = {1664-3224},
mesh = {Animals ; *Palaemonidae/virology/microbiology/genetics/immunology ; *Transcriptome ; *Disease Resistance/genetics ; Gene Expression Profiling ; *Gastrointestinal Microbiome ; Hepatopancreas/virology ; },
abstract = {Selective breeding for DIV1-resistant Macrobrachium rosenbergii is an effective strategy to mitigate aquaculture losses; however, the underlying resistance mechanisms remain poorly understood. In this study, approximately 2,300 prawns from 46 families were subjected to a DIV1 challenge test. Based on survival rate, viral load, histopathological observations, and viral gene detection in the transcriptome, one resistant family (R27-1) and one susceptible family (S2-2) were identified. Hepatopancreas transcriptomic (RNA-Seq) and gut microbiome analyses were conducted on samples at 0, 24, and 48 hours post-infection (hpi) from both families. A total of 144, 68, and 1,170 differentially expressed genes (DEGs) were identified at the respective timepoints. Three DEGs-including one corresponding to an uncharacterized lncRNA, an esterase E4-like protein, and a CUB-serine protease-were consistently differentially expressed at all timepoints. Transcriptomic data suggest that Melanogenesis, energy metabolism, and Steroid hormone biosynthesis pathways are associated with DIV1 resistance. Notable DEGs included hemocyanin, cytochrome P450, alkaline phosphatase-like, Friend leukemia integration 1 transcription factor-like, cytochrome P450 9e2-like, interferon regulatory factor 4-like, dual specificity protein phosphatase 10-like, trypsin II-P29-like, and cytochrome c oxidase subunit III. In addition, the potential probiotic Enterococcus casseliflavus (relative abundance: 0.51% vs 0.03%) was more abundant in the resistant family, whereas Lactococcus garvieae (RA: 20.18% vs 70%) was enriched in the susceptible one. These findings highlight the combined contribution of host transcriptomic responses and gut microbial communities to DIV1 resistance. To the best of our knowledge, this is the first study to integrate transcriptomic and microbiomic analyses for investigating DIV1 resistance in M. rosenbergii. These findings provide novel insights into the host-pathogen interaction and offer valuable targets for selective breeding of DIV1-resistant M. rosenbergii in aquaculture.},
}

Animals
*Palaemonidae/virology/microbiology/genetics/immunology
*Transcriptome
*Disease Resistance/genetics
Gene Expression Profiling
*Gastrointestinal Microbiome
Hepatopancreas/virology

@article {pmid40491838,
year = {2025},
author = {Tian, C and Zhang, Z},
title = {Sociobiome signals by high income for increased mobile genetic elements in the gut microbiome of Chinese individuals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1596101},
pmid = {40491838},
issn = {1664-302X},
abstract = {INTRODUCTION: Mobile genetic elements (MGEs) play a crucial role in the dissemination of antibiotic resistance genes (ARGs), posing significant public health concerns. Despite their importance, the impact of socioeconomic factors on MGEs within the human gut microbiome remains poorly understood.

METHODS: We reanalyzed 1,382 publicly available human gut metagenomic datasets from Chinese populations, including 415 individuals from high-income eastern regions and 967 individuals from low- and middle-income western regions. MGEs were identified and categorized into functional groups, and statistical analyses were conducted to assess regional differences and correlations with economic indicators.

RESULTS: A total of 638,097 nonredundant MGEs were identified. Among these, MGEs related to integration/excision had the highest mean abundance, while those involved in stability/transfer/defense had the lowest. The abundance of MGEs was significantly higher in the eastern population compared to the western population. Moreover, MGE abundance was positively correlated with regional GDP per capita and with ARG abundance within individuals.

DISCUSSION: Our findings suggest that socioeconomic development and industrialization are associated with increased MGE abundance in the human gut microbiome, which may in turn facilitate the spread of ARGs. These results highlight a potential unintended consequence of economic advancement on public health through microbiome-mediated antibiotic resistance.},
}

@article {pmid40491716,
year = {2025},
author = {Zhang, Y and Wu, H and Jin, M and Feng, G and Wang, S},
title = {The gut-heart axis: unveiling the roles of gut microbiota in cardiovascular diseases.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1572948},
pmid = {40491716},
issn = {2297-055X},
abstract = {The gut microbiome refers to the collective genomes of the approximately 1,000-1,150 microbial species found in the human gut, called the gut microbiota. Changing the gut microbiota composition has been shown to affect cardiovascular health significantly. Numerous studies have demonstrated the part that gut microbiota and its metabolites play in the development and course of several illnesses, including colon cancer, heart failure, stroke, hypertension, and inflammatory bowel disease. With cardiovascular diseases responsible for more than 31% of all fatalities globally, conditions like hypertension, atherosclerosis, and heart failure are serious global health issues. Developing preventive measures to fight cardiovascular diseases requires understanding how the gut microbiota interacts with the cardiovascular system. Understanding the distinctive gut microbiota linked to cardiovascular diseases has been made possible by microbial sequencing analysis. The gut microbiota and cardiovascular diseases are closely related, and more profound knowledge of this association may result in treatment strategies and broad guidelines for enhancing cardiovascular health through gut microbiome modification. This review summarizes the role of gut microbiota in cardiovascular diseases, highlighting their influence on disease progression and potential therapeutic implications.},
}

@article {pmid40491555,
year = {2025},
author = {Cheng, H and Li, H and Li, Z and Wang, Y and Liu, L and Wang, J and Ma, X and Tan, B},
title = {The role of glycosylated mucins in maintaining intestinal homeostasis and gut health.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {439-446},
pmid = {40491555},
issn = {2405-6383},
abstract = {The intestinal mucus barrier is a crucial component of the host's innate defense system, playing a vital role in regulating intestinal microecology and maintaining intestinal homeostasis. Glycosylated mucins, the core components of this barrier, are essential for preserving its integrity by preventing bacterial degradation. Additionally, mucins significantly contribute to establishing a balanced symbiotic relationship between the host and microbes. These mucins have the potential to mitigate intestinal epithelial damage by capturing and transporting cell debris and pathogenic bacteria. Meanwhile, certain bacteria help maintain the equilibrium and stability of the gut microbiome by degrading glycosylated mucins to utilize the carbohydrate chains, thus affecting the cytokine expression to regulate the synthesis and secretion of specific glycans. Investigating the complex connections between the mucus barrier and mucin glycosylation holds great promise for advancing our understanding of gastrointestinal disease mechanisms, paving the way for innovative prevention and treatment strategies.},
}

@article {pmid40491539,
year = {2025},
author = {Ronchetti, F and Schmitt, T and Keller, A and García-Reina, A and De la Rua, P and Steffan-Dewenter, I and Polidori, C},
title = {The Significance of Genetic Relatedness and Nest Sharing on the Worker-Worker Similarity of Gut Bacterial Microbiome and Cuticular Hydrocarbon Profile in a Sweat Bee.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71519},
pmid = {40491539},
issn = {2045-7758},
abstract = {The cuticular hydrocarbon (CHC) profile and the gut microbiome (GM) are crucial traits which have a significant impact on the life of bees. In honey bees, the CHC profile and the GM interact finely through trophallaxis, such that the characteristics of the GM are partially defined by the chemical recognition among sisters. However, most of the known primitively eusocial bees show simpler social traits, including moderate genetic relatedness among colony members, often due to workers' nest drifting or dispersal, and lack of trophallaxis. Hence, primitively eusocial bees offer a great opportunity to evaluate the respective role of worker-worker genetic relatedness and of the environment in which the adult lives (residency nest) on the interaction between CHC profile and GM. Here, we investigated such relationships in the primitively eusocial digger bee Halictus scabiosae (Halictidae). We found a high rate of nest-drifting by workers, which leads to a consequent highly variable intra-colonial genetic relatedness. Genetically closely related workers, even occupying distant nests, did possess both a more similar microbiome profile and a more similar CHC profile. Additionally, sharing the same nest seemed to account for the similarity of both CHC profile and GM among workers. Interestingly, differences in microbiome profile and in CHC profile were highly and positively correlated across workers, even after controlling for genetic relatedness. The results of our study point towards an impact of genetic relatedness on the GM and the CHC profile, but also suggest that microbiome and CHC profile are partially acquired through adult nest environment, and that microbiome possibly has a role in shaping the cuticular chemistry.},
}

@article {pmid40491474,
year = {2025},
author = {Vuong, N and Alomia, M and Byne, A and Gade, P and Philipson, TR and Alhammad, RI and Skislak, CJ and Alruwaili, I and Alsaab, FM and Zhou, W and Howard, M and Brothers, A and Still, AH and Araujo, RP and Van Hoek, M and Birkaya, B and Espina, V and Hoefer, RA and Liotta, L and Luchini, A},
title = {Lactobacillus rhamnosus-derived extracellular vesicles influence calcium deposition in a model of breast cancer intraductal calcium stress.},
journal = {iScience},
volume = {28},
number = {6},
pages = {112538},
pmid = {40491474},
issn = {2589-0042},
abstract = {Extracellular calcium export by the breast ductal epithelium is crucial during lactation and plays a significant role in breast cancer progression. Intraductal calcium deposition is a hallmark of aggressive premalignant lesions. This study tested the hypothesis that microbiome-derived extracellular vesicles (EVs) influence calcium modulation in premalignant breast cancer lesions. Based on the analysis of plasma, serum, saliva, and tissue collected from breast cancer patients and controls (N = 150), Lactobacillus rhamnosus (Lr) was chosen as the model microbiota. In a BT-474 human breast cancer cell line monolayer culture under acute calcium stress, Lr EVs enhanced intracellular calcium intake. In a BT474 3D spheroid model under chronic calcium stress, Lr EVs increased extracellular calcium deposition and mRNA expression of calcium export channel plasma membrane calcium-transporting ATPase 2 (PMCA2) and stromal interaction molecule 1 (STIM1) in a dose-dependent manner. We propose that Lr EVs influence calcium regulation and mineral deposition, thereby affecting premalignant breast cancer progression.},
}

@article {pmid40491460,
year = {2025},
author = {Manning, SK and Taylor, SL and Leong, LEX and Papanicolas, LE and Canoy, I and Morgan, LC and Rogers, GB},
title = {Direct assessment of airway microbiota in primary ciliary dyskinesia end-stage lung disease.},
journal = {ERJ open research},
volume = {11},
number = {3},
pages = {},
pmid = {40491460},
issn = {2312-0541},
abstract = {Microbiome assessment of sputum and lung tissue in primary ciliary dyskinesia identified rapid replacement by a single P. aeruginosa clone during end-stage lung disease https://bit.ly/4eV5s0H.},
}

@article {pmid40491436,
year = {2025},
author = {Li, D and Zhang, DY and Chen, SJ and Lv, YT and Huang, SM and Chen, C and Zeng, F and Chen, RX and Zhang, XD and Xiong, JX and Chen, FD and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Zhu, XL and Zhang, LJ and Bai, FH},
title = {Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1565887},
pmid = {40491436},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; *Fungi/classification/genetics/isolation & purification ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Feces/microbiology ; SARS-CoV-2 ; *Mycobiome ; Probiotics ; Metagenomics ; China ; },
abstract = {OBJECTIVE: COVID-19 has had a profound impact on public health globally. However, most studies have focused on patients with long COVID or those in the acute phase of infection, with limited research on the health of individuals who have recovered from mild COVID-19. This study investigates the long-term changes in bacterial and fungal communities in individuals recovering from mild COVID-19 and their clinical relevance.

METHODS: Healthy individuals from Hainan Province were enrolled before the COVID-19 outbreak, along with individuals recovering from COVID-19 at 3 months and 6 months post-recovery. Stool, blood samples, and metadata were collected. Metagenomic sequencing and Internal Transcribed Spacer (ITS) analysis characterized bacterial and fungal communities, while bacterial-fungal co-occurrence networks were constructed. A random forest model evaluated the predictive capacity of key taxa.

RESULTS: The gut microbiota of COVID-19 recoverees differed significantly from that of healthy individuals. At 3 months post-recovery, probiotics (e.g., Blautia massiliensis and Kluyveromyces spp.) were enriched, linked to improved metabolism, while at 6 months, partial recovery of probiotics (e.g., Acidaminococcus massiliensis and Asterotremella spp.) was observed alongside persistent pathogens (e.g., Streptococcus equinus and Gibberella spp.). Dynamic changes were observed, with Acidaminococcus massiliensis enriched at both baseline and 6 months but absent at 3 months. Co-occurrence network analysis revealed synergies between bacterial (Rothia spp.) and fungal (Coprinopsis spp.) taxa, suggesting their potential roles in gut restoration. The bacterial random forest model (10 taxa) outperformed the fungal model (8 taxa) in predicting recovery status (AUC = 0.99 vs. 0.80).

CONCLUSION: These findings highlight the significant long-term impacts of mild COVID-19 recovery on gut microbiota, with key taxa influencing metabolism and immune regulation, supporting microbiome-based strategies for recovery management.},
}

Humans
*COVID-19/microbiology
*Gastrointestinal Microbiome
*Fungi/classification/genetics/isolation & purification
Female
*Bacteria/classification/genetics/isolation & purification
Male
Adult
Middle Aged
Feces/microbiology
SARS-CoV-2
*Mycobiome
Probiotics
Metagenomics
China

@article {pmid40491434,
year = {2025},
author = {Liu, L and Guo, L and Dai, J and Cai, X and Wu, B},
title = {Fecal 16S rRNA sequencing and metabolomics reveal abnormal metabolism activity in preterm infants with different gestational ages.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1530653},
pmid = {40491434},
issn = {2235-2988},
mesh = {Humans ; *Infant, Premature/metabolism ; *Feces/microbiology ; *Gestational Age ; *RNA, Ribosomal, 16S/genetics ; Infant, Newborn ; *Metabolomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Metabolome ; Metabolic Networks and Pathways ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; },
abstract = {OBJECTIVE: This study aims to conduct a comprehensive analysis of the differences in gut microbiota and metabolomics in preterm infants stratified by gestational age.

METHODS: Fresh fecal samples were collected from neonates within the first 3 days after birth. The gut microbiota composition and the changes in specific taxa abundance were analyzed using 16S rRNA sequencing. Metabolomic profiling was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Participants were categorized into four groups based on gestational age at birth: PreA group (34-36 weeks), PreB group (32-33 weeks), PreC group (28-31 weeks), and control group (37-42 weeks). Metabolic pathways were identified through metabolomics analysis, referencing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

RESULTS: Notably, Principal Coordinates Analysis (PCoA) showed clear separation among samples from all groups, with significant differences noted in the PreC group when compared with the other three. We found a strong association between Escherichia-Shigella and Ureaplasma genera with infants born before 32 weeks of gestation, suggesting a higher risk of opportunistic infections for preterm infants under this gestational threshold. As gestational age increases, Megamonas and Prevotella gradually emerged, while Escherichia-Shigella and Ureaplasma progressively diminished. KEGG enrichment analysis indicated that Pyrimidine metabolism was a differentially regulated pathway between the PreA group and the control group. Interestingly, the only major differential metabolic pathway between the PreB group and the control group was Arachidonic acid metabolism. The bubble diagram revealed significant enrichment of differential metabolites in Pyrimidine and beta-Alanine metabolism pathways when comparing the PreC group with the control group.

CONCLUSION: Significant differences were observed in the fecal microbiome and metabolome between preterm and full-term infants, particularly in those born before 32 weeks of gestation. These findings suggested that the gut microbial system in preterm infants undergone progressive maturation, approaching a "healthy" state characteristic of full-term infants as gestational age increases.},
}

Humans
*Infant, Premature/metabolism
*Feces/microbiology
*Gestational Age
*RNA, Ribosomal, 16S/genetics
Infant, Newborn
*Metabolomics/methods
*Gastrointestinal Microbiome/genetics
Female
Male
*Bacteria/classification/genetics/isolation & purification/metabolism
Chromatography, Liquid
Tandem Mass Spectrometry
Metabolome
Metabolic Networks and Pathways
Sequence Analysis, DNA
DNA, Bacterial/genetics/chemistry

@article {pmid40491237,
year = {2025},
author = {Rosas, HD and Morgan, XC and Tao, Y and Lai, F and Mercaldo, ND},
title = {Gut dysbiosis in Down syndrome: A potentially unexplored culprit for early Alzheimer's disease.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {6},
pages = {e70330},
doi = {10.1002/alz.70330},
pmid = {40491237},
issn = {1552-5279},
support = {//Libbi Thomas Foundation/ ; /NH/NIH HHS/United States ; /AG/NIA NIH HHS/United States ; U01 AG051406/AG/NIA NIH HHS/United States ; U01 AG051412/AG/NIA NIH HHS/United States ; U19 AG068054/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Down Syndrome/microbiology/complications ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; *Alzheimer Disease/microbiology/etiology ; Male ; Female ; *Cognitive Dysfunction/microbiology ; Middle Aged ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Adult ; },
abstract = {INTRODUCTION: Gut dysbiosis has been found to play a role in sporadic Alzheimer's disease (AD) but has not been explored in Down syndrome (DS), despite the strong relationship between DS and early AD. Here, we compared the gut microbiomes of 20 adults with DS, either cognitively stable or with mild cognitive impairment.

METHODS: DNA from stool samples was profiled using 16S rRNA sequencing.

RESULTS: Cognitive status was associated with a significant difference in overall microbiome composition (p < 0.01) and with significant differences in the abundance of Bacteroidaceae, Enterobacteriaceae, and Christensenellaceae.

CONCLUSION: Just as in sporadic AD, AD in DS is associated with gut dysbiosis. Our work suggests that this is an important area for future investigation, one that may provide a novel and important target for therapeutic intervention.

HIGHLIGHTS: Alterations in the gut microbiome are present in adults with Down syndrome (DS) with mild cognitive impairment (MCI). Increased taxa in DS-MCI that contribute to inflammation and disrupt blood-brain barrier. Suggests a possible role of gut dysbiosis in Alzheimer's disease in adults with DS.},
}

Humans
*Down Syndrome/microbiology/complications
*Dysbiosis/microbiology/complications
*Gastrointestinal Microbiome/genetics
*Alzheimer Disease/microbiology/etiology
Male
Female
*Cognitive Dysfunction/microbiology
Middle Aged
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Aged
Adult

@article {pmid40491066,
year = {2025},
author = {Elisia, I and Yeung, M and Kowalski, S and Wong, A and Dietrich, C and Chang, V and Wu, S and Hollman, S and Dyer, R and Nguyen, KN and Krystal, G},
title = {Low Carbohydrate Diet Containing Soy Protein and Fish Oil Reduces AOM/DSS-Induced Colon Cancer, in Part, by an Acetate-Mediated Reduction in TH17 Cell Differentiation.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70113},
doi = {10.1002/mnfr.70113},
pmid = {40491066},
issn = {1613-4133},
abstract = {Since our previous studies found a low-carbohydrate (CHO) diet containing soy protein and fish oil (i.e., 15%Amylose/Soy/FO) significantly reduced tobacco carcinogen-induced lung nodules in A/J mice, breast tumors in C3(1)/Tag mice, and myelomalignancy in miR-146a knockout mice, we asked herein if this CHO diet could also reduce colorectal cancer. We tested the efficacy of the 15%Amylose/Soy/FO diet in preventing colitis-induced colorectal cancer using an azoxymethane/dextran sodium sulfate BALB/c mouse model. The 15%Amylose/Soy/FO diet significantly reduced colon tumor numbers compared to a Western diet and this was associated with a reduction in blood glucose, and a trend towards an increase in plasma β-hydroxybutyrate and an increase in liver fatty acid synthase, suggesting a systemic metabolic shift from glucose to fatty acids as an energy source. In addition, our CHO diet reduced proinflammatory cytokines, induced a marked change in the fecal microbiome, an increase in cecal and fecal acetate, and a reduction in interleukin-17A expressing cells in the colonic tumors of mice on the 15%Amylose/Soy/FO diet. Taken together, our results suggest the 15%Amylose/Soy/FO diet ameliorates colitis and prevents the subsequent development of colorectal cancer, in part by an acetate-mediated reduction in TH17 cell development.},
}

@article {pmid40490836,
year = {2025},
author = {Zhang, L and Fei, Z and Ding, Y and Zhang, Y and Ding, Z and Huang, Y and Wang, J and Liu, G and Bai, L and Wu, J},
title = {Inonotus obliquus fermentation product improves growth performance and meat quality probably through intestine and antioxidant capacity enhanced by gut microbes and metabolites regulation in rabbits.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {61},
pmid = {40490836},
issn = {2524-4671},
support = {SDAIT-21-12//Shandong Province Modern Agricultural Industry Technology System/ ; 2023YFD1800301//National Key R&D Program of China/ ; ts201511069//Distinguished Talent Projects/ ; },
abstract = {BACKGROUND: Inonotus obliquus is a medicinal edible fungus that contains a variety of biologically active ingredients and has multiple physiological effects. When supplemented in avian diet, Inonotus obliquus has proved to be beneficial. However, information regarding these effects on mammals is scanty. The present study aims to investigate the effect of supplementation of Inonotus obliquus fermentation product (IOFP) on the growth performance, antioxidant capacity, meat quality, intestinal function and gut microbiota of rabbit exploratorily, which may act as an important feed additive and also as an antibiotic alternative with its medicinal properties.

RESULTS: Dietary supplementation of IOFP increased body weight (P < 0.01) at the initial 21 d and improved feed efficiency throughout the 35 d experimental period when compared to control group. At the same time it was observed that meat quality and carcass parameters improved upon supplementation of IOFP. Additionally, IOFP supplementation resulted in significant increases (P < 0.05) in total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and nitric oxide (NO) activity or concentration in the serum and muscle. The crypt depth decreased significantly, whereas the villus height/crypt depth (V/C) value increased (P < 0.05). The concentration of secrete IgA (sIgA) of the intestine also increased (P < 0.05). IOFP supplementation significantly increased the fold change expression of Claudin 1, Occludin, ZO1, and ZO2 (P < 0.05) when compared to the respective gene expression levels of the duodenum and jejunum tissues of control group. Further study on cecum microbiota revealed that IOFP supplementation increased the microbiota diversity by increasing the number of beneficial bacteria and reducing the numbers of pathological bacteria. It was observed that cecum metabolites produced in the treated group were related to antioxidants, antiinflammation and antidepressive effects. The harmful metabolites related to fat deposition, loss of appetite and cytotoxic conditions decreased. Pearson's correlation studies between different bacteria and metabolites revealed that the metabolites produced were regulated by the beneficial and harmful bacteria respectively.

CONCLUSIONS: IOFP enhanced intestinal morphology and function, and organismic antioxidant capacity, probably by increasing the concentration of beneficial microbiota and metabolites resulting in improvement of body weight, feed efficiency, and parameters related to meat quality and carcass traits of rabbits.},
}

@article {pmid40490712,
year = {2025},
author = {Wang, W and Liu, M and Wang, Z and Ma, L and Zhao, Y and Ye, W and Li, X},
title = {Causal associations between gut microbiota, metabolites, and idiopathic normal pressure hydrocephalus: a two‑sample Mendelian randomization study.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {249},
pmid = {40490712},
issn = {1471-2377},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Mendelian Randomization Analysis/methods ; *Hydrocephalus, Normal Pressure/genetics/microbiology/metabolism ; Genome-Wide Association Study ; Aged ; Male ; Female ; },
abstract = {BACKGROUND: Implying connections with gut microbiome and serum metabolites, idiopathic normal pressure hydrocephalus (INPH) emerges as a prevalent neuropsychiatric condition in the elderly. Our objective was to systematically evaluate the potential causality between gut microbiome, derived metabolites, and INPH through the implementation of Mendelian randomization (MR) methodology.

METHODS: We utilized summary data from extensive genome-wide association studies, encompassing 196 gut microbiomes from the MiBioGen consortium (n = 18,340), 486 serum metabolites from the KORA and TwinsUK studies (n = 7,824), and individuals with INPH (case = 767, control = 375,610), for MR causal estimates. The leading analysis utilized the inverse-variance weighted (IVW) method, supplemented by weighted mode, MR-Egger, weighted median and simple mode approaches. Sensitivity analyses included MR-Egger intercept, Cochran's Q test, leave-one-out analysis and MR-PRESSO.

RESULTS: Our study primarily relied on the IVW method, confirming a causality between 9 genetically predicted abundance of gut microbiomes and INPH. We found an adverse correlation with genetically predicted abundance of order Clostridiales, genus Eubacteriumeligensgroup, genus Gordonibacter, genus Ruminococcus1 concerning INPH. Conversely, class Melainabacteria, genus Eubacteriumruminantiumgroup, genus Adlercreutzia, genus Dialister, genus RikenellaceaeRC9gutgroup potentially correlated with increased INPH risk. As for derived metabolites, IVW estimates indicated a causal connection between 25 genetically predicted serum metabolites and INPH. Sensitivity analysis underscored the robustness of our findings.

CONCLUSION: Our MR analysis provides evidence supporting the causality of certain gut microbial taxa and their derived metabolites on INPH. This underscores the potential for interventions targeting specific gut microbiota and derived metabolites in the treatment and prevention of INPH.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Mendelian Randomization Analysis/methods
*Hydrocephalus, Normal Pressure/genetics/microbiology/metabolism
Genome-Wide Association Study
Aged
Male
Female

@article {pmid40490500,
year = {2025},
author = {Robinson, CM and Carreño, D and Weber, T and Chen, Y and Riglar, DT},
title = {A discovery platform for identification of host-induced bacterial biosensors from diverse sources.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40490500},
issn = {1744-4292},
support = {211230/Z/18/Z//Wellcome Trust (WT)/ ; President's PhD Scholarship//Imperial College London (ICL)/ ; },
abstract = {Synthetic biology approaches such as whole-cell biosensing and 'sense-and-respond' therapeutics aim to enlist the vast sensing repertoire of gut microbes to drive cutting-edge clinical and research applications. However, well-characterised circuit components that sense health- and disease-relevant conditions within the gut remain limited. Here, we extend the flexibility and power of a biosensor screening platform using bacterial memory circuits. We construct libraries of sensory components sourced from diverse gut bacteria using a bespoke two-component system identification and cloning pipeline. Tagging unique strains using a hypervariable DNA barcode enables parallel tracking of thousands of unique clones, corresponding to ~150 putative biosensors, in a single experiment. Evaluating sensor activity and performance heterogeneity across various in vitro and in vivo conditions using mouse models, we identify several biosensors of interest. Validated hits include biosensors with relevance for autonomous control of synthetic functions within the mammalian gut and for non-invasive monitoring of inflammatory disease using faecal sampling. This approach will promote rapid biosensor engineering to advance the development of synthetic biology tools for deployment within complex environments.},
}

@article {pmid40490486,
year = {2025},
author = {Hendricks, H and Israel, S and Weitkamp, JH and Pakala, S and Rajagopala, S and Banerjee, R},
title = {Associations between antibiotic exposure intensity, intestinal microbiome perturbations, and outcomes in premature neonates with bacteremia.},
journal = {Journal of perinatology : official journal of the California Perinatal Association},
volume = {},
number = {},
pages = {},
pmid = {40490486},
issn = {1476-5543},
support = {5UL1TR002243-03//Vanderbilt Institute for Clinical and Translational Research (VICTR)/ ; },
abstract = {BACKGROUND: Neonatal microbiome dysbiosis is associated with infectious complications.

METHODS: Prospective weekly stools were collected over 1 year from hospitalized preterm infants with birthweight ≤2000 g and postnatal age (PNA) ≤2 months. Neonates with bacteremia (cases) were matched to uninfected controls. Stools were analyzed using whole metagenome sequencing. Intensity of antibiotic exposure was compared using an Antibiotic Spectrum Index (ASI).

RESULTS: We analyzed 398 stools from 40 cases and 39 controls. Cases had lower α diversity beyond 4 weeks PNA. Cases with subsequent infections after index bacteremia had persistently lower α diversity, while cases without subsequent infections demonstrated recovery of microbiome diversity. Compared to controls, cases had greater ASI at multiple timepoints, higher Enterococcus spp. and lower anaerobe abundance.

CONCLUSIONS: Compared to controls, premature neonates with bacteremia had intestinal microbiomes with lower α diversity, higher Enterococcus spp. and lower anaerobe abundance. These changes were associated with recurrent infectious complications.},
}

@article {pmid40490465,
year = {2025},
author = {Yong, SB and Ha, M and Cho, S},
title = {Microbiome Metabolite-Incorporated Lipid Nanoparticles Augment CD8[+] T Cell Memory Potential and Immunity for mRNA Cancer Vaccines.},
journal = {ACS biomaterials science & engineering},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsbiomaterials.5c00738},
pmid = {40490465},
issn = {2373-9878},
abstract = {Recently, mRNA/lipid nanoparticle (LNP)-based vaccines have been successfully applied to prevent infectious diseases, and several types of neoantigen-encoding mRNA cancer vaccines are currently under clinical trials. While mRNA vaccines effectively induce adaptive immune responses to antigens, mRNA vaccine-induced immunity is shortly maintained, and the longevity of the immune memory, especially improving the CD8[+] T cell memory potential, could be even more important. Previously, microbiome metabolites have shown T cell memory potential-augmenting effects via regulating the immunometabolism. Herein, we develop microbiome metabolite-incorporated LNPs (mmi-LNPs) and evaluate their potential to enhance T cell memory responses following mRNA vaccination. In various ionizable LNP formulations, mmi-LNPs elicited more stem cell-like memory T cells (T-SCMs) and augmented central and effector memory T cell responses, which indicates the general applicability of mmi-LNPs. Notably, butyrate-incorporated mmi-LNP exhibited the strongest effects. In conclusion, we suggest microbiome metabolite-incorporated LNP as a next-generation delivery vehicle for mRNA vaccines.},
}

@article {pmid40490101,
year = {2025},
author = {Lev-Tov, H and Balukoff, NC and Gonzalez, T and Chopra, D and Yaghi, M and Amornpairoj, W and Strbo, N and Tomic-Canic, M and Pastar, I},
title = {Minimally Invasive Procedure for Hidradenitis Suppurativa Using Antimicrobial Wound Gel Resolves Tunnels, Reverses Microbial Dysbiosis, Decreases Inflammation, and Improves Quality of Life: Prospective, Single-Center, Single-Arm Trial.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2025.06.008},
pmid = {40490101},
issn = {1097-6787},
}

@article {pmid40490097,
year = {2025},
author = {Ortiz, AM and Casta, FC and Bodykevich, EG and Flynn, JK and Fennessey, CM and Brooks, K and Ruiz, D and Yee, DS and Simpson, J and Rahmberg, AR and Keele, BF and Brenchley, JM},
title = {Repeated enema administration in rhesus macaques is not sufficient to promote bacterial dysbiosis or gastrointestinal dysfunction.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.06.002},
pmid = {40490097},
issn = {1935-3456},
abstract = {Chronic gastrointestinal diseases are a significant global health burden that can require the use of gastrointestinal-cleansing regimens for diagnostics or therapeutic treatment. These regimens are beneficial for facilitating surgical preparation, drug delivery, colorectal cancer screenings, and personal use is common among proponents of natural health and among certain populations at high risk of HIV acquisition. It remains unclear, however, whether repeated clearance of the colonic microbiome induces persistent changes in the microbiome, intestinal immunity, and viral disease susceptibility. We addressed these parameters by repeatedly administering iso-osmolar enemas to rhesus macaques prior to low-dose intra-rectal challenge with simian immunodeficiency virus (SIV). Considering both longitudinal and cross-sectional analyses, we observed no consistent changes in the fecal microbiome or intestinal immune parameters of treated animals, nor were significant differences observed in susceptibility to SIV acquisition. Unexpectedly, enema-treated animals exhibited significantly lower setpoint viral loads after infection, although we were unable to clearly identify attributing causes. Our study demonstrates that repeated microbiome clearance using clinically administered iso-osmolar enemas is not sufficient to restructure the fecal microbiome, perturb intestinal immune parameters, or increase susceptibility to mucosal SIV challenge. This research framework serves as a model for the development of colonic-administered diagnostics and interventions.},
}

@article {pmid40489796,
year = {2025},
author = {Andersen, S and Kennedy, GA and Banks, M and Flanagan, BM and Henden, AS},
title = {Prebiotic fibre enteral supplementation post allogeneic transplantation; feasibility and impact on the microbiome.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024015703},
pmid = {40489796},
issn = {2473-9537},
abstract = {The decline in diversity of the gastrointestinal microbiome during haematopoietic stem cell transplantation (HSCT) is associated with poorer clinical outcomes. While provision of enteral nutrition (EN) is common during HSCT, provision of a prebiotic fibre containing formula has not been explored. This pilot study compared tolerance, clinical, microbiome and metabolomic outcomes between patients who received standard EN (n= 10) versus prebiotic fibre EN (n=20) post allogeneic HSCT. Stool samples were collected at baseline and at peri-engraftment and were analysed with shotgun metagenomic sequencing. Provision of prebiotic EN increased daily fibre intake post-transplant to an average 22g per day compared with 4g per day in the standard care group. High tolerance of both EN formulas was observed with only 20% (n=2) of the standard and 15% of the prebiotic group (n=3) requiring parenteral nutrition (p=1.0). There was no difference in the amount of EN provided, EN duration or clinical outcomes. Microbial diversity declined in both groups with no difference post EN provision (p=0.93), however, there was a significant difference in relative abundance of lactobacillus_C rhamnosus with an increase in the prebiotic group only (p=0.022). The relative abundance of faecalicatena gnavus increased in the standard group and declined in the prebiotic group (p=0.0027). Functional analysis of the microbial genome showed decreased expression of antibiotic resistance genes in the prebiotic group only post EN provision (p = 0.00035). A longer fibre intervention should be trialled to optimise clinical outcomes and a more diverse microbiome. The trial was registered at www.anzctr.org.au as ACTRN12621000832875.},
}

@article {pmid40489582,
year = {2025},
author = {Zhou, X and Zheng, W and Kong, W and Zhang, J and Liao, Y and Min, J and Zeng, T},
title = {Glucose Parameters, Inflammation Markers, and Gut Microbiota Changes of Gut Microbiome-Targeted Therapies in Type 2 Diabetes Mellitus: a Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1210/clinem/dgaf340},
pmid = {40489582},
issn = {1945-7197},
abstract = {PURPOSE: This meta-analysis aims to summarize the effects of gut microbiome-targeted therapies (MTTs) on glucometabolic, inflammatory factors and gut microbiota in patients with type 2 diabetes mellitus (T2DM).

METHODS: 4 databases were searched for randomized controlled trials (RCTs) that included subjects with T2DM who received MTTs. All results were presented as standardized mean difference (SMD)/MD and 95% confidence intervals (95% CIs). In addition, subgroup analyses were performed according to region, type of MTTs, number of probiotic strains, probiotics dose, prebiotics dose, duration of MTTs, mean age, and baseline body mass index.

RESULTS: Fifty-four RCTs were included, encompassing 60 groups and 3,390 subjects. Overall, MTTs intervention decreased fasting plasma glucose (MD = -7.97 mg/dL, 95%CI =-10.82, -5.12; p ＜0.00001), 2h-postprandial blood glucose (MD = -43.30 mg/dL, 95%CI = -75.83, -10.77; p = 0.009), fasting insulin (MD = -1.73uU/ml, 95%CI = -2.63, -0.84; p = 0.0001), HbA1c (MD = -0.28%, 95%CI = -0.39, -0.17; p ＜0.00001), and Homeostatic Model Assessment of Insulin Resistance (MD =-0.53, 95%CI = -0.85, -0.20; P=0.0002). Furthermore, MTTs supplementation reduced high-sensitivity C-reactive protein, tumor necrosis factor alpha, and lipopolysaccharides. Meanwhile, the levels of Interleukin-10 were increased. Moreover, the abundance of Actinobacteria, Lactobacillus, and Lactobacillus casei subgroup increased.

CONCLUSION: MTTs modestly improved glucometabolic parameters, reduced pro-inflammatory cytokines, and enriched beneficial microbes (e.g., Actinobacteria, Lactobacillus) in T2DM. However, heterogeneity and limited long-term data highlight the need for large-scale RCTs.},
}

@article {pmid40489496,
year = {2025},
author = {Boddu, SS and Martini, KM and Nemenman, I and Vega, NM},
title = {Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics.},
journal = {PLoS computational biology},
volume = {21},
number = {6},
pages = {e1013110},
doi = {10.1371/journal.pcbi.1013110},
pmid = {40489496},
issn = {1553-7358},
abstract = {Variation in bacterial composition inside a host is a result of complex dynamics of microbial community assembly, but little is known about these dynamics. To deconstruct the factors that contribute to this variation, we used a combination of experimental and modeling approaches. We found that demographic stochasticity and stationary heterogeneity in the host carrying capacity or bacterial growth rate are insufficient to explain quantitatively the variation observed in our empirical data. Instead, we found that the data can be understood if the host-bacteria system can be viewed as stochastically switching between high and low growth rates phenotypes. This suggests the dynamics significantly more complex than logistic growth used in canonical models of microbiome assembly. We develop mathematical models of this process that can explain various aspects of our data. We highlight the limitations of snapshot data in describing variation in host-associated communities and the importance of using time-series data along with mathematical models to understand microbial dynamics within a host.},
}

@article {pmid40489211,
year = {2025},
author = {Gautam, P and Yadav, R and Vishwakarma, RK and Shekhar, S and Pathak, A and Singh, C},
title = {An Integrative Analysis of Metagenomic and Metabolomic Profiling Reveals Gut Microbiome Dysbiosis and Metabolic Alterations in ALS: Potential Biomarkers and Therapeutic Insights.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00254},
pmid = {40489211},
issn = {1948-7193},
abstract = {ALS is a severe neurodegenerative disorder characterized by motor neuron degeneration, gut dysbiosis, immune dysregulation, and metabolic disturbances. In this study, shotgun metagenomics and [1]H nuclear magnetic resonance (NMR)-based metabolomics were employed to investigate the altered gut microbiome and metabolite profiles in individuals with ALS, household controls (HCs), and nonhousehold controls (NHCs). The principal component analysis (PCA) explained 33% of the variance, and the partial least-squares discriminant analysis (PLS-DA) model demonstrate R[2] and Q[2] values of 0.97 and 0.84, respectively, indicating an adequate model fit. The relative bacterial abundance was 99.34% in the ALS group and 98.94% in the HC group. Among the ten identified genera, Bifidobacterium, Lactobacillus, and Enterococcus were more prevalent in ALS individuals, while Lactiplantibacillus and Klebsiella were more abundant in the HC group. We identified 70 metabolites, including short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), carbohydrates, and aromatic compounds, using NMR. Orthogonal partial least-squares discriminant analysis (O-PLS-DA) explained 15.8% of the variance, with a clear separation between the ALS and HC groups. Univariate receiver operating characteristic (ROC) analysis identified three fecal metabolites with AUC values above 0.70, including butyrate (0.798), propionate (0.727), and citrate (0.719). These metabolites may serve as potential biomarkers for ALS. The statistical model for metabolic pathway analysis revealed interconnected pathways, highlighting the complexity of metabolic dysregulation, as well as potential microbial and metabolic biomarkers in ALS. These results highlight the role of gut microbiome alterations in ALS and suggest potential avenues for therapeutic intervention.},
}

@article {pmid40488951,
year = {2025},
author = {Liu, Y and Huang, G and Wei, F and Hu, Y},
title = {Non-negligible role of gut morphology in shaping mammalian gut microbiomes.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40488951},
issn = {1869-1889},
abstract = {Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome, the gut morphology is seldom independently considered and even often ignored. To address this research gap, we investigated a large-scale dataset of mammalian gut microbiomes, comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders. We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories (foregut/hindgut/simple, foregut/hindgut, functional ruminant/ruminant-like, and colon fermenter/cecum fermenter) and uncovered the synergistic effect between phylogeny and gut morphology. Moreover, we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches, as well as those within the same taxonomic order but with different gut morphologies. We also identified three enterotype indices-Fusobacterium, UCG-005, and Prevotella-which could predict the three gut morphology types of mammals: simple, foregut, and hindgut. These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.},
}

@article {pmid40488937,
year = {2025},
author = {Paul, C and Roy, T and Roy, M and Rajeev, AC and Pan, A and Maitra, M and Das, N},
title = {Genome wide analysis of Priestia aryabhattai_OP, an endobacterium, modulating growth, development and biochemical compositions of sporophores in edible oyster mushroom Pleurotus ostreatus (MTCC 1802).},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {6},
pages = {194},
pmid = {40488937},
issn = {1573-0972},
support = {G.O. No. 52-Edn (B)/5B-15/2017//by Higher Education Department, Govt. of West Bengal, India as fellowship/ ; BT/INF/22/SP41296/2020//Department of Biotechnology (DBT), Govt. of India as DBT Builder Grant/ ; },
mesh = {*Pleurotus/growth & development/metabolism ; *Genome, Bacterial ; Phylogeny ; Laccase/metabolism/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Siderophores/metabolism ; Whole Genome Sequencing ; Fruiting Bodies, Fungal/growth & development ; },
abstract = {The increasing global interest in the consuming and producing of edible oyster mushrooms (Pleurotus spp.) is driven by their well-documented nutritional and health benefits. The metagenomic analysis of fruiting body revealed a distinct microbial composition in P. ostreatus, predominantly comprising Pseudomonodota (~ 82%) and Bacillota (~ 10%). An endobacterium Priestia aryabhattai_OP, associated with internal tissue of P. ostreatus (MTCC 1802), was isolated and characterized through biochemical and microscopic analyses as well as 16 S rRNA and whole genome sequencing. Co-cultivation of P. ostreatus with this bacterium significantly enhanced the in vitro production of laccase, a key growth-promoting enzyme. Additionally, the endobacterium improved the biological efficiency (BE) of the mushroom, enriched its nutraceutical profile, and facilitated the biosynthesis of beneficial compounds, including IAA, siderophores, and antimicrobials like lassopeptides, phosphonates, non-ribosomal iron-binding siderophores (NI- siderophore), carotenoids, paeninodins, synechobactins, and surfactins. The present findings offer novel insights into microbe-microbe interactions and their pivotal roles in fungal biology, with significant implications for sustainable mushroom production as well as nutrient enrichment and biotechnological advancements.},
}

*Pleurotus/growth & development/metabolism
*Genome, Bacterial
Phylogeny
Laccase/metabolism/biosynthesis
RNA, Ribosomal, 16S/genetics
Metagenomics
Siderophores/metabolism
Whole Genome Sequencing
Fruiting Bodies, Fungal/growth & development

@article {pmid40488826,
year = {2025},
author = {Lee, CJ and Carpenter, PA},
title = {Modern-Era Challenges in the Clinical Management of Graft-Versus-Host Disease.},
journal = {Advances in experimental medicine and biology},
volume = {1475},
number = {},
pages = {103-128},
pmid = {40488826},
issn = {0065-2598},
mesh = {*Graft vs Host Disease/therapy/diagnosis/immunology/etiology ; Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Animals ; Disease Management ; },
abstract = {For several decades, graft-versus-host disease (GVHD) has been a long-standing barrier to successful allogenic hematopoietic cell transplantation and a significant cause of post-transplant morbidity and mortality. Initially described as secondary disease or wasting syndrome in transplanted mice, the pathobiology of GVHD is increasingly understood as a dynamic interplay between innate and adaptive immunity in response to initial tissue damage, leading to inflammation and end-organ damage. In parallel, more uniform symptom capture, diagnosis, and response criteria have facilitated rigorous clinical trial design and conduct; together, these advancements have facilitated the development of novel GVHD prevention and treatment strategies. While these advancements have improved the GVHD treatment paradigm, new questions arise within this complex patient population. This chapter discusses several of the most pertinent current clinical practice challenges in GVHD, including its earlier diagnosis, risk stratification, initial and more advanced stage management, as well as a renewed focus on supportive care, given our increased understanding of key roles played by the human microbiome.},
}

*Graft vs Host Disease/therapy/diagnosis/immunology/etiology
Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
Animals
Disease Management

@article {pmid40488812,
year = {2025},
author = {Bajaj, P and Sharma, M},
title = {Chrononutrition and Gut Health: Exploring the Relationship Between Meal Timing and the Gut Microbiome.},
journal = {Current nutrition reports},
volume = {14},
number = {1},
pages = {79},
pmid = {40488812},
issn = {2161-3311},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Meals/physiology ; *Feeding Behavior/physiology ; Lipid Metabolism ; },
abstract = {PURPOSE OF REVIEW: This review explores the relationship between circadian rhythms and meal timing, or chrononutrition, and how it affects gut health. Since the gut microbiota plays a critical role in immunological response, metabolic control, and digestion, it is critical to comprehend how circadian misalignment impacts gut microbial equilibrium. This review examines research from the last ten years to assess the effects of circadian rhythm disturbances and meal time variations on the composition of the gut microbiota, the integrity of the gut barrier, and metabolic consequences.

RECENT FINDINGS: Using search terms like "Chrononutrition AND Gut health," "Circadian Rhythm AND Meal timing," and similar combinations, 31 peer-reviewed publications from PubMed, Google Scholar, and Scopus were included. There is evidence that circadian misalignment, which can be brought on by shift work, irregular eating habits, or social jet lag, affects lipid metabolism, short-chain fatty acid (SCFA) synthesis, and gut microbial rhythms. According to research, microbial diversity and function are enhanced by early-time-restricted feeding (eTRF), which synchronizes with circadian cycles. Changes in tight junction proteins have been linked to irregular meal timing, which increases intestinal permeability and inflammation. Additionally, new research indicates a bidirectional relationship in which the gut bacteria might affect the central and peripheral circadian clocks. Chrononutrition is a promising non-pharmacological approach to preventing metabolic dysregulation and promoting gut health. Consistently timing meals, especially early-time-restricted feeding, can help maintain microbial balance, improve gut barrier function, and lower the risk of chronic diseases by bringing food intake into alignment with circadian cycles. The need for integrated approaches to food and lifestyle changes in future research and clinical practice is highlighted by the bidirectional relationship between the gut microbiota and circadian systems.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Circadian Rhythm/physiology
*Meals/physiology
*Feeding Behavior/physiology
Lipid Metabolism

@article {pmid40488793,
year = {2025},
author = {Liu, S and Tai, Z and Li, M and Zhang, R and Shao, G and Guo, J and Lu, W},
title = {Improving intestinal barrier function and intestinal microbiome of weaned piglets fed a low-protein diet through tryptophan and N-Acetylglutamic acid supplementation.},
journal = {Tropical animal health and production},
volume = {57},
number = {5},
pages = {252},
pmid = {40488793},
issn = {1573-7438},
mesh = {Animals ; *Tryptophan/administration & dosage/metabolism ; *Gastrointestinal Microbiome/drug effects ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Diet, Protein-Restricted/veterinary ; Weaning ; *Glutamates/administration & dosage/metabolism ; *Sus scrofa/microbiology/physiology/growth & development ; Animal Nutritional Physiological Phenomena ; *Intestines/physiology/drug effects/microbiology ; Swine ; Male ; Diet/veterinary ; Intestinal Barrier Function ; },
abstract = {The research aimed to evaluate how incorporating NAG and Trp into a low-protein diet affects intestinal functions and alterations in the microbiota, ultimately focusing on enhancing the growth and stress resistance of weaned piglets aged 3-4 weeks.A total of 120 weaned piglets were categorized into five distinct groups: a control group (CON), a low-protein diet group (LP), a low-protein diet group with 0.2% N-acetylglutamic acid (LP + NAG), a low-protein diet group with 0.2% tryptophan (LP + Trp), and a low-protein diet group with 0.2% N-acetylglutamic acid and 0.2% tryptophan (LP + NAG + Trp). The results revealed that the LP + NAG + Trp group exhibited a higher feed-to-gain ratio and improved growth performance, with significantly greater average daily gain and feed intake than the control group. Antioxidant capacity was enhanced, as indicated by elevated levels of catalase and glutathione peroxidase. The expression of tight junction proteins ZO-1 and claudin-1 increased, strengthening the intestinal barrier. Additionally, immunoglobulin levels and the abundance of actinomycetes in the gut microbiota rose, indicating improved immune function and gut health.The increased digestive capacity of the intestine may be linked to the growth in the population of actinomycetes, which is attributed to the combined addition of the NAG + Trp group.},
}

Animals
*Tryptophan/administration & dosage/metabolism
*Gastrointestinal Microbiome/drug effects
Dietary Supplements/analysis
Animal Feed/analysis
*Diet, Protein-Restricted/veterinary
Weaning
*Glutamates/administration & dosage/metabolism
*Sus scrofa/microbiology/physiology/growth & development
Animal Nutritional Physiological Phenomena
*Intestines/physiology/drug effects/microbiology
Swine
Male
Diet/veterinary
Intestinal Barrier Function

@article {pmid40488777,
year = {2025},
author = {Chen, Y and Zhang, R and Zhang, Y and Guo, J and Guo, Z and Han, Y and Wang, F and Zhao, X and Ren, T},
title = {Integrated Microbiome, Transcriptome, and Physiology Analyses Reveal the Response Of Kuruma Shrimp (Penaeus japonicus) to Oxygen Nanobubble Exposure.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {3},
pages = {92},
pmid = {40488777},
issn = {1436-2236},
support = {No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; No. 2022YFE0117900//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Penaeidae/microbiology/physiology/genetics/drug effects/growth & development ; *Oxygen/pharmacology ; *Transcriptome ; *Gastrointestinal Microbiome/drug effects ; Aquaculture ; Adaptation, Physiological ; },
abstract = {Penaeus japonicus is a high-value crustacean species, but its response to oxygen nanobubble (NB-O2) remains poorly understood. This study evaluated the effects of NB-O2 exposure on juvenile P. japonicus cultured in two recirculating aquaculture systems (RAS). The control group (LS) was maintained with low-saturation dissolved oxygen (DO) at 7.5 ± 0.5 mg/L, while the experimental group (HS) was exposed to high-saturation DO of 15.0 ± 0.5 mg/L using NB-O2 technology. The investigation focused on changes in intestinal microbiota, transcriptomic responses, and physiological adaptation. Results demonstrated that NB-O2 significantly improved growth performance metrics, including specific growth rate (SGR), feed conversion ratio (FCR), molting rate (MR), and survival rate (SR). The intestinal microbiota exhibited an increased abundance of beneficial microorganisms, such as Lactobacillales and Rhodopseudomonas palustris, while maintaining microbial stability. Transcriptome analysis identified key pathways associated with adaptation to hyperoxia, particularly those involved in amino acid metabolism, energy metabolism, and antioxidant capacity. These findings were supported by physiological analysis, which showed changes in the amino acid profile and total free amino acids (T-AA), as well as a balanced interaction between glycogen (Gn), adenosine triphosphatase (ATP), and lactate dehydrogenase (LDH) in energy regulation. Antioxidant enzyme activities were all elevated under hyperoxia, including peroxidase (POD), catalase (CAT), total antioxidant capacity (T-AOC), total superoxide dismutase (T-SOD), and glutathione peroxidase (GSH-Px). Additionally, the expression of stress-resistance genes (HSP70, CAP3, LYZ-C) indicated no adverse effects. Overall, P. japonicus exhibited strong physiological and molecular adaptations to NB-O2-induced hyperoxia, highlighting the potential of this technology to enhance aquaculture productivity.},
}

Animals
*Penaeidae/microbiology/physiology/genetics/drug effects/growth & development
*Oxygen/pharmacology
*Transcriptome
*Gastrointestinal Microbiome/drug effects
Aquaculture
Adaptation, Physiological

@article {pmid40488530,
year = {2025},
author = {Gao, H and Zhuang, D and Zhou, H and Su, Q and Hu, X and Wang, Y and Bao, W and Zhu, L},
title = {A comprehensive analysis of human gut microbial biosynthesis gene clusters unveiling the dominant role of Paenibacillus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0061025},
doi = {10.1128/msystems.00610-25},
pmid = {40488530},
issn = {2379-5077},
abstract = {The secondary metabolites produced by the gut microbiota serve as crucial signaling molecules and substrates for gastrointestinal metabolic reactions, thereby playing a pivotal role in human physiological and pathological processes. In this study, we explore the complex symbiotic relationship between the gut microbiota and the human host by systematically annotating the biosynthetic gene clusters (BGCs) across 4,744 human gut microbiota genomes, sourced from the Unified Human Gastrointestinal Genome database. Our comprehensive analysis compares the differential biosynthetic potentials of microbiota from diverse continents and phyla while also elucidating the biosynthetic profiles of gut archaea. Notably, our findings identify Paenibacillus as a dominant genus within the human gut microbiota, characterized by its extensive biosynthetic capacity. This study presents the first global atlas of BGCs within the human gut microbiome, offering valuable insights into gut-derived secondary metabolic pathways and their intricate interactions with host physiology. These results lay the groundwork for future investigations into the microbiota's role in health and disease, underscoring the importance of understanding microbiota-derived metabolites in microbiology and gastroenterology.IMPORTANCEThis study provides a comprehensive analysis of biosynthetic gene clusters in the human gut microbiome, revealing a vast diversity of natural products with potential therapeutic applications. We identified Paenibacillus as a key genus with exceptional biosynthetic capabilities, including the production of leinamycin, a potent anticancer compound previously thought to be exclusive to Streptomyces. The findings highlight the gut microbiome as a rich, untapped resource for novel drug discovery, particularly in cancer therapy and immune modulation.},
}

@article {pmid40488505,
year = {2025},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Mapping of urban garden soil microbiomes in Bangladesh.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/mra.00375-25},
pmid = {40488505},
issn = {2576-098X},
abstract = {Shotgun metagenomics revealed distinct microbiome profiles in the garden soils of Dhaka and Gazipur district, Bangladesh, with Bacillus spp. demonstrating ecological dominance (>53% relative abundance) and location-specific distribution patterns. These findings highlight Bacillus species as prevalent microbes in urban garden soils.},
}

@article {pmid40488500,
year = {2025},
author = {Berríos-Farías, V and Guajardo-Leiva, S and Gallardo-Cerda, J and Galbán-Malagón, C and Ballesteros, G and Egas, C and Molina-Montenegro, M and Castro-Nallar, E},
title = {Rhizosphere and soil metagenomes and metagenome-assembled genomes from the Byers Peninsula, Livingston Island (62°S), Antarctica.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0017125},
doi = {10.1128/mra.00171-25},
pmid = {40488500},
issn = {2576-098X},
abstract = {Rhizosphere microbes establish functional interactions with their hosts, impacting plant fitness. To further understand plant effects on microbial composition and functional diversity, we present 52 metagenomes and 1,484 metagenome-assembled genomes (MAGs) from soil and the rhizosphere of Colobanthus quitensis and Deschampsia antarctica.},
}

@article {pmid40488467,
year = {2025},
author = {Liu, Y and Qiu, Q and Chen, Y and Deng, Y and Huang, W and Sun, C and Shang, X and Chen, X and Wang, C and Han, L and Chen, S and Yuan, J and Xu, F and Yang, Z and Fang, X and Huang, L},
title = {Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0145924},
doi = {10.1128/spectrum.01459-24},
pmid = {40488467},
issn = {2165-0497},
abstract = {Pre-diabetes (PD) represents a critical stage in the progression toward type 2 diabetes, with significant alterations observed in the human microbial community among pre-diabetic individuals in observational studies. However, understanding the interaction between human microbiota and the host during pre-diabetes remains limited. Therefore, this study aims to understand the alterations in the human microbial community during pre-diabetes, a critical stage toward type 2 diabetes. Using an integrated analysis of human microbiota and metabolomics data, we seek to identify the functional signature associated with PD and gain insights into potential mechanisms driving its progression to type 2 diabetes. These findings could inform the development of early intervention strategies for those at high risk. Samples were collected from pre-diabetes, diabetes, and healthy control groups. Through metagenome and 16S rRNA sequencing, we analyzed the gut microbial and tongue coating compositions, respectively. Untargeted metabolomics techniques were also applied for comprehensive plasma data. Using integrated multi-omics analysis, we aim to understand the metabolic potentials of the human microbiome, its molecular links with host targets, and their effects on pre-diabetes, thereby deepening our understanding of microbiome-host interactions in this context. The pre-diabetes group exhibited distinct clinical characteristics, particularly in blood glucose levels and a higher average level of γ-glutamyl transferase. We identified 509 intestinal bacterial species, with Megamonas funiformis and Parabacteroides merdae showing higher abundance in the PD group. In tongue coating samples, we found 1,122 bacterial genera, with the PD group showing altered levels of Corynebacterium and Johnsonella. Furthermore, we detected 795 metabolites, primarily involved in carbohydrate and lipid metabolism. Importantly, our integrated multi-omics analysis suggested Flavonifractor plautii's role in modulating blood glucose through influencing carbohydrate metabolism. Our integrated multi-omics analysis revealed significant alterations in several regulatory pathways associated with pre-diabetes, particularly emphasizing the impact of gut bacterium Flavonifractor plautii on blood glucose levels through its influence on carbohydrate metabolism. These intricate relationships among gut microbiota, metabolites, and blood glucose levels underscore the significance of personalized treatment approaches and preventive strategies for pre-diabetes. The insights gained from this research hold considerable promise for advancing our understanding and management of pre-diabetes.IMPORTANCEThis study investigates alterations in the human microbial community during PD, a critical stage leading to type 2 diabetes. Through integrated analysis of metagenomic and metabolomics data from pre-diabetes, diabetes, and healthy control groups, we identified distinct clinical characteristics in the PD group, including elevated blood glucose levels and γ-glutamyl transferase. A total of 509 intestinal bacterial species were identified, with Flavonifractor plautii playing a key role in modulating blood glucose levels via its influence on carbohydrate metabolism. Our findings underscore the complex interactions among gut microbiota, metabolites, and blood glucose levels, highlighting the potential for personalized treatment approaches and early intervention strategies for individuals at high risk of developing type 2 diabetes.},
}

@article {pmid40488407,
year = {2025},
author = {Grossman, AS and Lei, L and Botting, JM and Liu, J and Nahar, N and Liu, J and McLean, JS and He, X and Bor, B},
title = {Saccharibacteria deploy two distinct type IV pili, driving episymbiosis, host competition, and twitching motility.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf119},
pmid = {40488407},
issn = {1751-7370},
abstract = {All cultivated Patescibacteria, also known as the candidate phyla radiation, are obligate episymbionts residing on other microbes. Despite being ubiquitous in many diverse environments, including mammalian microbiomes, molecular mechanisms of host identification and binding amongst ultrasmall bacterial episymbionts remain largely unknown. Type 4 pili are well conserved in this group and could potentially facilitate these symbiotic interactions. To test this hypothesis, we genetically targeted pili genes in Saccharibacteria Nanosynbacter lyticus strain TM7x to assess their essentiality and roles in symbiosis. Our results revealed that Nanosynbacter lyticus assembles two distinct type 4 pili: a non-essential thin pilus that has the smallest diameter of any type 4 pili and contributes to host-binding and episymbiont growth; and an essential thick pilus involved in twitching motility. To understand the role of these pili in vivo we developed Saccharibacteria competition assays and species specific Fluorescence in situ hybridization probes. Competition between different Saccharibacteria within mock communities demonstrated consistent competitive outcomes that were not driven by priority effects but were dependent on the thin pilus. Collectively our findings demonstrate that Saccharibacteria encode unique extracellular pili that enable their underexplored episymbiotic lifestyle and competitive fitness within a community.},
}

@article {pmid40488306,
year = {2025},
author = {Yoshimura, E and Hamada, Y and Hatamoto, Y and Nakagata, T and Nanri, H and Nakayama, Y and Iwasaka, C and Hayashi, T and Suzuki, I and Ando, T and Ishikawa-Takata, K and Tanaka, S and Ono, R and Araki, M and Kawashima, H and Chen, YA and Park, J and Hosomi, K and Mizuguchi, K and Kunisawa, J and Miyachi, M},
title = {Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514137},
doi = {10.1080/19490976.2025.2514137},
pmid = {40488306},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/chemistry/microbiology ; Cross-Over Studies ; Male ; *Serotonin/analysis/metabolism ; Adult ; Female ; Young Adult ; *Tryptophanase/metabolism/analysis/genetics ; Energy Metabolism ; *Diet ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, we investigated the effects of short-term energy loads on changes in gut microbiome-derived tryptophanase and fecal serotonin levels and their association with variations in energy absorption. This randomized crossover energy-load intervention study included 15 healthy participants subjected to three dietary conditions - overfeeding, control, and underfeeding - for eight days. The effects of the dietary conditions on energy absorption (digestible and metabolizable energy) were assessed using a bomb calorimeter. Fecal serotonin levels were assessed using LC-MS/MS, and the gut microbiota was analyzed using the 16S rRNA gene and metagenomic shotgun analysis. Significant differences were observed in digestible energy (p < 0.001), with higher values in the overfeeding than in the control (p = 0.032) conditions. Furthermore, significant differences were noted in metabolizable energy and gut transit time (p < 0.001), both of which were higher in the overfeeding than in the control (metabolizable energy: p = 0.001; gut transit time: p = 0.014) and underfeeding (metabolizable energy: p < 0.001; gut transit time: p = 0.004) conditions. Fecal serotonin levels differed significantly (p < 0.001), with significantly lower levels in the overfeeding than in the control (p = 0.005) and underfeeding (p < 0.001) conditions. Tryptophanase exhibited significant differences (p = 0.0019), with lower gene abundance in the overfeeding than in the underfeeding (p = 0.001) condition. Tryptophanase positively correlated with Bacteroides abundance under all conditions (correlation coefficient: 0.696-0.896). Intra-individual variability in fecal serotonin levels was significantly negatively associated with digestible energy (β = -0.077, p = 0.019). The findings suggest that short-term energy loads dynamically alter fecal serotonin, Bacteroides, and tryptophanase levels. Moreover, changes in fecal serotonin levels might be indirectly associated with energy absorption.},
}

Humans
*Gastrointestinal Microbiome
*Feces/chemistry/microbiology
Cross-Over Studies
Male
*Serotonin/analysis/metabolism
Adult
Female
Young Adult
*Tryptophanase/metabolism/analysis/genetics
Energy Metabolism
*Diet
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid40487791,
year = {2025},
author = {Stewart, AG and Harris, PNA and Graham, RMA and Jennison, AV and Schlebusch, S and Kakkanat, A and Harris-Brown, T and Paterson, DL and Forde, BM},
title = {Differences in antimicrobial resistance gene abundance and microbial diversity of the gut microbiome in patients on antibiotics enrolled in a clinical trial.},
journal = {Therapeutic advances in infectious disease},
volume = {12},
number = {},
pages = {20499361251337597},
pmid = {40487791},
issn = {2049-9361},
abstract = {BACKGROUND: Understanding how the gut microbiome adapts on exposure to individual antibiotics, with respect to antimicrobial resistance gene (ARG) enrichment, is important.

OBJECTIVES: To characterise the changes that occur in the gut microbiome of patients enrolled in an antibiotic clinical trial and to propose methods in which to embed gut microbiome analysis into clinical trials.

DESIGN: This was a prospective cohort study of hospitalised patients who were successfully enrolled and randomised into two clinical trials between January 2021 to December 2021.

METHODS: Adult patients admitted to the hospital with a bloodstream infection have been randomised to receive either benzylpenicillin, ampicillin, cefazolin, ceftriaxone, piperacillin-tazobactam or meropenem at a single institution. Faecal specimens were collected at enrolment and every second day until discharge. Each specimen underwent DNA sequencing to determine microbial diversity and ARG abundance.

RESULTS: Ten patients (including six females) were included. DNA concentration and sampling quality were markedly lower for rectal swabs compared to stool samples. Relative abundance of Enterococcus faecium was increased in individual patients where treatment included ampicillin, meropenem and piperacillin-tazobactam. Piperacillin-tazobactam also increased the abundance of key beta-lactamase genes (bla SHV-100, bla OXA-392, bla CMY-18). Ampicillin increased the abundance of bla TEM-1A. There were no extended-spectrum beta-lactamase (ESBL) or carbapenemase genes detected in our study. The presence of key anaerobes such as Clostridium and Bifidobacterium species appeared to play an important role in colonisation resistance of E. faecium and Clostridioides difficile.

CONCLUSION: Differential changes in anaerobic bacterial genera on exposure to antibiotics may be a key determinant of colonisation resistance. The pre-analytical phase of microbiome analysis is a critical factor in data quality and interpretation.},
}

@article {pmid40487754,
year = {2025},
author = {Wang, M and Zhu, Y},
title = {Gut microbiome versus thyroid cancer: Association and clinical implications (Review).},
journal = {Oncology letters},
volume = {30},
number = {1},
pages = {368},
pmid = {40487754},
issn = {1792-1082},
abstract = {Thyroid cancer (TC) is one of the most prevalent endocrine tumors, and its incidence rates are increasing. Recent studies have shown that TC disrupts the gut microbiomes (GM) by influencing the levels of thyroid hormones, estrogen levels, weight and insulin resistance. Traditional treatments, including thyroid surgery, radioactive iodine (RAI) therapy and checkpoint inhibitors, also alter the GM. Additionally, GM affects the proliferation of TC by influencing chronic inflammation and metabolism (e.g., effects on short-chain fatty acids and amino acid metabolism). Notable changes in the GM of patients with TC include increased numbers of Clostridium, Streptococcus, Proteus and Lachnospiraceae, and decreased numbers of Lactobacillus, Prevotella and Ruminococcaceae bacteria. In addition, the GM may serve as a biomarker for diagnosis, prognosis and predicting metastasis in patients with TC, potentially enhancing diagnostic efficiency. Furthermore, the GM presents an opportunity to improve the efficacy of RAI therapy and immunotherapy in patients with TC. Probiotic combination approaches may also enhance clinical outcomes and the quality of life for individuals with TC. In conclusion, the present review discussed how there are bidirectional causal relationships between the GM and TC, emphasizing the role of the 'gut-thyroid' axis. Clostridium, Streptococcus, Proteus and Lachnospiraceae may be potential risk factors, whereas Lactobacillus, Prevotella and Ruminococcaceae may have protective roles for TC. Further investigations into macrobiotics-associated mechanisms should prove to be helpful in terms of optimizing strategies for the early prevention and treatment of TC.},
}

@article {pmid40487637,
year = {2025},
author = {Chen, M and Peng, Y and Hu, Y and Kang, Z and Chen, T and Zhang, Y and Chen, X and Li, Q and Yuan, Z and Wu, Y and Xu, H and Zhou, G and Liu, T and Zhou, H and Yuan, C and Huang, W and Zhang, W},
title = {A critical role for Phocaeicola vulgatus in negatively impacting metformin response in diabetes.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {5},
pages = {2511-2528},
pmid = {40487637},
issn = {2211-3835},
abstract = {Metformin has been demonstrated to attenuate hyperglycaemia by modulating the gut microbiota. However, the mechanisms through which the microbiome mediates metformin monotherapy failure (MMF) are unclear. Herein, in a prospective clinical cohort study of newly diagnosed type 2 diabetes mellitus (T2DM) patients treated with metformin monotherapy, metagenomic sequencing of faecal samples revealed that Phocaeicola vulgatus abundance was approximately 12 times higher in nonresponders than in responders. P. vulgatus rapidly hydrolysed taurine-conjugated bile acids, leading to ceramide accumulation and reversing the improvements in glucose intolerance conferred by metformin in high-fat diet-fed mice. Interestingly, C22:0 ceramide bound to mitochondrial fission factor to induce mitochondrial fragmentation and impair hepatic oxidative phosphorylation in P. vulgatus-colonized hyperglycaemic mice, which could be exacerbated by metformin. This work suggests that metformin may be unsuitable for P. vulgatus-rich T2DM patients and that clinicians should be aware of metformin toxicity to mitochondria. Suppressing P. vulgatus growth with cefaclor or improving mitochondrial function using adenosylcobalamin may represent simple, safe, effective therapeutic strategies for addressing MMF.},
}

@article {pmid40487442,
year = {2025},
author = {Hisamatsu, D and Masuoka, H and Takeshige-Amano, H and Kurokawa, R and Ogata, Y and Suda, W and Hatano, T and Asaoka, D and Mabuchi, Y and Naraoka, Y and Sato, N and Asada, T and Hattori, N and Hattori, M and Akazawa, C},
title = {Acetylcholinesterase inhibitors considerably affect the salivary microbiome in patients with Alzheimer's disease.},
journal = {iScience},
volume = {28},
number = {6},
pages = {112593},
pmid = {40487442},
issn = {2589-0042},
abstract = {Microbiome alterations are reportedly linked to systemic disease progression and medication. However, the effects of central nervous system drugs on the microbiome of patients with neurodegenerative diseases, such as Alzheimer's or Parkinson's disease, are poorly understood. Here, we comprehensively analyzed the effects of medication on the salivary and gut microbiomes of patients with Alzheimer's or Parkinson's disease. Comparative analyses of the effects of disease severity and drug use revealed that anti-dementia (DE) drugs, particularly acetylcholinesterase inhibitors, had a greater effect on compositional changes in the salivary microbiome than on those in the gut microbiome. Multivariate analyses incorporating anti-DE drug use showed that microbial signatures may serve as promising disease biomarkers, enabling the development of more precise predictors of cognitive function. Our findings will facilitate the advancement of diagnostic tools leveraging the salivary microbiome.},
}

@article {pmid40487326,
year = {2025},
author = {Bornbusch, SL and Dami, KA},
title = {Connecting microbial ecology to human fertility and reproduction: perspectives from the reproductive microbiomes of animals.},
journal = {F&S reports},
volume = {6},
number = {Suppl 1},
pages = {45-49},
pmid = {40487326},
issn = {2666-3341},
abstract = {In all vertebrates, reproduction occurs in the context of host-associated microbiomes, which are increasingly recognized for their contributions to reproductive success. Although host-associated microbiomes are species specific, synthesizing patterns in microbial ecology across human and animal taxa provides perspectives for understanding the factors that shape microbial communities and their contributions to reproduction. Additionally, the fertility and reproductive physiology of animals under human care-particularly endangered species-is often meticulously monitored to maximize reproductive opportunities. In this mini-review, we examine current knowledge on reproductive microbiomes in animals, focusing, when available, on the sparse literature for wildlife species. We suggest ways in which studying animal microbial ecology may advance human fertility and reproduction by focusing on 3 microbial communities-vaginal, milk, and seminal microbiomes-which represent a large portion of literature and have clear implications for reproductive health. We identify avenues of future research that will further strengthen the linkages between reproductive research in wildlife species and humans and provide potential guidelines for practical applications of microbiome science to human reproductive health.},
}

@article {pmid40487272,
year = {2025},
author = {Phipps, AI and Hill, CM and Lin, G and Malen, RC and Reedy, AM and Kahsai, O and Ammar, H and Curtis, K and Ma, N and Randolph, TW and Ma, J and Ogino, S and Newcomb, PA and Hullar, MA},
title = {Fusobacterium nucleatum Enrichment in Colorectal Tumor Tissue: Associations With Tumor Characteristics and Survival Outcomes.},
journal = {Gastro hep advances},
volume = {4},
number = {6},
pages = {100644},
pmid = {40487272},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Fusobacterium nucleatum (Fn) is linked to colorectal cancer (CRC) etiology and survival. We hypothesized that CRC tumor attributes and survival are associated with the amount and presence of Fn in tumors.

METHODS: Fn abundance was measured via droplet digital polymerase chain reaction in patient-matched CRC tumor and normal tissue samples from 859 Puget Sound CRC Cohort participants. Fn enrichment was defined as the continuous difference in normalized abundance between patient-matched tumor and normal tissue samples. Fn presence in tumor was classified categorically as not present, low, or high, regardless of Fn status in matched normal tissue. Associations of Fn enrichment and presence with tumor site, stage, DNA mismatch repair (MMR) status, CpG island methylator phenotype (CIMP) status, BRAF and KRAS mutation status, and molecular subtypes based on combinations of tumor markers were assessed using logistic regression. Associations of Fn enrichment and presence with CRC survival was estimate with Cox regression.

RESULTS: Fn was present in 20% of tumor tissues and 10% of normal tissues, with higher average abundance in tumors. High Fn presence was independently associated with deficient MMR (dMMR) status and in the context of molecular subtypes for type 1 tumors (dMMR, CIMP-high, BRAF-mutated) and type 5 tumors (dMMR, CIMP-low or negative, BRAF-wildtype). Fn enrichment was associated with type 5 and type 2 tumors (proficient MMR, CIMP-high, BRAF-mutated). Fn enrichment and presence were associated with poorer CRC survival, with some suggestion that associations differed by MMR status.

CONCLUSION: Detectable Fn in CRC tissue is associated with certain CRC tumor attributes and survival; however, associations may vary based on Fn definition.},
}

@article {pmid40487213,
year = {2025},
author = {Wu, S and Tian, B and Shan, C and Wang, X and Xie, X and Xie, H and Jia, X and Zhang, F and Han, J},
title = {Integrated physiological, microbial, and metabolomics analyses revealed the differences in different varieties of Paeonia lactiflora Pall.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1577695},
pmid = {40487213},
issn = {1664-462X},
abstract = {Paeonia lactiflora Pall (P. lactiflora) is a perennial herb with high medicinal and economic value. In the growth process of P. lactiflora, the plant's root secondary metabolism is intricately linked to the microbial communities that surround it. However, few systematic studies have reported the changes in the microbiome and metabolites during P. lactiflora cultivation thus far. In this study, amplicon sequencing technology was used to determine the difference in rhizosphere microorganisms of P. lactiflora. The non-targeted metabolomics method was used to determine the changes in root metabolites, and the relationship between microorganisms and metabolites was demonstrated by co-expression network analysis. The paeoniflorin content (PC) was determined by HPLC. The total phenol content (TPC) was determined by the Folin-Ciocalteu method, and the total flavonoid content (TFC) was determined by the NaNO2-Al (NO3)3 method. The antioxidants were evaluated with the DPPH, ABTS, and FRAP methods. Results showed that Proteobacteria had the highest relative abundance among all phyla, Halomonas had the highest relative abundance among all genera. The results of metabolomics showed that 693 metabolites and 207 differential metabolites were detected in the four groups, which were mainly enriched in the biosynthesis of phenylpropanoids, phenylpropanoid biosynthesis, taste transduction, central carbon metabolism in cancer, and biosynthesis of plant secondary metabolites. The results also showed that the PC, TPC, TFC, and antioxidant capacity of the white P. lactiflora group were higher than those of the other groups. This study revealed the differences between different varieties of P. lactiflora and provided theoretical support for breeding and data reference for improving the quality of P. lactiflora by regulating microbial species.},
}

@article {pmid40487195,
year = {2025},
author = {Geese, T and Dempfle, A},
title = {From variability to stability: Sensitivity of network properties in IBD human gut microbiome studies.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1945-1961},
pmid = {40487195},
issn = {2001-0370},
abstract = {BACKGROUND: The gut microbiome's role in inflammatory bowel disease (IBD) is well-established, but capturing its complexity is challenging. Network analysis offers a valuable approach, but selecting suitable measures is crucial. This study examines the sensitivity of network properties to abundance variations. It evaluates whether these properties reflect the microbiome in IBD or are too sensitive to variability from e.g. laboratory conditions or intra-individual changes.

METHODS: Using genetically unrelated individuals from the KINDRED cohort (IBD n = 522, healthy controls n = 365) and the PRISM cohort (IBD n = 42, healthy controls n = 42), microbial networks were constructed with genera as nodes and significant pairwise correlations as edges, separately for IBD patients and controls. Important IBD-related nodes, identified through centrality measures, and non-disease-related nodes were varied in abundance ( ± 30 %), and networks were re-constructed and compared with initial networks regarding local and global properties.

RESULTS: Network properties in IBD were sensitive to abundance variations, with small and large changes producing similar effects. Sensitivity to increasing read counts of disease-related and non-disease-related genera was similar. Local properties showed magnitude-dependent changes of up to 50 % in response to the depletion of disease-related genera, relative to no modification applied, and an almost binary sensitivity pattern when modifying non-disease-related genera. Global case network properties changed less than 10 % in most settings, potentially indicating a certain stability of dysbiosis.

CONCLUSION: Caution is needed with network-based approaches, as even small variations, stemming from sources of microbiome variability, can affect results and reproducibility. The relatively stable dysbiosis in IBD could pose challenges for microbiome-directed therapies.},
}

@article {pmid40487108,
year = {2025},
author = {Ortiz-Chura, A and Corral-Jara, KF and Tournayre, J and Cantalapiedra-Hijar, G and Popova, M and Morgavi, DP},
title = {Rumen microbiota associated with feed efficiency in beef cattle are highly influenced by diet composition.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {378-389},
pmid = {40487108},
issn = {2405-6383},
abstract = {Given the role of the rumen microbiome in providing nutrients to the host ruminant, it is expected that rumen microbes contribute to inter-animal variations in feed efficiency. However, the link between microbial structure and an "efficient" host phenotype is unclear. We hypothesized that extreme residual feed intake (RFI) phenotypes would display distinctive microbiome features regardless of the diet. In this study, we selected the 32 most extreme RFI Charolais bulls from a cohort of 100 animals fed corn-silage (CS; n = 50) or grass-silage (GS; n = 50) based diets. Rumen samples were obtained 3 h after feeding, at slaughter, for fermentation and metataxonomic and metatranscriptomic microbial analysis. Volatile fatty acid profiles showed no differences between diets and between extreme RFI phenotypes (P > 0.05). Total bacteria and methanogen populations did not differ between extreme RFI phenotypes (P > 0.05), although methanogens expressed per liquid rumen digesta weight tended to decrease in the most efficient bulls compared to the least efficient ones (P = 0.10). The rumen microbial community structure differed between diets (P < 0.001), and between extreme RFI phenotypes in the GS diet. In the whole dataset, we identified Succiniclasticum, Saccharofermentans, Clostridia_258483 and CAG-238 as bacteria discriminant between extreme RFI phenotypes (q < 0.10). Within diets, these four genera were also discriminant in the GS diet and were all associated with the least efficient bulls. In contrast, in bulls fed the CS diet, only Saccharofermentans and Succiniclasticum were discriminant but they were positively associated with the most efficient bulls. Rumen microbial functional features did not differ between extreme RFI phenotypes but did differ between diets. In conclusion, the rumen microbiome was mainly influenced by diet, with the RFI phenotype being a marginal effector. Succiniclasticum, Saccharofermentans, Clostridia_258483, and CAG-238 were discriminant between extreme RFI phenotypes regardless of diet. However, the direction of the association with RFI was diet dependent, indicating a diet-RFI interaction and suggesting that these discriminating microbes may be suitable microbial indicator species for RFI only when considered in conjunction with the diet information.},
}

@article {pmid40487096,
year = {2025},
author = {Han, H and Liu, K and Wang, Y and Song, M and Lian, H and Gao, T and Zhang, L and Fu, T},
title = {Supplementation of the probiotic Lactobacillus rhamnosus GG to pre-weaning calves decreases diarrhea incidence by modulating gut bacteria and associated metabolites.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {21},
number = {},
pages = {234-244},
pmid = {40487096},
issn = {2405-6383},
abstract = {The aim of the present study was to investigate whether Lactobacillus rhamnosus GG (LGG) could be utilized as an effective strategy to promote growth performance of calves and to further study its impact on decreasing diarrhea. A total of 18 healthy Holstein calves (age 8 ± 3 days, weight 42.48 ± 1.04 kg) were raised in a centralized manner to minimize differences and then divided into two groups: one group received LGG supplementation (1 × 10[10] CFU per calf per day), while the other served as the control (CON). Each group consisted of 9 replicates, with 1 calf per replicate. The experimental period spanned 6 weeks. The experimental results demonstrated an increase of the average daily growth (P = 0.094) and a highly significant reduction in diarrhea (P = 0.001) for the LGG group compared with the CON group. The supplementation of LGG resulted in an increased abundance of endogenous beneficial bacteria in the gut including Lysinbacillus (P = 0.012) and Rikenellaceae_RC9_gut_group (P = 0.041) while reducing levels of pathogenic bacteria in the Escherichia-Shigella (P = 0.066). These particular groups could serve as biomarker bacteria for calf diarrhea and gut health. The alteration of metabolite production and metabolic pathways were also closely associated with the variation of bacterial composition in the gut microbiome of calves, of which included enrichment of biosynthesis of unsaturated fatty acids, α-linolenic acid and steroid biosynthesis. Overall, LGG administration had a positive impact on improving the intestinal homeostasis, alleviating diarrhea, and enhancing growth performance by modulating gut bacteria and metabolites in pre-weaning calves. Thus, LGG could be a potential alternative to prophylactic antibiotic treatment that would lower associated costs and provide new insights into preventing and treating calf diarrhea.},
}

@article {pmid40486854,
year = {2025},
author = {Qian, D and Xu, P and Wang, X and Du, C and Zhao, X and Xu, J},
title = {Bacterial extracellular vesicles for gut microbiome-host communication and drug development.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {4},
pages = {1816-1840},
pmid = {40486854},
issn = {2211-3835},
abstract = {As the intricate interplay between microbiota and the host garners increasing research attention, a significant parallel surge has emerged in the investigation of intestinal bacterial extracellular vesicles (BEVs). Most intestinal bacteria secrete BEVs, which harbor specific cargo molecules and exhibit diverse functions, encompassing interactions among bacteria themselves and between bacteria and the host. These interactions can either bolster host health or contribute to various pathologies. By integrating the characteristics of BEVs, we summarized the current research landscape, delving into the intricate interplay between BEVs and different diseases. Furthermore, we offer a succinct overview of the challenges faced in BEVs-based research, encompassing separation, detection, engineering for drug purposes, clinical diagnostics, safety, and future study. In essence, these summaries may serve as invaluable guides for BEVs as communication tools between the gut microbiome and host, ultimately propelling the discovery of novel studies and drug discovery.},
}

@article {pmid40486513,
year = {2025},
author = {Chen, LZ and Cai, Q and Zheng, PF},
title = {Mitochondrial metabolic rescue in post-COVID-19 syndrome: MR spectroscopy insights and precision nutritional therapeutics.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1597370},
pmid = {40486513},
issn = {1664-3224},
mesh = {Humans ; *COVID-19/metabolism/complications/diet therapy ; *Mitochondria/metabolism ; *SARS-CoV-2 ; Magnetic Resonance Spectroscopy/methods ; Precision Medicine ; *Nutrition Therapy/methods ; Energy Metabolism ; Oxidative Stress ; Ubiquinone/analogs & derivatives ; },
abstract = {Post-COVID-19 Condition (PCC), impacting 30-90% of survivors, is characterized by persistent fatigue and metabolic dysfunction, often linked to underlying mitochondrial impairment. This review examines current evidence on mitochondrial-targeted nutrition therapies, with a focus on magnetic resonance spectroscopy (MRS) as a tool for assessing metabolic recovery. Key findings highlight reduced adenosine triphosphate (ATP) production, heightened oxidative stress, and disrupted mitochondrial biogenesis- metabolic abnormalities that closely mirror those seen in chronic fatigue syndromes. While mitochondrial dysfunction is recognized as central, debate continues on whether systemic inflammation or direct viral damage primarily drives these abnormalities. Current evidence supports nutrients, such as, CoQ10, NAC, and creatine for restoring energy metabolism and reducing oxidative stress. MRS biomarkers (τPCr, Qmax), offer valuable tools for monitoring personalized intervention. However, several limitations persist, including variability in nutritional protocols, inconsistencies in MRS methodologies, and limited consideration of microbiome-psychosocial interactions. Most clinical trials focus on short-term outcomes, lacking data on long-term efficacy or stratification based on mitochondrial dysfunction severity. Future research priorities include multi-omics investigations into mitochondrial-epigenetic interactions, the development of targeted antioxidants, and exploration of engineered microbial metabolites. Standardizing MRS protocols, validating composite endpoints, and optimizing nutrient delivery systems require interdisciplinary collaboration. This review advocates for a precision medicine approach, combining MRS-based metabolic profiling with personalized nutritional strategies, to address the multifactorial nature of PCC and advance clinical translation.},
}

Humans
*COVID-19/metabolism/complications/diet therapy
*Mitochondria/metabolism
*SARS-CoV-2
Magnetic Resonance Spectroscopy/methods
Precision Medicine
*Nutrition Therapy/methods
Energy Metabolism
Oxidative Stress
Ubiquinone/analogs & derivatives

@article {pmid40486510,
year = {2025},
author = {Yang, P and Song, Y and Li, M},
title = {Biological mechanisms of pulmonary inflammation and its association with seropositive rheumatoid arthritis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1530753},
pmid = {40486510},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/complications ; Extracellular Traps/immunology ; *Pneumonia/immunology ; *COVID-19/immunology ; SARS-CoV-2/immunology ; Animals ; Lung/immunology/pathology ; Gastrointestinal Microbiome/immunology ; },
abstract = {Although the pathogenesis of seropositive rheumatoid arthritis (RA) remains unclear, studies suggest that pulmonary inflammation-related biological mechanisms play a significant role in its development. This review thoroughly explores the mechanisms underlying early pulmonary lesions in seropositive RA, focusing on the mucosal barrier hypothesis, neutrophil extracellular traps, pathogenic microbial infections like COVID-19, Vitamin D, the microbiome and gut-lung axis, inhalation exposures and chronic pulmonary diseases. This study seeks to provide novel insights and theoretical foundations for the prevention and treatment of seropositive rheumatoid arthritis.},
}

Humans
*Arthritis, Rheumatoid/immunology/complications
Extracellular Traps/immunology
*Pneumonia/immunology
*COVID-19/immunology
SARS-CoV-2/immunology
Animals
Lung/immunology/pathology
Gastrointestinal Microbiome/immunology

@article {pmid40486234,
year = {2025},
author = {Shilov, S and Korotetskiy, I and Kuznetsova, T and Zubenko, N and Ivanova, L and Solodova, E and Tugeyeva, A and Kaziyev, A and Korotetskaya, N and Izmailov, T},
title = {The chicken gut resistome data from different regions of Kazakhstan.},
journal = {Data in brief},
volume = {60},
number = {},
pages = {111608},
pmid = {40486234},
issn = {2352-3409},
abstract = {Antibiotic resistance (AR) is a serious global health problem affecting both human medicine and animal agriculture. The poultry farming, especially industrial poultry, antibiotics are widely used for disease prevention and growth promotion, leading to the accumulation and dissemination of antibiotic resistance genes (ARGs) within the intestinal microbiomes of birds. Poultry, which often have close contact with humans, can serve as reservoirs for resistant microorganisms, posing potential public health risks. Determination of avian intestinal resistomes through metagenomic sequencing and bioinformatics analysis enables the identification of diversity and transmission dynamics of ARGs, and to evaluate the influence of environmental factors and conditions of poultry on resistance gene distribution. The article presents data of resistome analysis of gut microbiota in populations of chickens from different regions of Kazakhstan. The data obtained will allow to develop a strategy to reduce the spread of antibiotic-resistant pathogens and improve safety in poultry farming, as well as to predict the risk of transmission of resistant microorganisms between animals and humans.},
}

@article {pmid40485985,
year = {2025},
author = {Cerioni, NL and Uhl, HL and Welty, MA and Adler, JJ},
title = {Soil microbiome analysis of cultivated tomato (Solanum lycopersicum) plants.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40485985},
issn = {2578-9430},
abstract = {Microbial biodiversity is critical to tomato plant health. The symbiotic relationship between tomato plants and their soil microbiome influences the plants' ability to absorb nutrients and adapt to environmental stresses. This study compared the soil microbiome between tomato plants appearing healthy versus those appearing unhealthy. There were no significant differences in overall bacterial biodiversity between the conditions. However, a specific beneficial genus (Sphingomonas) and its phylum Proteobacteria (Pseudomonadota) were found at significantly higher amounts in healthy plants' soil compared to unhealthy plants' soil. Our findings show the need for further examination of the benefits of Sphingomonas for tomato plants.},
}

@article {pmid40485830,
year = {2025},
author = {Magagula, P and Swart, V and Fourie, A and Vermeulen, A and Nelson, JH and van Rooyen, Z and van den Berg, N},
title = {Avocado rhizosphere community profiling: white root rot and its impact on microbial composition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1583797},
pmid = {40485830},
issn = {1664-302X},
abstract = {INTRODUCTION: The avocado rhizosphere supports diverse microbial communities essential for plant health and defence against pathogens. This study aimed to investigate the impact of Dematophora necatrix, the causal agent of white root rot (WRR), on the microbial composition and soil physicochemical properties of infected and non-infected avocado trees in two South African orchards.

METHODS: ITS and 16S metabarcoding was used to compare the composition and diversity of the rhizosphere microbiome. Soil physicochemical properties were also assessed, and culturable bacterial and fungal isolates from the rhizosphere were screened for antagonistic activity against D. necatrix.

RESULTS: We found that D. necatrix did not significantly alter overall microbial diversity but influenced relative abundance of specific taxa. In Orchard A, dominant bacterial genera included Sphingomonas, Rokubacteriales and Lysobacter, while Orchard B featured Sphingomonas and Acidothermus while beneficial microbes such as Streptomyces and Bacillus were enriched in WRR non-infected (WRR-N) soils. The fungal profiles revealed Trichoderma and Penicillium as potential biocontrol agents enriched in WRR-N soils. Furthermore, dual-culture assays demonstrated that Bacillus, Pseudomonas, Penicillium and Trichoderma isolates inhibited D. necatrix, highlighting their biocontrol potential. Key parameters, such as soil pH and iron (Fe), correlated strongly with microbial composition, suggesting they play an important role in pathogen resilience.

DISCUSSION: These findings underscore the complexity of the avocado rhizosphere and its role in managing WRR, offering a foundation for developing integrated disease management strategies to enhance avocado productivity.},
}

@article {pmid40485679,
year = {2025},
author = {Fargue, S and Suryavanshi, M and Wood, KD and Crivelli, JJ and Oster, RA and Assimos, DG and Miller, A and Knight, J},
title = {Inducing Oxalobacter formigenes Colonization Reduces Urinary Oxalate in Healthy Adults.},
journal = {Kidney international reports},
volume = {10},
number = {5},
pages = {1518-1528},
pmid = {40485679},
issn = {2468-0249},
abstract = {INTRODUCTION: Oxalate-degrading intestinal bacteria, including the oxalate-degrading specialist, Oxalobacter formigenes (O formigenes), have the potential to reduce urinary oxalate excretion in humans, and thus limit the risk of calcium oxalate kidney stone formation. The aim of this proof-of-concept study, which was performed in healthy adults, was to demonstrate that ingestion of live O formigenes is safe, can establish sustainable gut colonization, and reduce urinary oxalate excretion.

METHODS: Twenty-two healthy adults without a history of kidney stones and not colonized with O formigenes ingested diets controlled in oxalate and calcium. In these participants, 24-hour urine and stool oxalate levels were quantified using ion chromatography coupled with mass spectrometry before and after ingestion of O formigenes.

RESULTS: All 22 participants were successfully colonized after a single dose of O formigenes (∼10[10] cells); 10 remained colonized for at least 1 year. Colonization was lost in 11 participants, of whom 9 reported antibiotic use. Six participants who lost colonization were redosed, and 5 were successfully recolonized. Stool oxalate concentration and urine oxalate excretion significantly decreased by 54% and 14%, respectively, with varied responses after colonization. Microbiome molecular analyses of precolonized stool samples highlighted the abundance and diversity of other potential oxalate-degrading bacteria, which may have influenced the effect of O formigenes colonization on urinary oxalate excretion.

CONCLUSION: These findings support future investigations to examine the effectiveness of O formigenes colonization in reducing urinary oxalate excretion in disease cohorts, including calcium oxalate kidney stone formers with enteric hyperoxaluria.},
}

@article {pmid40485603,
year = {2025},
author = {Ma, J and Fu, S and Tan, J and Han, Y and Chen, Y and Deng, X and Shen, H and Zeng, S and Peng, Y and Cai, C},
title = {Mechanistic Foundations of KRAS-Driven Tumor Ecosystems: Integrating Crosstalk among Immune, Metabolic, Microbial, and Stromal Microenvironment.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e02714},
doi = {10.1002/advs.202502714},
pmid = {40485603},
issn = {2198-3844},
support = {82173342//National Natural Science Foundation of China/ ; 82203015//National Natural Science Foundation of China/ ; 82373275//National Natural Science Foundation of China/ ; 82403920//National Natural Science Foundation of China/ ; 2024JJ6662//Natural Science Foundation of Hunan Province/ ; 2025JJ20077//Natural Science Foundation of Hunan Province/ ; 2024RC3042//Science and Technology Innovation Program of Hunan Province/ ; 2023Q01//Youth Science Foundation of Xiangya Hospital/ ; GZC20242044//Postdoctoral Fellowship Program of the CPSF/ ; 2024M753679//China Postdoctoral Science Foundation/ ; kq2403008//Nature Science Foundation of Changsha/ ; },
abstract = {Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most frequently mutated member of the RAS family of small GTPases (RAS). It affects about one-fifth of cancer cases. The tumor microenvironment (TME) is a multifaceted network of immune cells, metabolites, microbiota, stromal components, and extracellular matrix. It creates a dynamic ecosystem that supports malignant initiation, progression, and therapy resistance through bidirectional crosstalk with tumor cells. Emerging evidence reveals distinct TME landscapes shaped by wild-type versus oncogenic KRAS variants. Additionally, TME rewiring occurs during KRAS-targeted therapies. Deciphering these KRAS-dependent TME architectures and their therapeutic vulnerabilities represents a critical frontier for precision oncology. This review synthesizes key milestones and persistent challenges in KRAS inhibitor development. And it systematically evaluates how KRAS mutations orchestrated immunosuppressive niches, metabolic symbiosis, stromal remodeling, and microbiome dysbiosis, supported by mechanistic insights from preclinical and clinical studies. It further explores therapeutic opportunities arising from targeting TME interactions, including rational combinations of KRAS inhibitors with immune checkpoint blockade, metabolic agents, or microbiota-modulating strategies.},
}

@article {pmid40485371,
year = {2025},
author = {Wang, SJ and Glass, R and Jiang, B and Kirkwood, C and Parashar, U and Duan, ZJ and Wang, XY},
title = {A report for the fifth International Workshop on Rotavirus and Norovirus in China.},
journal = {Human vaccines & immunotherapeutics},
volume = {21},
number = {1},
pages = {2512647},
doi = {10.1080/21645515.2025.2512647},
pmid = {40485371},
issn = {2164-554X},
mesh = {Humans ; China/epidemiology ; *Rotavirus Infections/prevention & control/epidemiology/immunology ; *Norovirus/immunology ; *Rotavirus/immunology ; *Gastroenteritis/prevention & control/virology/epidemiology ; *Rotavirus Vaccines/immunology/administration & dosage ; *Caliciviridae Infections/prevention & control/epidemiology/immunology ; },
abstract = {The fifth International Workshop on Rotavirus and Norovirus in China was convened in Shanghai May 8-9, 2024. The workshop was organized by Fudan University and China Center for Disease Control and Prevention (China CDC), with strong support from Bill & Melinda Gates Foundation and the Centers for Disease Control and Prevention in the United States (US CDC). Over 230 participants from 10 countries, including experts and representatives from government and non-government organizations, academia and vaccine manufacturers, attended the meeting. Progress on reduced rotavirus disease burden, the impact of currently licensed oral vaccines, new vaccines and technologies under development to control and prevent acute gastroenteritis caused by rotavirus and norovirus, mucosal immunity and its measurement, as well as the association between the effectiveness of rotavirus vaccine and intestinal microbiome were discussed extensively. This report summarized the latest information shared at the convening.},
}

Humans
China/epidemiology
*Rotavirus Infections/prevention & control/epidemiology/immunology
*Norovirus/immunology
*Rotavirus/immunology
*Gastroenteritis/prevention & control/virology/epidemiology
*Rotavirus Vaccines/immunology/administration & dosage
*Caliciviridae Infections/prevention & control/epidemiology/immunology

@article {pmid40485285,
year = {2025},
author = {Sze, SH},
title = {An Exact Matching Method for 16S rRNA Taxonomy Classification.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0615},
pmid = {40485285},
issn = {1557-8666},
abstract = {One popular approach to taxonomy classification in the microbiome utilizes 16S ribosomal RNA sequences. The main challenge is that 16S rRNA sequences could be almost identical in closely related species, and it is difficult to distinguish them at the species level. Recent approaches are able to achieve almost single nucleotide resolution by constructing an error model of the reads. We develop an exact matching algorithm to utilize the single nucleotide resolution directly. We show that our algorithm is able to obtain improved accuracy in recent samples of mock communities and in samples of high compositional complexity when compared to existing algorithms. A software program implementing this algorithm is available at http://faculty.cse.tamu.edu/shsze/kmpmatch.},
}

@article {pmid40484980,
year = {2025},
author = {Tang, G and Millar, EKA and Graham, PH and Beretov, J},
title = {Interaction between the breast tumor microenvironment and gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514136},
doi = {10.1080/19490976.2025.2514136},
pmid = {40484980},
issn = {1949-0984},
mesh = {Humans ; *Breast Neoplasms/microbiology/immunology/pathology/metabolism ; *Tumor Microenvironment ; *Gastrointestinal Microbiome ; Female ; Dysbiosis/microbiology ; Probiotics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; },
abstract = {Previously believed to be sterile, the breast microenvironment has been revealed by modern DNA sequencing technologies to harbor a diverse community of microorganisms. The breast tumor microenvironment (TME) has a microbial signature unique to that of other breast pathologies as well as between breast cancer subtypes and stage. Among the plethora of microorganisms identified, Methylobacterium radiotolerans and Sphingomonas yanoikuyae stand out, both elevated in breast cancer tissue and associated with cancer stage. Breast cancer is the most common malignancy affecting women and the second most common cause of cancer-specific death in women worldwide. Gut dysbiosis has recently emerged as a key player, although the exact mechanisms are still unclear. Hypothesized mechanisms include bacterial metabolites inducing genomic instability, imbalances in the local and systemic immune system, the role of gut microbiota in the regulation of estrogen metabolism. Probiotic commensals Akkermansia muciniphila and Bifidobacterium appear to have a protective effect, with evidence of gut wall protection, correlation with less advanced disease and better treatment efficacy and tolerability. This review outlines the relationship between the breast microbiome, the gut microbiome, the 'estrabolome', and the immune system in breast cancer. This characterization could make a significant clinical contribution, potentially leading to new methods of primary prevention, better prognostication and prediction, as well as new avenues of treatment.},
}

Humans
*Breast Neoplasms/microbiology/immunology/pathology/metabolism
*Tumor Microenvironment
*Gastrointestinal Microbiome
Female
Dysbiosis/microbiology
Probiotics
*Bacteria/classification/genetics/metabolism/isolation & purification

@article {pmid40484974,
year = {2025},
author = {Smith, ME and Kavamura, VN and Hughes, D and Mendes, R and Lund, G and Clark, I and Mauchline, TH},
title = {Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {64},
pmid = {40484974},
issn = {2524-6372},
support = {FR2021-02017//Svenska Forskningsrådet Formas/ ; BB/N016246/1//Bilateral BBSRC-Embrapa gran/ ; BBS/E/C/00005196//Bilateral BBSRC-Embrapa grant/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; },
abstract = {BACKGROUND: During the Green Revolution, one of the biggest developments of wheat domestication was the development of new cultivars that respond well to fertilisers and produce higher yields on shorter stems to prevent lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of modern cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of pre-green revolution (heritage) cultivars to compare the impact of modern wheat breeding on rhizosphere microbiome functions.

RESULTS: We found distinct taxonomic and functional differences between heritage and modern wheat rhizosphere communities and identified that modern wheat microbiomes were less distinct from the communities in the surrounding soil. Of the 113 functional genes that were differentially abundant between heritage and modern cultivars, 95% were depleted in modern cultivars and 65% of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules).

CONCLUSIONS: Overall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture will benefit from deliberately incorporating the development of beneficial plant-microbiome interactions, alongside traditional yield traits, to advance sustainable wheat production.},
}

@article {pmid40484955,
year = {2025},
author = {Lin, A and Huang, L and Jiang, A and Zhu, L and Mou, W and Li, Y and Zhang, C and Liu, Z and Zhang, J and Cheng, Q and Wei, T and Luo, P},
title = {Microbiota boost immunotherapy? A meta-analysis dives into fecal microbiota transplantation and immune checkpoint inhibitors.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {341},
pmid = {40484955},
issn = {1741-7015},
support = {2021A1515012593//Natural Science Foundation of Guangdong Province/ ; 82373129//National Natural Science Foundation of China/ ; 82172750//National Natural Science Foundation of China/ ; 2022A1515111212//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A04J1257//Science and Technology Program of Guangzhou/ ; NO.2023RC3074//Hunan Youth Science and Technology Talent Project/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; *Neoplasms/therapy ; *Gastrointestinal Microbiome ; *Immunotherapy/methods ; Treatment Outcome ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) are a cornerstone of modern cancer treatment, but their effectiveness is limited. Fecal microbiota transplantation (FMT), which alters the gut microbiome, has shown promise in enhancing ICIs' therapeutic effects.

METHODS: We conducted a comprehensive search of relevant studies available up to September 30, 2024, to analyze the clinical efficacy and safety of combining FMT with ICIs in cancer treatment. The primary endpoint was the objective response rate (ORR), with secondary evaluations of survival outcomes and safety.

RESULTS: A total of 10 studies involving 164 patients with solid tumors were included. The pooled ORR was 43% (95% CI: 0.35-0.51). Subgroup analysis revealed that the combination of anti-PD-1 and anti-CTLA-4 therapies was associated with a significantly higher ORR (60%) compared to anti-PD-1 monotherapy (37%; P = 0.01). The incidence of grade 1-2 adverse events (AEs) was 42% (95% CI: 0.32-0.52), while grade 3-4 AEs occurred in 37% of patients (95% CI: 0.28-0.46).

CONCLUSIONS: This meta-analysis provides preliminary evidence supporting the use of FMT as a strategy to enhance the efficacy of ICIs in patients with advanced or refractory solid tumors. However, larger-scale randomized controlled trials with long-term follow-up are required to confirm and optimize treatment protocols.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Immune Checkpoint Inhibitors/therapeutic use
*Neoplasms/therapy
*Gastrointestinal Microbiome
*Immunotherapy/methods
Treatment Outcome

@article {pmid40484738,
year = {2025},
author = {Nohesara, S and Mostafavi Abdolmaleky, H and Dickerson, F and Pinto-Tomas, AA and Jeste, DV and Thiagalingam, S},
title = {Corrigendum to "Associations of microbiome pathophysiology with social activity and behavior are mediated by epigenetic modulations: Avenues for designing innovative therapeutic strategies" [Neurosci. Biobehav. Rev. 174 (2025) 106208].},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106240},
doi = {10.1016/j.neubiorev.2025.106240},
pmid = {40484738},
issn = {1873-7528},
}

@article {pmid40484562,
year = {2025},
author = {Feng, Y and Xiao, Y and Li, X and Guo, M and Huang, L and Lu, W and Zhao, J and Chen, W},
title = {Prebiotic roles and anti-aging effects of xylo-oligosaccharide: Keystone responsive bacteria and their metabolic interactions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {215},
number = {},
pages = {116673},
doi = {10.1016/j.foodres.2025.116673},
pmid = {40484562},
issn = {1873-7145},
mesh = {*Prebiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/pharmacology ; Humans ; Feces/microbiology ; Animals ; *Aging/drug effects ; Mice ; Male ; Metabolomics ; *Glucuronates/pharmacology ; *Bacteria/metabolism/drug effects/genetics/classification ; Mice, Inbred C57BL ; Female ; Fermentation ; Adult ; },
abstract = {Xylo-oligosaccharide (XOS), a prebiotic oligosaccharide, has been reported to exert the beneficial effects on the host, primarily by modulating the gut microbiota and associated metabolism. However, the specific microbes, their metabolic interactions and mechanistic insights remain understudied. In this study, we aim to investigate the response of gut microbiota to XOS at the fine-grained level using combined approaches of microbiome sequencing, genomic analyses, and metabolomic analyses based on in vitro fecal fermentation using healthy human fecal samples. The results showed that XOS significantly altered the composition of the gut microbiota and enriched numerous bacterial taxa, such as Blautia, Bifidobacterium longum subsp. longum, and Faecalibacterium prausnitzii. Functional genomic analyses further confirmed that specifically identified XOS-responsive bacteria harbored varied XOS-utilizing capacities, consistent with the levels of their abundance elevation. The fecal metabolomics analysis revealed that XOS intervention significantly altered the metabolic profile (γ-aminobutyric acid, serotonin, and inosine). The microbe-microbe and microbe-metabolite interaction networks consistently identified three independent groups, potentially representing different levels of XOS degradation and/or other response mechanisms. Finally, the beneficial effects of XOS on the gut microbiota and metabolism were confirmed by the alleviation D-galactose-induced aging in mouse model. This study supports the role of XOS as prebiotics and highlights the potential of XOS in alleviating host aging-associated phenotypes in a D-galactose-induced aging mouse model in terms of improvements on cognitive function, inflammatory markers, and oxidative stress levels.},
}

*Prebiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Oligosaccharides/pharmacology
Humans
Feces/microbiology
Animals
*Aging/drug effects
Mice
Male
Metabolomics
*Glucuronates/pharmacology
*Bacteria/metabolism/drug effects/genetics/classification
Mice, Inbred C57BL
Female
Fermentation
Adult

@article {pmid40484540,
year = {2025},
author = {Grant-St James, A and Lee, AC and Lee, AJ and Wist, J and Sohel, F and Wong, KW and Yeap, BB and Loo, RL and Henry, A and Susic, D and El-Omar, E and Nicholson, JK and Holmes, E and Whiley, L and Gray, N},
title = {Analytical quality control in targeted lipidomics: Evaluating the performance of commercial plasma as a surrogate for pooled study samples.},
journal = {Analytica chimica acta},
volume = {1365},
number = {},
pages = {344225},
doi = {10.1016/j.aca.2025.344225},
pmid = {40484540},
issn = {1873-4324},
mesh = {*Lipidomics/standards ; Quality Control ; *Lipids/blood ; Humans ; },
abstract = {BACKGROUND: Pooled quality control (PQC) samples are the gold standard for data quality monitoring in metabolic phenotyping studies. Typically composed of equal parts from all study samples, PQCs can be challenging to generate in large cohorts or when sample volumes are low. As an alternative, externally sourced matrix-matched surrogate QCs (sQC) have been proposed. This study evaluates the performance of sQCs against PQCs for assessing analytical variation, data pre-processing, and downstream data analysis in a targeted lipidomics workflow.

RESULTS: Plasma samples (n = 701) from the Microbiome Understanding in Maternity Study, along with PQC (n = 80) and sQC (n = 80) samples, were analyzed using a lipidomics assay targeting 1162 lipids. QC samples were injected throughout acquisition, and data pre-processing was performed using each strategy. For simplicity, a subset (n = 381) of the study samples was used to assess differences in downstream statistical analyses. Both QC approaches demonstrated high analytical repeatability. While PQC and sQC compositions differed, use of PQCs retained less than 4 % more lipid species during pre-processing. Univariate analysis identified more statistically significant lipids with PQC-based pre-processing, but multivariate model performance was similar between datasets.

SIGNIFICANCE: This study provides a comprehensive comparison of QC strategies and emphasizes the importance of careful QC workflow selection. While PQCs offer advantages, sQCs serve as a suitable alternative for quality assessment and pre-processing. Their commercial availability also supports use as intra- and inter-laboratory long-term references, aiding data harmonization across studies and laboratories.},
}

*Lipidomics/standards
Quality Control
*Lipids/blood
Humans

@article {pmid40484397,
year = {2025},
author = {Adachi, A and Dominguez, JJ and Utami, YD and Fuji, M and Kirita, S and Imai, S and Murakami, T and Hongoh, Y and Shinjo, R and Kamiya, T and Fujiwara, T and Minamisawa, K and Ono, N and Kanaya, S and Saijo, Y},
title = {Field Dynamics of the Root Endosphere Microbiome Assembly in Paddy Rice Cultivated under No Fertilizer Input.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf045},
pmid = {40484397},
issn = {1471-9053},
abstract = {Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared to a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars-Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.},
}

@article {pmid40484360,
year = {2025},
author = {Wu, H and He, K and Wang, H and Li, W and Huo, R and Jiang, SH and Xue, J},
title = {The Gut-Brain Axis in the Context of Colorectal Cancer.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107816},
doi = {10.1016/j.phrs.2025.107816},
pmid = {40484360},
issn = {1096-1186},
abstract = {The gut-brain axis (GBA) plays a pivotal role in the pathophysiology of colorectal cancer (CRC), influencing tumor progression, immune responses, and therapeutic outcomes. Bidirectional communication between the gut and the brain, mediated through microbial metabolites, neurotransmitters, and neural signaling pathways, shapes the tumor microenvironment and systemic inflammation. CRC cells not only modify the gut microbiota but also release neuroactive molecules that influence neural circuits, further impacting tumor growth. The autonomic nervous system regulates gut motility, immune responses, and inflammation, contributing to CRC progression. The gut microbiome's production of bioactive molecules, such as short-chain fatty acids and neurotransmitters, further modulates brain activity, promoting tumor metastasis and immune evasion. This review summarizes the complex interactions within the GBA and their implications for CRC, with a focus on immune modulation, microbial dysbiosis, and neuroimmune interactions. We highlight the therapeutic potential of targeting the GBA, including microbiome modulation, neurotransmitter-specific therapies, and psychological interventions, which could complement existing CRC treatments. Future research is essential to further elucidate the precise molecular mediators of the GBA and their impact on CRC biology, laying the groundwork for novel, targeted therapeutic strategies that could improve patient outcomes.},
}

@article {pmid40484186,
year = {2025},
author = {Ayres, KR and Liuzzi, JP and Lewis, FC and Mobarki, HM},
title = {Investigating Zinc's role in Mitigating Blood Lead Levels' Toxicity on Gut Microbiota Diversity: NHANES 2007-2010.},
journal = {Toxicology letters},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.toxlet.2025.06.001},
pmid = {40484186},
issn = {1879-3169},
abstract = {INTRODUCTION: Zinc serves as a cofactor for numerous vital processes across species. Microorganisms that make up the gut microbiome rely on these zinc-dependent mechanisms to perform essential functions, contributing to a diverse and stable microbial environment. Environmental contaminants, such as lead, has been shown to disrupt diversity and stability. The purpose of this study was to determine whether zinc serves as an effect modifier against elevated blood lead levels (BLL) on gut microbiota diversity.

METHODS: The 2007-2008 and 2009-2010 NHANES datasets were utilized to conduct a cross-sectional complex survey analysis aimed at determining whether zinc intake acts as a protective factor against changes in microbiome diversity associated with BLL, using enterolactone (ENL) as a biomarker. A multiple linear regression was conducted to evaluate whether an interaction between BLL and zinc intake could predict ENL. The model included fiber intake and BMI as covariates.

RESULTS: BMI and fiber intake were identified as covariates. Fiber intake was a confounding variable in the relationship between zinc and ENL levels. Lead was found to decrease ENL levels (p= 0.002). The interaction between zinc and BLL was marginally significant (p=0.089).

CONCLUSION: This study suggests that lead's impact on gut microbial diversity may depend on zinc status. These findings emphasize the importance of accounting for dietary confounders, such as fiber intake, to improve model accuracy and interpretation. While additional research is needed to confirm zinc's potential protective role, public health strategies encouraging adequate zinc and fiber intake may in part help support microbial resilience and reduce lead's effects on the gut microbiota.},
}

@article {pmid40484124,
year = {2025},
author = {Liu, Y and Li, Z and Shen, L and Shuai, K and Zhang, C and Ning, Z},
title = {Trends in Food Protein-Induced Allergic Proctocolitis (FPIAP): Mechanisms and Treatment Targeting Gut Microbiome.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102634},
doi = {10.1016/j.clinre.2025.102634},
pmid = {40484124},
issn = {2210-741X},
abstract = {BACKGROUND: Food protein-induced allergic proctocolitis (FPIAP) is a non-IgE-mediated food allergy characterized by subacute or chronic inflammatory processes in the gut. Unlike IgE-mediated food allergies that may cause multi-organ syndromes, non-IgE-mediated food allergies mainly affect the gastrointestinal tract. The incidence of FPIAP is rising globally, becoming a significant health concern.

OBJECTIVES: This article aims to systematically review the epidemiological characteristics, pathogenesis, cell death programs involved in FPIAP, and its relationship with the gut microbiota. It also explores therapeutic developments targeting the intestinal microbiota.

METHODS: We conducted a comprehensive literature search across multiple databases, including PubMed, Web of Science, and Scopus, up to December 2024. Studies were selected based on predefined inclusion and exclusion criteria. Data extraction and quality assessment were performed by two independent reviewers.

RESULTS: The review identified key epidemiological trends, highlighting the increasing incidence of FPIAP. The pathogenesis section elucidates the mechanisms underlying non-IgE-mediated allergies, emphasizing the role of the gut microbiome in mediating dietary factors and immune responses. Specific cell death programs, such as apoptosis and pyroptosis, were found to be involved in the progression of FPIAP. Therapeutic strategies targeting the gut microbiota show promise in managing FPIAP, with probiotics and prebiotics emerging as potential interventions.

CONCLUSIONS: This review provides valuable insights into the mechanisms of FPIAP and highlights the potential of microbiota-targeted therapies. Future research should focus on large-scale clinical trials to validate the efficacy of these interventions and further explore the complex interplay between diet, gut microbiota, and immune responses in FPIAP.},
}

@article {pmid40484118,
year = {2025},
author = {Jin, MJ and Barron, AB and He, SY and He, XJ and Huang, Q and Zhang, LZ and Wang, ZL and Wu, XB and Yan, WY and Zeng, ZJ},
title = {Bombella intestini: A probiotic honeybee(Apis mellifera) gut bacterium.},
journal = {Journal of insect physiology},
volume = {},
number = {},
pages = {104836},
doi = {10.1016/j.jinsphys.2025.104836},
pmid = {40484118},
issn = {1879-1611},
abstract = {Honey bee colonies are facing increasing environmental stressors that threaten their health and lifespan. While the gut microbiota may play a role in honey bee physiology, the specific functions of certain bacterial species remain unclear. This study investigates whether Bombella intestini, a bacterium highly enriched in the queen gut but nearly absent in worker bees, can act as a probiotic to promote honey bee growth, metabolism, and lifespan. Our results show that B. intestini can survive in larval food and the larval gut. When larval food is inoculated with B. intestini there is increased tryptophan in both the larval diet and larval hemolymph. Bees fed this diet had a longer lifespan. This study identifies B. intestini as a potential probiotic for honey bees, providing a microbiome-based strategy to enhance their growth and longevity. These findings open new avenues for improving honey bee health management through microbial supplementation.},
}

@article {pmid40483843,
year = {2025},
author = {Azevedo, MJ and Ferreira, AF and Loginov, D and Novák, P and Falcão-Pires, I and Ramalho, C and Buijs, MJ and Brandt, BW and Zaura, E and Trindade, F and Sampaio-Maia, B},
title = {Salivary proteome and microbiome in pregnancy and postpartum: An exploratory study on the relation with arterial hypertension.},
journal = {Archives of oral biology},
volume = {177},
number = {},
pages = {106319},
doi = {10.1016/j.archoralbio.2025.106319},
pmid = {40483843},
issn = {1879-1506},
abstract = {OBJECTIVES: Arterial hypertension (AH) influences salivary gland physiology and oral health, being associated with a higher incidence of periodontal disease in pregnant women. Evidence points to a bidirectional relationship between the oral microbiota and blood pressure regulation. Therefore, this study aimed to characterize the oral health of pregnant women and AH-associated changes in the salivary proteome and microbiome during pregnancy and postpartum.

DESIGN: Ten healthy women and ten women with AH were enrolled. Saliva was collected during pregnancy and six months postpartum. The salivary proteome was characterized by shotgun label-free mass spectrometry analysis. Specific proteins were validated through parallel reaction monitoring (PRM). The oral microbiota was characterized via 16S rRNA gene amplicon sequencing (V4 region). The periodontal health and the caries history was assessed during pregnancy.

RESULTS: Pregnant women with AH had lower junction plakoglobin (JUP)- and desmoplakin (DSP)-specific peptide levels than healthy women, confirmed by the PRM approach. The levels of these proteins correlated negatively with periodontal health indexes, which were higher in pregnant women with AH. In AH, nitrate-reducing microorganisms had lower abundance, correlating positively with JUP and DSP-specific peptides.

CONCLUSIONS: The salivary proteome and microbiota are shaped by AH during and after pregnancy. Further research is required to understand the underlying mechanisms impairing oral health in AH.},
}

@article {pmid40483796,
year = {2025},
author = {Liu, MY and He, SF and Li, YY and Shen, JJ and Li, JJ and Li, YS and Liu, YY and Wu, T and Li, JB and Hu, LF},
title = {Alterations in the intestinal fungal microbiome of patients with severe fever with thrombocytopenia syndrome.},
journal = {Journal of infection and public health},
volume = {18},
number = {9},
pages = {102837},
doi = {10.1016/j.jiph.2025.102837},
pmid = {40483796},
issn = {1876-035X},
abstract = {BACKGROUND: Aspergillus coinfection in patients with severe fever with thrombocytopenia syndrome (SFTS), is a serious clinical challenge associated with increased mortality. Understanding the factors contributing to this co-infection is crucial for improving patient outcomes. This study aimed to reveal the role of the intestinal mycobiome in SFTS severity and the risk of Aspergillus coinfection, with the goal of identifying potential therapeutic targets.

METHODS: Fecal samples were collected from 80 patients both during their hospitalization and post-discharge. Internal transcribed spacer (ITS) amplicon sequencing and fungal profiling of intestine were performed. R statistical software (version 3.5.1) was used for data processing and analysis.

RESULTS: The intestinal mycobiomes of SFTS patients showed strong alterations characterized by increased Aspergillus species, and a highly heterogeneous mycobiome configuration compared to healthy controls. The Aspergillus had a positive correlation with coinfection of invasive pulmonary aspergillosis (IPA) and disease severity of SFTS (p < 0.001), whereas Saccharomycetales and Candida were more abundant in SFTS patients without IPA (p < 0.001). In SFTS patients with IPA, A. subversicolor, A. flavus and A. penicillioides were the three most common fungal species. Longitudinal dynamic detection revealed that patients who experienced significant fluctuations in their intestinal mycobiome tended to have more severe illness. After recovering, the gut mycobiome of patients can recover and stabilize within a month.

CONCLUSION: The research highlighted enrichment of intestinal Aspergillus was conducive to IPA and disease severity in SFTS patients. Monitoring the gut mycobiome could potentially be used as a biomarker to assess disease severity of SFTS.},
}

@article {pmid40481438,
year = {2025},
author = {Babalola, OO and Osuji, IE and Akanmu, AO},
title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {40},
pmid = {40481438},
issn = {2730-6844},
abstract = {OBJECTIVES: The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.).

DATA DESCRIPTION: The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).},
}

@article {pmid40462893,
year = {2025},
author = {Xiong, X and Ho, M and Jaber, K and Mishra, R and Charytan, A and Zaidan, N and Schlamp, F and Fishman, GI and Nazzal, L},
title = {Colonization with Oxalobacter formigenes slows the progression of CKD and reduces cardiac remodeling in CKD.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40462893},
issn = {2692-8205},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK129675/DK/NIDDK NIH HHS/United States ; R01 DK137473/DK/NIDDK NIH HHS/United States ; },
abstract = {Accumulation of oxalate in patients with chronic kidney disease (CKD) is associated with CKD progression and increased risk of cardiac death. Whether reducing plasma or urine oxalate slows CKD progression and prevents cardiovascular complications remains unexplored. We colonized the intestines of control and CKD mice with Oxalobacter formigenes (Oxf), an oxalate-degrading microorganism. The mice were fed with the oxalate precursor hydroxyproline for 23 weeks at which time we assessed pathological changes in the kidney and heart. We demonstrate that Oxf reduces plasma oxalate (pOx) and creatinine levels, mitigates inflammation and fibrosis in the kidney, and reduces pathologic cardiac remodeling in the hearts of CKD mice. RNA-seq analysis of ventricular tissue of CKD mice reveals dysregulated expression of metabolic pathways while Oxf colonization reverses these changes. These findings demonstrate that oxalate accumulation plays a role not only in CKD progression but also in associated cardiovascular complications and suggest that strategies to reduce plasma oxalate levels may have therapeutic benefit.},
}

@article {pmid40483759,
year = {2025},
author = {Zhang, F and Peng, R and Xie, Y and Ji, X and Liu, S and Jiang, H},
title = {Cultivar-specific response of a root-associated microbiome assembly of rice to cadmium pollution.},
journal = {Plant physiology and biochemistry : PPB},
volume = {227},
number = {},
pages = {110128},
doi = {10.1016/j.plaphy.2025.110128},
pmid = {40483759},
issn = {1873-2690},
abstract = {Rice (Oryza sativa L.) cadmium (Cd) contamination is a serious threat to global food security and human health. However, the response of rice root-associated microbiomes to Cd pollution remains unclear. This study investigate the interactions between the root-associated microbiome and plant metals using environmental and microbial analysis methods, to reveal the potential mechanisms of the root microbiomes regulating the Cd accumulation in rice. The results showed that the grain Cd concentrations of the two low-Cd accumulation (LA) cultivars were 34-46 % lower than that of the high-Cd accumulation (HA) cultivars, whereas the iron (Fe) content in the LA roots was significantly higher than that in the HA roots. The root Fe content was significantly negatively correlated with the Cd concentration of grain (R = -0.681, p < 0.05). 16S rRNA amplicon sequencing showed that rice planting significantly changed the diversity of the root-associated bacterial community and formed a unique core endophytic microbiome (such as Xanthobacteraceae and Sphingomonas) under Cd stress. LA cultivars assembled more root core microbial taxa, which promoted siderophore secretion and root Fe uptake, thereby inhibiting Cd uptake by rice. Chrome azurol S plate detection confirmed that the LA rhizosphere was enriched with 1-9-fold more siderophore-secreting microorganisms than the HA rhizosphere. This study provides new insights into the effects of root-associated microbiomes on Cd accumulation in plant and will help develop new strategies for the safe production of rice.},
}

@article {pmid40483691,
year = {2025},
author = {Burgmer, S and Meyer Zu Altenschildesche, FL and Gyenis, A and Lee, HJ and Vilchez, D and Giavalisco, P and Fichant, A and Uhlirova, M and Storelli, G},
title = {Endosymbiont control through non-canonical immune signaling and gut metabolic remodeling.},
journal = {Cell reports},
volume = {44},
number = {6},
pages = {115811},
doi = {10.1016/j.celrep.2025.115811},
pmid = {40483691},
issn = {2211-1247},
abstract = {Animals coexist with bacteria and need to keep these microorganisms under tight control. To achieve such control, pattern recognition receptors (PRRs) sense bacterial cues and induce the production of antimicrobials. Here, we uncover a metabolic arm in the control of symbionts by PRRs. We show that, in Drosophila, the PRRs PGRP-LC and PGRP-LE act independently of canonical NF-κB signaling to repress essential metabolic functions in the gut, such as digestion and central carbon metabolism. This metabolic switch affects commensal populations and drastically reduces intestinal and systemic populations of the intracellular parasite Wolbachia. We propose that intestinal metabolic remodeling complements immune responses by imposing nutrient restriction on intracellular bacteria, whose lifestyle protects them from antimicrobials. Our findings reveal a role for PRRs in bacterial control beyond canonical immune pathways and provide insights into how microbial signals modulate symbiotic populations but also nutrition and metabolism in animals.},
}

@article {pmid40483623,
year = {2025},
author = {Chi, Y and Luo, M and Ding, C},
title = {The role of microbiota in fish spoilage: biochemical mechanisms and innovative preservation strategies.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {7},
pages = {89},
pmid = {40483623},
issn = {1572-9699},
support = {202411049301XJ//National College Student Innovation and Entrepreneurship Training Program Funding Project/ ; },
mesh = {*Fishes/microbiology ; *Microbiota ; Animals ; *Food Preservation/methods ; *Food Microbiology ; *Seafood/microbiology ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Fish spoilage is a microbially-mediated biochemical process resulting in quality deterioration, economic losses, and food safety risks. Studies have indicated that spoilage microbiota are phylogenetically diverse, with Gram-negative bacteria (Pseudomonas, Shewanella, Photobacterium) representing primary spoilage organisms, and Gram-positive bacteria (Lactobacillus, Brochothrix) causing spoilage only under specific conditions. Microorganisms cause spoilage through the utilization of three main metabolic processes: (i) proteolytic degradation of muscle proteins, (ii) lipolytic breakdown of triglycerides, and (iii) production of volatile bioactive organic compounds and biogenic amines. By combining high-throughput sequencing with metabolomics, researchers have been uncovering strain-specific metabolic networks and how they are influenced by environmental factors such as temperature, pH, and packaging. This review systematically examines: (1) patterns of taxonomic succession in spoilage microbiota, (2) enzymatic and biochemical pathways involved in spoilage, and (3) innovative preservation strategies targeting spoilage consortia. Emerging technologies, such as bacteriocin-mediated biopreservation, phage therapy, and modified atmosphere packaging, show considerable promise in inhibiting spoilage organisms while maintaining the sensory qualities of the fish. Microbiome-directed interventions combined with predictive modeling and precision storage systems also represent a novel approach to fish preservation. There is a critical need to integrate traditional microbiology with the use of multi-omic technologies for the development of sustainable, microbiota-based preservation strategies that address global seafood security challenges.},
}

*Fishes/microbiology
*Microbiota
Animals
*Food Preservation/methods
*Food Microbiology
*Seafood/microbiology
*Bacteria/metabolism/classification/genetics

@article {pmid40483501,
year = {2025},
author = {Cuthbertson, L and Hatfield, L and Gavillet, H and Hardman, M and Marsh, R and Rivett, DW and van der Gast, C},
title = {Species turnover within cystic fibrosis lung microbiota is indicative of acute pulmonary exacerbation onset.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {140},
pmid = {40483501},
issn = {2049-2618},
support = {NE/H019456/1//Natural Environment Research Council/ ; NE/H019456/1//Natural Environment Research Council/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; VIA 045//Cystic Fibrosis Trust/ ; },
mesh = {*Cystic Fibrosis/microbiology ; Humans ; *Lung/microbiology ; *Microbiota ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Disease Progression ; Young Adult ; },
abstract = {BACKGROUND: Acute pulmonary exacerbations (PEx) are associated with increased morbidity and earlier mortality for people living with cystic fibrosis (pwCF). The most common causes of PEx in CF are by bacterial infection and concomitant inflammation leading to progressive airway damage. To draw attention to the seriousness of PEx they have been labelled as 'lung attacks', much like a 'heart attack' for acute myocardial infarction. Treatment typically starts when a pwCF presents with worsening respiratory symptoms. Hence, there is a pressing need to identify indicative biomarkers of PEx onset to allow more timely intervention. Set within an ecological framework, we investigated temporal microbiota dynamics to connect changes in the lung microbiota of pwCF to changes in disease states across a PEx event.

RESULTS: Species-time relationships (STR) describe how the richness of a community changes with time, here STRs were used to assess temporal turnover (w) within the lung microbiota of each pwCF (n = 12, mean sample duration 315.9 ± 42.7 days). STRs were characterised by high interpatient variability, indicating that turnover and hence temporal organization are a personalized feature of the CF lung microbiota. Greater turnover was found to be significantly associated with greater change in lung function with time. When microbiota turnover was examined at a finer scale across each pwCF time series, w-values could clearly be observed to increase in the exacerbation period, then peaking within the treatment period, demonstrating that increases in turnover were not solely a result of perturbations caused by PEx antibiotic interventions. STR w-values have been found to have a remarkable degree of similarity for different organisms, in a variety of habitats and ecosystems, and time lengths (typically not exceeding w = 0.5). Here, we found w-values soon increased beyond that. It was therefore possible to use the departure from that expected norm up to start of treatment to approximate onset of PEx in days (21.2 ± 8.9 days across the study participants).

CONCLUSIONS: Here, we illustrate that changes in turnover of the lung microbiota of pwCF can be indicative of PEx onset in considerable advance of when treatment would normally be initiated. This offers translational potential to enable early detection of PEx and consequent timely intervention. Video Abstract.},
}

*Cystic Fibrosis/microbiology
Humans
*Lung/microbiology
*Microbiota
Male
Female
*Bacteria/classification/genetics/isolation & purification
Adult
Disease Progression
Young Adult

@article {pmid40483308,
year = {2025},
author = {Behel, V and Hait, S and Noronha, V and Chowdhury, A and Chandrani, P and Patil, V and Menon, N and Mishra, R and Bawaskar, B and Dahimbekar, G and Shah, M and Kaushal, R and Veldore, V and Goswami, H and Bharde, A and Khandare, J and Shafi, G and Choughule, A and Tyagi, N and Desai, S and Prabhash, K and Dutt, A},
title = {Assessment of plasma derived microbiome profiles in lung cancer using targeted and whole exome sequencing.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {62},
pmid = {40483308},
issn = {2056-7189},
support = {01/ICMRCAREP-2023-0000278/AD/DevDiv//Indian Council of Medical Research/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/blood/genetics ; *Exome Sequencing/methods ; *Microbiota/genetics ; Female ; Computational Biology/methods ; Male ; Adenocarcinoma of Lung/microbiology ; Middle Aged ; Aged ; },
abstract = {Microbial infections contribute to ~20% of malignancy. Plasma-derived cell-free DNA presents a promising avenue for non-invasive cancer diagnostics, capturing microbial signatures. We analyzed 261 plasma from 50 patients with lung adenocarcinoma by targeted and whole exome sequencing at 10,000 × and 340 × depth, respectively. Comparative analyses of Kraken 2 and IPD2 reveal substantial discrepancies, highlighting challenges in microbial DNA quantification and the need for stringent bioinformatics approaches to ensure accurate cancer microbiome profiling.},
}

Humans
*Lung Neoplasms/microbiology/blood/genetics
*Exome Sequencing/methods
*Microbiota/genetics
Female
Computational Biology/methods
Male
Adenocarcinoma of Lung/microbiology
Middle Aged
Aged

@article {pmid40483298,
year = {2025},
author = {Leeflang, J and Wright, JA and Worthley, DL and Din, MO and Woods, SL},
title = {Evolutionary adaptation of probiotics in the gut: selection pressures, optimization strategies, and regulatory challenges.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {96},
pmid = {40483298},
issn = {2055-5008},
support = {2020305//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Bushell fellowship//Gastroenterological Society of Australia (GESA)/ ; 1R01 EB030134-01A1//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/growth & development ; *Gastrointestinal Tract/microbiology ; Selection, Genetic ; *Adaptation, Physiological ; Biological Evolution ; },
abstract = {Probiotics and live bacterial therapeutics are garnering increased attention for use in human health and have the potential to revolutionise the treatment of gastrointestinal diseases. However, a pervasive feature of bacteria that must be considered in the design of safe and effective probiotics and live bacterial therapeutics is their capacity for rapid evolution, both at the individual (epi)genetic level and in terms of population dynamics. Here we summarise gastrointestinal-specific evolution of bacteria, focussing on genetic and population levels of adaptation to factors such as carbon source availability, environmental stressors, and interactions with the native microbiome. We also address regulatory and safety considerations for the development of probiotics and live biotherapeutics from an evolutionary perspective, with a discussion of methods that utilise evolution to improve probiotic safety and efficacy via directed evolution, in comparison to another popular approach, genetic engineering.},
}

*Probiotics
Humans
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/growth & development
*Gastrointestinal Tract/microbiology
Selection, Genetic
*Adaptation, Physiological
Biological Evolution

@article {pmid40483244,
year = {2025},
author = {Duong, JT and Hayden, HS and Verster, AJ and Pope, CE and Miller, C and Kelsi Penewit, and Salipante, SJ and Rowe, SM and Solomon, GM and Nichols, D and Kelly, A and Schwarzenberg, SJ and Freedman, SD and Hoffman, LR},
title = {Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.05.006},
pmid = {40483244},
issn = {1873-5010},
abstract = {BACKGROUND: People with cystic fibrosis (PwCF) often have fecal dysbioses relative to those without CF, characterized by increased pro-inflammatory microbiota and gastrointestinal (GI) inflammation as measured by fecal calprotectin, suggesting that inflammation contributes to CF GI disease. The multicenter observational PROMISE study (NCT04038047) found that calprotectin decreased in PwCF treated with elexacaftor/tezacaftor/ivacaftor (ETI). To better understand the dynamics between fecal dysbiosis and GI inflammation, we characterized the microbiomes of fecal samples from PROMISE and the relationships with calprotectin before, 1-month post, and 6-months post ETI.

METHODS: Fecal microbiota from participants ≥12 y/o were determined by shotgun metagenomic sequencing with random forest modeling and multivariate linear regression analysis to define relationships between microbiota, calprotectin, and deltaF508 genotype before and after ETI.

RESULTS: We analyzed 345 samples from 124 participants. At baseline, we observed community-level differences in the fecal microbiota among participants with abnormal compared to normal calprotectin. With ETI, the relative abundances of 7 bacterial species - Escherichia coli, Staphylococcus aureus, Clostridium scindens, Enterocloster clostridioformis, Clostridium butyricum, Anaeroglobus geminatus, and Ruminococcus gnavus - decreased significantly, correlating with calprotectin decrease. We detected community-level differences in the fecal microbiota based on CFTR genotype and a distinct pattern of microbiota change in F508del homozygous compared to heterozygous participants after ETI.

CONCLUSIONS: We identified 7 species for which fecal abundances decreased with ETI and correlated with calprotectin decrease, supporting a close relationship between fecal microbiota and inflammation in PwCF. Future work will define these relationships with metabolites and GI symptoms during long-term ETI therapy.},
}

@article {pmid40483188,
year = {2025},
author = {Arif, SJ and Graham, SP and Abdill, RJ and Blekhman, R},
title = {Analyzing human gut microbiome data from global populations: challenges and resources.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.05.008},
pmid = {40483188},
issn = {1878-4380},
abstract = {Research on the human gut microbiome is expanding rapidly; yet, most published studies focus on populations from high-income regions such as North America and Europe. Underrepresentation of populations from low- and middle-income countries in the microbiome literature limits the generalizability of microbiome-health associations. These challenges are compounded by computational barriers, including biases in reference databases, nonrepresentative metadata, and infrastructure limitations in low- and middle-income countries. However, recent efforts in large-scale global sampling have begun to address these problems. This review provides recommendations for future research efforts applying computational analysis to global microbiome data, including guidelines to initiate and maintain equitable partnerships, identify representative datasets, overcome technical limitations, and contextualize results at the global scale.},
}

@article {pmid40482930,
year = {2025},
author = {Adiningrat, A and Maulana, I and Fadhlurrahman, AG and Yumoto, H},
title = {Probiotic bacteria from asymptomatic necrotic tooth can regulate the microbiome homeostasis.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107791},
doi = {10.1016/j.micpath.2025.107791},
pmid = {40482930},
issn = {1096-1208},
abstract = {OBJECTIVE: This study was performed to identify and isolate the dominant bacteria from a chronic asymptomatic necrotic root canal and investigate in vitro its potential postbiotics effect at the biofilm maturation maintaining root canal microbiome homeostasis.

METHODS: For bacterial identification of an in vivo root canal sample, metagenomic analysis was applied, followed by single colony isolation and PCR analysis. Cell free supernatant (CFS) was then cultivated through serial L paracasei culture procedures prior antibiofilm analysis. Antibiofilm effects of the CFS product were evaluated using in vitro biofilm analysis against S. mutans and E. faecalis. Biofilm mass analysis was measured by using colorimetric approach with cresyl-vast violet staining, morphological appearance was observed using both phase-contrast and scanning electron microscope (SEM). Shapiro-Wilk analysis was applied for normality test, followed by the ANOVA to compare multiple groups or a student t-test for independent two groups mean comparisons.

RESULTS: The isolated root canal bacteria produced biofilm mass that was similar to the Enterococcus faecalis control pathogenic biofilm. From the morphological analysis suggested that population of the isolated bacteria were predominantly occupied by rod-shaped rather than cocci-shaped inhabitants. Further metagenomic analysis indicated that the isolated dominant bacteria in the mixed culture were mainly identified as probiotic bacteria, Lacticaseibacillus paracasei. Moreover, the functional analysis revealed that the L. paracasei cell free supernatant product (CFS) exhibited a promising positive effect in biofilm structure integrity disturbances of S. mutans and E. faecalis.

CONCLUSIONS: The isolated Lacticaseibacillus paracasei from the root canal of a chronic asymptomatic necrotic tooth, produces potential postbiotic products that demonstrated a disruptive ability against Streptococcus mutans and Enterococcus faecalis biofilm integrity.},
}

@article {pmid40482893,
year = {2025},
author = {Ning, Z and Dou, D and Liu, J and Qin, X and Ang, YH and Yang, T and Zhang, J},
title = {Sulfur modification enhances promotion of carbon-iron composites on carbon chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132776},
doi = {10.1016/j.biortech.2025.132776},
pmid = {40482893},
issn = {1873-2976},
abstract = {Efficient synthesis of caproate is crucial for efficient recovery of organic wastes. However, the yield and selectivity of caproate are limited by the efficiency of carbon chain elongation (CCE). This study presents sulfur-modified carbon-iron composites (BC[S-Fe]) as an innovative approach to enhance CCE for efficient caproate biosynthesis. Unlike conventional carbon-iron materials (BC[Fe]), sulfur modification stabilized nano-zero-valent iron (Fe[0]) against oxidation and amplified redox activity, achieving an 83 % higher caproate yield (6914 mg·L[-1]) and 58 % carbon conversion efficiency. BC[S-Fe [1/5]] (S:Fe = 1:5) outperformed BC, Fe[0] and BC[Fe] by enriching electroactive bacteria (e.g., Rummeliibacillus suwonensis, Seramator thermalis, and Rubeoparvulum massiliense) that upregulated electron transfer genes and CCE metabolic genes. Additionally, BC[S-Fe [1/5]] enhanced biofilm formation and quorum sensing, fostering microbial synergy to optimize electron flux. This work pioneers the integration of sulfur-modified composites into microbial CCE systems, offering a novel strategy to optimize caproate synthesis through enhanced electron transfer and functional microbiome engineering.},
}

@article {pmid40482791,
year = {2025},
author = {Gazi, U and Bahceciler, NN},
title = {Oral microbiota in allergic diseases, and sublingual allergen immunotherapy.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {},
number = {},
pages = {110538},
doi = {10.1016/j.clim.2025.110538},
pmid = {40482791},
issn = {1521-7035},
abstract = {Allergic diseases with their epidemic prevalence on the rise have been one of the major global health problems of the 21st century. The association of increased prevalence with lifestyle changes including increased urbanization, and hygiene practices highlighted the importance of host-microbiome interactions for maintaining immune homeostasis. In support, numerous studies demonstrated altered gut microbiome composition in allergic patients, and suggested dysbiosis as a possible cause of allergic diseases. Nevertheless, despite being the second largest microbiota in the human body, oral microbiota has not yet received the attention it deserves in the literature. With this review article, we aim to highlight its significance by summarizing the data obtained from studies evaluating oral microbiome composition in patients with allergic respiratory diseases. Additionally, their importance will be further elaborated by discussing the findings presented by animal and human studies investigating the possible effect of oral probiotic uptake to the clinical efficacy of sublingual allergen immunotherapy.},
}

@article {pmid40482721,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Root architecture and the rhizosphere microbiome: shaping sustainable agriculture.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {112599},
doi = {10.1016/j.plantsci.2025.112599},
pmid = {40482721},
issn = {1873-2259},
abstract = {Understanding root architecture and exudation is fundamental for enhancing crop productivity and promoting sustainable agriculture. Historically, plant researchers have focused on above-ground traits to increase yield and reduce input dependence. However, below-ground traits, especially those related to the root system, are equally critical yet often overlooked due to phenotyping challenges. Root architecture, including some root traits, i.e., lateral root density, root hair abundance, and root tip number, plays central roles in plant establishment, stress tolerance, and the recruitment of beneficial microbes in the rhizosphere. Root exudates, a complex array of chemical compounds released by roots, vary with plant species, developmental stage, and environmental conditions. These compounds act as signals and nutrients, shaping the composition and function of rhizosphere microbial communities. In turn, the microbiome of rhizosphere contributes to plant health by facilitating nutrient uptake, enhancing stress resilience, and providing defense against pathogens. Integrating root traits into breeding programs offers promising opportunities to select for genotypes that are more efficient in recruiting beneficial microbes. Heritable root traits, such as increased branching, finer roots, and higher exudation capacity, can enhance microbiome assembly and stability. The assessment of genes can also regulate of these traits and represent targets for genomics-assisted selection. Some strategies, such as microbiome engineering, particularly through the design of synthetic microbial communities (SynComs), can be used to modulate root architecture and optimize plant-microbe interactions. Despite these promising outcomes, challenges remain in translating SynCom applications to the field due to environmental variability, native microbial competition, and limited understanding of host genetic controls. This review discusses how root architecture shapes the rhizosphere microbiome and explores strategies, such as trait-based breeding and microbiome engineering, for advancing sustainable crop production.},
}

@article {pmid40482640,
year = {2025},
author = {DeLeon, O and Mocanu, M and Tan, A and Sidebottom, AM and Koval, J and Ceccato, HD and Kralicek, S and Colgan, JJ and St George, MM and Lake, JM and Cooper, M and Xu, J and Moore, J and Su, Q and Xu, Z and Ng, SC and Chan, FKL and Tun, HM and Cham, CM and Liu, CY and Rubin, DT and Martinez-Guryn, K and Chang, EB},
title = {Microbiome mismatches from microbiota transplants lead to persistent off-target metabolic and immunomodulatory effects.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.014},
pmid = {40482640},
issn = {1097-4172},
abstract = {Fecal microbiota transplant (FMT) is an increasingly used intervention, but its suitability to restore regional gut microbiota, particularly in the small bowel (SB), must be questioned because of its predominant anaerobic composition. In human subjects receiving FMT by upper endoscopy, duodenal engraftment of anaerobes was observed after 4 weeks. We hypothesized that peroral FMTs create host-microbe mismatches that impact SB homeostasis. To test this, antibiotic-treated specific-pathogen-free (SPF) mice were given jejunal, cecal, or fecal microbiota transplants (JMTs, CMTs, or FMTs, respectively) and studied 1 or 3 months later. JMT and FMT altered regional microbiota membership and function, energy balance, and intestinal and hepatic transcriptomes; JMT favored host metabolic pathways and FMT favored immune pathways. MTs drove regional intestinal identity (Gata4, Gata6, and Satb2) and downstream differentiation markers. RNA sequencing (RNA-seq) of metabolite-exposed human enteroids and duodenal biopsies post-FMT confirmed transcriptional changes in mice. Thus, regional microbial mismatches after FMTs can lead to unintended consequences and require rethinking of microbiome-based interventions.},
}

@article {pmid40482531,
year = {2025},
author = {Yan, R and Manjunatha, V and Thomas, A and Shankar, V and Lumpkins, B and Hoerr, FJ and Greene, A and Jiang, X},
title = {Comparative effects of vegetarian diet and rendered animal by-product on the chicken gut health.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105360},
doi = {10.1016/j.psj.2025.105360},
pmid = {40482531},
issn = {1525-3171},
abstract = {Rendered animal proteins and fats can provide vital nutrients for poultry at affordable prices. With growing interest in reintroducing rendered animal by-products into poultry diets, this study investigated the effects of replacing a portion of soybean meal and vegetable fat with rendered animal proteins and fats in a standard vegetarian chicken diet. The study focused on the changes in gut and liver histopathology, and gut microbiome composition and functions. Five diet treatments were formulated to be isocaloric and isonitrogenous and balanced for amino acids, including a standard vegetarian control diet and four diets containing rendered animal by-products. A total of 15 pens with 50 chickens each were assigned one of the five diets from hatch to 42 days of age, with three replicate pens per treatment. On days 28 and 42, six birds were randomly selected from two pens per treatment and humanely euthanized by cervical dislocation. Cecal samples were collected for microbial enumeration and DNA extraction, while gut and liver histopathology analyses were conducted on day 42. Enumeration of Clostridium perfringens was performed under anaerobic conditions using selective media and metagenomic sequencing was used to assess taxonomic and functional profiles of the microbiome. Statistical analysis included data transformation, permutational multivariate analysis of variance, and differential abundance testing. No significant differences were observed between the vegetarian control and rendered animal by-product diets in gut or liver histopathology, C. perfringens levels, or microbiome composition, indicating that inclusion of animal by-products did not significantly affect broiler intestinal health or microbial functions over a 42-day period. These findings suggest that partially replacing soybean meal and vegetable fat with rendered animal by-products can be a safe and cost-effective alternative to plant-based ingredients in poultry diets.},
}

@article {pmid40482059,
year = {2025},
author = {Rendina, M and Turnbaugh, PJ and Bradley, PH},
title = {Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf131},
pmid = {40482059},
issn = {2160-1836},
abstract = {Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all known human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; two of these, 6-mercaptopurine by xanthine dehydrogenase (XDH) and 5-fluorouracil by dihydropyrimidine dehydrogenase (DPYD), have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism.},
}

@article {pmid40481968,
year = {2025},
author = {van Iersel, LEJ and Beijers, RJHCG and Simons, SO and Schuurman, LT and Shetty, SA and Roeselers, G and van Helvoort, A and Schols, AMWJ and Gosker, HR},
title = {Characterizing gut microbial dysbiosis and exploring the effect of prebiotic fiber supplementation in patients with COPD.},
journal = {European journal of nutrition},
volume = {64},
number = {5},
pages = {210},
pmid = {40481968},
issn = {1436-6215},
support = {10.2.16.119//Longfonds/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Prebiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Male ; *Dietary Fiber/administration & dosage ; Female ; *Dysbiosis/microbiology ; *Dietary Supplements ; Middle Aged ; Double-Blind Method ; Aged ; Feces/microbiology ; Cross-Sectional Studies ; Vitamin D/administration & dosage ; Tryptophan/administration & dosage ; },
abstract = {PURPOSE: Chronic Obstructive Pulmonary Disease (COPD) is associated with poor dietary quality that may lead to gut microbiota imbalances. A healthy gut microbiome contributes to metabolic health and immune function through production of metabolites like short-chain fatty acids. Prebiotic fibers positively influence microbiota by promoting the production of beneficial metabolites. This study aimed to assess altered gut microbiota composition in patients with COPD and to explore the effects of targeted multi-nutrient supplementation including prebiotic fibers on these outcomes.

METHODS: An exploratory analysis was performed within the double-blinded placebo-controlled NUTRECOVER-trial to gain preliminary insights into the effects of the nutritional intervention. The cross-sectional baseline comparison included 32 patients with COPD and 32 age-matched healthy references. Subsequently, patients were randomly assigned to a multi-nutrient supplement including prebiotic fibers, vitamin D, tryptophan, and N-3 long-chain poly unsaturated fatty acids (n = 16) or placebo (n = 16) for three months. Stool samples, blood samples and food diaries were obtained before and after the intervention.

RESULTS: Higher relative abundance of Bacteroidota (0.50 ± 0.13 vs. 0.41 ± 0.14, p = 0.010), and lower Firmicutes (0.40 ± 0.14 vs. 0.49 ± 0.12, p = 0.007) were found in patients compared with healthy controls. Patients also showed lower alpha diversity (5.80 ± 0.32 vs. 5.99 ± 0.30, p = 0.017) and higher inter-individual variability (0.51 ± 0.16 vs. 0.48 ± 0.10, p < 0.001). No effects of the nutritional intervention on gut microbiome and systemic inflammation were shown at 3 months.

CONCLUSION: Patients with COPD exhibit differences in gut microbiota composition compared with healthy controls. Three months of multi-nutrient supplementation is insufficient to show changes in microbiome composition. The ongoing NUTRECOVER-trial will show the potential of long-term prebiotic fiber supplementation in this susceptible patient population.

TRIAL REGISTRATION NUMBER: clinicaltrials.gov: NCT03807310.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology
*Prebiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
Male
*Dietary Fiber/administration & dosage
Female
*Dysbiosis/microbiology
*Dietary Supplements
Middle Aged
Double-Blind Method
Aged
Feces/microbiology
Cross-Sectional Studies
Vitamin D/administration & dosage
Tryptophan/administration & dosage

@article {pmid40481696,
year = {2025},
author = {Martínez-Montoro, JI and Sancho-Marín, R and Ocaña-Wilhelmi, L and Arranz-Salas, I and Ruiz-Campos, N and García-López, MJ and Tinahones, FJ and Gutiérrez-Repiso, C},
title = {Gastric microbiota-specific signatures in adults with obesity and Helicobacter pylori-negative gastritis.},
journal = {European journal of clinical investigation},
volume = {},
number = {},
pages = {e70085},
doi = {10.1111/eci.70085},
pmid = {40481696},
issn = {1365-2362},
support = {//Centro de Investigación Biomédica en Red-Fisiopatología de la Obesidad y Nutrición/ ; CM22/00217//Instituto de Salud Carlos III/ ; CP20/00066//Instituto de Salud Carlos III/ ; JR24/00006//Instituto de Salud Carlos III/ ; //European Regional Development Fund/ ; PTA2022-021854-I//Ministerio de Ciencia e Innovación/ ; //Funding for open access charge: Universidad de Málaga/CBUA/ ; },
abstract = {BACKGROUND: The role of the gastric microbiome in the pathophysiology of gastritis beyond Helicobacter pylori (HP) infection is poorly understood and has remained unexplored in patients with obesity. The aim of this study was to analyse gastric mucosa-associated microbiota in patients with obesity and nonatrophic chronic gastritis in the absence of HP infection or history of HP eradication.

METHODS: This was a case-control study conducted at Virgen de la Victoria University Hospital in Malaga, performed in patients with severe obesity (body mass index ≥40 kg/m[2]) undergoing sleeve gastrectomy, without HP infection and no history of HP eradication. Gastric biopsy specimens were collected at surgery and were analysed by 16S rRNA sequencing. Participants were divided into two groups according to the histological evaluation: nonatrophic chronic gastritis and nongastritis. An exploratory prospective analysis to determine the influence of gastritis on short-term outcomes after surgery was also performed.

RESULTS: Sixty-seven participants (38 in the gastritis and 29 in the nongastritis group) were included. A lower alpha diversity (evenness and Shannon diversity indexes) and beta diversity (weighted Unifrac distance) were shown in the gastritis group. Higher relative abundances in the families Micrococcaceae, Streptococcaceae and Leuconostocaceae and the genera Streptococcus, Weissella and Cryptobacterium were observed in the gastritis group, compared with the nongastritis group. An enrichment in pathways involved in toluene degradation, heterolactic fermentation and secondary metabolites biosynthesis, such as ergothioneine and terpenoids, was found in the gastritis group. Also, higher total cholesterol levels 1 year after the surgery were observed in the gastritis group compared with the nongastritis group, although no within-group differences from baseline to 1 year were detected in this parameter.

CONCLUSION: Our results suggest a relationship between the gastric microbiome and nonatrophic chronic gastritis in obesity, beyond HP infection.},
}

@article {pmid40481630,
year = {2025},
author = {Parthasarathy, S and Aly, SH and Tharumasivam, SV and Giridharan, B and Chandran, J and Thirumurthy, P and Abd El Hafeez, MS and El-Shazly, M},
title = {Unlocking nature's secrets: a review on the pharmacokinetics of plant-based medicines and herbal remedies.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/14786419.2025.2513583},
pmid = {40481630},
issn = {1478-6427},
abstract = {Herbal and plant-based medicines have been used for centuries for their therapeutic properties. However, understanding their pharmacokinetics is essential for optimising their efficacy, ensuring their safety and guiding appropriate dosing regimens. Herbal and plant-based medications can be ingested, inhaled, applied topically or injected. Factors such as solubility, formulation and interactions with gut enzymes and transporters influence their absorption characteristics. Distribution of these compounds involves their movement throughout the body, influenced by factors like blood flow, tissue permeability and plasma protein binding. Herbal and plant-based medications are metabolised in the liver by cytochrome P450 enzymes and conjugation routes. Metabolism can vary by genetics and gut microbiome. These compounds can be excreted by the kidneys, liver, faeces, lungs, sweat and saliva. This review aims to decode the pharmacokinetics of herbal and plant-based medicines by providing a comprehensive overview of their absorption, distribution, metabolism and elimination processes.},
}

@article {pmid40481550,
year = {2025},
author = {Zhu, F and Ying, H and Siadat, SD and Fateh, A},
title = {The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {40},
pmid = {40481550},
issn = {1757-4749},
abstract = {Non-tuberculous mycobacteria (NTM) are emerging pathogens of global concern, particularly in regions with declining tuberculosis rates. This review synthesizes current evidence on the epidemiology, immune pathogenesis, and microbiome interactions underlying NTM infections. The rising incidence of NTM is driven by environmental factors, immunocompromised populations, and advanced diagnostics. Clinically, NTM manifests as pulmonary, lymphatic, skin/soft tissue, or disseminated disease, with Mycobacterium avium complex (MAC) and M. abscessus being predominant pathogens. Host immunity, particularly Th1 responses mediated by IL-12/IFN-γ and TLR2 signaling, is critical for controlling NTM, while dysregulated immunity (e.g., elevated Th2 cytokines, PD-1/IL-10 pathways) exacerbates susceptibility. Emerging research highlights the gut-lung axis as a pivotal mediator of disease, where microbiome dysbiosis-marked by reduced Prevotella and Bifidobacterium-impairs systemic immunity and promotes NTM progression. Short-chain fatty acids (SCFAs) and microbial metabolites like inosine modulate macrophage and T-cell responses, offering therapeutic potential. Studies reveal distinct airway microbiome signatures in NTM patients, characterized by enriched Streptococcus and Prevotella, and reduced diversity linked to worse outcomes. Despite advances, treatment remains challenging due to biofilm formation, antibiotic resistance, and relapse rates. This review underscores the need for microbiome-targeted therapies, personalized medicine, and longitudinal studies to unravel causal relationships between microbial ecology and NTM pathogenesis.},
}

@article {pmid40481461,
year = {2025},
author = {Yang, S and Li, J and Wu, Y},
title = {The association of lead and cadmium exposure with periodontitis: a systematic review and meta-analysis.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {935},
pmid = {40481461},
issn = {1472-6831},
mesh = {Humans ; *Cadmium/adverse effects/toxicity ; *Lead/adverse effects/toxicity ; *Periodontitis/chemically induced/epidemiology ; *Environmental Exposure/adverse effects ; },
abstract = {OBJECTIVE: Periodontitis, a microbiome-driven chronic inflammatory disease that destroys the supporting structures of the teeth, is influenced by various environmental factors, including exposure to heavy metals such as lead and cadmium. This systematic review and meta-analysis aimed to evaluate the association between exposure to lead and cadmium and periodontitis.

METHODS: A comprehensive literature search was conducted in PubMed, Web of Science, Scopus, and Embase up to February 1, 2025, following PRISMA guidelines. Observational studies examining the association between lead and/or cadmium exposure and periodontitis were included. Required clinical data were extracted, and study quality was assessed using the Newcastle-Ottawa Scale. Random-effects models were used to compute either standardized mean differences (SMD) of concentration or pooled adjusted odds ratios (aORs). Heterogeneity was assessed with I².

RESULTS: Fourteen studies (13 datasets for either lead or cadmium) comprising 72,467 participants were eligible for inclusion. The meta-analysis found that cadmium and lead exposure were significantly associated with higher odds of periodontitis, with pooled aORs of 1.22 (95% CI: 1.08-1.37) and 1.85 (95% CI: 1.42-2.41), respectively. Sensitivity analyses confirmed the robustness of the findings.

CONCLUSION: This study provides evidence that exposure to lead and cadmium is significantly associated with periodontitis. These findings highlight the importance of reducing environmental exposure to these heavy metals as part of preventive strategies for periodontal disease. Further research is needed to explore the underlying biological mechanisms and evaluate potential interventions to reduce exposure-associated periodontitis.},
}

Humans
*Cadmium/adverse effects/toxicity
*Lead/adverse effects/toxicity
*Periodontitis/chemically induced/epidemiology
*Environmental Exposure/adverse effects