@article {pmid41421479,
year = {2025},
author = {Schneller-Pavelescu, L and Mora-Martínez, C and Sánchez-Pujol, MJ and Sanz, Y and Caparrós-Cayuela, E and Francés-Guarinos, R and Ramos-Rincón, JM and Belinchón-Romero, I},
title = {Relation between gut microbiome and inflammatory interleukins in psoriasis patients compared to healthy controls: an observational study.},
journal = {Actas dermo-sifiliograficas},
volume = {},
number = {},
pages = {104579},
doi = {10.1016/j.ad.2025.104579},
pmid = {41421479},
issn = {1578-2190},
abstract = {BACKGROUND: The gut microbiota interacts with the immune system and plays an important role in many inflammatory diseases such as psoriasis, although the exact mechanisms in this disease are not yet well understood.

OBJECTIVES: To characterize differences in the microbiota between patients with psoriasis and healthy controls, and to assess the relationship between these differences and the interleukins involved in psoriasis.

METHODS: A cross-sectional observational study was conducted in which sociodemographic data, blood samples, and stool samples were collected from patients with psoriasis and healthy controls attending our center between June 2019 and May 2020. Cytokines (interleukin (IL) 17, 22, 23, 31, 33, 36, interferon (IFN) γ, and transforming growth factor (TGF) β) were analyzed using ELISA, and microbiota was analyzed through 16S amplicon sequencing.

RESULTS: Thirty-six patients and 23 controls were included. Absolute abundance analysis found a higher abundance of the phylum Synergistota in the control group (p<0.05). Differential abundance analysis found higher abundance of the genus Subdoligranulum and Lactobacillus, and the species Bacteroides plebeius (p<0.05), and lower abundance of the species Senegalimassilia anaerobia and the genus Ruminococcus (p<0.05) in the psoriasis group. A relationship was observed between Subdoligranulum and TNFα, IL17, IL22, IL23, IL31, IL33, IL36, IFNγ, and TGFβ (p<0.05), as well as between Lactobacillus and IL17, IL23, IL36, TNFα, and TGFβ (p<0.05).

CONCLUSIONS: Significant alterations in the gut microbiota of patients with psoriasis were detected and a relationship with inflammatory interleukins, suggesting their involvement in the disease. These findings could aid in the development of future probiotic treatments for psoriasis.},
}

@article {pmid41421426,
year = {2025},
author = {Nam, J and Lee, Y and Lee, S and Choi, H and Lee, SY and Yang, D},
title = {Synthetic biology strategies for engineering probiotics and commensal bacteria for diagnostics and therapeutics.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108782},
doi = {10.1016/j.biotechadv.2025.108782},
pmid = {41421426},
issn = {1873-1899},
abstract = {Microorganisms inhabit diverse environments, including nearly every organ in the human body. The human microbiome-a complex community of microorganisms residing in the human body-has gained increasing attention as a key contributor to human health and disease, making it an important target for the development of diagnostic and therapeutic strategies. However, the inherent complexity of microbial communities and the challenges of engineering diverse, non-model microorganisms present significant barriers. To address these challenges, synthetic biology has provided powerful tools and strategies to engineer microorganisms capable of sensing disease-specific environments and performing targeted therapeutic functions. In particular, the development of synthetic genetic circuits has significantly improved the precision and reliability of disease diagnosis and treatment, enabling real-time disease monitoring, therapeutic, and even preventive interventions. This review highlights state-of-the-art synthetic biology tools and strategies for engineering the probiotics and commensal bacteria aimed at the diagnosis and treatment of human diseases, with accompanying examples. Future challenges and prospects are also discussed.},
}

@article {pmid41421411,
year = {2025},
author = {Chaudhary, R and Bag, S and Bansal, N and Lal, R and Bishnoi, M and Kondepudi, KK and Chopra, K and Bansal, S},
title = {Soy Isoflavone Ameliorates Gut-brain axis Dysfunction via ER-β Activation and β-glucuronidase Modulation in Estrogen-Deficient Rats.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {178503},
doi = {10.1016/j.ejphar.2025.178503},
pmid = {41421411},
issn = {1879-0712},
abstract = {The Gut-brain axis (GBA) plays a crucial role in neuroendocrine homeostasis, and its dysregulation due to estrogen deficiency is associated with cognitive decline, mood disorders, and gut microbiome disturbances in postmenopausal women. The gut microbiome involved in estrogen metabolism, known as the estrobolome, regulates β-glucuronidase activity, which influences estrogen reactivation and systemic availability. Reduced estrobolome function and altered β-glucuronidase activity in post-menopause may exacerbate GBA dysfunction. Thus, strategies that modulate the estrobolome and enhance β-glucuronidase may be beneficial in improving postmenopausal GBA dysfunction. With this background, our study aims to determine the effect of soy isoflavone (SIF) on GBA dysfunction in estrogen-deficient rats. To induce GBA dysfunction, rats were first bilaterally ovariectomized (OVX) and, after one week, treated with SIF (40 and 80 mg/kg)/17β-estradiol (17βE2) for 28 days. In OVX rats, one-month administration of SIF maintained estrogen receptor-β (ER-β) expression over estrogen receptor-α (ER-α), preserved gut eubiosis by modulating the estrobolome, increased β-glucuronidase enzyme and GUSB gene levels. Additionally, SIF also restores physiological and neurobehavioral parameters. In addition to this, SIF regulates mucosal integrity, tight junction genes, inflammatory markers, oxidative stress, monoamine neurotransmission, hypothalamic-pituitary axis regulations, and apoptosis. Comparative profiling of SIF with 17βE2 shows that 17βE2 improves gut and brain health, while preserving serum estradiol levels and uterine horn weight. This may enhance the feminizing side effects of 17βE2. However, SIF did not show any uterotrophic effect. SIF at doses of 40 and 80 mg/kg may offer a safer alternative to 17βE2 for managing GBA dysfunction in postmenopausal women.},
}

@article {pmid41421358,
year = {2025},
author = {Wang, J and Qian, X and Li, Q and Jin, Z and Liu, N and Zhao, J and Chen, W and Wang, S and Tian, P},
title = {Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101106},
doi = {10.1016/j.xgen.2025.101106},
pmid = {41421358},
issn = {2666-979X},
abstract = {The ecological persistence of Bifidobacterium breve across life stages reflects adaptive strategies beyond the classical infant- versus adult-type dichotomy, historically attributed to differential nutrient utilization. Here, comparative genomics revealed no major differences in shared carbohydrate-related genes or accessory genome content between infant- and adult-derived strains. Instead, a distinct type III lanthipeptide bacteriocin cluster, lanKC, was specifically detected in adult-derived isolates. Functional assays combining gene knockout, in vitro co-cultivation, and human intervention demonstrated that lanKC enhances strain-level competitive fitness and promotes community stability. Phylogenetic and metagenomic analyses of 5,475 lanKC homologs and 6,122 infant gut metagenomes further suggested a possible early-life acquisition via intra-genus horizontal gene transfer. These findings uncover a previously unrecognized genetic basis underlying B. breve adaptation to the gut environment and support a multi-factorial model in which metabolic flexibility and interference competition jointly sustain bifidobacterial persistence and host-microbe symbiosis throughout life.},
}

@article {pmid41421351,
year = {2025},
author = {Newsome, RC and Liu, H and Agbodzi, B and Gharaibeh, RZ and Zhou, L and Jobin, C},
title = {Microbial-derived immunostimulatory small molecule augments anti-PD-1 therapy in lung cancer.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102519},
doi = {10.1016/j.xcrm.2025.102519},
pmid = {41421351},
issn = {2666-3791},
abstract = {We previously showed that enrichment of the Bacteroides genus is associated with improved anti-PD-1-mediated tumor therapy. Here, we isolate 183 Bacteroides isolates from the feces of humanized anti-PD-1 responder mice. Supernatants from 6 of 183 isolates stimulate IFNγ production from primary CD8[+] T cells. These six isolates (6-consort) enhance anti-PD-1-induced anti-tumor efficacy in syngeneic and orthotopic lung cancer models compared to non-responder feces-colonized mice, an effect dependent on the production of IFNγ. Bioassay-guided fractionation and comparative metabolomics lead to the discovery of an active N-acyl amide (cis-Bac429) produced by Bacteroides. cis-Bac429 stimulates IFNγ production by CD8[+] T cells but not synthetic saturated Bac429 (sat-Bac429), indicating structural specificity. Intratumorally administered cis-Bac429, but not sat-Bac429, significantly decreases subcutaneous lung and colon tumor growth in combination with anti-PD-1 therapy and drives IFNγ+ CD8[+] T cell tumor infiltration. These findings pave the way for development of Bacteroides-type N-acyl-amides as adjuvant treatments for anti-PD-1-refractory NSCLC.},
}

@article {pmid41421350,
year = {2025},
author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L},
title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102516},
doi = {10.1016/j.xcrm.2025.102516},
pmid = {41421350},
issn = {2666-3791},
abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.},
}

@article {pmid41421305,
year = {2025},
author = {Zhou, H and McCarthy, FM and Kim, TH and Warren, W and Zhang, G},
title = {Emerging technologies in poultry genomics: Unlocking innovation for the future of sustainable production.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106240},
doi = {10.1016/j.psj.2025.106240},
pmid = {41421305},
issn = {1525-3171},
abstract = {Over the past decade, poultry genomics has undergone a transformative shift from genome assembly to functional annotation, mechanistic discovery, and integrative applications that advance sustainable poultry production. This symposium highlights emerging tools and resources that enable researchers to move beyond statistical associations toward biological causality and breeding application. Functional annotation through the FAANG (Functional Annotation of Animal Genomes) initiative and ChickenGTEx Project has produced comprehensive regulatory maps and expression QTL datasets across tissues, cell types, and developmental stages, forming a foundation for identifying causal regulatory variants. Advances in CRISPR-based editing provide scalable platforms for in vitro validation of regulatory elements and dissect gene function, bridging genotype to phenotype. Single-cell RNA sequencing technologies are now delivering high-resolution immune cell atlases and developmental maps, offering novel insights into host defense and tissue regulation. Integrative omics frameworks that combine genomics, transcriptomics, epigenomics, and 3D chromatin data are revealing systemic regulatory networks controlling complex traits such as egg production, growth, and fat deposition, with functional validation of candidate variants accelerating their translation into precision breeding. Equally important, microbiome-based approaches are emerging as powerful tools to improve poultry health, nutrient utilization, and disease resistance, providing environmentally sustainable strategies that complement genetic selection. Challenges remain in statistical power, tissue- and development-specific context specificity, and bridging discoveries to genomic prediction. However, new opportunities, including multi-omics integration, causal inference, and iterative validation pipelines facilitate the development of predictive and mechanistically informed approaches to genetic improvement. Together, these advances mark a paradigm shift in poultry genomics, positioning the field to close the genotype-molecular-phenotype loop, and equipping the industry with tools to enhance production efficiency, resilience, and animal welfare for long-term sustainability.},
}

@article {pmid41420986,
year = {2025},
author = {Kao, CS and Jiang, CB and Yang, CC and Wang, YL and Chen, YH and Chao, HJ and Hsi, HC and Chien, LC},
title = {Combined exposure to microplastics and cadmium alters gut microbiota composition in preschool children: A cross-sectional study.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140854},
doi = {10.1016/j.jhazmat.2025.140854},
pmid = {41420986},
issn = {1873-3336},
abstract = {Early childhood is a critical developmental stage during which the gut microbiota strongly influences nutrient absorption, immunity, and neurodevelopment. Diet is considered a primary route of exposure to both microplastics (MPs) and cadmium (Cd), raising concerns about their potential joint impacts on child health. However, the effects of combined exposure to MPs and Cd on the early-life gut microbiota remain poorly understood. Fecal samples from 68 preschool children under 6 years of age were analyzed using pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) and inductively coupled plasma mass spectrometry (ICP-MS) to quantify MPs and Cd, respectively. MPs were detected in all samples, with a median concentration of 123.7 μg/g dry weight (DW) (interquartile range, IQR: 70.6-197.8). The predominant polymers were polyethylene (PE, 100 %), polyamide-66 (PA66, 100 %), and polyvinyl chloride (PVC, 93 %). Cd was also detected in all children, with a median concentration of 0.31 μg/g DW (range: 0.21-0.48). Cd concentrations were significantly higher in the low-MP-exposure group compared to the high-exposure group, indicating an inverse association between fecal MP and Cd levels in children. Under combined exposure to MPs and Cd, children with lower Cd levels exhibited higher abundances of beneficial taxa, such as Bifidobacterium and Faecalibacterium. In contrast, higher MP exposure was associated with enrichment of Bacilli and enhanced Bacilli-associated functional activity, particularly in amino acid, energy, and carbohydrate metabolism. KEGG functional predictions also showed that carbohydrate and nucleotide metabolism pathways are more prominent in both low Cd-MP and high Cd-MP exposure groups, indicating a non-monotonic trend. These findings provide novel evidence that combined exposure to MPs and Cd is associated with distinct alterations in the gut microbiota of preschool children, underscoring the need to consider multiple pollutants in early-life microbiome research.},
}

@article {pmid41420859,
year = {2025},
author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA},
title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116724},
doi = {10.1016/j.celrep.2025.116724},
pmid = {41420859},
issn = {2211-1247},
abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.},
}

@article {pmid41420751,
year = {2025},
author = {Varia, J and Herbert, M and Hooker, B},
title = {The Neuroimmunology of Autism.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {316},
pmid = {41420751},
issn = {1559-1182},
mesh = {Humans ; Animals ; *Autism Spectrum Disorder/immunology ; *Neuroimmunomodulation ; *Autistic Disorder/immunology ; Microbiota ; *Immune System/immunology ; },
abstract = {Alterations and maladaptations of the immune system remain some of the most controversial concepts in autism spectrum disorder (ASD). Nonetheless, intensifying evidence confirms that much of what ASD involves is related not to a static encephalopathy-based model of autism but rather to the consequences of environmental insult and complex and dynamic psychological and physiological processes involving the interdependence of the nervous, immune, and host microbiome. This narrative review provides a conceptual framework, focuses on clinical research, and is written for specialists and non-specialists. To provide access to multi- and interdisciplinary perspectives with wide-ranging cutting-edge implications for all people with ASD. Beginning with historical, epidemiological, and etiological underpinnings, we elaborate on a contemporary understanding of the immune system in the pathophysiology of ASD. Theoretical and scientific discourse on the relationship of the immune system with the nervous system and host microbiota in homeostasis/allostasis, neurodevelopment, and psychological and physiological health and disease is also provided. As a basis for conceptual advances detailing the interconnection, interdependence, and interference with or subjugation (as would be the case for autoinflammatory and autoimmune conditions) of the nervous system and host microbiota by the immune system, and the role of these interactions in the pathogenesis of ASD. This gives us a platform for not only examining the role of the immune system in the etiology, pathogenesis, and pathophysiology of ASD but also understanding social and higher-level processes of consciousness for individuals on the spectrum. Finally, taking a neuroimmunological perspective, we highlight the need for a multi-scale, holistic approach to understanding and developing future therapeutic modalities to address the core symptoms of ASD that go beyond the current reductionist and "magic-bullet" medical paradigm.},
}

Humans
Animals
*Autism Spectrum Disorder/immunology
*Neuroimmunomodulation
*Autistic Disorder/immunology
Microbiota
*Immune System/immunology

@article {pmid41420750,
year = {2025},
author = {Motevalli, H and Mehrani, A and Zolfaghari, K and Khodaee, P and Yazdanpanah, N and Saleki, K and Rezaei, N},
title = {TLRs and NLRs modulate oral microbiome involvement in Alzheimer's disease.},
journal = {Metabolic brain disease},
volume = {41},
number = {1},
pages = {7},
pmid = {41420750},
issn = {1573-7365},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; *Microbiota/physiology ; *Toll-Like Receptors/metabolism ; Animals ; *Mouth/microbiology ; Dysbiosis/metabolism ; },
abstract = {Alzheimer's disease (AD) is the most common and irreversible type of dementia, accounting for more than half of all dementia cases. Early diagnosis of AD plays a role in slowing the progression of the disease and also preserving the quality of life of patients. However, there is often a time lag of several decades between the biological onset of the disease and the time of clinical diagnosis. At the time of diagnosis, the patient often has noticeable cognitive decline, which reduces the effectiveness of available treatments. This diagnostic time lag from onset to the onset of symptoms highlights the need to identify accessible and cost-effective screening tools, such as biomarker-based diagnostic and screening methods. Studies have implicated disorders of the oral-brain axis in the pathogenesis of neurodegenerative diseases such as AD. Oral dysbiosis has been epidemiologically associated with an increased risk of cognitive decline and AD, making the oral microbiome a potential biomarker for screening and early diagnosis of AD. Oral dysbiosis also plays a role in the pathogenesis of AD by increasing systemic inflammation and neuroinflammation. TLR/NLR signaling has been identified as a key intrinsic pathway in the pathogenesis of these neuroinflammations and systemic inflammation, which may suggest the use of inhibitors such as TAK-242/MCC950 as a potential therapeutic approach in the treatment of AD, although preclinical and clinical evidence for the use of these inhibitors in the course of AD is still very limited. In this review, we discuss oral dysbiosis in AD and review studies investigating the mouth-brain axis as an effective pathway in AD from diagnosis to treatment.},
}

Humans
*Alzheimer Disease/metabolism/microbiology
*Microbiota/physiology
*Toll-Like Receptors/metabolism
Animals
*Mouth/microbiology
Dysbiosis/metabolism

@article {pmid41420663,
year = {2025},
author = {Frederick, RM and Lam, K and Han, JK},
title = {Acute Exacerbations of Chronic Rhinosinusitis.},
journal = {Current allergy and asthma reports},
volume = {25},
number = {1},
pages = {61},
pmid = {41420663},
issn = {1534-6315},
mesh = {Humans ; *Sinusitis/diagnosis/drug therapy ; Chronic Disease ; *Rhinitis/diagnosis/drug therapy ; Acute Disease ; Disease Progression ; Asthma ; Anti-Bacterial Agents/therapeutic use ; Rhinosinusitis ; },
abstract = {PURPOSE OF REVIEW: We aim to highlight recent advancements on the evolving chronic rhinosinusitis (CRS) phenotype: acute exacerbations of chronic rhinosinusitis (AECRS). We focused on studies that expanded the current understanding of its pathophysiology, patient characteristics, and disease burden.

RECENT FINDINGS: Defining AECRS has been a topic of discussion for many years. A recent regulatory definition of AECRS in the literature incorporates a > 3 day requirement of worsened symptoms and an escalation of treatment. It is important not to rely on patient-reported rescue medication frequency as it was recently demonstrated these are only obtained for 1/3 of reported AECRS episodes. The pathophysiology behind AECRS is still being evaluated but it appears irritants such as viral insult to the sinonasal microbiome can create a dysbiosis and worsens host immune system breakdown, facilitating a subsequent bacterial infection. Many studies are using loose definitions of AECRS because no formal definition has existed until recently. Clinical trials and other studies are relying on patient-reported illnesses, CRS-related antibiotics, and CRS-related corticosteroids to determine an episode of AECRS. Formally defining AECRS is vital in order to conduct future literature on its etiology and clinical outcomes so results may be translatable. Additionally, our review demonstrates that CRS patients with asthma and/or concomitant allergic rhinitis appear to be at an increased risk for developing AECRS and future research should continue to investigate their interplay. Many patients are being overprescribed antibiotics and corticosteroids for reported AECRS episodes. This increases total healthcare spending and increases the risk for adverse effects from corticosteroids and antibiotic resistance. Future research should investigate methods to mitigate this practice.},
}

Humans
*Sinusitis/diagnosis/drug therapy
Chronic Disease
*Rhinitis/diagnosis/drug therapy
Acute Disease
Disease Progression
Asthma
Anti-Bacterial Agents/therapeutic use
Rhinosinusitis

@article {pmid41420661,
year = {2025},
author = {Ngangbam, AK and Nongmaithem, BD and Haojam, RS and Khundrakpam, L and Singh, LL and Meetei, KB},
title = {First functional and taxonomic insights into the microbiome of edible snail, Cipangopaludina lecythis via shotgun metagenomics.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {18},
pmid = {41420661},
issn = {1572-9699},
mesh = {*Snails/microbiology ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The freshwater snail Cipangopaludina lecythis holds both ecological and medicinal importance, yet its microbiome remains unexplored. This study presents the first shotgun metagenomic profiling of edible tissues of C. lecythis. Illumina HiSeq sequencing generated over 42 million high-quality reads, revealing 38 bacterial phyla dominated by Pseudomonadota (32%), followed by Bacillota and Actinomycetota. At the genus level, Pseudomonas, Klebsiella, Acinetobacter, Bacillus, Clostridium, Staphylococcus, and Streptomyces were prevalent. Functionally important genera such as Aeromonas, Vibrio, and Pseudoalteromonas which are known for their probiotic and immunomodulatory properties were also detected. The dominant species included Pseudomonas sp. REST10, Escherichia coli, Klebsiella pneumoniae, and Streptomyces sp. T12, many of which were associated with fermentation and host microbe interactions. Interestingly, the microbial profiles differed from those in marine snails, indicating environment-specific microbiome signatures. Functional annotation revealed key enzymes including 17 beta-hydroxysteroid dehydrogenase type 3 (HSD17B3) and malonyl-CoA:ACP transacylase, involved in fatty acid metabolism and energy regulation. Enzymes such as glutathione S-transferase and arylacetamide deacetylase were also detected, along with chitinase and chitin synthases, suggesting host microbe interactions in chitin metabolism. High alpha diversity showed a rich and functional microbiome. Overall, this study highlights the metabolic potential and ecological relevance of the C. lecythis microbiome, supporting its application in biotechnology and nutraceutical industry.},
}

*Snails/microbiology
*Metagenomics/methods
Animals
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41420422,
year = {2025},
author = {Cao, S and Yang, L and Wang, R and Liu, J},
title = {Worldwide Research Trends on Substance Use Disorder-Related Inflammatory Imbalances: A Bibliometric Analysis.},
journal = {CNS neuroscience & therapeutics},
volume = {31},
number = {12},
pages = {e70719},
doi = {10.1002/cns.70719},
pmid = {41420422},
issn = {1755-5949},
support = {1053320230244//the Fundamental Research Funds for the Central Universities of Central South University/ ; U22A20303//National Natural Science Foundation of China/ ; 2019SK2131//Innovative Province Special Construction Foundation of Hunan Province/ ; 2021RC4016//the Science and Technology Innovation Program of Hunan Province/ ; 2020SK4001//Clinical Research Center For Medical Imaging In Hunan Province in China/ ; },
mesh = {*Bibliometrics ; Humans ; *Substance-Related Disorders/epidemiology/complications ; *Inflammation ; *Biomedical Research/trends ; Animals ; },
abstract = {BACKGROUND: Substance use disorder (SUD) is a complex, chronic, and relapsing encephalopathy associated with inflammatory processes. This study aims to conduct a bibliometric analysis to elucidate the current landscape, research hotspots, and evolving trends in the field of SUD-related inflammation imbalance.

METHODS: Original research and review articles pertaining to "SUD-inflammation" subject were systematically retrieved from the Web of Science Core Collection (WoSCC) database, encompassing publications from its inception to January 1, 2025. Co-authorship, collaboration, co-citation, and co-occurrence analyses were performed using VOSviewer, and CiteSpace was utilized to identify strongest citation bursts and keyword trends.

RESULTS: A total of 2318 publications on "SUD-inflammation" realm were included. A marked increase in publication output was observed starting in 2019. The United States (US) and China emerged as the most prolific countries. The journal, institution, and author, with the largest number of total publications (NP), were respectively JOURNAL OF ETHNOPHARMACOLOGY, UNIVERSITY OF CALIFORNIA SYSTEM, and Michael Maes. Core terms "microglial activation," "oxidative stress," and "TLR4 signaling" were among the most frequently studied topics. Additionally, the roles of the "gut-immune-brain" axis and N-acetylcysteine in drug addiction have been receiving significant attention.

CONCLUSION: This bibliometric study delineates the foundational knowledge structural and mapping of the "SUD-inflammation" field over the past 25 years. The findings provide a comprehensive and data-driven perspective on the evolving research landscape, offering valuable insights for future investigations and resource allocation.},
}

*Bibliometrics
Humans
*Substance-Related Disorders/epidemiology/complications
*Inflammation
*Biomedical Research/trends
Animals

@article {pmid41420183,
year = {2025},
author = {Dai, Y and Song, J and Bai, G and Liu, J},
title = {A literature-based gut microbiota dietary index and its association with obstructive sleep apnea risk: a population-based, cross-sectional study.},
journal = {BMC nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40795-025-01199-8},
pmid = {41420183},
issn = {2055-0928},
support = {[2022] No.1//Zunyi Oral Disease Immune Prevention and Medical Biomaterials Research and Development Innovation Talent Team, Zunyi Science Talent/ ; [2022] No.1//Zunyi Oral Disease Immune Prevention and Medical Biomaterials Research and Development Innovation Talent Team, Zunyi Science Talent/ ; [2022] No.1//Zunyi Oral Disease Immune Prevention and Medical Biomaterials Research and Development Innovation Talent Team, Zunyi Science Talent/ ; },
abstract = {BACKGROUND: Limited research has explored the link between the Literature-Based Dietary Index for Gut Microbiota (LBDI-GM) and Obstructive Sleep Apnea (OSA). This study aims to examine the relationship between these two conditions.

METHODS: This cross-sectional analysis utilized data from the 2015-2018 National Health and Nutritional Examination Survey (NHANES). Obstructive sleep apnea (OSA) served as the independent variable, evaluated through self-reported questionnaires. The dependent variable was the novel literature-Based Dietary Index for Gut Microbiota, which quantified dietary patterns linked to intestinal microbiome characteristics. Weighted multivariable logistic regression modeling explored associations between LBDI-GM and OSA. Supplementary subgroup and interaction evaluations were performed.

RESULT: A total of 8,707 participants were included in the final analysis, with a mean age of 47.66 years (SD = 0.43). The study population was nearly equally distributed by sex, with 4,460 males (51.2%) and 4,247 females (48.8%). Following comprehensive adjustment for potential confounders in the weighted logistic regression model (Model III), LBDI-GM demonstrated a statistically significant inverse association with OSA risk (OR = 0.967, 95% CI: 0.938-0.996, p = 0.025). Sex-stratified analyses indicated that this protective association was particularly evident among female participants.

CONCLUSIONS: This cross-sectional study identified an inverse association between LBDI-GM and OSA, suggesting that dietary patterns promoting gut microbiota health may play a role in reducing the risk of OSA. These findings highlight the potential for integrating dietary interventions into clinical practice to improve OSA management.},
}

@article {pmid41420109,
year = {2025},
author = {McCormick, C and Degregori, S and Johnson, GC and Blumstein, DT and Barber, PH},
title = {Marmot gut microbiomes are stable against dietary variation.},
journal = {Oecologia},
volume = {208},
number = {1},
pages = {15},
pmid = {41420109},
issn = {1432-1939},
support = {1557130//National Science Foundation/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Diet ; *Marmota/microbiology ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {Animal gut microbiomes, particularly those of herbivorous mammals, are strongly shaped by the host diet. However, how dietary composition impacts gut microbiome variation across a population of wild hosts is unknown. To examine the relationship between gut microbiome composition and diet composition across individuals, we employed a multi-omic approach leveraging both 16S rRNA amplicon sequencing and plant DNA metabarcoding (tRNL primer) in 39 wild yellow-bellied marmot fecal samples from the Rocky Mountains. We utilized the 16 s rRNA primer to target microbes and the tRNL primer to target plants. Our results indicate that the marmot gut microbiomes appear to be stable against dietary variation, even across individuals with significantly different diets. We also show that colony membership significantly impacts marmot dietary variation, while age does not. Thus, while diet clearly plays a significant role in shaping mammalian gut microbiomes, our study suggests that diet composition within the same species has a minimal impact on gut microbiome variation, particularly in the absence of experimental manipulations and dietary interventions.},
}

*Gastrointestinal Microbiome
Animals
*Diet
*Marmota/microbiology
RNA, Ribosomal, 16S
Feces/microbiology

@article {pmid41419805,
year = {2025},
author = {Hussain, M and Ahmed, N and Xie, X and Teng, Z and Hou, X and Li, X and Yang, Z and Zhu, Z},
title = {Characterization of the mango phyllosphere microbiome during fruit-setting unveils unique community assembly and coexisting beneficial-pathogenic microbiota.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07943-3},
pmid = {41419805},
issn = {1471-2229},
support = {2025KY0769//Basic Ability Enhancement Projects for Young and Middle-aged Teachers/ ; 2024011670 and 2019011394//Scientific Research Startup Fund of Baise University/ ; 2024011670 and 2019011394//Scientific Research Startup Fund of Baise University/ ; },
abstract = {BACKGROUND: Mango is an economically important fruit tree with rich genetic diversity, but has been threatened by a diverse range of pathogens, causing substantial losses annually. While the plant-associated microbiomes are well studied, the assembly patterns and composition of phyllosphere microbial communities for deciphering potential pathogenic and beneficial microbiota during the mango fruit-setting phase remain largely unexplored.

RESULTS: This study profiled the bacterial and fungal communities in mango leaves, flowers, and fruitlets using high-throughput amplicon sequencing. Both flowers and fruitlets exhibited significantly less diverse microbial communities than leaves, and the bacterial and fungal microbiota compositions of all three organs were distinct from one another. Importantly, organ-specific preferences were observed among the dominant bacterial families, with mango flowers characterized by a high abundance of Erwiniaceae, fruitlets by Acetobacteraceae, and leaves by Microbacteriaceae and Bifidobacteriaceae. In contrast, fungal families were less differentiated, with only Didymellaceae and Symmetrosporaceae showing leaf-specific enrichment relative to flowers and fruitlets. Analysis of the shared microbial genera across the three phyllosphere organs revealed the presence of core bacterial taxa Pseudomonas and Sphingomonas, while the fungal core genera were Alternaria, Aureobasidium, Cladosporium, Epicoccum, Fusarium, Hannaella, Nectria, Neodidymella, and Vishniacozyma. Notably, several of these concurrently detected microbial genera have been previously documented as either pathogenic (e.g., Alternaria, Cladosporium and Fusarium) or beneficial (Aureobasidium, Vishniacozyma, Sphingomonas and Pseudomonas). Furthermore, we found that the mango phyllosphere bacterial and fungal communities were established by parallel selection of the microbiota, instead of consecutive selection. Deciphering the functional profile of the phyllosphere microbiota revealed the association of microbial taxa with functions such as chemoheterotrophy, aerobic chemoheterotrophy, fermentation, aromatic compound degradation, plant pathogens, endophytes, and saprotrophs, indicating a balanced ecosystem in which future fruit health outcomes may be determined by subtle shifts in the microbial community structure.

CONCLUSION: Our findings offer a checklist of the core beneficial and pathogenic microbes inhabiting the mango phyllosphere, while also highlighting the selective role of mango organs in recruiting specific subsets of microbiota, which can be harnessed for disease protection and improving mango production.},
}

@article {pmid41419476,
year = {2025},
author = {Gustin, AT and Broedlow, CA and Hager, K and Coronado, E and Wangari, S and Iwayama, N and Ahrens, CY and Garrison, WD and Guerriero, KA and De Paris, K and Londono-Renteria, B and Gale, M and Klatt, NR and Kublin, JG and Manuzak, JA},
title = {Distinct gastrointestinal microbial signatures predict parasite levels in controlled Plasmodium infections in both rhesus macaques and humans.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67241-2},
pmid = {41419476},
issn = {2041-1723},
support = {K01OD024876//U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD)/ ; },
abstract = {Functions of the gastrointestinal (GI) microbiome include maintenance of immune homeostasis and protection against infectious disease. Current assessments of the role of the GI microbiome in Plasmodium infection have been primarily conducted using mouse models and observational human cohorts. Here, we experimentally assessed associations between pre-infection GI microbiome composition and acute Plasmodium parasitemia using 16S rRNA sequencing and samples from rhesus macaques (RMs) and adult humans enrolled in a previously conducted controlled human malaria infection (CHMI) trial (NCT04072302) originally designed to test the efficacy of KAF156, a novel imidazolopiperazine class of antimalarial drugs. We identified distinct pre-infection 16S microbial signatures that were associated with increased risk for above median parasitemia in RMs infected with P. fragile and CHMI participants infected with P. falciparum. Further, we identified a Bifidobacterium feature set that accurately stratified parasitemia risk and could therefore serve as a foundation for a potential biomarker panel to aid prevention efforts in malaria endemic regions. Together, our findings demonstrate that pre-infection GI microbiome composition is indicative of risk for Plasmodium parasitemia, and our observation that the pre-infection microbiome-P. fragile dynamic in RMs mirrors the pre-infection microbiome-P. falciparum interaction in CHMI participants supports the future use of this model in pre-clinical investigations of novel microbiome-targeting approaches to reduce malaria burden.},
}

@article {pmid41419359,
year = {2025},
author = {Bourdin, T and Carrera Páez, LC and Massard, M and Hocquet, D},
title = {Studying low-dose antibiotic effects on the gut microbiome.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.014},
pmid = {41419359},
issn = {1878-4380},
abstract = {Antibiotics at sub-minimal inhibitory concentrations (sub-MICs), which are commonly present in food and the environment, can reach the human gut microbiome and silently disrupt the balance of microbes, contributing to the emergence and persistence of antimicrobial resistance (AMR). The gastrointestinal (GI) tract presents spatially heterogeneous antibiotic exposures, making it challenging to assess their full impact with conventional experimental approaches. Although in vitro and in vivo models provide some insight, they often lack physiological relevance or scalability. This highlights the need to reconsider the criteria used to determine 'safe' upper concentration limits in food, as current standards may underestimate the risks of sub-MIC exposures. Therefore, better integrative modeling approaches are essential to uncover hidden drivers of resistance and guide effective interventions.},
}

@article {pmid41419211,
year = {2025},
author = {Airan, Y and Fedorova, O and Heer, C and Rees, MG and Ronan, MM and Roth, JA and Bindra, RS and Herzon, SB},
title = {Synthesis and Biological Evaluation of Colibactin Derivatives.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.5c00639},
pmid = {41419211},
issn = {1554-8937},
abstract = {Colibactin is a pseudo-C2-symmetric gut microbiome metabolite that induces DNA interstrand cross-links and plays a causal role in colorectal cancer. Since efforts to isolate colibactin have not been successful, we developed colibactin 742 (3a/b) as a stable colibactin mimetic. However, colibactin 742 (3a/b) exists as a mixture of ring and chain isomers, which complicates analysis of its activity. We report here the discovery of colibactin 686 (9) as a superior colibactin mimetic. Colibactin 686 (9) is more potent than colibactin 742 (3a/b) and recapitulates the bacterial genotoxic phenotype. Colibactin 686 (9) possesses a C2-symmetric structure, which will expedite its synthesis, and is incapable of ring-chain isomerization, which will simplify analysis of its biological activity. We additionally establish that colibactins do not passively diffuse into cells, and are substrates for monocarboxylate transporter pumps. These latter findings have implications for trafficking of natural colibactin, which remains poorly understood.},
}

@article {pmid41419129,
year = {2025},
author = {Tan, IJ and Zieneldien, T and Ma, S and Grant-Kels, JM},
title = {Ethical Considerations in Skin Microbiome Data Ownership.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2025.12.040},
pmid = {41419129},
issn = {1097-6787},
}

@article {pmid41419102,
year = {2025},
author = {Alvarado Chavarría, P and Shah, FS and Hafeez, A and Zafar, S and Khan, K},
title = {The Vyarna Bio Information Booster: Maximization of microbiome bioinformation diversity through the combination of the lyophilized Human Breast Milk of multiple providers.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108243},
doi = {10.1016/j.micpath.2025.108243},
pmid = {41419102},
issn = {1096-1208},
abstract = {Human breast milk is increasingly recognized not only as nourishment but as a dynamic medium of biological information-delivering nutrients, immune molecules, and microbial ecosystems critical to early development. While each mother transmits a unique immunological and microbiota profile, the developmental impact of amplifying this diversity remains unexplored. Here, we introduce the Vyarna Booster: a novel, shelf-stable powder formed by combining lyophilized breast milk from multiple verified providers to intentionally exceed the microbial diversity found in any single sample. Using 16S rRNA gene sequencing, we analyzed bacterial composition across fresh (F), individually lyophilized (L), and mixed composite (M) samples from 13 mothers. The composite formulation exhibited greater microbial richness and evenness than any source sample, with consistently elevated abundance of commensals such as Streptococcus salivarius and Lactococcus raffinolactis. This increased diversity was reproducible across independently assembled mixes. While we do not claim viability or clinical outcomes, the observed taxonomic amplification suggests a previously untested mechanism for engineering postnatal microbial exposure. We propose the Vyarna Booster as a new class of infant nutritional supplement-one that augments the natural limits of human milk through deliberate bioinformational combination, and raises foundational questions about the boundaries of maternal transmission, microbial design, and early life programming.},
}

@article {pmid41419097,
year = {2025},
author = {Yusta, B and Wong, CK and Matthews, D and Koehler, JA and Baggio, LL and Drucker, DJ},
title = {Loss of GLP-2R signaling in Glp2r[-/-] mice increases the long-term severity of graft versus host disease.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102311},
doi = {10.1016/j.molmet.2025.102311},
pmid = {41419097},
issn = {2212-8778},
abstract = {BACKGROUND: Glucagon-like peptide-2 (GLP-2 reduces systemic and gut inflammation while preserving mucosal integrity. Preclinical and clinical reports implicate GLP-2 receptor (GLP-2R) agonism as a potential therapy for graft vs. host disease (GvHD) METHODS: Here we assessed whether enhanced vs. loss of GLP-2R signaling modifies gut injury and inflammation in experimental murine acute GvHD (aGvHD). Allogeneic hematopoietic cell transplantation (HCT) was performed using bone marrow and splenocytes from BALB/cJ donor mice to induce aGvHD in C57BL/6J recipients. Chimerism was determined by flow cytometry of immune cell compartments. Inflammation was assessed by measuring circulating cytokines and histological scoring of gut mucosal damage. GLP-2 responsivity was assessed using histology and gene expression analyses. The gut microbiome was assessed by 16S rRNA sequencing.

RESULTS: Allogeneic chimerism was > 90% in peripheral blood and in the gut epithelial compartment. Gut GLP-2R signaling was preserved following allogeneic bone marrow transplantation. Surprisingly, GLP-2R agonism using teduglutide did not reduce circulating cytokines, gut injury, immune cell infiltration or the severity of aGvHD. In contrast, transplant recipient Glp2r[-/-] mice exhibited reduced survival, associated with increased bacteremia. Shifts in microbial species abundance with gain or loss of GLP-2R signaling were not correlated with aGvHD clinical outcomes.

CONCLUSIONS: Activation of GLP-2R signaling did not reduce the severity of experimental aGvHD, failing to replicate a previous study using an identical aGvHD protocol. Nevertheless, loss of GLP-2R signaling in transplant recipients decreased survival and increased bacteremia, implicating an essential role for endogenous GLP-2R signaling in maintaining barrier function in the context of immune-mediated gut epithelial injury.},
}

@article {pmid41419086,
year = {2025},
author = {Robbins, E and Koueik, J and Singh, AM and Frischmeyer-Guerrerio, PA and Hourigan, SK},
title = {Role of the Early-Life Microbiome in the Development of Food Allergy.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2025.12.007},
pmid = {41419086},
issn = {2213-2201},
abstract = {Food allergies (FA) affect millions of children worldwide, often emerging during the critical early-life period when the gut microbiota and the immune system co-develop. This review examines the current evidence linking infant gut microbiome development to FA risk, gaps in current knowledge, and future directions. Substantial evidence from animal models and human studies implicates the developing gut microbiome in shaping immune tolerance to food antigens through various mechanisms. Early life gut microbiome dysbiosis or imbalance, with associated altered metabolite profiles, has been associated with increased FA risk, especially in infants delivered by Cesarean section, exposed to antibiotics, or lacking certain dietary and environmental exposures. However, findings remain heterogeneous across cohorts, and direct causal mechanisms in humans are not fully established, in part due to logistical challenges and variability in microbiome sequencing and FA definitions. Key gaps include a paucity of mechanistic human studies, limited understanding of the timing and functional impact of dysbiosis, and insufficient standardization of research methodologies. Moreover, while environmental factors such as maternal health, delivery mode, and early-life exposures are linked to microbiome development and FA risk, disentangling their specific contributions remains difficult. Future research focused on standardized, longitudinal studies integrating functional metabolomics and immune profiling to establish causal pathways is critical. Elucidating the precise microbial and metabolic drivers of immune tolerance may enable the development of targeted microbial therapeutics, such as probiotics, dietary modifications, or metabolite supplementation, to reduce FA in at-risk infants. Addressing these gaps is essential to mitigate the rising global burden of pediatric food allergies.},
}

@article {pmid41418978,
year = {2025},
author = {Selesner, L and Hedges, M and Pung, R and Vaughn, C and Burns, A and Aloia, M and Henson, J and Tobias, J and Olyaei, A and Nizich, S and Swift, K and Veshagh, A and Andres, SF and Fialkowski, E and Jordan, BK and Scottoline, B},
title = {Increase in Necrotizing Enterocolitis with Cessation of Bifidobacterium longum Subspecies. infantis Administration in Very Low Birthweight Infants: A Single-Center Retrospective Cohort Study.},
journal = {The Journal of pediatrics},
volume = {},
number = {},
pages = {114961},
doi = {10.1016/j.jpeds.2025.114961},
pmid = {41418978},
issn = {1097-6833},
abstract = {OBJECTIVE: To evaluate the incidence of necrotizing enterocolitis (NEC) before probiotic introduction, during probiotic administration, and after its cessation following the 2023 FDA advisory discouraging probiotic use in preterm infants.

STUDY DESIGN: Retrospective cohort study of very low birthweight (VLBW) infants (birthweight <1500 grams), admitted to a level IV neonatal intensive care unit (NICU) from 2014 through 2024. Infants were grouped into three epochs according to Bifidobacterium longum ssp. infantis (B. infantis) EVC001 administration: Pre-EVC001 (no probiotic), EVC001 (routine use), and Post-EVC001 (post-discontinuation). The primary outcome was NEC incidence. Secondary outcomes included NEC-associated mortality, all-cause mortality, NEC severity, and NEC incidence among extremely low birthweight (ELBW; <1000 grams) infants. Multivariable log-binomial and ordinal logistic regression models were used.

RESULTS: Among 733 VLBW infants, NEC incidence was 12% Pre-EVC001, 2.6% EVC001, and 16% Post-EVC001 (p<0.001). NEC risk was higher both Pre-EVC001 (aRR 4.4, 95% CI 2.2-9.0) and Post-EVC001 (aRR 4.5, 95% CI 2.0-9.9; both p<0.001) compared with during EVC001 administration. ELBW infants showed similar trends. EVC001 use was associated with reduced odds of severe NEC compared with epochs without EVC001use (VLBW OR 5.3, 95% CI 2.5-11.0; ELBW OR 5.0, 95% CI 2.2-11.7; both p<0.001). NEC-related mortality was lowest during EVC001 use compared with epochs without EVC001 (0.9%, p=0.05).

CONCLUSIONS: NEC incidence was higher before and lower during EVC001 administration and rose then after its discontinuation in this single center retrospective study. There is a need for multicenter trials evaluating B. infantis for NEC prevention.},
}

@article {pmid41418974,
year = {2025},
author = {Muthuraman, KR and Kato, T and Kusano, K and Moriya, Y and Park, EY},
title = {β-Glucans and their roles in immune and metabolic regulation: A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149746},
doi = {10.1016/j.ijbiomac.2025.149746},
pmid = {41418974},
issn = {1879-0003},
abstract = {β-Glucans are non-starch polysaccharides derived from various natural sources, including cereals, fungi, yeast, algae, and bacteria. Their structures determine their functions: cereal-derived β-glucans from oats and barley have mixed β-(1,3) and β-(1,4) linkages for heart and blood sugar benefits, while fungal and yeast types have β-(1,3) backbones with β-(1,6) branches that confer potent immunomodulatory properties through their interaction with pattern recognition receptors on immune cells. This review comprehensively explores the various physiological effects of β-glucans, focusing on their mechanisms of action in metabolic health, antiinflammatory, antioxidant, and immunotherapeutic applications. It examines how β-glucans improve glycemic control by increasing insulin sensitivity, modulating the gut microbiome, and reducing cholesterol levels through enhanced bile acid excretion. Additionally, it discusses their antiinflammatory actions through the modulation of key signaling pathways, antioxidant effects via the Nrf2 activation, and their immunomodulatory role in neonatal and therapeutic contexts, showcasing their potential as biological response modifiers for a wide range of diseases, including chronic inflammation, metabolic disorders, and infections. The findings confirm that the specific source and structural properties of β-glucans are crucial for their efficacy, making them valuable components in the development of functional foods, nutraceuticals, and pharmaceuticals.},
}

@article {pmid41418891,
year = {2025},
author = {Caetano-Silva, ME and Hilt, ME and Valishev, I and Lim, C and Kasperek, M and Shrestha, A and Fu, H and Eck, E and McCusker, R and Armstrong, H and Loman, B and Bailey, MT and Allen, JM},
title = {Social stress worsens colitis through β-adrenergic-driven oxidative stress in intestinal mucosal compartments.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106222},
doi = {10.1016/j.bbi.2025.106222},
pmid = {41418891},
issn = {1090-2139},
abstract = {Psychological stress is a known risk factor for inflammatory bowel disease (IBD), but the mechanisms linking stress to worsened disease remain unclear. Because distinct stress paradigms activate different neuroimmune circuits, it is critical to investigate model-specific effects. We examined how social stress primes the gut for heightened inflammation and whether this is mediated by specific neuroendocrine pathways, including α2-/β-adrenergic (sympathetic) or glucocorticoid/ corticotropin-releasing hormone receptor (CRHR1) (HPA axis) signaling. Mice were exposed to social disruption (SDR) stress and pre-treated with pharmacological antagonists targeting α2-adrenergic receptors (idazoxan), β-adrenergic receptor (β-AR) (propranolol), glucocorticoid receptor (mifepristone), or CRHR1 (antalarmin). Intestinal epithelial cell (IEC) gene expression and microbiota composition were assessed following SDR. To determine disease impact, SDR was combined with either Citrobacter rodentium infection or dextran sulfate sodium (DSS)-induced colitis, with interventions including the β-AR inhibitors and the NADPH oxidase inhibitor apocynin. SDR significantly upregulated expression of Dual oxidase 2 (Duox2), Dual oxidase maturation factor 2 (Duoxa2), and inducible nitric oxide synthase 2 (Nos2) in IECs (2- to 8-fold, p < 0.0001), effects reversed by β-AR blockade but not α2-adrenergic, CRH, or glucocorticoid inhibition. SDR also induced microbial dysbiosis, characterized by reduced α -diversity and compositional shifts, which was rescued by propranolol. Stress exacerbated disease severity in both infectious (C. rodentium) and chemically induced (DSS) colitis, amplifying colonic expression of Duox2, Nos2, and Ccl2, especially. Apocynin mitigated stress-induced ROS/RNS production and body weight loss even prior to colitis onset, reduced colonic expression of key oxidative enzymes, especially DUOX2, and alleviated both chemically and infectious colitis severity. These findings provide strong evidence that social stress sensitizes the gut to inflammation through β-adrenergic and NADPH oxidase-driven oxidative stress, highlighting potential therapeutic targets for mitigating stress-exacerbated IBD.},
}

@article {pmid41418855,
year = {2025},
author = {Laue, HE and Kook, D and Khatchikian, C and Coto, SD and Jackson, BP and Palys, TJ and Peacock, JL and Karagas, MR and O'Toole, GA and Hoen, AG and Madan, JC},
title = {Early-life arsenic exposure modulates the developing microbiome in a rural cohort.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123588},
doi = {10.1016/j.envres.2025.123588},
pmid = {41418855},
issn = {1096-0953},
abstract = {BACKGROUND: Studies reported associations between arsenic and the infant gut microbiome measured contemporaneously. We tested the hypothesis that early-life arsenic associates with longitudinal microbiome differences and examined sex-specific effects.

METHODS: Participants provided urine and fecal samples at six weeks (6W; n=219) or twelve months (12M; n=219), a subset of whom provided samples at both (n=167). Total arsenic (tAs), inorganic arsenic, monomethylarsinic acid, and dimethylarsinic acid (DMA) were quantified in 6W and 12M urine with high-performance liquid chromatography with inductively-coupled plasma mass spectrometry. We estimated gut microbiome composition at 6W and 12M with metagenomic sequencing. Using generalized linear and mixed-effect models, we evaluated cross-sectional and longitudinal associations of arsenic concentrations with bacterial diversity and species/ gene pathway relative abundance.

RESULTS: DMA and tAs at 6W were associated with bacterial species at 6W but similar associations were not observed at 12M. At 6W, associations between arsenic and metabolic pathways tended to be sex-specific. In longitudinal analyses, tAs associated with higher Shannon diversity [β=0.07 per doubling (95%CI: 0.05, 0.09)], with a diminishing trend in this association with sampling age [β=-0.04 per doubling (95%CI: -0.07, -0.004)]. We observed a similar longitudinal pattern between at least one arsenic measure and ten bacterial species, with stronger associations among males than females.

CONCLUSIONS: We observed longitudinal and cross-sectional associations of arsenic and the gut microbiome in the first year of life. Early-life arsenic concentrations were more strongly associated with disruptions in the infant gut microbiome than later infancy, highlighting the importance of early-life exposures in microbiome dysbiosis.},
}

@article {pmid41418853,
year = {2025},
author = {Shi, W and Delgado-Baquerizo, M and Liao, H and Gong, Y and Zhou, G and Li, S and Jiang, H and Yang, Y and Ye, C and Zhang, Q},
title = {Intensive Flooding Enhances Methane but Reduces Carbon Dioxide and Nitrous Oxide Emissions in Reservoir Drawdown Areas.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123563},
doi = {10.1016/j.envres.2025.123563},
pmid = {41418853},
issn = {1096-0953},
abstract = {Riparian ecosystems, vital interfaces for soil-atmosphere greenhouse gases (GHG) exchange, are increasingly subject to perturbations from extreme flooding events and artificial hydrological alterations. The resultant effects on soil microbiomes and GHG emissions, particularly under varying flooding regimes, remain poorly elucidated. Here, we conducted an in-situ flooding manipulation experiment across three elevation gradients in a reservoir drawdown area, applying continuous flooding (Extreme), 3-day flooding alternating with 3-day drainage (Moderate), and no flooding (Control) to evaluate responses of CH4, CO2, and N2O emissions and associated microbiomes. Flooding exerted stronger control than elevation on GHG fluxes. CH4 emissions increased dramatically under both extreme and moderate flooding (24-fold and 25-fold, respectively), whereas CO2 and N2O emissions decreased: extreme flooding reducing CO2 by 51% and N2O by 108%, and moderate flooding reducing N2O by 67% with minimal effect on CO2 emissions. CH4 emissions increased primarily due to elevated water tables and enhanced soil anaerobic conditions, stimulating methanogenic activity via methylotrophic pathways (up-regulated mtaC gene) and greater availability of labile plant litter. CO2 emissions declined as flooding reduced aboveground plant biomass, thereby lowering plant respiration. N2O emissions decreased because higher soil moisture promoted complete denitrification, converting N2O to N2. Using co-occurrence network analysis, the bacterial order Xanthomonadales emerged as keystone taxa, showing strong associations with microbial functional groups involved in GHG-related metabolic pathways. Overall, our findings indicate that riparian ecosystems may become CH4 emission hotspots under future climatic extremes and highlight the critical role of hydrological dynamics-microbiome interactions in shaping riparian carbon and nitrogen cycles.},
}

@article {pmid41418718,
year = {2025},
author = {Dwivedi, J and Shukla, MM and Upadhyay, A and Wal, A and Sharma, KK and Gasmi, A},
title = {From 16S rRNA to deep learning: Evolution of computational approaches in human microbiome studies.},
journal = {Computational biology and chemistry},
volume = {121},
number = {},
pages = {108852},
doi = {10.1016/j.compbiolchem.2025.108852},
pmid = {41418718},
issn = {1476-928X},
abstract = {The human microbiome plays a vital role in maintaining physiological balance and influencing immunity, metabolism, and disease development. Over the past decade, the field has witnessed a remarkable transition from traditional 16S rRNA sequencing and culture-based assays to advanced computational frameworks that integrate multiomics datasets. Modern computational tools now enable researchers to move beyond descriptive taxonomy toward functional, predictive, and mechanistic insights, with techniques such as network modeling, genome-scale metabolic reconstruction, and deep learning algorithms facilitating the accurate profiling of microbial communities and the identification of biomarkers associated with complex disorders. AI-based platforms including QIIME, MetaPhlAn, and DeepMicro have further strengthened microbiome analysis by integrating genomic, proteomic, and metabolomic data to model host-microbe interactions. Despite these advances, challenges such as data heterogeneity, limited interpretability of AI models, and ethical issues in data sharing continue to impede clinical translation. Future progress will rely on explainable AI, federated learning, and standardized data frameworks to promote transparency, reproducibility, and applicability in precision medicine. Overall, the integration of AI-driven bioinformatics marks a paradigm shift in human microbiome research, transforming it from an observational discipline into a predictive and translational science with the potential to revolutionize personalized healthcare.},
}

@article {pmid41418709,
year = {2025},
author = {Kingkaw, A and Mok, K and Nakphaichit, M and Koffas, M and Vongsangnak, W},
title = {Engineering the gut microbiome and its impact on human health.},
journal = {Current opinion in biotechnology},
volume = {97},
number = {},
pages = {103415},
doi = {10.1016/j.copbio.2025.103415},
pmid = {41418709},
issn = {1879-0429},
abstract = {The gut microbiome plays a crucial role in maintaining health by supporting digestion, immunity, and overall well-being. Disruptions to the gut microbiome can result in dysbiosis, which is correlated with disease states. Recent advances in engineering the gut microbiome, functional ingredients designed through prebiotics, probiotics, and synbiotics have progressed together with synthetic microbial communities (SynComs), which influence the modulation of microbiome composition and functional role, offering a promising strategy to restore balance and enhance health. This field is rapidly advancing with broad applications focused on improving animal and human health. This review explores the significance and current applications of the engineering microbiome and its impact on gut health, as well as the challenges and sustainable future.},
}

@article {pmid41418677,
year = {2025},
author = {Zhang, L and Du, A and Chen, Y and Zheng, D and Lu, Y},
title = {Supragingival Biomarker flora of Children With and Without Cariogenic Disease and Black Stains, Aged 3 to 6 Years.},
journal = {International dental journal},
volume = {76},
number = {1},
pages = {103982},
doi = {10.1016/j.identj.2025.103982},
pmid = {41418677},
issn = {1875-595X},
abstract = {BACKGROUND: The oral microbiome plays a pivotal role in the occurrence and progression of dental caries and black stain (BS) pigment.

OBJECTIVES: The aim of this study was to explore the keystone microbiota and potential biomarkers of caries and BS pigment in 3 to 6-year-old children.

METHODS: A total of 122 children were included, namely, healthy controls (HC, n = 32), those with severe early childhood caries (SECC, n = 31), those with BS pigment but caries-free (BSCF, n = 29), and those with SECC and BS pigment (SECCBS, n = 30). Supragingival plaques were collected for 16S rRNA sequencing followed by bioinformatics analysis.

RESULTS: Seven phyla and 14 genera were identified in all the samples, and differences in relative abundance were observed. Alpha diversity analysis revealed that the richness and diversity of the bacterial communities were similar across the HC, BSCF, SECC and SECCBS groups (P > .05). Different bacterial species were identified in the six paired groups (P < .05). With respect to the disparities in keystone nodes, the SECC group had the highest value of 66, followed by the SECCBS and BSCF groups and the HC group (56, 47 and 33, respectively). The areas under roc curve for the 10 machine learning models were systematically evaluated, and seven models yielded exceptional results, including support vector machine (SVM)-linear and SVM-RBF for BSCF-SECC, naïve Bayes classification for BSCF-SECCBS, decision trees for HC-BSCF, LASSO for HC-SECC, and SVM-poly for HC-SECCBS and K nearest neighbour for SECC-SECCBS.

CONCLUSIONS: The diversity of the microbial community has little influence on the development of dental caries and black staining. However, specific bacteria exhibited different relative abundances across the HC, SECC, BSCF, and SECCBS groups; therefore, those bacteria may serve as candidate biomarkers. Co-occurrence network approaches and differential machine learning models can be used to predict a spectrum of dental caries in primary dentition, providing a convenient and preventive strategy.},
}

@article {pmid41418374,
year = {2025},
author = {Bhuiyan, MNI and Rahman, MS and Rahman, MM and Islam, S and Suchi, PD and Saha, BK},
title = {From ocean to table: marine contaminants and their risks to human health and biodiversity.},
journal = {Marine pollution bulletin},
volume = {224},
number = {},
pages = {119134},
doi = {10.1016/j.marpolbul.2025.119134},
pmid = {41418374},
issn = {1879-3363},
abstract = {Marine ecosystems are increasingly threatened by human-made pollutants such as microplastics (MPs), heavy metals, persistent organic pollutants (POPs), and pathogenic microorganisms. These contaminants endanger biodiversity, disrupt ecosystem functions, and compromise seafood safety. This review synthesized current knowledge on pollutant sources, environmental transport, and trophic transfer, emphasizing their accumulation and magnification through marine food webs and ultimately in humans. Quantitative evidence-such as MP loads of 0.2-5 particles g[-1] in bivalves and MeHg concentrations of 0.3-1.5 ppm in predatory fish-illustrates the scale of exposure across trophic levels. Ecotoxicological impacts include endocrine disruption, reproductive impairment, immune suppression, and neurobehavioral alterations, with case studies documenting coral bleaching, shellfish larval mortality, and predator-prey destabilization. Human health risks arise from long-term dietary exposure to MeHg, PCBs, phthalates, and microbial toxins, contributing to neurodevelopmental deficits, carcinogenesis, metabolic disorders, and microbiome-mediated toxicity-defined as pollutant-driven alterations in gut microbial communities that impair immunity and metabolic regulation. The novelty of this review lies in its integration of region-specific contaminant datasets, multi-stressor interaction pathways, and emerging mechanistic biomarkers, offering a systems-level perspective on marine pollution. Despite regulatory progress, gaps remain in enforcement, monitoring, and multi-contaminant risk assessment. Research priorities include multigenerational exposure studies, standardized analytical workflows, and improved detection of emerging hazards such as nanoplastics. Advances in high-resolution metabolomics, AI-based exposure diagnostics, and gnotobiotic models provide promising tools for future research. A holistic strategy combining technological innovation, coordinated policy, and community engagement is essential to safeguard the ocean-to-table continuum.},
}

@article {pmid41418359,
year = {2025},
author = {Toledo, LT and Polveiro, RC and Silva-Júnior, A and Moreira, MAS and Marks, FS},
title = {Interactions between Mycoplasma hyopneumoniae strains and the resident lung microbiota in swine.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110840},
doi = {10.1016/j.vetmic.2025.110840},
pmid = {41418359},
issn = {1873-2542},
abstract = {Enzootic pneumonia (EP) in swine, caused by Mycoplasma hyopneumoniae (M. hyopneumoniae), is a chronic respiratory disease that leads to significant economic losses in pig production. Infection with M. hyopneumoniae can induce pulmonary dysbiosis; however, the impact of different strains with varying degrees of virulence on the composition of a healthy microbiota remains incompletely understood. This study investigated alterations in the lung microbiome of pigs experimentally infected with two distinct strains of M. hyopneumoniae (UFV1 and UFV2) using 16S rRNA gene-based metataxonomic analyses and bioinformatics approaches. Pigs were divided into three experimental groups: Control (uninfected), UFV1 (infected with strain UFV1), and UFV2 (infected with strain UFV2). Bronchoalveolar lavage fluid were collected for DNA extraction and sequencing. Alpha diversity was significantly lower in the infected groups compared to the Control. Beta diversity analysis revealed significant differences in microbiota composition among the groups, with a clear separation between the Control group and the infected groups. Mycoplasma was the most abundant genus in both UFV1 and UFV2 groups, whereas the Control group exhibited greater genus-level diversity, including Stenotrophomonas, Comamonas, and Pseudomonas. Linear discriminant analysis (LDA) confirmed the enrichment of Mycoplasma in the infected groups and identified additional differentially abundant genera. Predictive modeling based on microbiota composition demonstrated high accuracy in classifying the groups, with Varibaculum, Pseudomonas, and Actinobacillus emerging as key genera for prediction. The UFV1 and UFV2 strains exhibited distinct lung microbiota profiles, suggesting different infection dynamics and interactions with the resident microbiota. This study provides new insights into the impact of diverse M. hyopneumoniae strains on the porcine lung microbiome, with implications for the development of preventive and control strategies for EP.},
}

@article {pmid41418133,
year = {2025},
author = {Sharma, S and Rawal, P and Kalra, S},
title = {Gut Guardianship: Recommendations for Rational Use of Proton Pump Inhibitors in Chronic Kidney Disease.},
journal = {JPMA. The Journal of the Pakistan Medical Association},
volume = {75},
number = {11},
pages = {1822-1824},
doi = {10.47391/JPMA.25-94},
pmid = {41418133},
issn = {0030-9982},
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/adverse effects ; *Renal Insufficiency, Chronic/complications ; Nephritis, Interstitial/chemically induced ; },
abstract = {The widespread use of proton pump inhibitors (PPIs) has raised safety concerns, especially among patients with chronic kidney disease (CKD), where long-term use has been linked with acute interstitial nephritis (AIN), hypomagnesaemia, and potential progression to endstage kidney disease (ESKD). Recent observational studies and meta-analyses have yielded mixed evidence, calling for a nuanced and individualized approach to acid suppression in CKD. The concept of gut guardianship emphasizes cautious, indication-based prescribing, dose minimization, and structured deprescribing to preserve gut-renal health. This article reviews the current evidence and proposes a clinical toolkit for rational PPI use in CKD, based on risk stratification, guideline-based indications, and ongoing monitoring.},
}

Humans
*Proton Pump Inhibitors/therapeutic use/adverse effects
*Renal Insufficiency, Chronic/complications
Nephritis, Interstitial/chemically induced

@article {pmid41417796,
year = {2025},
author = {Kumari, P and Devi, P and Banerjee, B and Tarai, B and Budhiraja, S and Sethi, TP and Pandey, R},
title = {Functional dynamics between resident transcriptionally active microbes (TAMs) and host genes underlie Dengue severity.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {12},
pages = {e0013836},
pmid = {41417796},
issn = {1935-2735},
mesh = {Humans ; *Dengue/microbiology/genetics/immunology/pathology ; Female ; Male ; *Host Microbial Interactions/genetics ; Transcriptome ; Machine Learning ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; Gene Expression Profiling ; Adult ; Severity of Illness Index ; },
abstract = {Host-microbe interactions are increasingly recognized as an important module to understand disease progression and potential treatment strategies. Increasing evidence points to the microbiome's ability to modulate host gene expression, and thereby influencing host physiology. By integrating dual RNA sequencing with machine learning, we uncover how transcriptionally active microbes (TAMs) may influence host genes involved in immune and metabolic functions in the hospital admitted dengue patients. Towards this, we analyzed 112 whole transcriptomes from the blood samples of patients with differential dengue disease severity. Using a machine learning-based integrated host-microbial transcriptomic analysis framework, combining Lasso regression and sparse canonical correlation analysis (SCCA), we identified both shared and disease-specific associations between the microbes and the host transcriptomic pathways. Notably, opportunistic microbes such as Acetobacter-ghanensis, Achromobacter sp. B7, Bacillus licheniformis, and Clostridium cochlearium, along with the host genes, namely, PPME1, TIMP2, NLRC4, and RhoB, were associated with immune dysregulation in the severe dengue patients. These microbes and genes appear to influence pathophysiology through distinct molecular pathways, highlighting their disease-specific roles in host-microbe interactions.},
}

Humans
*Dengue/microbiology/genetics/immunology/pathology
Female
Male
*Host Microbial Interactions/genetics
Transcriptome
Machine Learning
*Microbiota
*Bacteria/genetics/classification/isolation & purification
Gene Expression Profiling
Adult
Severity of Illness Index

@article {pmid41417758,
year = {2025},
author = {Wang, Z and Zhou, M and Dang, Y and Huang, X and Xu, C and Xu, F and Xu, X and Li, P and Zhang, S and Shi, H and Wu, J},
title = {Fecal microbiota composition and function are associated with anxiety and depression in patients with inflammatory bowel disease.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337941},
pmid = {41417758},
issn = {1932-6203},
mesh = {Humans ; *Feces/microbiology ; Male ; Female ; *Depression/microbiology/complications ; Adult ; *Anxiety/microbiology/complications ; *Inflammatory Bowel Diseases/microbiology/complications/psychology ; *Gastrointestinal Microbiome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND AND AIMS: Increasing prevalence of anxiety and depression are found in patients with inflammatory bowel disease (IBD). Altered gut microbiome may affect the brain, resulting in psychiatric symptoms. We aimed to analyze the feature of gut microbiota in IBD patients with anxiety or depression.

METHODS: Anxiety and depression symptoms were assessed by the Hospital Anxiety and Depression Scale (HADS). Stool samples were collected from IBD patients, and the 16S rRNA sequencing was used to detect fecal microbiota. Metabolites were detected by Liquid Chromatography-Mass Spectrometry (LC-MS).

RESULTS: Among the involved IBD patients (n = 59), 28.81% had anxiety and 33.90% had depression. Linear discriminant analysis Effect Size (LEfSe) (LDA > 3.0) revealed that 4 genera (Klebsiella, Alloprevotella, Barnesiella, Bacillus) were enriched, while Sellimonas was depleted in the anxiety group. Enrichment of 2 genera (Ruminococcus, Barnesiella) were found in the depression group. In the anxiety group, valine, leucine and isoleucine degradation was enriched in fecal microbiota, with upregulation of 3-methyl-2-oxobutanoic acid involved in the above pathway. In the depression group, butanoate metabolism was enriched in fecal microbiota, with alpha-ketoglutaric acid involved. Lysine degradation were enriched in fecal microbiota, with pipecolic acid involved. Primary bile acid biosynthesis was depleted in fecal microbiota, with glycocholic acid involved. Pearson correlation analysis revealed a positive correlation between Alloprevotella and 3-methyl-2-oxobutanoic acid in the anxiety group. In patients with both anxiety and depression, four genera (Subdoligranulum, Alloprevotella, Christensenellaceae R-7 group, Barnesiella) were positively correlated with alpha-ketoglutaric acid.

CONCLUSION: In this study, the alteration of composition of fecal microbiota was identified, and differential genus associated with IBD patients with anxiety or depression or both were explored. Change in function of microbiota was also discovered by the detection of differential pathways and fecal metabolites, which were associated with IBD patients with anxiety or depression or both.},
}

Humans
*Feces/microbiology
Male
Female
*Depression/microbiology/complications
Adult
*Anxiety/microbiology/complications
*Inflammatory Bowel Diseases/microbiology/complications/psychology
*Gastrointestinal Microbiome
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid41417755,
year = {2025},
author = {Harlow, K and Service, EK and Geiger, JE and Carlson, BE and Kimble, SJA},
title = {The relationships between box turtle gut microbiomes and personality.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0339132},
pmid = {41417755},
issn = {1932-6203},
mesh = {Animals ; *Turtles/microbiology/physiology ; *Gastrointestinal Microbiome ; Female ; Male ; *Personality ; *Behavior, Animal ; Bacteria/genetics/classification ; },
abstract = {Though well understood in model animals, the microbiome-brain axis has only recently been found to be important in wildlife health. Host behavior is an important component of this axis, and variation in individual animal personalities can shape the dynamics, composition, and evolutionary trajectory of an ecosystem. Relative boldness or shyness is a commonly used personality metric across vertebrate animals, and the composition of an organism's microbiome may be important in shaping this trait. Turtles have been poorly characterized in terms of behavior and microbiome, though they are the most threatened vertebrate group on Earth and therefore warrant more study. To address this gap, we compared the gut microbiota of bold and shy Eastern Box Turtles to investigate any correlation between microbial composition and personality type. Free-ranging Eastern Box Turtles were captured and assayed for their personality, and cloacal, skin, and oral swab samples were collected. Microbial DNA from swabs was amplified and sequenced. Female turtles had significantly higher alpha microbial diversities than male turtles and shy turtles had a significantly higher microbial diversity than bold turtles. Four significantly overabundant bacteria were found (two in bold turtles and two in shy turtles). The steroid biosynthesis pathway was significantly overrepresented in bold turtles, while the bile acid biosynthesis pathway and purine degradation to urea modules were significantly overrepresented in shy turtles. Firmicutes, Actinobacteria, and Proteobacteria are implicated in the classification of Eastern Box Turtle personality. While our conclusions should be considered in the context of limited sample sizes, our data suggest prominent metabolic pathways, modules, and bacteria that are implicated in different Eastern Box Turtle personality types, suggesting a possible microbial influence on the personality of this well-known but threatened species.},
}

Animals
*Turtles/microbiology/physiology
*Gastrointestinal Microbiome
Female
Male
*Personality
*Behavior, Animal
Bacteria/genetics/classification

@article {pmid41417606,
year = {2025},
author = {Piñero, J and Kolchinsky, A and Redner, S and Solé, R},
title = {Neutral theory of cooperative dynamics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {51},
pages = {e2515423122},
doi = {10.1073/pnas.2515423122},
pmid = {41417606},
issn = {1091-6490},
support = {2021 SGR 0075//Government of Catalonia | Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR)/ ; Grant No. 62417//John Templeton Foundation (JTF)/ ; No. 101068029.//National Science Foundation (NSF)/ ; },
mesh = {Biodiversity ; Microbiota ; *Symbiosis ; *Models, Biological ; Ecosystem ; Humans ; *Cooperative Behavior ; },
abstract = {Mutualistic interactions are widespread in nature, from plant communities and microbiomes to human organizations. Along with competition for resources, cooperative interactions shape biodiversity and contribute to the robustness of complex ecosystems. We present a stochastic neutral theory of cooperator species. Our model shares with the classic neutral theory of biodiversity the assumption that all species are equivalent, but crucially differs in requiring cooperation between species for replication. With low migration, our model displays a bimodal species-abundance distribution, with a high-abundance mode associated with a core of cooperating species. This core is responsible for maintaining a diverse pool of long-lived species, which are present even at very small migration rates. We derive analytical expressions of the steady-state species abundance distribution, as well as scaling laws for diversity, number of species, and residence times. With high migration, our model recovers the results of classic neutral theory. We briefly discuss implications of our analysis for research on the microbiome, synthetic biology, and the origin of life.},
}

Biodiversity
Microbiota
*Symbiosis
*Models, Biological
Ecosystem
Humans
*Cooperative Behavior

@article {pmid41417588,
year = {2025},
author = {Fenclová, K and Murínová, I},
title = {Probiotics in antibiotic treatment - an overview of effectiveness, risks, and recommended practices.},
journal = {Casopis lekaru ceskych},
volume = {164},
number = {6},
pages = {259-261},
pmid = {41417588},
issn = {0008-7335},
mesh = {*Probiotics/therapeutic use/adverse effects ; Humans ; *Anti-Bacterial Agents/adverse effects ; *Diarrhea/prevention & control/chemically induced ; Gastrointestinal Microbiome/drug effects ; },
abstract = {The administration of antibiotics is associated with the risk of diarrhea due to disruption of the natural gut microbiome, a condition that may persist for several months after the completion of treatment. Probiotics are often used to prevent antibiotic-associated diarrhea; however, their effectiveness in this indication remains a subject of discussion. Meta-analyses confirming the benefits of probiotics are critically assessed by the professional community, and for a long time, their administration was not included in the recommended practices of professional societies. The situation changed in 2023 when probiotics were included in the recommended practices of the World Gastroenterology Organization. This article focuses on the possibilities of administering probiotics in the Czech context, emphasizing currently available medicinal products, their composition, benefits, and potential risks.},
}

*Probiotics/therapeutic use/adverse effects
Humans
*Anti-Bacterial Agents/adverse effects
*Diarrhea/prevention & control/chemically induced
Gastrointestinal Microbiome/drug effects

@article {pmid41417490,
year = {2026},
author = {Jessani, A},
title = {Beyond Demographics: Sex, Gender, and Sexuality in Oral Health Research.},
journal = {Advances in dental research},
volume = {33},
number = {1},
pages = {26-30},
doi = {10.1177/00220345251392073},
pmid = {41417490},
issn = {1544-0737},
mesh = {Humans ; *Oral Health ; *Sexuality ; *Dental Research ; Sexual and Gender Minorities ; Male ; Female ; Sex Factors ; },
abstract = {Sex, gender, and sexuality are crucial and interrelated factors influencing oral health outcomes, yet they are often overlooked and inadequately addressed in human studies on oral health. Biological sex influences oral disease susceptibility through hormonal, immunological, and microbiome-related mechanisms. Concomitantly, gender as a social construct modulates health through psychosocial stress, health care access, and societal norms. Sexuality intersects with oral health through behavioral risks, stigma, and discrimination, especially among lesbian, gay, bisexual, transgender, and queer or questioning populations. Despite their importance, oral health research often treats sex as a binary demographic variable, excluding sexual and gender minority individuals. There is a lack of meaningful integration of these variables across all phases of research, from proposal development and data collection to analysis and knowledge creation. This results in limited generalizability, perpetuates health inequities, and impedes the development of inclusive, evidence-based, and person-centered interventions. Furthermore, dental education and research training programs often lack comprehensive content on sex, gender, and sexuality, contributing to research approaches and training that reinforce binary-centered investigations. Substantial gaps in mentorship, representation, and inclusive curricula largely contribute to the underrepresentation of gender-diverse scholars and leaders in oral health. To address these gaps, a multipronged action plan is necessary, including an inclusive research design, robust data collection tools, curriculum reform that integrates person-centered frameworks, community engagement and service-learning, policy change, and accountability mechanisms. The integration of intersectionality, pertinent sex, gender, sexuality, and social determinants of health in oral health research and education is essential for achieving scientific rigor, health equity, and culturally responsive care for all populations.},
}

Humans
*Oral Health
*Sexuality
*Dental Research
Sexual and Gender Minorities
Male
Female
Sex Factors

@article {pmid41417461,
year = {2025},
author = {Drew, G and Kraft, CS and Mehta, N},
title = {Fecal Microbiota Therapy: Clinical Laboratory Testing and Metabolomic Approaches for Donor Screening, Product Assessment, and Patient Monitoring.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvaf156},
pmid = {41417461},
issn = {1530-8561},
abstract = {BACKGROUND: The safety and efficacy of fecal microbiota transplantation for prevention of recurrent Clostridioides difficile infection relies on complex interactions between the donor and recipient microbiome.

CONTENT: Screening of donor stool has largely aimed to ensure safety; however, metagenomic and metabolic features of the stool, which may affect efficacy of the fecal microbiota transplantation (FMT), have been largely overlooked.

SUMMARY: In this review, we discuss the nascent field of metagenomic and metabolic donor and recipient characteristics that may affect efficacy of FMT and future directions for this field to allow for more precise and personalized therapies.},
}

@article {pmid41417284,
year = {2025},
author = {Meher, MM and Afrin, M and Jahan, MR and Yanai, A and Islam, MN},
title = {The role of enteroendocrine cells, hormones, and gut microbiota in anorexia nervosa: a complex interplay of the microbiome-gut-brain axis.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {215},
pmid = {41417284},
issn = {1573-4978},
support = {KAKENHI, grant number 22K02092//Japan Society for the Promotion of Science/ ; KAKENHI, grant number 22K06792//Japan Society for the Promotion of Science/ ; },
}

@article {pmid41417214,
year = {2025},
author = {Czyz, S and Quan, J and Yang, K and Alhusayen, R and Hardin, J},
title = {Clinical Implications of the Skin Microbiota in the Therapy of Cutaneous T Cell Lymphoma: A Scoping Review.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {41417214},
issn = {2193-8210},
abstract = {Cutaneous T cell lymphomas (CTCL) are non-Hodgkin T cell malignancies defined by malignant T cell transformation and accumulation in the skin. Limited understanding of CTCL pathogenesis, including the role of the tumor microenvironment, hinders effective treatment. Emerging evidence implicates the skin microbiota as a key modulator of disease, with microbial dysbiosis contributing to progression and representing a novel therapeutic target. This review synthesizes findings from 37 rigorously selected studies, outlining current knowledge of the CTCL-associated microbiome, mycobiome, and virome. It evaluates therapeutic strategies aimed at microbial colonization, emphasizing the potential of modulating host-microbe interactions. Additionally, we provide comprehensive clinical insight into the indications for microbial-modulating strategies of the microbiota in CTCL.},
}

@article {pmid41416890,
year = {2025},
author = {Fouquier, J and Stanislawski, M and O'Connor, J and Scadden, AS and Lozupone, C},
title = {EXPLANA: A user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf658},
pmid = {41416890},
issn = {1367-4811},
abstract = {MOTIVATION: Longitudinal microbiome studies (LMS) are increasingly common but have analytic challenges including non-independent data requiring mixed-effects models. Furthermore, large amounts of data motivate exploratory analysis to identify factors related to outcome variables. Although change analysis (ie, calculating feature changes between timepoints) can be powerful, how to best conduct these analyses is often unclear. For example, observational LMS measurements show natural fluctuations, so baseline might not be a reference of primary interest, whereas, for interventional LMS, baseline is typically a key reference point, often indicating the start of treatment.

RESULTS: To address these challenges, a feature selection workflow, called EXPLANA (EXPLoratory ANAlysis), was developed for LMS that supports numerical and categorical data, and also accommodates cross-sectional studies. Machine-learning methods were combined with different types of change calculations and downstream interpretation methods to identify statistically meaningful variables and explain their relationship to outcomes. EXPLANA generates an interactive report that textually and graphically summarizes methods and results. EXPLANA had good performance on simulated longitudinal data, with a balanced accuracy score of 0.91 (range: 0.79-1.00, SD = 0.05), outperformed an existing tool, QIIME 2 feature-volatility (balanced accuracy: 0.95 vs. 0.56) and identified novel order-dependent categorical feature changes (e.g., different effect for A_B vs B_A). EXPLANA is broadly applicable and simplifies analytics for identifying features related to outcomes of interest.

AVAILABILITY: Software is available at https://github.com/JTFouquier/explana and https://zenodo.org/records/17478745 (10.5281/zenodo.17478744). Documentation and demos are available at www.explana.io.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid41416749,
year = {2025},
author = {Wright, F and Grand, S and Sanders, I and Arraiano-Castilho, R},
title = {Mycorrhizal control of microbial gene transcription and taxonomic composition in the rhizosphere and bulk soil.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf282},
pmid = {41416749},
issn = {1751-7370},
abstract = {Interactions between arbuscular mycorrhizal fungi (AMF) and soil microbial communities that support plant nutrient acquisition remain poorly understood. Here, we investigate how the model AMF species Rhizophagus irregularis influences microbial mRNA transcription and microbial taxonomic composition in rhizosphere and bulk soil compartments of Zea mays mesocosms. Using metatranscriptomic profiling alongside 16S rRNA and ITS amplicon sequencing, we show that AMF alter bacterial gene expression without shifting community composition and significantly increase fungal richness and evenness. We identify genotype-specific effects of AMF on microbial diversity and function and find that AMF colonisation stimulates microbial B-vitamin biosynthesis. We also link elevated plant leaf phosphorus levels under AMF colonisation with changes in root gene expression and increased abundance of AMF-stimulated rhizosphere bacterial taxa. These findings highlight the importance of feedback loops between plant, AMF and soil microorganisms and show how these interactions can contribute to increases in plant nutrient uptake. It is hoped these results will be useful for sustainable crop production and ecosystem regeneration through microbiome-informed management strategies.},
}

@article {pmid41416604,
year = {2025},
author = {Rychlik, A},
title = {Fecal microbiome transplantation in the treatment of chronic enteropathies.},
journal = {Polish journal of veterinary sciences},
volume = {28},
number = {4},
pages = {691-700},
doi = {10.24425/pjvs.2025.157285},
pmid = {41416604},
issn = {2300-2557},
mesh = {*Fecal Microbiota Transplantation/veterinary ; Animals ; *Intestinal Diseases/therapy/veterinary ; *Gastrointestinal Microbiome ; Chronic Disease ; },
abstract = {The intestinal microbiome is essential for the proper functioning of the immune system and the course of metabolic processes in the living organism. Intestinal bacteria produce a variety of metabolites that affect the health of many organs, especially the intestines. Disturbances in the composition of the intestinal microflora are referred to as dysbiosis. Dysbiosis occurring in chronic enteropathies may exacerbate intestinal inflammation. Therefore, effective methods of treating enteropathy are still being sought, which involve restoring the proper composition of the intestinal microbiome. In recent years, many scientific centers have drawn attention to the possibility of treating enteropathy by transplanting intestinal contents from a healthy donor. This review presents the advantages and disadvantages of this therapeutic method, described in the latest available literature and the newest guidelines regarding the donor and transplant administration methods.},
}

*Fecal Microbiota Transplantation/veterinary
Animals
*Intestinal Diseases/therapy/veterinary
*Gastrointestinal Microbiome
Chronic Disease

@article {pmid41416302,
year = {2025},
author = {Mohamed, M and Ullah, A and Hassan, R and Hamza, M and Mohamed, I and Salam, M},
title = {The Impact of Probiotics on Acne Vulgaris: A Meta-Analysis of Randomized Controlled Trials.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97010},
pmid = {41416302},
issn = {2168-8184},
abstract = {Acne vulgaris is a multifactorial inflammatory skin disorder influenced by hormonal activity, microbial imbalance, and immune dysregulation. While conventional treatments such as antibiotics and retinoids remain effective, their long-term use is often limited by side effects, resistance, and poor adherence. This meta-analysis evaluated the efficacy of probiotics as an adjunct or alternative therapy for acne management. Four randomized controlled trials involving 227 participants were analyzed, showing that probiotic supplementation reduced acne severity scores (OR 0.48; 95% CI 0.29-0.79) and non-inflammatory lesion counts (mean difference (MD) -4.62; 95% CI -8.10 to -1.15) compared with controls. A trend toward improvement in inflammatory lesions was observed (MD -2.03; 95% CI -5.46 to 1.41) but was not statistically significant. Heterogeneity across studies ranged from moderate to high, reflecting variation in probiotic strains, formulations, and treatment durations. While these findings suggest a potential benefit of probiotics, the limited number and quality of trials warrant cautious interpretation. Larger, standardized clinical studies are needed to confirm efficacy and identify optimal probiotic regimens for acne management.},
}

@article {pmid41416172,
year = {2025},
author = {Yao, H and Sun, C and Wang, S and Zhou, Y and Zhang, Z and Song, F and Luo, H},
title = {[Advances in the Application of Forensic Microbiome Analysis in Tissue Source Inference].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {56},
number = {5},
pages = {1419-1426},
pmid = {41416172},
issn = {1672-173X},
mesh = {Humans ; *Microbiota ; *Forensic Sciences/methods ; *Forensic Medicine/methods ; },
abstract = {Forensic microbiology, a pivotal discipline within forensic science, focuses on microorganisms as the primary subject of study and applies life science technologies to analyze microbial evidence in criminal and civil investigations. Tissue source inference plays a crucial role in forensic investigations, facilitating case assessment and crime scene reconstruction. The application of microbiome analysis in tissue source inference benefits from the tissue specificity and spatiotemporal stability of human microbial communities. This article provides a systematic review of recent advances in tissue source inference based on microbiome analysis, covering technological development, research trends, and practical applications. Finally, the challenges confronted in practice in forensic microbiology and the future prospects for its development are summarized.},
}

Humans
*Microbiota
*Forensic Sciences/methods
*Forensic Medicine/methods

@article {pmid41416156,
year = {2025},
author = {Yang, R},
title = {[Integration of Microbiome Research and the One Health Approach Promotes Innovation and Development in Public Health Laboratory Sciences].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {56},
number = {5},
pages = {1171-1176},
pmid = {41416156},
issn = {1672-173X},
mesh = {*Microbiota ; Humans ; *Public Health ; *One Health ; Animals ; },
abstract = {As global health challenges become increasingly complex and multidimensional, microbiome research and the One Health approach-along with their integration-actively promote the development of the field of public health laboratory sciences. The microbiome is an essential component of the human body, animals, and the environment. Microbiome research not only elucidates the interaction mechanisms between microorganisms and their hosts but also provides an irreplaceable material basis for the well-being of humans, animals, and the environment, offering new perspectives for the prevention, diagnosis, and treatment of human diseases. Additionally, the One Health approach emphasizes the interconnectedness of human, animal, and environmental health, establishing a theoretical foundation for interdisciplinary collaboration and global health management. The integration of the microbiome and the One Health approach establishes the notion of "the balance of dynamic factors" as a scientific principle underpinning One Health. This integration holds far-reaching implications for expanding new fields and developing new technologies in public health laboratory sciences, as well as informing public health practices.},
}

*Microbiota
Humans
*Public Health
*One Health
Animals

@article {pmid41416110,
year = {2025},
author = {Jun, L and Wan, X and Zhang, D and Zheng, Y and Chen, X and Mi, L and Xiao, B},
title = {Mixed vaginal infection status in women infected with Trichomonas vaginalis: comparison of microscopy method and metagenomic sequencing analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638464},
pmid = {41416110},
issn = {2235-2988},
mesh = {Female ; Humans ; *Trichomonas vaginalis/genetics/isolation & purification ; *Metagenomics/methods ; Adult ; *Vagina/microbiology/parasitology/pathology ; *Trichomonas Vaginitis/diagnosis/microbiology ; *Microscopy/methods ; Microbiota/genetics ; *Coinfection/microbiology/diagnosis/parasitology ; Young Adult ; Middle Aged ; Lactobacillus/isolation & purification/genetics ; },
abstract = {Trichomonas vaginalis (TV) infection is a common non-viral sexually transmitted infection, often combined with mixed vaginal infections. These mixed infections worsen inflammation, disrupt vaginal microbiota, and affect treatment. Currently, TV and its mixed infections are mainly diagnosed by wet mount microscopy, which has low sensitivity and cannot identify complex microbes well. This study compared microscopy with metagenomic sequencing to explore vaginal microbiota changes and improve diagnosis of TV-related mixed infections. We enrolled 30 participants: 20 TV-infected patients (diagnosed by wet mount microscopy) and 10 healthy controls (with Lactobacillus as dominant vaginal microbiota). Then tested by Gram staining, microscopy, and metagenomic sequencing. We analyzed microbial composition and identified different abundant taxa. We also measured clinical indices (Lactobacillus grade, vaginal pH, Nugent score for BV, Donders score for AV) to assess vaginal microecology. Among 20 TV patients, microscopy and clinical criteria found a 65% mixed infection rate (13/20), including TV+AV (5 cases), TV+BV+AV (7 cases), and TV+VVC (1 case). Metagenomic sequencing showed TV patients had higher alpha diversity (Shannon index: p=0.0276) and different beta diversity (ANOSIM, r=0.21, p=0.000167) than controls. At the genus level, TV patients had more anaerobic taxa (Fannyhessea, Atopobium, Peptostreptococcus, FDR<0.05) and less Lactobacillus (FDR<0.05) than controls. All TV patients were CST IV (low Lactobacillus, high mixed bacteria), including 12 cases of CST IV-C and 7 cases of CST IV-B. Microscopy and sequencing had low diagnostic consistency in diagnosing mixed infections, especially for mixed vaginitis. TV infection causes significant vaginal microecological imbalance (less Lactobacillus, more anaerobes, high mixed infection rate). Metagenomic sequencing is better than microscopy at identifying complex microbes and low-abundance pathogens, making it more accurate for diagnosing TV-related mixed infections. These results suggest molecular diagnostic methods should be used as complementary tools for precise analysis improve TV and its mixed infection diagnosis and treatment.},
}

Female
Humans
*Trichomonas vaginalis/genetics/isolation & purification
*Metagenomics/methods
Adult
*Vagina/microbiology/parasitology/pathology
*Trichomonas Vaginitis/diagnosis/microbiology
*Microscopy/methods
Microbiota/genetics
*Coinfection/microbiology/diagnosis/parasitology
Young Adult
Middle Aged
Lactobacillus/isolation & purification/genetics

@article {pmid41416106,
year = {2025},
author = {Yang, X and Tannous, J and Rush, TA and Del Valle, I and Xiao, S and Maharjan, B and Liu, Y and Weston, DJ and De, K and Tschaplinski, TJ and Lee, JH and Morgan, M and Jacobson, D and Islam, MT and Chen, F and Abraham, PE and Tuskan, GA and Doktycz, MJ and Chen, JG},
title = {Utilizing plant synthetic biology to accelerate plant-microbe interactions research.},
journal = {Biodesign research},
volume = {7},
number = {2},
pages = {100007},
pmid = {41416106},
issn = {2693-1257},
abstract = {Plant-microbe interactions are critical to ecosystem resilience and substantially influence crop production. From the perspective of plant science, two important focus areas concerning plant-microbe interactions include: 1) understanding plant molecular mechanisms involved in plant-microbe interfaces and 2) engineering plants for increasing plant disease resistance or enhancing beneficial interactions with microbes to increase their resilience to biotic and abiotic stress conditions. Molecular biology and genetics approaches have been used to investigate the molecular mechanisms underlying plant responses to various beneficial and pathogenic microbes. While these approaches are valuable for elucidating the functions of individual genes and pathways, they fall short of unraveling the complex cross-talk across pathways or systems that plants employ to respond and adapt to environmental stresses. Also, genetic engineering of plants to increase disease resistance or enhance symbiosis with microbes has mainly been attempted or conducted through targeted manipulation of single genes/pathways of plants. Recent advancements in synthetic biology tool development are paving the way for multi-gene characterization and engineering in plants in relation to plant-microbe interactions. Here, we briefly summarize the current understanding of plant molecular pathways involved in plant interactions with beneficial and pathogenic microorganisms. Then, we highlight the progress in applying plant synthetic biology to elucidate the molecular basis of plant responses to microbes, enhance plant disease resistance, engineer synthetic symbiosis, and conduct in situ microbiome engineering. Lastly, we discuss the challenges, opportunities, and future directions for advancing plant-microbe interactions research using the capabilities of plant synthetic biology.},
}

@article {pmid41415842,
year = {2025},
author = {Sun, L and Liu, C},
title = {The modifying effect of dietary index for gut microbiota on the association between urinary arsenic exposure and bladder cancer risk: a nationwide cohort study.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1723496},
pmid = {41415842},
issn = {2296-861X},
abstract = {OBJECTIVE: Arsenic exposure is a well-established risk factor for bladder cancer, but substantial individual variability in susceptibility suggests the potential role of effect modifiers. The gut microbiome, which is influenced by diet, may regulate arsenic metabolism and toxicity. The Dietary Index for Gut Microbiota (DIGM) quantifies the potential of diet to foster a beneficial gut ecosystem, yet its role in modifying arsenic-related carcinogenesis remains unclear. This study aimed to investigate the potential interaction between urinary arsenic levels and DIGM on bladder cancer risk.

METHODS: We conducted a cross-sectional analysis using data from the National Health and Nutrition Examination Survey (NHANES) 2007-2018. Bladder cancer status was obtained through self-reported medical questionnaires. Total urinary arsenic was measured using ICP-DRC-MS, and arsenobetaine was subtracted to estimate toxic inorganic arsenic exposure. DIGM was constructed based on 24-h dietary recall data. Weighted multivariable logistic regression models were used to evaluate associations, and interaction was tested by including a product term (urinary arsenic*DIGM) and assessed on both additive and multiplicative scales.

RESULTS: Among 4,889 participants (mean age 47.47 years; 50.34% male), 585 had bladder cancer. After adjusting for covariates, elevated urinary arsenic was associated with increased bladder cancer risk (OR: 2.22, 95% CI: 1.53-3.22). Interaction analysis revealed a significant multiplicative interaction between urinary arsenic and DIGM (P-interaction = 0.022). Stratified analysis showed a strong positive association between urinary arsenic and bladder cancer in participants in the lowest DIGM tertile (OR: 1.95, 95% CI: 1.46-2.61). This association was significantly attenuated and became non-significant in those in the highest DIGM tertile (OR: 1.13, 95% CI: 0.89-1.44). Measures of additive interaction (RERI = 0.47, AP = 0.31) further supported a synergistic effect.

CONCLUSION: Our findings suggest that a diet promoting a healthier gut microbiota, as indicated by a higher DIGM score, may attenuate the association between urinary arsenic exposure and bladder cancer risk. These results indicate that dietary intervention could be a strategic approach to mitigate urinary arsenic-related cancer risk, highlighting the importance of diet-gut-microbiome interactions in environmental carcinogenesis.},
}

@article {pmid41415835,
year = {2025},
author = {Hao, Z and Li, X and Li, Z and Ma, M and Xi, Y and Yu, L and Wang, Y and Zhang, B and Xu, Y and Zhang, L},
title = {Serum metabolomics and gut microbiota analysis reveal the lipid-lowering effects of fermented triple-bean soup in high-fat diet-fed mice.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1705483},
pmid = {41415835},
issn = {2296-861X},
abstract = {Triple-bean soup (TBS), a traditional Chinese functional food, was innovatively fermented with lactic acid bacteria (FTBS) to enhance its hypolipidemic potential. Using a multi-omics approach integrating 16S rRNA sequencing and serum metabolomics, we systematically investigated FTBS's effects on high-fat diet (HFD)-induced metabolic disorders in mice. FTBS significantly alleviated HFD-induced metabolic disorders, outperforming UFTBS. It remodels the microbial ecosystem by suppressing obesogenic bacteria, restoring microbial diversity and F/B balance, and increasing the abundance of Prevotella, Coprococcus, and Oscillospira. The levels of short-chain fatty acids (SCFAs), notably butyrate and propionate, increased by 1.8-fold following a substantial enrichment of key beneficial bacterial species, including Prevotella and Coprococcus. Metabolomic profiling identified that FTBS modulates the levels of 192 metabolites, reprogrammed key pathways, such as valine, leucine, and isoleucine biosynthesis, glycerophospholipid metabolism, citrate cycle, and primary bile acid biosynthesis. Consequently, systemic metabolomic profiles improved, manifesting as reduced hepatic steatosis and improved blood lipid levels. Our study demonstrates that FTBS ameliorates metabolic syndrome by modulating the gut-liver axis via specific microbial and metabolic shifts. These findings position FTBS as a promising nutraceutical for metabolic liver disease, merging traditional dietary knowledge with modern microbiome science.},
}

@article {pmid41415829,
year = {2025},
author = {Wang, X and Li, J and Ge, Z and Fan, J and Ma, D and Cao, H and Shen, J and Wang, Y and Liu, Z and Gomaa, SE and Li, X and Ji, X and Teng, T},
title = {Phage therapy for intestinal infections: efficacy, challenges, and future directions in translational research.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1672198},
pmid = {41415829},
issn = {1664-302X},
abstract = {Phage therapy has emerged as a promising alternative to conventional antibiotics for combating intestinal bacterial infections, especially in the era of rising antimicrobial resistance. Despite its therapeutic potential, the clinical translation of phage therapy remains hindered by limited large-scale trial data and incomplete mechanistic understanding. This review systematically evaluates the efficacy of phage therapy in animal models of intestinal diseases, encompassing bacterial infection-induced diarrhea (e.g., cholera, typhoid fever), bacterial enteritis, and sepsis. By synthesizing evidence from bacterial colonization assays, histopathological analyses, and disease severity assessments, we highlight features such as phage-mediated pathogen clearance, changes in inflammatory factors, and intestinal pathology. Furthermore, challenges including phage selection difficulties, host specificity issues, and safety considerations are discussed, along with future research directions aimed at bridging the gap between experimental models and clinical applications.},
}

@article {pmid41415821,
year = {2025},
author = {Wang, C and Zhai, C and Hu, S and Lü, Y},
title = {Microbiome-immune crosstalk in allergic rhinitis: lung and intestinal microbiota mechanisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1697226},
pmid = {41415821},
issn = {1664-302X},
abstract = {Allergic rhinitis (AR) is a prevalent immune-mediated upper respiratory disorder that manifests as an itchy nose, nasal congestion, a runny nose, and other symptoms. Emerging research suggests that AR, beyond its IgE-mediated hypersensitivity, indirectly influences the immune system by altering the equilibrium of the lung and intestinal microbiota. Therefore, future research should systematically characterize the mechanistic involvement of the respiratory and intestinal microbiomes in AR development, which may reveal innovative therapeutic targets. This review highlights the mechanisms by which the lung and intestinal microbiota contribute to the pathogenesis of AR and discusses potential therapeutic strategies.},
}

@article {pmid41415809,
year = {2025},
author = {Li, E and Wang, S and Li, Y and Liuli, A and Liang, M and Huang, J and Li, Y and Li, H and Feng, Z},
title = {Characterization of the gut microbiota in people with different levels of obesity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1679119},
pmid = {41415809},
issn = {1664-302X},
abstract = {PURPOSE: With the evolution of dietary habits, obesity has emerged as a significant global health issue. Numerous studies have demonstrated a close association between obesity and gut microbiota; however, the specific contribution of gut microbiota to varying degrees of obesity remains inadequately understood. Consequently, this study aims to characterize the gut microbiota of individuals across different obesity severity levels.

METHODS: We conducted a comprehensive characterization of the gut microbiome in Chinese obese patients and a healthy control group through the application of 16S rRNA gene sequencing, supplemented by metagenomic sequencing. The study cohort was stratified into five distinct categories based on body mass index (BMI): healthy, overweight, and obesity grades I, II, and III.

RESULTS: In obese populations, the gut microbiome structure shifted significantly, with beneficial genera like Faecalibacterium, Roseburia, and Ruminococcus decreasing, and potentially harmful genera such as Blautia, Collinsella, and Streptococcus increasing. These changes impacted host metabolic pathways, including ribosome synthesis, RNA polymerase activity, and DNA repair. Clinical analyses also revealed strong links between specific genera and metabolic markers like lipid metabolism and insulin resistance.

CONCLUSION: Populations with different obesity traits show unique changes in gut flora. The level of dysbiosis, or imbalance in intestinal microbiota, rises with obesity. These microbial changes are linked to host metabolism, indicating that targeting harmful bacteria and supplementing with beneficial ones from normal-weight populations could effectively reduce obesity.},
}

@article {pmid41415685,
year = {2025},
author = {Zhang, L and Chen, N and Chen, H and Tang, C and Wang, J and Wang, Y and Zhang, Y and Guo, H and Yuan, J},
title = {Recent advances of engineered probiotics for therapeutic applications.},
journal = {Biodesign research},
volume = {7},
number = {3},
pages = {100039},
pmid = {41415685},
issn = {2693-1257},
abstract = {A great number of multifactorial diseases, including neoplastic, metabolic, and autoimmune diseases, have been associated with microbiota dysbiosis. Recently, there has been an increasing understanding of the importance of microbiome and their impact on human health. Advances in synthetic biology have led to the development of probiotics as diagnostic tools and disease treatment approaches. In this review, we briefly summarize recent examples of engineered probiotic-based therapeutics in human diseases, including cancers, gastrointestinal disorders, infectious diseases, and metabolic disorders. Finally, we discuss the challenges and opportunities in developing engineered probiotics for disease treatments.},
}

@article {pmid41415417,
year = {2025},
author = {Bracken, AK and Malarney, KP and Chang, PV},
title = {Chemical proteomics reveals regulation of bile salt hydrolases via oxidative post-translational modifications.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.11.693737},
pmid = {41415417},
issn = {2692-8205},
abstract = {The gut microbiome is the vast, diverse ecosystem of microorganisms that inhabits the human intestines and provides numerous essential functions for the host. One such key role is the metabolism of primary bile acids that are biosynthesized in the host liver into a plethora of secondary bile acids produced by gut bacteria. These metabolites serve as both antimicrobial and chemical signaling agents within the host. The critical microbial enzyme that plays a gatekeeping role in secondary bile acid metabolism is bile salt hydrolase (BSH), a cysteine hydrolase that is primarily known for its deconjugating and reconjugating activities on bile acid substrates. Despite the crucial nature of these biotransformations, regulation of BSH activity is not well understood. Here, we found that the catalytic cysteine 2 (Cys2) within the BSH active site exists in multiple sulfur oxidation states including sulfenic acid (Cys-SOH). Importantly, we show this reversible oxidative post-translational modification (oxPTM) ablates BSH catalytic activity. We have leveraged this discovery to develop a chemoproteomic platform featuring a sulfenic acid-reactive bile acid probe to profile BSH Cys2 oxPTMs throughout the gut microbiome. Our results reveal that though most gut microbiota-associated BSHs exist in the active Cys2-SH state, some are preferentially and reversibly inactivated in the Cys2-SOH state. This reversible oxidation of Cys2 may serve as a general mechanism to regulate BSH activity in vivo in response to a changing physiological environment.},
}

@article {pmid41415394,
year = {2025},
author = {Barcena-Varela, M and Shang, J and Mogno, I and Lozano, A and Liebling, I and Mead, KR and Li, Z and Grinspan, LT and Lindblad, KE and Ruiz de Galarreta, M and Donne, R and Gnjatic, S and Merad, M and Jun, T and Ang, C and Marron, TU and Faith, J and Lujambio, A},
title = {Bacteroidetes promote hepatocellular carcinoma progression and resistance to immunotherapy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.09.693238},
pmid = {41415394},
issn = {2692-8205},
abstract = {BACKGROUND AND AIMS: Growing evidence highlight the critical role of the gut microbiome in tumorigenesis and response to immunotherapies. However, the impact of gut microbes on hepatocellular carcinoma (HCC) progression and response to immune-checkpoint blockade (ICB) remains unclear due to the lack of combined preclinical and clinical studies.

APPROACH & RESULTS: We performed 16S rRNA of cross-cohort stool samples from 10 HCC responders (R) and 40 non-responders (NR) to ICB at baseline and on-treatment time-points. We identified an enrichment of Bacteroidetes in NR. To study the role of the microbiome in the cancer immune response, we generated an immunogenic mouse model of HCC via hydrodynamic tail-vein injection (HDTVI) of DNA plasmids mimicking common HCC alterations and immunogenicity by expressing model antigens (MYC-lucOS;CTNNB1 tumors). We found that antibiotic (ABX)-induced dysbiosis promoted a pro-tumorigenic effect in the MYC-lucOS;CTNNB1 HCC model by the expansion of a specific Bacteroidetes , Parabacteroides distasonis . Colonization of mice carrying MYC-lucOS;CTNNB1 HCCs with Parabacteroides distasonis confirmed its pro-tumorigenic effect in vivo. Furthermore, we explored the effects of colonizing with microbiotas from patients and showed that microbiota from a NR donor enriched in Bacteroidetes promoted faster tumorigenesis than microbiota from a R donor with reduced Bacteroidetes . We isolated 6 Bacteroidetes species from the NR donor, cultured them, and used them as a cocktail to colonize mice; similarly, mice transplanted with this cocktail showed increased tumorigenesis and reduced survival.

CONCLUSIONS: This study identified Bacteroidetes enrichment as a potential biomarker of ICB resistance in HCC and, by using immunogenic mouse models, established that Bacteroidetes abundance influences tumor development.},
}

@article {pmid41415387,
year = {2025},
author = {Tjo, H and Jiang, V and Jeffrey, PD and Zhu, A and Link, AJ and Joseph, JA and Conway, JM},
title = {Structural insights into xyloglucan recognition by an ABC transporter from a Gram-positive, thermophilic bacterium.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.13.694138},
pmid = {41415387},
issn = {2692-8205},
abstract = {Xyloglucan (an α-1,6-xylosyl-substituted β-1,4-glucan) is a major hemicellulose of the primary cell wall of many plants and an important growth substrate for biomass-degrading bacteria in diverse ecological niches, including the gut microbiome and hot springs. In Gram-positive bacteria, xyloglucan is deconstructed into soluble oligosaccharides in the extracytoplasmic space before import by ATP-Binding Cassette (ABC) transporters, but the structural basis for this process remains poorly understood. Here, we identified an ABC transporter for xyloglucan uptake (Athe_2052-2054) in the Gram-positive, plant biomass-degrading thermophile Anaerocellum bescii , which is conserved across the Anaerocellum genus. We solved the apo crystal structure of its extracellular substrate-binding protein (SBP), Athe_2052, revealing a unique tertiary fold found only in a small subset of SBPs that bind complex oligosaccharides. This structure represents the first ABC SBP known to bind xyloglucan oligosaccharides. Biophysical analysis showed that while Athe_2052 binds unsubstituted β-glucan chains, recognition of xyloglucan side chains in the binding pocket markedly increases affinity (K d = 14 nM) for xyloglucan heptasaccharide (XXXG), the principal oligosaccharide released during xyloglucan deconstruction. Molecular modeling revealed that xyloglucan heptasaccharide, owing to its branched substitutions, is bound in a distinct conformation compared to unsubstituted β-glucans. This represents a unique mode of xyloglucan recognition driven by α-linked side-chain interactions rather than β-glucan backbone recognition alone. Together, these findings provide the first structural basis for xyloglucan oligosaccharide recognition by an ABC transporter in Gram-positive bacteria.},
}

@article {pmid41415303,
year = {2025},
author = {Witte Paz, M and Bitzer, A and Nieselt, K and Heilbronner, S},
title = {A landscape of metallophore synthesis and uptake potential of the genus Staphylococcus.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf183},
pmid = {41415303},
issn = {2631-9268},
mesh = {*Staphylococcus/genetics/metabolism/classification ; Multigene Family ; Humans ; *Metals/metabolism ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Metallophores are secondary metabolites that enable bacterial growth in metal-limited environments such as the human nasal microbiome. While synthesis and uptake of metallophores in Staphylococcus aureus are well characterized, the diversity across the Staphylococcus genus remains unclear. We performed a comprehensive bioinformatic analysis of 77 representative species, as well as over 1800 strains, to map metallophore biosynthetic gene clusters (BGCs) and uptake systems. Staphyloferrin A (SF-A) biosynthesis was widely conserved, though disrupted loci were found in some species, with some of them appearing to have replaced SF-A with a newly discovered, still uncharacterized, BGC. In contrast, staphyloferrin B and staphylopine production were restricted to select species. Uptake systems were more broadly distributed, showing evidence of "cheating" species that lack biosynthesis, but retain the required lipoproteins for metallophore usage. Staphylococcus lugdunensis exemplifies this, encoding multiple uptake systems without producing known metallophores. Strain-level variation was also observed, particularly with specific cases of SF-A truncation, but also for the diversity of lipoprotein receptors. These findings highlight the diversity of metallophore systems, suggesting diverse metallophore-dependent cooperation and competition within the Staphylococcus genus. This work provides a foundation for future experimental studies to identify the role of metallophores in microbial community interactions.},
}

*Staphylococcus/genetics/metabolism/classification
Multigene Family
Humans
*Metals/metabolism
Bacterial Proteins/genetics/metabolism

@article {pmid41415293,
year = {2025},
author = {Murugan, AK and Alzahrani, AS},
title = {COVID-19 vaccine-induced autoimmune hyperthyroidism: Graves' disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1699210},
pmid = {41415293},
issn = {1664-3224},
mesh = {Humans ; *Graves Disease/immunology/etiology ; *COVID-19 Vaccines/adverse effects/immunology ; *SARS-CoV-2/immunology ; *COVID-19/prevention & control/immunology ; Autoantibodies/immunology ; Autoimmunity ; },
abstract = {Graves' disease (GD) is an autoimmune disorder that results in hyperthyroidism, in which the immune system mistakenly targets the thyroid gland, causing it to produce excessive amounts of thyroid hormones. Genetic predisposition, environmental factors such as infections and stress, disruptions in the gut microbiome, excessive iodine intake, and epigenetic changes have all been implicated in the development of GD. The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) posed a serious global health crisis. The emergence of COVID-19 vaccines has been pivotal in combating the viral infection and its spread. However, reports of rare adverse events, including the development of autoimmune disorders such as GD following vaccination, have raised concerns. Autoimmune factors play a critical role in the pathogenesis of GD, particularly through the production of autoantibodies targeting the thyroid gland. In this review, reported cases are critically analyzed to elucidate commonalities and potential triggers for the development of this autoimmune disorder, highlighting the vital role of autoimmune mechanisms in inducing GD. We also discuss the molecular mechanisms underlying vaccine-induced autoimmunity, including antigen presentation, bystander activation, molecular mimicry, and the induction of inflammatory factors following vaccination. Understanding these mechanisms in COVID-19 vaccine-induced GD could enhance patient care and guide vaccination policies.},
}

Humans
*Graves Disease/immunology/etiology
*COVID-19 Vaccines/adverse effects/immunology
*SARS-CoV-2/immunology
*COVID-19/prevention & control/immunology
Autoantibodies/immunology
Autoimmunity

@article {pmid41414728,
year = {2025},
author = {Hrustemović, E},
title = {The interaction between the gut microbiota, nutrition, and human health.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70395},
pmid = {41414728},
issn = {1097-0010},
abstract = {The biodiversity of the gut flora is widely accepted as a key indicator of human health. The diversity of gut flora depends on age, lifestyle, diet and the use of certain drugs, especially antibiotics. The normal flora is called the microbiota, and the entire genetic material of all microorganisms makes up the microbiome. Probiotics have functions from digesting food, absorbing nutrients to modulating immunity. The purpose of this review is to point out the importance of proper nutrition, as well as the importance of the rational use of antibiotics in order to preserve the biodiversity of the gut flora, which contributes to human health. Articles were retrieved from ScienceDirect, Google Scholar, PubMed and SciELO databases. The research was limited to articles published between 2010 and 2026. Irrational use of antibiotics disrupts the gut flora, which can cause inflammatory bowel diseases, increase intestinal permeability, impairing individual health. The use of oral probiotics with antibiotics can be important in preserving the gut microbiota, and can also help in the treatment of autoimmune diseases. Taking probiotics helps build a diverse population of beneficial gut bacteria before infection occurs, so it is especially recommended to take them during the season of foodborne infections (like summer). The combination of Lactobacillus rhamnosus and Saccharomyces boulardii has proven to be beneficial. After stopping oral probiotics, the microbiota continues to form depending on the diet. Biodiversity of gut flora is different in each person, although it is quite similar among family members with a common environment and diet. © 2025 Society of Chemical Industry.},
}

@article {pmid41413928,
year = {2025},
author = {Dawson, SL and Collier, F and O'Hely, M and Holmes, E and Holland, L and Morgan, R and Lodge, S and Gray, N and Phipps, S and Burgner, D and Mansell, T and Molloy, J and Marx, W and Ponsonby, AL and Vuillermin, P and , },
title = {Maternal prenatal urinary metabolites associate with infant food allergy.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {12},
pages = {e70252},
doi = {10.1111/pai.70252},
pmid = {41413928},
issn = {1399-3038},
mesh = {Humans ; Female ; Pregnancy ; *Food Hypersensitivity/epidemiology/urine ; Infant ; *Hippurates/urine ; Adult ; Male ; Gastrointestinal Microbiome ; Australia/epidemiology ; Diet ; Infant, Newborn ; *Prenatal Exposure Delayed Effects ; },
abstract = {BACKGROUND: Interplay between the maternal diet and gut microbiome may impact fetal immune development and allergic disease risk. This study investigated associations between maternal prenatal urinary metabolites and infant food allergy and then extended to potentially relevant dietary and microbial precursors.

METHODS: We investigated 599 mother-infant dyads from an Australian population-derived prebirth cohort. Maternal dietary data and fecal and urine samples were collected in the third trimester. NMR was used to measure prenatal urinary metabolites. Infant food allergy status was determined at 1 year by skin prick allergy testing and food challenge. Regression techniques were used to investigate associations and adjust for pre-specific confounding factors.

RESULTS: Higher concentration of hippuric acid in maternal urine, an end-product of dietary polyphenol metabolism, was associated with a lower risk of infant food allergy (odds ratio (OR) 0.62 (95% CI 0.42, 0.93)). Consistent with this, dietary proanthocyanidins, a polyphenol, were positively associated with both higher urinary hippuric acid concentration (0.11 log units, CI 0.01, 0.22) and lower risk of infant food allergy (OR 0.58 (CI 0.36, 0.96)). Maternal carriage of the gut commensal Prevotella copri, previously associated with protection against infant allergic disease, was associated with 21% higher urinary hippuric acid concentrations (CI 4%, 40%, corresponding to 0.19 log units CI 0.04, 0.34); however there was no evidence of mediation.

CONCLUSION: Further studies are required to confirm whether higher dietary intake of proanthocyanidins during pregnancy is associated with protection against allergic disease in the infant via gut microbiome production of hippuric precursors and other immune-active metabolites.},
}

Humans
Female
Pregnancy
*Food Hypersensitivity/epidemiology/urine
Infant
*Hippurates/urine
Adult
Male
Gastrointestinal Microbiome
Australia/epidemiology
Diet
Infant, Newborn
*Prenatal Exposure Delayed Effects

@article {pmid41413903,
year = {2025},
author = {Buddhasiri, S and Jantrakajorn, S and Daochai, C and Keawchana, N and Sornying, P and Thiennimitr, P and Suyapoh, W},
title = {Pathogenic piscine intestinal coccidia infection alters gut microbiome in juvenile Asian seabass (Lates calcarifer).},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-025-05168-y},
pmid = {41413903},
issn = {1746-6148},
support = {N24A671189//Innovation and the National Research Council of Thailand (NRCT)/ ; },
}

@article {pmid41413769,
year = {2025},
author = {Medina-Méndez, JM and Iruzubieta, P and Fernández-López, R and Crespo, J and de la Cruz, F},
title = {Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04549-5},
pmid = {41413769},
issn = {1471-2180},
support = {PI22/01853//Spanish Carlos III Health Institute (ISCIII)/ ; PID2020-1179236B-100//Spanish MINECO/ ; },
}

@article {pmid41413743,
year = {2025},
author = {Wang, ZZ and Chen, YK and Li, X and Lin, L and Chen, B and Chen, M and Zheng, H},
title = {Altered molecular signature of the intestinal microbiota in irritable bowel syndrome patients versus healthy controls: An updated systematic review.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {41413743},
issn = {0975-0711},
abstract = {BACKGROUND AND AIMS: Irritable bowel syndrome (IBS), a prevalent functional gastrointestinal disorder, poses significant challenges for both patients and medical practitioners. Recent investigations have indicated the gut microbiome as a potential therapeutic target for IBS. Nevertheless, the exact association between these microorganisms and IBS symptoms remains incompletely elucidated. This updated systematic analysis aims to assess the extant research correlating the gut microbial community with IBS.

METHODS: A systematic search was performed in major electronic databases including PubMed, EMBASE and Web of Science, spanning from their inception to December 2024. The objective was to identify case-control studies that examined and compared the composition of the fecal or colonic microbiota in individuals diagnosed with IBS against healthy controls.

RESULTS: Our systematic search included 44 articles, which collectively revealed that IBS patients exhibit lower intestinal microbiome diversity compared to healthy controls. Fecal microbiome analysis demonstrated an imbalance in the phyla Firmicutes and Bacteroidetes among IBS patients. Specifically, IBS with diarrhea (IBS-D) patients showed reduced levels of Butyricimonas and Proteobacteria, while IBS with constipation (IBS-C) patients exhibited decreased Firmicutes and Actinobacteria, along with increased Verrucomicrobiota and Proteobacteria. Additionally, disruptions in the gut microbiome were noted, particularly in the duodenum and jejunum, as well as changes in key bacterial populations within the colon and rectum.

CONCLUSION: Our review confirms significant gut microbiota dysbiosis in IBS patients, characterized by reduced microbial diversity and altered abundances of Firmicutes and Bacteroidetes. These findings support the potential for microbiota-targeted therapies in IBS management, though further research is needed to establish causal mechanisms and clinical applications.},
}

@article {pmid41413663,
year = {2025},
author = {McAdams, Z and Gustafson, K and Ericsson, A},
title = {Biological and technical variability in mouse microbiota analysis and implications for sample size determination.},
journal = {Lab animal},
volume = {},
number = {},
pages = {},
pmid = {41413663},
issn = {1548-4475},
support = {U42 OD010918/CD/ODCDC CDC HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; },
abstract = {The gut microbiota (GM) affects host development, behavior and disease susceptibility. Biomedical research investigating GM-mediated influences on host phenotypes often involves collecting fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice. While efforts are made to minimize this variation, biological and technical variability exists and may influence outcomes. Here we employed a hierarchical fecal sampling strategy (that is, sequenced multiple libraries generated from multiple pellets collected from multiple mice) to quantify the effect size of biological and technical variation and to provide practical guidance for the development of microbiome studies involving laboratory mice. We found that while biological and technical sources of variation contribute significant variability to alpha- and beta-diversity outcomes, their effect size is 3-30-times lower than that of the experimental variable in the context of an experimental group with high intergroup variability. After quantifying the variability of alpha-diversity metrics at the technical and biological levels, we simulated whether sequencing multiple fecal samples from mice improves effect size in a two-group experimental design. Our simulation determined that collecting five fecal samples per mouse increased effect size, reducing the minimum number of animals per group required by 5% while dramatically increasing sequencing costs. Our data suggest that the effect size of biological and technical factors may contribute appreciable variability to an experimental paradigm with relatively low mean differences. In addition, repeated sampling improves statistical power; however, its application is probably impractical given the increased sequencing costs.},
}

@article {pmid41413612,
year = {2025},
author = {Zheng, L and Lv, X and Fu, A and Fang, H and Li, M and Huang, S and Hsiang, T},
title = {Bacillus amyloliquefaciens PP19 regulation of microbial communities and suppression of Peronophythora litchii.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02239-y},
pmid = {41413612},
issn = {2049-2618},
support = {2022A1515010470//Guangdong Basic and Applied Basic Research Foundation/ ; 202102//Key Laboratory of Biology and Genetic Resources Utilization of South Tropical Fruit Trees, Ministry of Agriculture and Rural Affairs/ ; },
abstract = {BACKGROUND: Litchi downy blight (LDB) is a major disease affecting litchi (Litchi chinensis), damaging fruits, inflorescences, and leaves, and significantly hindering the development of the litchi industry in China and globally. Bacillus amyloliquefaciens PP19 has demonstrated significant biocontrol efficacy against LDB, but its mechanism of action remains unclear.

RESULTS: This study used microbiome analysis and bacterial interaction studies to investigate the biocontrol mechanism by which PP19 regulates core microbial communities on litchi exocarps to suppress LDB. First, 16S rRNA diversity analysis revealed that PP19 pretreatment effectively prevented bacterial diversity imbalances caused by Peronophythora litchii infection, maintaining microbial stability by regulating the abundance of specific genera (Actinomycetospora, Paenibacillus, and Spirosoma). Microbial interaction networks and functional prediction revealed that PP19 might modulate bacterial motility pathways, resulting in changes to the abundance of specific microbial communities on litchi exocarps. These changes facilitated the formation of a core microbiome negatively correlated with the abundance of P. litchii. By isolating and genetically identifying 83 cultivable bacterial strains from litchi exocarps and using correlation analysis, 16 candidate strains with potentially significant interactions with PP19 and P. litchii SC18 were identified. Plate antagonism, liquid co-culture, and leaf biocontrol efficacy analyses ultimately identified four representative strains (Sphingomonas sp. F14, Rhizobium sp. F26, Pseudomonas sp. F32, and Enterobacter cloacae F63) with significant interactions with either PP19 or P. litchii. Interaction, motility, and biofilm production analyses showed that PP19 interacted with the four litchi exocarp bacteria to prevent disease through various mechanisms, and enhanced their motility and biofilm production to varying degrees.

CONCLUSIONS: PP19 regulates core microbial communities on litchi exocarps, maintaining community stability and enriching interacting strains which together inhibit the growth of P. litchii, thereby achieving biocontrol efficacy. Video Abstract.},
}

@article {pmid41413553,
year = {2025},
author = {Shah, S and Mallick, BC and Devi, B and Kumar, M},
title = {Exploring black soil microbiota for industrial enzymes: cellulase and xylanase characterization from Bacillus subtilis SSMK413.},
journal = {Microbial cell factories},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12934-025-02898-4},
pmid = {41413553},
issn = {1475-2859},
}

@article {pmid41413507,
year = {2025},
author = {Saponara, S and Scicchitano, F and D'Alterio, MN and Chilà, C and Daniilidis, A and Vitale, SG and Angioni, S},
title = {Could the estrobolome have a role in endometriosis pathogenesis and infertility? A systematic review.},
journal = {BMC women's health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12905-025-04195-z},
pmid = {41413507},
issn = {1472-6874},
abstract = {BACKGROUND: Endometriosis is a chronic, estrogen-dependent condition affecting 10% of reproductive-aged women, often associated with infertility and chronic pelvic pain. Recent evidence suggests that gut microbiota dysbiosis and alterations in the estrobolome, defined as the collection of bacterial genes involved in estrogen metabolism, may play a role in the pathogenesis of endometriosis and infertility.

METHODS: This systematic review was registered with PROSPERO (ID: CRD42024627464). A comprehensive search was conducted across PubMed, Embase, Scopus, Web of Science, Cochrane CENTRAL, ClinicalTrials.gov, and grey literature sources up to December 2024, without a lower date limit. The search included terms such as "estrobolome," "endometriosis," "infertility," and "estrogen metabolism". Original articles and clinical trials investigating the role of the estrobolome in endometriosis pathogenesis and infertility were included. Abstract-only studies, reviews, and non-English articles were excluded.

RESULTS: Five studies were analyzed, highlighting gut dysbiosis, estrobolome alterations, and immunological factors in endometriosis and infertile patients. Some investigations reported dysregulated or increased β-glucuronidase activity, suggesting a potential link between microbial estrogen metabolism and disease pathophysiology. These microbial and enzymatic alterations were accompanied by elevated inflammatory cytokines and persistent activation of immune cells, possibly contributing to local and systemic estrogen stimulation and lesion progression.

CONCLUSIONS: Our analysis emphasizes how disruptions in estrogen-metabolizing bacterial pathways may contribute to the inflammatory and hormonal features observed in endometriosis and infertility. Given the associations observed, future studies should explore whether modulating the microbiota or estrogen metabolism can improve clinical outcomes in patients with endometriosis or infertility.},
}

@article {pmid41413446,
year = {2025},
author = {Nguyen, NH and Lee, YI and Jang, YS and Lee, HK and Jung, I and Lee, SJ and Lee, JH},
title = {In vitro and in vivo exploration of microbiome-derived yeast extract for anti-aging and skin rejuvenation.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04593-1},
pmid = {41413446},
issn = {1471-2180},
}

@article {pmid41413443,
year = {2025},
author = {Wang, Z and Bai, L and Dong, S and Yang, D and Tong, Z and Zhong, F and Zi, H and Zeng, Y and Chen, M and Xu, H and Zhang, B and Lin, W and Zhang, Z},
title = {Regulatory role of rhizosphere microbial structure and function in yield formation of ratooning season rice.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07915-7},
pmid = {41413443},
issn = {1471-2229},
support = {2021J01093//National Natural Science Foundation of Fujian/ ; KFB24059//the Sci-tech Innovation Fund Project of Fujian Agriculture and Forestry University/ ; },
abstract = {In ratoon rice cultivation, the formation of tillers from stubble following the harvest of the main crop rice is crucial for achieving high and stable yields during the ratooning season. This study employed two rice varieties, YongYou1540 (YY1540) and JinHui809 (JH809), which exhibited comparable yields in the main crop season but markedly different yields in the ratooning season. We systematically compared changes in the physicochemical properties of the rhizosphere soil, as well as the microbial community structure and functional characteristics, between the two varieties at different growth stages during their ratooning seasons (0, 10, and 20 days after harvest). Our results revealed that microbial nutrient-acquiring enzyme activities were significantly higher in YY1540 compared to JH809. Analysis of rhizosphere microbial communities indicated that community diversity (e.g., Chao1) and network properties (e.g., robustness) had limited effects on the yield of ratooning season rice. In contrast, the functional features of the microbiome-particularly the abundances of carbon fixation genes (e.g., acsA, acsB), carbon degradation genes (e.g., malQ, pulA), and phosphorus cycling genes (e.g., pstS, ppx)-were significantly higher in YY1540. Furthermore, Mantel tests indicated that nutrient-cycling functional genes in the rhizosphere microbiome were significantly associated with soil nutrient indices, such as available phosphorus (AP), extractable organic carbon (EOC), and dissolved organic carbon (DOC), as well as the status of microbial nutrient limitation (e.g., VA) and yield of ratooning season rice. Notably, functional genes involved in carbon and phosphorus cycling exhibited particularly strong associations with AP, EOC, and yield of ratooning season rice. Collectively, the increased abundances of key functional genes (e.g., acsA and pstS), along with elevated activities of β-1,4-glucosidase and acid phosphatase, alleviated carbon and phosphorus limitations, improved nutrient supply efficiency during the regrowth stage, and ultimately enabled YY1540 to achieve higher yields in ratooning season rice. This study provides initial evidence for the crucial role of rhizosphere microbial functions in the yield formation of ratooning season rice. It offers a novel theoretical framework and practical pathway for the precision management and sustainable intensification of ratoon rice through microbial regulation.},
}

@article {pmid41413233,
year = {2025},
author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S},
title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.},
journal = {Hypertension research : official journal of the Japanese Society of Hypertension},
volume = {},
number = {},
pages = {},
pmid = {41413233},
issn = {1348-4214},
abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.},
}

@article {pmid41413047,
year = {2025},
author = {Li, X and Perino, A and Sulc, J and Jalil, A and von Alvensleben, GVG and Morel, JD and Wang, Q and Rapin, A and Li, H and Schoonjans, K and Auwerx, J},
title = {Genetic and dietary determinants of gut microbiome-bile acid interactions in the BXD genetic reference population.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67680-x},
pmid = {41413047},
issn = {2041-1723},
support = {ERC-AdG-787702//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 310030-189178//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; RF 2017K1A1A2013124//National Research Foundation of Korea (NRF)/ ; },
abstract = {The gut microbiome is crucial in regulating overall physiology and communicates with the host through various microbial-derived metabolites, including secondary bile acids (BAs). However, mechanisms underlying the gut microbiome-BA crosstalk (gMxB) are still poorly understood. Here, we assess the postprandial cecal microbiome, BA levels, and colon transcriptome of male BXD mice fed with a chow or high-fat diet, and find that genetic and dietary factors shift microbiome composition and affect gMxB. Four diet-dependent co-mapping genetic loci associated with gMxB, including the interaction between Turicibacter sanguinis - plasma cholic acid, are identified using systems genetics approaches. By integrating human MiBioGen database, we prioritize PTGR1 and PTPRD as candidate genes potentially regulating identified gMxB. The human relevance of these candidates on metabolic health is investigated using data from the UK biobank, FinnGen, and million veteran program databases. Overall, this study illustrates potential modulators regulating gMxB and provides insights into gut microbiome-host communication.},
}

@article {pmid41413022,
year = {2025},
author = {Tonnelé, H and Chen, D and Morillo, F and Garcia-Calleja, J and Chitre, AS and Johnson, BB and Sanches, TM and Cheng, R and Bonder, MJ and Gonzalez, A and Kosciolek, T and George, AM and Han, W and Holl, K and Horvath, A and Ishiwari, K and King, CP and Lamparelli, AC and Martin, CD and Martinez, AG and Netzley, AH and Tripi, JA and Wang, T and Bosch, E and Doris, PA and Stegle, O and Chen, H and Flagel, SB and Meyer, PJ and Richards, JB and Robinson, TE and Solberg Woods, LC and Polesskaya, O and Knight, R and Palmer, AA and Baud, A},
title = {Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10126},
pmid = {41413022},
issn = {2041-1723},
support = {105941/Z/14/Z//Wellcome Trust (Wellcome)/ ; LCF/BQ/PI21/11830006//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; P50DA037844//U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; U01DA051234//U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; },
mesh = {Animals ; Rats ; *Gastrointestinal Microbiome/genetics ; Sialyltransferases/genetics ; Humans ; Male ; Cohort Studies ; Phenotype ; Multifactorial Inheritance ; *Host Microbial Interactions/genetics ; Female ; },
abstract = {The intestinal microbiome influences health and disease. Its composition is affected by host genetics and environmental exposures. Understanding host genetic effects is critical but challenging in humans, due to the difficulty of detecting, mapping and interpreting them. To address this, we analyse host genetic effects in four cohorts of outbred laboratory rats exposed to distinct but controlled environments. We show that polygenic host genetic effects are consistent across cohort environments. We identify three replicated microbiome-associated loci, one of which involves the sialyltransferase gene St6galnac1 and Paraprevotella. We find a similar association in a human cohort, between ST6GAL1 and Paraprevotella, both of which have been linked with immune and infectious diseases. Moreover, we find indirect (i.e. social) genetic effects on microbiome phenotypes, which substantially increase the total genetic variance. Finally, we identify a novel mechanism whereby indirect genetic effects can contribute to "missing heritability".},
}

Animals
Rats
*Gastrointestinal Microbiome/genetics
Sialyltransferases/genetics
Humans
Male
Cohort Studies
Phenotype
Multifactorial Inheritance
*Host Microbial Interactions/genetics
Female

@article {pmid41412926,
year = {2025},
author = {Autenrieth, IB and Bury, L and Rooney, AM and Willmann, M and Vehreschild, MJGT and Egli, A},
title = {Paradigms for microbiome analysis in infectious and non-communicable diseases.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.016},
pmid = {41412926},
issn = {1878-4380},
abstract = {Next-generation sequencing and bioinformatics paved the way in deciphering the human gut microbiome and challenged fundamental postulates on the causal role of the microbiota for health and pathogenesis of infectious and noncommunicable diseases. To exploit the clinical relevance and potential of microbiome diagnostics and therapy, deep metagenomic sequencing with standardized, validated laboratory procedures, aiming at deciphering the microbiome at strain level and applying index-scores to allow classification of individual microbiomes as dysbiotic (associated with disease) or eubiotic (associated with health) should be implemented. By this means, metagenomically informed therapies with live biotherapeutic products, fecal microbiota transfer, pro-, pre-, or postbiotics might become a standard in personalized prevention and treatment of infectious and non-communicable diseases.},
}

@article {pmid41412728,
year = {2025},
author = {Marx, W and Suo, C and Dissanayaka, T and Maleki, S and Nguyen, L and Travica, N and Mohebbi, M and Lotfaliany, M and Yucel, M and McGuinness, AJ and Berk, M and Aslam, H and Jacka, FN},
title = {Effects of a probiotic fermented dairy product on hippocampal metabolites, structure and function: an 8-week randomised, placebo-controlled trial in healthy women.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335398},
pmid = {41412728},
issn = {1468-3288},
abstract = {BACKGROUND: Fermented foods are a promising yet underexplored intervention for influencing brain function and mental health through the gut-brain axis.

OBJECTIVE: The objective of this study was to evaluate the impact of a dairy product fermented with probiotic bacteria on aspects of brain structure and function.

DESIGN: In a triple-blind, randomised, placebo-controlled trial, 40 healthy women aged 18-55 years were randomised to consume either 130 g per day of a fermented probiotic yoghurt or a placebo for 8 weeks. The primary outcome was the between-group differential change from baseline to week 8 in left hippocampal metabolites, measured using magnetic resonance spectroscopy. Secondary outcomes included changes in brain structure and function, faecal microbiome composition and functional potential, mental health, gastrointestinal symptoms, memory and blood markers of oxidative stress and inflammation.

RESULTS: There was a between-group difference in the change in average left hippocampal glutathione concentration (mean difference in change: -0.49; 95% CI -0.95 to -0.04), as well as brain volume in the hippocampus and nucleus accumbens, although these results did not withstand correction for multiple comparisons. There were between-group differences in the change in average functional connectivity between the left hippocampus and left frontal pole. There was also a significant between-group change in gut microbiome beta diversity. There were no differences in other secondary measures.

CONCLUSION: This study provides preliminary evidence that a probiotic fermented dairy product can modulate hippocampal-related outcomes.

TRIAL REGISTRATION NUMBER: ACTRN12622000622707.},
}

@article {pmid41412727,
year = {2025},
author = {Osswald, A and Wortmann, E and Wylensek, D and Kuhls, S and Coleman, OI and Peuker, K and Strigli, A and Ducarmon, QR and Larralde, M and Liang, W and Treichel, NS and Schumacher, F and Volet, C and Matysik, S and Kleigrewe, K and Gigl, M and Rohn, S and Guo, CJ and Kleuser, B and Liebisch, G and Schnieke, A and Ridlon, JM and Bernier-Latmani, R and Zeller, G and Zeissig, S and Haller, D and Flisikowski, K and Clavel, T and Ocvirk, S},
title = {Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-332243},
pmid = {41412727},
issn = {1468-3288},
abstract = {BACKGROUND: Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that secondary BAs produced by 7α-dehydroxylating (7αDH+) gut bacteria are increased in CRC, a causal proof of their tumour-promoting effects is lacking.

OBJECTIVE: Investigate the causal role of BAs produced by 7αDH+ gut bacteria in CRC.

DESIGN: We performed feeding studies in a porcine model of CRC combined with multi-omics analyses and gnotobiotic mouse models colonised with 7αDH+ bacteria or a genetically modified strain to demonstrate causality.

RESULTS: Western diet exacerbated the CRC phenotype in APC [1311/+] pigs. This was accompanied by increased levels of the secondary BA deoxycholic acid (DCA) and higher colonic epithelial cell proliferation. The latter was counteracted by the BA-scavenging drug colestyramine. Metagenomic analysis across multiple human cohorts revealed higher occurrence of bai (BA inducible) operons from Clostridium scindens and close relatives in faeces of patients with CRC. Addition of these specific 7αDH+ bacteria (C. scindens/Extibacter muris) to defined communities of gut bacteria led to DCA production and increased colon tumour burden in mouse models of chemically or genetically induced CRC. A mutant strain of Faecalicatena contorta lacking 7αDH caused fewer colonic tumours in azoxymethane/dextran sodium sulfate treated mice and triggered less epithelial cell proliferation in human colon organoids compared with wild-type F. contorta.

CONCLUSION: This work provides functional evidence for the causal role of secondary BAs produced by gut bacteria through 7αDH in CRC under adverse dietary conditions, opening avenues for future preventive strategies.},
}

@article {pmid41412647,
year = {2026},
author = {Chen, T and Mo, S and Shen, M and Du, W and Yu, Q and Chen, Y and Xie, J},
title = {Therapeutic potential of Ficus pumila L. in chronic obstructive pulmonary disease through modulation of the gut microbiota-SCFA-lung signaling pathway.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117952},
doi = {10.1016/j.foodres.2025.117952},
pmid = {41412647},
issn = {1873-7145},
mesh = {*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Ficus/chemistry ; *Signal Transduction/drug effects ; *Lung/metabolism/drug effects ; Mice ; *Fatty Acids, Volatile/metabolism ; *Plant Extracts/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Polysaccharides/pharmacology ; },
abstract = {Ficus pumila L. has been reported to alleviate pulmonary inflammation, its impact on chronic obstructive pulmonary disease (COPD) pathobiology-specifically via modulation of the gut-lung signaling pathway-has yet to be mechanistically defined. This study investigated how Ficus pumila L. polysaccharides (FP-P) and aqueous extracts (FP-E) remodel the gut microbiome-SCFA network and restore microbial metabolic function in a cigarette smoke-induced COPD mouse model. Microbiota composition was profiled by high-resolution 16S rRNA amplicon sequence variant (ASV) analysis, with concomitant quantification of caecal SCFA using targeted gas chromatography-mass spectrometry (GC-MS) and inference of metagenome function by PICRUSt2. Results demonstrated that FP-P and FP-E alleviated pulmonary pathology, reduced inflammatory cytokine secretion, and significantly restored gut microbiota α-diversity in COPD mice. At the family level, FP-P selectively expanded SCFA-producing Clostridiaceae, and Staphylococcaceae, whereas it contracted pro-inflammatory Helicobacteraceae and Campylobacteraceae. Caecal total SCFA concentration increased by 41.90 %, driven primarily by elevations in butyrate (+23.41 %) and propionate (+45.45 %), without significant changes in acetate. PICRUSt2-inferred metagenomes showed up-regulation of butanoate biosynthesis (PWY-5677), metabolism of cofactors and amino acid (P162-PWY and NAD-BIOSYNTHESIS-II), and carbohydrate degradation (P341-PWY), all of which underpin SCFA production. These functional shifts were accompanied by increased abundance of microbial genes encoding ribosomal proteins and ATP-binding cassette transporters, indicating barrier reinforcement. Collectively, FP-P and FP-E mitigate CS-induced COPD pathology through a gut microbiota-SCFA-lung signaling signaling pathway, highlighting the gut-to-lung communication within the broader gut-lung axis. These findings establish a mechanistic link between microbial metabolism and pulmonary inflammation while acknowledging that the reverse lung-to-gut feedback remains to be elucidated. Future studies will investigate this bidirectional crosstalk and the receptor-mediated signaling of SCFAs in lung tissue.},
}

*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
Animals
*Ficus/chemistry
*Signal Transduction/drug effects
*Lung/metabolism/drug effects
Mice
*Fatty Acids, Volatile/metabolism
*Plant Extracts/pharmacology
Male
Mice, Inbred C57BL
Disease Models, Animal
Polysaccharides/pharmacology

@article {pmid41405656,
year = {2025},
author = {Ingegnoli, F and Gandolfo, S and Ciccia, F and Caporali, R},
title = {Integrating Nutrition into Precision Medicine for Controlling Systemic Inflammation in Rheumatoid Arthritis.},
journal = {Inflammation},
volume = {49},
number = {1},
pages = {6},
pmid = {41405656},
issn = {1573-2576},
abstract = {The management of rheumatoid arthritis (RA) has evolved from the conventional “treat-to-target” approach to strategies that emphasize individualized, patient-centered care. Concepts such as “therapeutic matchmaking” and “smart-to-target” highlight the importance of biomarkers, comorbidities, and quality-of-life priorities in selecting treatments. There is increasing evidence that identifies the gut-joint axis as a critical factor in RA pathogenesis. This axis links gut microbiota composition, intestinal barrier integrity, and systemic inflammation. Dysbiosis, reduced short-chain fatty acid production, and increased gut permeability can lead to immune dysregulation and joint inflammation. Nutritional interventions, such as high-fiber diets, prebiotics, probiotics, polyphenols, and omega-3 fatty acids, can restore microbial balance, enhance barrier function, and reduce inflammation. Precision nutrition, which tailors dietary recommendations based on genetic, microbiome, metabolic, and lifestyle factors, provides a framework for incorporating gut health into RA management. Microbiome-guided dietary strategies may improve responses to pharmacologic treatments, enable early intervention, and provide preventive benefits for high-risk individuals. Combining personalized nutrition with pharmacotherapy could optimize disease control, mitigate side effects, and promote sustainable, patient-empowering care. Future research should focus on randomized controlled trials and advanced analytic tools to refine predictive models and establish personalized nutrition as a cornerstone of holistic RA management.},
}

@article {pmid41280052,
year = {2025},
author = {Johnson, D and Sundararaj, KP and Subramanian, S and Qiu, Y and Samuel, I and Cheng, D and Salman, T and Luo, Z and Fitting, S and Keen, L and Call, E and Maddi, A and Stoops, W and Hartley, A and McKinnon, JE and Wan, Z and Berto, S and Jiang, W},
title = {Characterize Oral-to-Blood Microbial DNA Translocation in Individuals with Cocaine Use Disorder.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41280052},
issn = {2692-8205},
abstract = {BACKGROUND: Cocaine disrupts gut barriers in animal models, potentially enabling microbial translocation and inflammation in the periphery and central nervous system (CNS), but its direct role in inducing inflammation remains controversial. This study aimed to determine if the oral cavity is a source of circulating microbial DNA translocation in individuals with current cocaine use disorder (COC).

RESULTS: A cross-sectional case-control study was conducted, comparing COC and demographically matched non-drug controls. Ten COC (via smoking or vaping) and 24 controls provided paired saliva and blood samples. Microbial 16S rRNA V4 region was sequenced in isolated microbial DNA from saliva and plasma. Single-cell RNA sequencing (scRNAseq) was analyzed in human peripheral blood mononuclear cells. Saliva from COC, but not plasma, exhibited reduced alpha diversity and altered beta diversity, characterized by enriched Streptococcus and depleted Fusobacterium, Neisseria, and other taxa relative to controls. Controls exhibited low to undetectable microbial translocation in plasma. By contrast, plasma Streptococcus and several S. species displayed COC-specific oral enrichment and evidence of translocation into the bloodstream. In vitro, cocaine selectively enhanced S. parasanguinis growth, consistent with COC-enriched oral pathobionts and translocation into circulation in vivo. S. parasanguinis, but not cocaine alone, induced IL-1β and TNF-α production in human primary monocytes. scRNAseq further revealed innate immune activation, impaired T cell function, and heightened susceptibility to infection in COC.

CONCLUSIONS: This is the first study demonstrating that COC via smoking or snorting exhibited oral microbial dysbiosis and selective oral-to-blood microbial translocation in vivo. These findings suggest that compromised oral-to-blood barrier, rather than cocaine itself, promotes immune perturbations in COC.},
}

@article {pmid41412637,
year = {2026},
author = {Ferrocino, I and Biolcati, F and Giordano, M and Bertolino, M and Zeppa, G and Cocolin, L},
title = {Dairy environment and seasons affect the microbiome of a traditional artisanal cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117927},
doi = {10.1016/j.foodres.2025.117927},
pmid = {41412637},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Seasons ; *Microbiota ; Animals ; *Food Microbiology ; Italy ; Fungi/classification/genetics/isolation & purification ; *Dairying/methods ; Bacteria/classification/genetics ; Milk/microbiology ; Food Handling/methods ; Cattle ; Metagenomics ; },
abstract = {Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow's milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product's sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.},
}

*Cheese/microbiology/analysis
*Seasons
*Microbiota
Animals
*Food Microbiology
Italy
Fungi/classification/genetics/isolation & purification
*Dairying/methods
Bacteria/classification/genetics
Milk/microbiology
Food Handling/methods
Cattle
Metagenomics

@article {pmid41412214,
year = {2025},
author = {Babalola, KT and Ganugula, R and Arora, M and Anderson, D and Agarwal, SK and Mohan, C and Mehrara, BJ and Kumar, MNVR},
title = {Dose optimization of lymph node-targeted cyclosporine-A for lupus-driven vasculopathy.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114553},
doi = {10.1016/j.jconrel.2025.114553},
pmid = {41412214},
issn = {1873-4995},
abstract = {Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by immune dysregulation, systemic inflammation, and vascular complications. Cyclosporine A (CsA) is a potent immunosuppressant, but its systemic toxicity often limits its clinical use. To address this, we developed a lymph node-targeting nanoparticle formulation of CsA (P2Ns-GA-CsA) designed for CD71-mediated uptake to improve therapeutic efficacy while minimizing off-target effects. We conducted a preclinical dose optimization study in the MRL-lpr mouse model of lupus to define the effective therapeutic window of P2Ns-GA-CsA. Our preclinical dose optimization revealed a complex, biphasic immunological response. While all doses (5, 10, and 15 mg/kg) reduced inflammatory cytokines and kidney injury markers, a nuanced effect on immune activation was observed. The 5 mg/kg and 10 mg/kg doses successfully suppressed lymphocyte proliferation and immune activation, which was evident from reduced splenomegaly, lymphadenopathy, and plasma levels of anti-dsDNA and total IgG. Conversely, the 15 mg/kg dose paradoxically triggered immune hyperactivation, leading to aggressive lymphadenopathy, splenomegaly, and elevated autoantibodies. Mechanistically, the optimal 10 mg/kg dose downregulated key mediators of inflammation-induced lymphangiogenesis, corrected gut microbial dysbiosis, and restored microbiome-mediated tryptophan catabolism, contributing to systemic immunomodulation. These findings highlight the critical importance of non-regulatory dose optimization for nanomedicines, revealing complex pharmacodynamic responses often missed in conventional single-dose studies. Our results not only establish the targeted delivery of CsA as a viable therapeutic strategy for managing the vascular complications of SLE but also provide a crucial framework for ensuring the safety and efficacy of other repurposed immunomodulatory drugs in autoimmune diseases.},
}

@article {pmid41412203,
year = {2025},
author = {Rosales-Islas, V and Montes-García, JF and Ramírez-Paz-Y-Puente, GA and Paniagua-Contreras, GL and Gutiérrez-Pabello, JA and Zenteno, E and Vázquez-Cruz, C and Negrete-Abascal, E},
title = {Epinephrine and norepinephrine increase the growth and expression of adhesins and proteases in Mannheimia haemolytica.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108250},
doi = {10.1016/j.micpath.2025.108250},
pmid = {41412203},
issn = {1096-1208},
abstract = {Mannheimia haemolytica (Mh) is an opportunistic pathogen that causes pneumonic infections in different ruminants. It is also part of the respiratory tract microbiome, but it descends into the lower respiratory tract under stress, causing shipping fever. The stress hormones epinephrine and norepinephrine have been suggested to induce Mh biofilm dispersion, but their roles in virulence have not been shown. In this study, the effects of these two hormones on Mh growth and on the expression of adhesins, proteases, and biofilm formation are evaluated. Physiological concentrations (1-5 ng/mL) of epinephrine and norepinephrine increase the growth of Mh and the expression of 42- and 75-kDa gelatin proteases, induce biofilm dispersion, and decrease biofilm protein and carbohydrate concentrations. At 50 or 500 ng/mL concentrations of epinephrine and norepinephrine, the expression of OmpA and OmpH adhesins and 42- and 100-kDa casein proteases increases. Bacterial adhesion to bovine monocytes or oral epithelial cells also increases, but antibodies against OmpH and OmpA diminish adhesion. Our results strongly suggest that epinephrine and norepinephrine modulate the expression of Mh virulence factors.},
}

@article {pmid41412124,
year = {2025},
author = {Deng, L and Fehr, K and Toe, LC and Allen, LH and Bode, L and Hampel, D and Manus, MB and Mertens, A and Robertson, B and Yonemitsu, C and Meulenaer, B and Lachat, C and Sonnenburg, JL and Azad, MB and Dailey-Chwalibóg, T},
title = {Time-specific bidirectional links between the maternal microbiome, milk composition, and infant gut microbiota.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.11.014},
pmid = {41412124},
issn = {1934-6069},
abstract = {Early-life gut microbiome development is shaped by complex maternal and nutritional influences, yet the temporal and directional structure of these interactions remains unclear. In a longitudinal study of 152 mother-infant dyads in rural Burkina Faso, we examine how maternal gut and milk microbiomes, alongside milk components, influence infant gut microbiome development during the first 6 months. At 1-2 months, the infant gut microbiome clusters into three types: Escherichia-dominated, Bifidobacterium-dominated, and a diverse, pathogen-prevalent profile, which become less distinct by 5-6 months. Early infant gut microbiomes associate with maternal prenatal gut microbiota and early milk microbiome and oligosaccharides, while later variation links to other milk nutrients. Furthermore, early infant gut profiles predict subsequent milk composition, suggesting potential bidirectional communication between infant needs and maternal lactational physiology. These findings offer insights into early-life microbial development and inform future mechanistic studies and microbiome-targeted interventions, particularly in low-resource settings.},
}

@article {pmid41412116,
year = {2025},
author = {Collins, MK and Darch, H and Olavarría-Ramírez, L and McCafferty, C and O'Riordan, KJ and Cryan, JF},
title = {Robust Hippocampal Synaptic Plasticity Despite Gut Microbiota Depletion in Adult Mice.},
journal = {The European journal of neuroscience},
volume = {62},
number = {12},
pages = {e70346},
doi = {10.1111/ejn.70346},
pmid = {41412116},
issn = {1460-9568},
support = {754535//H2020 Marie Skłodowska-Curie Actions, Marie Sklodowska-Curie/ ; IRC GOIPG/2021/942//H2020 Marie Skłodowska-Curie Actions, Marie Sklodowska-Curie/ ; //Irish Research Council/ ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; *Hippocampus/physiology/drug effects ; Male ; *Neuronal Plasticity/physiology/drug effects ; Female ; Mice ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred C57BL ; Long-Term Potentiation/drug effects ; },
abstract = {The microbiota-gut-brain axis describes the bidirectional communication between the brain and the trillions of microorganisms living in the gut. Moreover, current evidence suggests that this axis can influence host behaviour and brain physiology. Previously we have shown that adult mice that have not been exposed to microbes throughout their lives display sex-specific deficits in hippocampal synaptic plasticity. However, it is not known whether this phenomenon originates during neurodevelopment or whether similar effects could be recreated with microbiome depletion in adulthood. Therefore, we explored the vulnerability of hippocampal synaptic function to altered microbiome signals, depleting the microbiome of male and female mice for 2 weeks with either an antibiotic cocktail or a single antibiotic added to drinking water. The antibiotic cocktail contained a variety of antibiotics including broad-spectrum antibiotics to ensure widescale microbiota depletion (ampicillin, vancomycin and imipenem). In addition, a more targeted depletion of Gram-positive gut bacteria was conducted using the gut-restricted antibiotic vancomycin. Ex vivo hippocampal electrophysiology measures of basal synaptic efficacy, short-term plasticity, and long-term potentiation (LTP) were then examined. We found that there was no effect of antibiotic administration on any of these measures, demonstrating the robustness of these hippocampal circuits to microbiome depletion during early adulthood. Taken together, this shows the ability of adult hippocampal plasticity to withstand a gut microbiome insult.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
*Hippocampus/physiology/drug effects
Male
*Neuronal Plasticity/physiology/drug effects
Female
Mice
Anti-Bacterial Agents/pharmacology
Mice, Inbred C57BL
Long-Term Potentiation/drug effects

@article {pmid41412053,
year = {2025},
author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D},
title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140847},
doi = {10.1016/j.jhazmat.2025.140847},
pmid = {41412053},
issn = {1873-3336},
abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.},
}

@article {pmid41411975,
year = {2025},
author = {Dai, J and Cao, X and Xu, H and Wang, C and Hao, L and Xie, B and Li, S and Zhao, K and Cui, L and Yin, Z and Yao, B and Chen, T and Haderlein, SB and Wang, R and Xu, F},
title = {Anodic microbiota reassembly via cell-cell interactions confers oxygen resilience in microbial fuel cells.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133815},
doi = {10.1016/j.biortech.2025.133815},
pmid = {41411975},
issn = {1873-2976},
abstract = {An anaerobic environment is typically optimal for electrochemically active microorganisms to generate current. Previous studies have created an integrated chamber-free microbial fuel cell (iMFC) that enables anaerobic sludge-sourced EAMs to function under high dissolved oxygen (DO) for the first time, although the mechanism remained unclear. This study examined the power output and anode microbiome dynamics under DO exposure in the iMFC. Multi-omics revealed a three-phase microbiome reassembly during aeration. Indole-3-acetic acid (IAA) and its precursors from anaerobes, together with streptozocin, phenazine, and rhamnolipid produced sequentially by aerobes, drove the anaerobic-aerobic transition. Initially, DO suppressed anaerobes, alleviating their IAA-mediated inhibition of facultative aerobes. Subsequent cell-cell signaling guided anodic microbiome succession from Acinetobacter to Stenotrophomonas, and finally to Pseudomonas. These findings elucidate the anode microbiome transformation mechanism and confirm with a reassembled synthetic consortium that iMFCs can operate aerobically, providing key insights for scaling the technology.},
}

@article {pmid41411934,
year = {2025},
author = {Paul, SS and Dey, A and Chanu, YM and Paul, J and Andonissamy, J and Dahiya, SS and Punia, BS},
title = {Altered rumen microbiome of water buffalo (Bubalus bubalis) by dietary composite feed additive enhances growth and nutrient utilization with reduced enteric methane and nitrogen emissions.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128347},
doi = {10.1016/j.jenvman.2025.128347},
pmid = {41411934},
issn = {1095-8630},
abstract = {Environmental pollution through animal agriculture is a great concern in recent days owing to enhanced demand of animal products. In view of reduced greenhouse gas emissions from ruminants, this study investigated the effects of a novel composite feed additive (RESMI) having an optimum combination of methane inhibitors and alternate hydrogen sinks on rumen microbial community, methanogenesis, digestibility of feed, rumen fermentation, and performance of water buffaloes. The feed additive, RESMI was fed to fourteen Murrah buffalo calves divided into two groups (control and treatment) in a completely randomized design along with basal feed wheat straw, green fodder and concentrate mixture for a period of six months to study growth rate, nutrient utilization and methane emissions. Another four rumen fistulated adult buffaloes were selected to investigate the abundance and dynamics of rumen microbiota including potential adaptation of rumen microbes over five months of feeding experimentation. The treatment significantly (p < 0.05) decreased methane emission by up to 75 %, increased (p < 0.05) body weight gain by 9.7 %, feed efficiency by 15.2 % and also increased (p < 0.05) feed digestibility, resulting reduced faecal N excretion. The ruminal ammonia concentration was decreased (p < 0.05) and the abundances of total archaea at 1month as well as 5 months post dosing were decreased (p < 0.05) as compared to pre-dosing level but did not adversely (p > 0.05) affect the abundances of total bacteria and anaerobic fungi. A substantial difference (p < 0.05) in the relative abundance of different phylotypes of archaea, bacteria, and anaerobic fungi and unclassified bacteria were demonstrated indicating possible microbial community reorientation over time. The study revealed that supplementing the novel composite feed additive (RESMI) comprising of a combination of adequate electron acceptors or alternate hydrogen sinks with multiple inhibitors of methanogens can be an effective approach to decrease environmental pollution from ruminants and enhance production performance without development of substantial methanogenic archaeal resistance over long-term usage.},
}

@article {pmid41411657,
year = {2025},
author = {Chitre, S and Gharaibeh, RZ and Jobin, C},
title = {A defined bacterial consortium and spatial transcriptomics highlight the complex interaction between Campylobacter jejuni and the murine intestine.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2600053},
doi = {10.1080/19490976.2025.2600053},
pmid = {41411657},
issn = {1949-0984},
mesh = {Animals ; *Campylobacter jejuni/genetics/physiology/isolation & purification ; *Gastrointestinal Microbiome ; Mice ; *Campylobacter Infections/microbiology/immunology/genetics ; *Transcriptome ; Mice, Inbred C57BL ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Interleukin-10/genetics/deficiency ; Germ-Free Life ; *Intestines/microbiology/immunology ; Gene Expression Profiling ; },
abstract = {The intestinal microbiota influences host susceptibility to Campylobacter jejuni (C. jejuni) infection. However, the interaction between specific intestinal bacteria and the C. jejuni-mediated host response is unclear. We established a defined consortium of bacteria to delineate C. jejuni-induced host responses. Three groups of germ-free (GF) Il10[-/-] mice were used in this study: 1) mice colonized with a defined consortium of 13 bacterial isolates (C13) representing the four most prominent phyla in the mouse gut. 2) C13 plus C. jejuni 81-176 and 3) GF alone. The C13 + C. jejuni group induced significant intestinal inflammation and inflammatory mRNA gene expression compared to mice colonized with C13. 16S rRNA gene sequencing revealed an increased relative abundance of Escherichia and Paraclostridium in C13 + C. jejuni. Fluorescence in situ hybridization (FISH) and RNAscope integrated with spatial transcriptomics provided a high-resolution map of infection-induced gene expression, revealing localized immune responses and epithelial remodeling in defined colonic regions. Region-specific analysis further demonstrated that tissue-associated C. jejuni differentially modulates host gene expression compared to tissue-associated Enterobacteriaceae. Collectively, these findings demonstrate the potential of defined microbial consortia and spatially resolved transcriptomics to dissect the complex interplay between host, microbiota, and pathogens during enteric infection.},
}

Animals
*Campylobacter jejuni/genetics/physiology/isolation & purification
*Gastrointestinal Microbiome
Mice
*Campylobacter Infections/microbiology/immunology/genetics
*Transcriptome
Mice, Inbred C57BL
Mice, Knockout
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Interleukin-10/genetics/deficiency
Germ-Free Life
*Intestines/microbiology/immunology
Gene Expression Profiling

@article {pmid41411654,
year = {2025},
author = {Zhang, L and Xu, W and Meng, HYH and Ching, JYL and Liu, Y and Wang, S and Yan, S and Lin, L and Cheong, PK and Ip, KL and Peng, Y and Zhu, J and Cheung, CP and Leung, TF and Leung, ASY and Tam, WH and Leung, TY and Chan, PKS and Chang, EB and Rubin, DT and Claud, EC and Wu, WKK and Tun, HM and Chan, FKL and Ng, SC},
title = {Impacts of COVID-19 pandemic on early life gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2443117},
doi = {10.1080/19490976.2024.2443117},
pmid = {41411654},
issn = {1949-0984},
mesh = {Humans ; *COVID-19/epidemiology ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; SARS-CoV-2 ; Infant, Newborn ; China/epidemiology ; Pandemics ; Male ; Bacteria/genetics/classification/isolation & purification/drug effects ; Cohort Studies ; Hygiene ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Increased hygiene and sanitation are theorized to predispose to developing atopic diseases, a process potentially mediated by the gut microbiome. We hypothesized that the gut microbiome maturation has been altered by COVID-19 lockdown measures during the first year of life, a critical period when environmental exposure shapes human microbiome development. The two large pre- and during-COVID-19 mother-baby pairs cohorts in the Greater Bay Area of China provided the unique opportunity to assess the effect of increased hygiene standards on early gut microbiome maturation. Our results showed that the gut microbiome diversity, composition, and developmental trajectory were significantly altered between pre- and during-COVID-19 cohorts. Functionally, there was decreased richness in both antimicrobial peptide resistance genes and antibiotic resistance genes in the during-COVID cohort. Specially, Staphylococcus epidermidis carried a lower copy number of fluoroquinolone and beta-lactam antibiotics resistance genes while Klebsiella pneumoniae possessed a higher copy number of fluoroquinolone antibiotic resistance genes in gut microbiota of infants born during the COVID-19 pandemic. Our study underscores the importance of considering the microbiome when evaluating hygiene measures and the need for future research to ascertain the role of the gut microbiome in disease development.},
}

Humans
*COVID-19/epidemiology
*Gastrointestinal Microbiome/genetics
Infant
Female
SARS-CoV-2
Infant, Newborn
China/epidemiology
Pandemics
Male
Bacteria/genetics/classification/isolation & purification/drug effects
Cohort Studies
Hygiene
Anti-Bacterial Agents/pharmacology
Feces/microbiology
Drug Resistance, Bacterial/genetics

@article {pmid41410816,
year = {2025},
author = {He, JH and Wang, H and Qiu, E and Qi, Q and Wang, Z},
title = {Gut Microbiota and Atherosclerosis: Integrative Multi-Omics and Mechanistic Insights.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {1},
pmid = {41410816},
issn = {1534-6242},
support = {R01HL170904/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology/metabolism ; Metabolomics/methods ; Metagenomics ; Dysbiosis ; Proteomics ; Multiomics ; },
abstract = {PURPOSE OF REVIEW: This review synthesizes and discusses evidence from metagenomics, metabolomics, and proteomics on gut microbiome alterations in atherosclerotic cardiovascular disease (ACVD), with carotid atherosclerosis (CAS) serving as an example.

RECENT FINDINGS: Evidence on gut microbial α-diversity and β-diversity was mixed and differs by disease status. Pro-inflammatory/pathogenic gut bacterial taxa (e.g., Escherichia coli, Klebsiella spp., Streptococcus spp., and Ruminococcus gnavus) were often enriched in patients with ACVD or CAS, whereas short-chain fatty acid (SCFA) producers (e.g., Faecalibacterium prausnitzii, Roseburia spp., Bacteroides spp., and Eubacterium eligens) were depleted. Targeted and untargeted metabolomics implicated multiple microbial-derived metabolites in relation to ACVD and CAS, including trimethylamine N-oxide, short-chain fatty acids, bile acids, lipopolysaccharides, phenylacetylglutamine, indole-3-propionate and imidazole propionate. Gut dysbiosis contributes to ACVD or CAS possibly via metabolite-mediated effects on endothelial function, inflammation, and lipid metabolism. Future research prioritizing longitudinal and interventional studies integrating microbial metagenomics with host multi-omics are needed to elucidate causal pathways and identify clinically actionable targets.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Atherosclerosis/microbiology/metabolism
Metabolomics/methods
Metagenomics
Dysbiosis
Proteomics
Multiomics

@article {pmid41410755,
year = {2025},
author = {Rath, T and Neurath, MF},
title = {[Chronic inflammatory bowel diseases : What contribution can endoscopy make?].},
journal = {Innere Medizin (Heidelberg, Germany)},
volume = {},
number = {},
pages = {},
pmid = {41410755},
issn = {2731-7099},
abstract = {Chronic inflammatory bowel diseases (IBD), primarily ulcerative colitis and Crohn's disease, are chronic relapsing-remitting inflammations of the gastrointestinal tract. The pathogenesis involves a dysregulation of the intestinal immune system in response to commensal components of the intestinal microbiome. A genetic predisposition forms the foundation for the sustained inflammatory reaction. While treatment approaches in the past focused mainly on the control of clinical symptoms through medication, the results of recent studies indicate that an endoscopically detected remission is superior to mere clinical symptom control in terms of disease progression and prognosis. This review article highlights the importance of endoscopy in the management of IBD, presents established scoring systems for the endoscopic grading of inflammatory activity and outlines in which situations and according to which guidelines endoscopic diagnostics are indicated. Finally, yet importantly applications and algorithms of artificial intelligence as well as advanced technologies in microscopy are increasingly being integrated into endoscopic procedures for patients with IBD and are also discussed in this article.},
}

@article {pmid41410660,
year = {2025},
author = {Tulone, G and Pavan, N and Fasciana, TM and Martorana, A and Minasola, C and Tricoli, MR and Claps, F and Mariyam, L and Marmo, D and Serra, N and Giammanco, A and Simonato, A},
title = {Exploring the influence of the bladder microbiome on BCG immunotherapy outcomes for high-risk non muscle invasive bladder cancer.},
journal = {Minerva urology and nephrology},
volume = {77},
number = {6},
pages = {820-827},
doi = {10.23736/S2724-6051.25.06431-6},
pmid = {41410660},
issn = {2724-6442},
mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/drug therapy/pathology/therapy ; *BCG Vaccine/therapeutic use/administration & dosage ; Retrospective Studies ; Female ; Male ; *Microbiota ; Aged ; *Urinary Bladder/microbiology ; *Adjuvants, Immunologic/therapeutic use/administration & dosage ; Treatment Outcome ; Middle Aged ; Immunotherapy/methods ; Administration, Intravesical ; },
abstract = {BACKGROUND: Intravesical Bacillus Calmette-Guérin (BCG) is an established adjuvant therapy for high-risk superficial bladder cancer, though its efficacy varies among patients. Recent interest in the urinary microbiome comprising microorganisms inhabiting the urinary tract stems from its potential impact on various urological conditions, including bladder cancer. Our study investigates the possible relationship between the bladder microbiome and BCG therapy outcomes in a preliminary and explorative analysis.

METHODS: We conducted a retrospective, descriptive study involving 31 high-risk bladder cancer (BC) patients treated with BCG. BC tissues were collected pre-treatment, and formalin-fixed paraffin-embedded (FFPE) samples were analyzed. DNA extracted from these samples underwent high-throughput 16S rRNA amplicon sequencing targeting the V1-V3 regions.

RESULTS: Our cohort consisted of 15 BCG-resistant patients and 16 responders. Median instillation numbers were six (IQR: 6-9) for resistant patients and twelve (IQR: 14-15) for responders, with a median follow-up length of six months (IQR: 3.3-9.5) and 43 months (IQR: 24-55), respectively. Significant differences were observed in the microbiome: BCG responders showed higher median percentages of Firmicutes (1.1 vs. 0.3, P=0.0293) and Verrucomicrobiota (0.9 vs. 0.1, P=0.0285). Additionally, Fusobacteriota was more prevalent among responders (75% vs. 33.3%, P=0.0198), while Cyanobacteria were more common in resistant patients (73.3% vs. 31.3%, P=0.0191).

CONCLUSIONS: Our preliminary findings illuminate the bladder microbiome's role in influencing BCG therapy outcomes, underscoring the complex microbial interplay affecting treatment efficacy in urological diseases. This explorative study sets the groundwork for ongoing data collection and future research pathways aimed at further delineating these relationships.},
}

Humans
*Urinary Bladder Neoplasms/microbiology/drug therapy/pathology/therapy
*BCG Vaccine/therapeutic use/administration & dosage
Retrospective Studies
Female
Male
*Microbiota
Aged
*Urinary Bladder/microbiology
*Adjuvants, Immunologic/therapeutic use/administration & dosage
Treatment Outcome
Middle Aged
Immunotherapy/methods
Administration, Intravesical

@article {pmid41410609,
year = {2025},
author = {Drost, M and Fuhrmann, G},
title = {Pseudomonas aeruginosa and Its Unsuspected Ally Lactiplantibacillus plantarum: Enhanced Pathogenicity in A Combined Cystic Fibrosis Sputum - Epithelial Cell Model.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00759},
pmid = {41410609},
issn = {2373-8227},
abstract = {Pseudomonas aeruginosa is a notorious bacterial pathogen causing chronic pulmonary infections in people with cystic fibrosis (CF) due to its high tolerance to antibiotics and ability to form recalcitrant biofilms. A newer approach to attenuate the virulence of P. aeruginosa in CF could be the local reinforcement of a resilient community of competing bacteria in the lung. Lactobacilli can mediate antagonistic effects against P. aeruginosa by production of organic acids, but it is not entirely clear if they can exert this beneficial effect locally at the site of infection. While the nutritional environment of the airways in CF promotes P. aeruginosa, it does not support robust growth of lactic acid bacteria, thus attenuating their probiotic potential. To overcome this obstacle, we hypothesized that prebiotic fructooligosaccharides (FOS) could selectively stimulate Lactiplantibacillus plantarum during culture in synthetic cystic fibrosis sputum medium (SCFM2). Indeed, FOS supported the growth of L. plantarum and led to increased acid production. Co-cultivation of L. plantarum and P. aeruginosa reduced biofilm formation and FOS enabled L. plantarum to grow to higher densities in dual-species biofilms. However, this came at the cost of an increased production of the cytotoxic metabolite pyocyanin by P. aeruginosa. To examine whether L. plantarum would influence the pathogenicity of P. aeruginosa, we developed a dual-bacterial species infection model using a CF - relevant airway cell line exposed to the nutritional environment of SCFM2. L. plantarum, grown in SCFM2 or SCFM-FOS, did not inhibit the adhesion of P. aeruginosa. In contrast, the presence of live as well as heat-inactivated L. plantarum, or sterile L. plantarum supernatants drastically enhanced the cell damage during coinfection with P. aeruginosa. This effect was not exclusively dependent on differences in the proliferation of P. aeruginosa or addition of SCFM2 to the cell culture medium. Our data indicate that a potential benefit of bacteriotherapy is determined by the nutritional environment of the diseased body site and that the use of L. plantarum in the context of chronic pulmonary infections must be carefully evaluated.},
}

@article {pmid41410536,
year = {2025},
author = {Berruto, C and Grillo, E and Esturi, S and Demirer, GS},
title = {A 3D-printed capillary tube holder for high-throughput chemotaxis assays.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0038425},
doi = {10.1128/jb.00384-25},
pmid = {41410536},
issn = {1098-5530},
abstract = {Bacterial chemotaxis is an important behavior to study to understand spatial segregation of species in mixed communities and the assembly of host microbiomes. This is particularly relevant in the rhizosphere, where chemoattraction toward root exudates is an important determinant of plant colonization. However, current methods to screen chemoeffectors are limited in their throughput, creating a barrier to generating comprehensive data sets describing chemotactic profiles for species of interest. Here, we describe a novel 3D-printed capillary tube holder approach, which facilitates up to 384 simultaneous capillary tube chemotaxis assays. We optimized and benchmarked our assay using Escherichia coli K12 and Bacillus subtilis 3610 with known chemoattractants: serine and aspartate. We then tested the threshold concentration of these chemoattractants using our assay and found that we could detect chemoattraction toward concentrations spanning multiple orders of magnitude. In this paper, we describe our high-throughput chemotaxis assay in detail and provide the necessary files for 3D printing the capillary tube holder.IMPORTANCEChemotaxis is an important behavior to study to understand how microbial communities assemble and respond to their environment. Identifying chemoattractants may uncover key targets for microbiome engineering. However, the generation of large data sets describing chemotactic profiles has been limited by a lack of high-throughput tools to quantitatively screen chemotaxis. We designed a 3D-printed assay allowing for up to 384 simultaneous capillary tube chemotaxis assays and validated our method with two different bacterial species. The throughput of our approach is greatly increased by the ability to use lag time as a proxy for cell count. Our approach is easy to use and low cost, effectively lowering the barrier to expanding more comprehensive data sets describing the chemotactic profiles of different bacterial species.},
}

@article {pmid41410463,
year = {2025},
author = {Xie, Y and Cidan, Y and Cisang, Z and Ciwang, R and Liu, G and Wu, D and Cideng, D and Chilie, J and Kang, J and Zhu, Y and Basang, W},
title = {Effect of altitudes on serum parameters, metabolome, and gut microbiota in yaks on the Qinghai-Tibet Plateau.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0254925},
doi = {10.1128/spectrum.02549-25},
pmid = {41410463},
issn = {2165-0497},
abstract = {Yaks (Bos grunniens), native to the Qinghai-Tibet Plateau, have evolved extraordinary physiological resilience to chronic hypoxia, cold, and nutritional scarcity. However, the integrated metabolic and microbial mechanisms underlying these adaptations remain poorly defined. Here, a comprehensive multi-omics analysis was performed on thirty grazing heifer yaks (2.5 years old) from three altitudes-3,600 m (low altitude [LA]), 4,000 m (middle altitude [MA]), and 4,500 m (high altitude [HA])-to investigate how altitude affects host physiology, metabolism, and gut microbial ecology. Increasing altitude significantly reduced serum total protein, globulin, blood urea nitrogen, and alkaline phosphatase, indicating suppressed anabolic metabolism and nitrogen-sparing strategies. Antioxidant capacity (total superoxide dismutase, total antioxidant capacity) and pro-inflammatory cytokines (interleukin-2 [IL-2], IL-6, tumor necrosis factor-α, interferon-γ) increased (P < 0.05), while glutathione peroxidase, IL-4, IL-10, growth hormone, insulin-like growth factor-1, and growth hormone-releasing hormone declined (P < 0.05), reflecting energy reallocation from growth toward antioxidation and immune maintenance under hypoxia. Plasma metabolomics revealed distinct altitude-dependent reprogramming, with enrichment of retinol metabolism at 4,000 m and α-linolenic acid metabolism, tricarboxylic acid (TCA) cycle, and branched-chain amino acid biosynthesis at 4,500 m. These pathways link lipid remodeling, oxidative balance, and oxygen utilization. The gut microbiota displayed altitude-specific shifts, characterized by enrichment of Christensenellaceae_R-7_group and Monoglobus and reduced UCG-005 and Rikenellaceae_RC9_gut_group, accompanied by lower fecal volatile fatty acids (P < 0.05). Correlation analyses confirmed tight associations between fermentative taxa and volatile fatty acids production. Collectively, our results establish a serum-metabolome-microbiota axis as a central mechanism supporting yak adaptation to high altitude.IMPORTANCEThis study demonstrates that the gut microbiota plays a crucial role in how yaks adapt to high-altitude hypoxia. Rising altitude not only alters the composition of gut microbes but also shifts their metabolic activity toward improving fermentation efficiency and antioxidant capacity. These microbial changes are closely linked with host metabolism, forming a coordinated serum-metabolome-microbiota network that helps maintain energy balance and immune stability when oxygen is limited. The enrichment of retinol and α-linolenic acid metabolism as altitude-responsive pathways further highlights the metabolic interplay between host and microbes in supporting physiological resilience. Overall, our findings show that microbial flexibility and metabolic cooperation are key factors enabling ruminants to survive in extreme environments, providing a scientific basis for microbiome-informed strategies to enhance yak health and productivity on the Qinghai-Tibet Plateau.},
}

@article {pmid41410445,
year = {2025},
author = {Shin, R and Han, S and Ro, J and Lee, S and Ryu, S-H and Hur, H-G and Shin, H},
title = {Quantitative microbial risk assessment of antibiotic resistance genes and mobile genetic elements in orchard soils across South Korea.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0226025},
doi = {10.1128/aem.02260-25},
pmid = {41410445},
issn = {1098-5336},
abstract = {Antibiotic resistance is a global health crisis, but environmental pathways of resistance dissemination to farm workers remain poorly understood. Agricultural soils represent critical but underexplored reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), particularly in orchards where antibiotics such as streptomycin and oxytetracycline are widely used for fire blight control. Here, we conducted a nationwide investigation of orchard soils in South Korea, integrating high-throughput qPCR, 16S rRNA gene sequencing, and quantitative microbial risk assessment (QMRA). We detected 297 ARGs and 52 MGEs, with eight core genes [aac(3)-VIa, tetL, aadE, sul1, qacH_351, tnpA-1, IS6100, and intI1] significantly enriched in orchard soils but absent in non-orchard soils, such as national parks or mountain soils. Aminoglycoside- and tetracycline-resistance genes were dominant, directly reflecting the application of streptomycin and oxytetracycline. QMRA estimated that orchard farmers ingest resistance genes through soil contact, with aac(3)-VIa posing the highest risk (~29 ingestion events per farmer annually), followed by qacH_351, tetL, and tnpA-1. These results demonstrate the quantifiable occupational risks of ARG exposure in orchard environments. By combining resistome profiling, microbial networks, and QMRA, this study establishes a framework for assessing the public health implications. Although the ingestion of ARGs may not immediately cause impacts on human health, such exposure has the potential to enrich antibiotic resistance within the gut microbiome of farm workers, thereby increasing the probability of treatment complications if infections occur.IMPORTANCEAntibiotic resistance is widely recognized as one of the most concerning threats to public health, yet the pathways through which resistance emerges and spreads remain underexplored. Orchard soils, where antibiotics are sprayed to control plant diseases, represent an overlooked environment where resistance may develop and circulate to people who work the land. By examining soils from orchards at a nationwide scale, we found resistance genes that mirror the antibiotics used in these settings and showed that farm workers are regularly exposed to them through routine contact with soil. This study provides the direct evidence that orchard farming can contribute to human exposure to resistance, heralding the need to include agricultural environments in efforts to prevent the spread of resistance. Our work offers a way to measure these risks and can guide protective strategies for workers and communities.},
}