@article {pmid41253270,
year = {2025},
author = {Ding, L and Xu, JY and Zhang, LL and Liu, Y and Gu, KT and Liang, YZ and Hidayat, K and Wan, Z and Chen, GC and Qin, LQ},
title = {Lactoferrin alleviates non-alcoholic steatohepatitis via remodeling gut microbiota to regulate serotonin-related pathways.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.11.034},
pmid = {41253270},
issn = {2090-1224},
abstract = {INTRODUCTION: Lactoferrin (LF), a multifunctional glycoprotein, has been implicated in the regulation of glucose and lipid metabolism.

OBJECTIVES AND METHODS: This study employed in vivo and in vitro models to investigate the direct effects of LF on non-alcoholic steatohepatitis (NASH) and to elucidate its underlying mechanisms.

RESULTS: LF intervention alleviated hepatic lipid metabolic disorders and liver injury in high-fat, high-cholesterol cholate-containing diet (HFCCD)-fed mice by mitigating oxidative stress, suppressing the inflammatory cGAS/STING pathway, and reducing M1 proinflammatory macrophage polarization. These effects were validated in free fatty acid (FFA)-treated HepG2 cells and AML12 cells. Furthermore, LF ameliorated HFCCD-induced gut microbiota dysbiosis and increased short-chain fatty acid levels. The critical role of gut microbiota in mediating the hepatoprotective effects of LF was confirmed through antibiotic-induced microbiome depletion and fecal microbiota transplantation. Mechanistically, LF modulated gut-liver serotonin signaling and promoted fatty acid β-oxidation through the HTR2A-PPARα-CPT-1A pathway, an effect abolished by the HTR2A agonist DOI. In a co-culture system, LF treatment of the Caco-2/HT29 monolayer alleviated lipid accumulation and regulated the HTR2A-PPARα-CPT-1A pathway in FFA-treated HepG2 cells.

CONCLUSIONS: These findings indicate that LF attenuates NASH by remodeling gut microbiota to modulate microbiota-derived serotonin signaling and enhance fatty acid oxidation.},
}

@article {pmid41253145,
year = {2025},
author = {Shi, H and Newton, DP and Nguyen, TH and Estrela, S and Sanchez, J and Tu, M and Ho, PY and Zeng, Q and DeFelice, BC and Sonnenburg, JL and Huang, KC},
title = {Nutrient competition predicts gut microbiome restructuring under drug perturbations.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.10.038},
pmid = {41253145},
issn = {1097-4172},
abstract = {Human gut bacteria are routinely exposed to stresses, and community-level responses are difficult to predict. To interrogate these effects, we screened stool-derived in vitro communities with 707 clinically relevant drugs. Across ∼5,000 community-drug conditions, compositional and metabolomic responses were shaped by nutrient competition, with certain species expanding due to the suppression of competitors. Most compositional changes arose from strain extinction and were reversed by reintroducing extinct species, although certain drugs promoted alternative states long after treatment. Despite strong selection pressures, resistance emergence was infrequent. Responses to drugs were qualitatively conserved across communities, while nutrient competition quantitatively tuned species abundances, consistent with consumer-resource model predictions. Together, nutrient competition provides a predictive framework to anticipate and potentially mitigate drug side effects on the gut microbiota.},
}

@article {pmid41252854,
year = {2025},
author = {Chen, X and Huang, Y and Zhu, X and Gan, C and An, W and Liu, Y and Zhou, S and Xu, M},
title = {Global biogeographic patterns and assembly processes of landfill leachate microbiomes.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124922},
doi = {10.1016/j.watres.2025.124922},
pmid = {41252854},
issn = {1879-2448},
abstract = {Approximately 95 % of municipal solid waste is disposed of in landfill globally, generating leachate that is known as a complex mixture of biodegradable and persistent toxic compounds. Microbes are main forces for tackling the toxic leachate but the patterns of microbial assembly in such treatments are largely unknown, limiting the proper optimization of leachate treatment efficiency. This study, for the first time, presents a global-scale analysis involving 151 landfill leachate treatment samples for uncovering mechanisms of microbial assembly from an ecological perspective. The information of microbiome from 97 treatments in Asia, 41 treatments in Europe, and 13 treatments in North America were collected. The results revealed pronounced biogeographic divergence, with Asian samples (particularly those from India) exhibiting lower microbial diversity and richness compared to Europe and North America counterparts. Geographical-climatic and socio-economic factors significantly influenced microbial composition, with elevation and per capita GDP being primary drivers. Further, the community assembly was predominantly governed by deterministic processes. Co-occurrence network analyses demonstrated distinct microbial interaction patterns across continents, with Asian networks being more vulnerable to collapse under external disturbances. This study provides critical insights into the global microbial ecology of landfill leachate treatment, offering a foundation for developing targeted bioremediation strategies.},
}

@article {pmid41252749,
year = {2025},
author = {Welsh, TB and Dundas, CM},
title = {Genetically Reprogramming Crops and Rhizobacteria for Nutritional Iron Biofortification.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00614},
pmid = {41252749},
issn = {2161-5063},
abstract = {Iron is a critical micronutrient for both plants and humans, yet its declining availability across agricultural systems threatens global food security and health. Biofortification of food crops has emerged as a promising strategy to combat iron deficiency and anemia, leveraging both crop breeding and microbiome-based approaches to enhance iron mobilization and uptake. Advances in plant and bacterial synthetic biology could enable the precise programming of iron homeostasis and acquisition mechanisms, offering tailored solutions across diverse species and environments. Here, we outline key biomolecules, genes, and biosynthetic and transport pathways that represent underexplored synthetic biology targets for improving crop iron acquisition. We highlight opportunities to tune expression strength, tissue specificity, and cross-host pathway transfer to enhance chelation- and reduction-mediated solubilization of soil iron and augment plant uptake. Finally, we emphasize the broader importance of developing plant-microbe-metal actuators as modular components in genetic circuit design and discuss how their deployment across diverse plant and microbial chassis could accelerate agricultural biofortification and improve global nutrition.},
}

@article {pmid41252568,
year = {2025},
author = {Severino, A and Marchitto, SA and Bisegna, P and Porcari, S and Rondinella, D and Schepis, T and Barbaro, F and Pecere, S and Maida, M and Spada, C and Gasbarrini, A and Cammarota, G and Facciorusso, A and Ianiro, G},
title = {Measuring gut microbiome as a colorectal cancer screening tool: potential and challenges.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2592078},
pmid = {41252568},
issn = {1747-4132},
abstract = {INTRODUCTION: Colorectal cancer (CRC) represents a global public health challenge, ranking as the third most prevalent cancer globally. Population-based screening programs for average-risk populations have proven effective in reducing incidence and mortality of CRC through early detection of cancer. The fecal immunochemical test (FIT), the standard diagnostic method in many nations, still falls short in diagnostic effectiveness, resulting in undetected adenomas and, more significantly, unnecessary colonoscopies.

AREAS COVERED: One of the primary research focuses in the field of CRC is the discovery of new, noninvasive biomarkers. Recent studies, including metagenomic meta-analyses, have discovered common microbial signatures able to reproducibly discriminate between patients with CRC and healthy controls. Based on this evidence, international guidelines have recently recommended the use of microbiome-based biomarkers for CRC screening in clinical settings, although such studies have yet to be conducted.

EXPERT OPINION: This field of research needs considerable multidisciplinary efforts, including large and geographically different meta-cohorts, and the application of state-of-the-art computational approaches, to identify reproducible signatures able to predict early lesions. Such diagnostic tool would revolutionize CRC screening. More widely, it would provide a mind-set shift in the clinical and scientific community promoting the exploitation of diagnostic and therapeutic microbiome tools in clinical practice.},
}

@article {pmid41252467,
year = {2025},
author = {Soffa, DR and Hickman, KJ and Cain, JW and Spencer, JA and Poole, RK},
title = {Vaginal microbiota and circulating interferon-stimulated genes in lactating dairy cows at and following time of artificial insemination.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf399},
pmid = {41252467},
issn = {1525-3163},
abstract = {Reproductive tract microbiota has been shown to shift during early gestation in cattle. However, characterization of the vaginal microbiota during the establishment of pregnancy in lactating dairy cows has yet to be fully determined. Therefore, the objectives of this study were to characterize shifts in the vaginal microbiota from time of artificial insemination (AI) to maternal recognition of pregnancy and analyze its relationship with interferon-stimulated genes (ISGs) in lactating dairy cows. Vaginal swab samples for microbiota analysis and blood were collected from lactating Holstein dairy cows (n = 40) on day 0 (d0; time of AI) and day 18 (d18; post-AI during the time of maternal recognition of pregnancy). Pregnancy status was determined via transrectal ultrasonography on d32 (Open, n = 18 and Pregnant, n = 22). Microbiota analysis for phylum and genus taxonomic classification, as well as α- and β-diversity, was conducted targeting the V4 hypervariable region of the 16S rRNA gene on d0 and d18. RT-qPCR analysis was conducted to analyze expression of ISGs, interferon-stimulated gene 15 kDa (ISG15) and myxovirus resistance 2 (MX2), on d0 and d18. Phyla and genera greater than 1% relative abundance did not differ between Open and Pregnant cows (P > 0.10). Shifts in certain bacterial phyla and genera between d0 and d18 (P < 0.05), along with lower α-diversity matrices of Simpson's diversity index (P = 0.02) and Shannon's diversity index (P = 0.009) on d18, indicate that time-dependent shifts in bacterial communities may alter reproductive success. This is further supported by the difference between days for the weighted UniFrac β-diversity matrix (P = 0.005). Reduced MX2 expression on d18 (P = 0.002), and its correlation with Fusobacteria (r = -0.35; P = 0.09), may be indicative of pregnancy failure and thus result in Open cows. These results indicate that shifts in microbiota from day of AI to d18 may influence successful establishment of pregnancy in lactating dairy cows.},
}

@article {pmid41252442,
year = {2025},
author = {Zentgraf, J and Schmitz, JE and Rahmann, S},
title = {Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf632},
pmid = {41252442},
issn = {1367-4811},
abstract = {MOTIVATION: The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis, such as metagenomic binning or genome assembly. For large-scale metagenomics projects, fast and accurate removal of human contamination is therefore critical.

RESULTS: We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k-mers, or spaced seeds. Cleanifier uses a pangenome index of known human gapped k-mers, and the creation and use of alternative references is also possible. Reads are classified and filtered according to their gapped k-mer content. Cleanifier supports two filtering modes: one that queries all gapped k-mers and one that queries only a sample of them. A comparison of Cleanifier with other state-of-the-art tools shows that the sampling mode makes Cleanifier the fastest method with comparable accuracy. When using a probabilistic Cuckoo filter to store the complete k-mer set, Cleanifier has similar memory requirements to methods that use a sampled minimizer index. At the same time, Cleanifier is more flexible, because it can use different sampling methods on the same index.

Cleanifier is available via gitlab (https://gitlab.com/rahmannlab/cleanifier), PyPi (https://pypi.org/project/cleanifier/) and Bioconda (https://anaconda.org/bioconda/cleanifier). The pre-computed human pangenome index is available at Zenodo (https://doi.org/10.5281/zenodo.15639519).

SUPPLEMENTARY INFORMATION: Available online.},
}

@article {pmid41252333,
year = {2025},
author = {Bahji, A and Brietzke, E and Cooke, NCA and Clement, F and Frey, BN and Hofmeister, M and Kennedy, SH and Lam, R and Milev, R and Moinul, D and Parikh, SV and Patten, S and Ravindran, A and Rosenblat, JD and Samaan, Z and Schaffer, A and Saleem, A and Beaulieu, S and Tourjman, V and Van Ameringen, M and Vigod, S and Yatham, L and Taylor, V and , },
title = {The Canadian Network for Mood and Anxiety Treatments Task Force Recommendations for the Use of Probiotics, Prebiotics, Synbiotics, and Fecal Microbiota Transplants in Adults With Major Depressive Disorder: Recommandations du Groupe de travail du Réseau canadien pour le traitement des troubles de l'humeur et de l'anxiété (Canadian Network for Mood and Anxiety Treatments, CANMAT) concernant l'utilisation des probiotiques, des prébiotiques, des symbiotiques et de la transplantation de microbiote fécal chez les adultes atteints de trouble dépressif majeur.},
journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
volume = {},
number = {},
pages = {7067437251394363},
doi = {10.1177/07067437251394363},
pmid = {41252333},
issn = {1497-0015},
abstract = {BackgroundApproximately one-third of adults with major depressive disorder (MDD) experience limited response or intolerable side effects with existing pharmacotherapies. As such, innovative treatments targeting novel biological pathways are under investigation. One promising area of research is the gut microbiome and its influence on mood through the microbiota-gut-brain axis. Clinical studies have begun evaluating microbiome-targeted interventions such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) as potential treatments for MDD. The Canadian Network for Mood and Anxiety Treatments (CANMAT) convened a task force to evaluate the evidence for microbiome-targeted interventions in adults with MDD and to provide updated clinical recommendations.MethodsA systematic review of randomized controlled trials (RCTs) and meta-analyses was conducted, assessing interventions such as probiotics, prebiotics, synbiotics, and FMT in adults with MDD. The CANMAT methodology was used to determine levels of evidence and treatment line recommendations, which were presented in a question-and-answer format.ResultsTwenty-three RCTs and eight meta-analyses were included. Probiotics have been the most extensively studied and have demonstrated modest improvements in depressive symptoms, particularly when used in an adjunctive manner. However, recent high-quality trials yielded mixed results. Evidence for prebiotics and FMT was limited and inconclusive, while synbiotics were assessed in only one small RCT. Most interventions were well tolerated, with few serious adverse events.ConclusionsProbiotics may be cautiously considered as third-line adjunctive treatments for MDD, though findings remain inconsistent. There is currently insufficient evidence to recommend prebiotics, synbiotics, or FMT in clinical practice. Further large-scale, well-controlled trials are needed to clarify efficacy, safety, and optimal patient subgroups.},
}

@article {pmid41252249,
year = {2025},
author = {Febinia, CA and Luqman, H and Kusuma, P and Priliani, L and Lewis, J and Wihandani, DM and Pinatih, GN and Sudoyo, H and Almeida, A and Malik, SG and Jacobs, GS},
title = {From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116573},
doi = {10.1016/j.celrep.2025.116573},
pmid = {41252249},
issn = {2211-1247},
abstract = {Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.},
}

@article {pmid41252227,
year = {2025},
author = {van Loenen, MR and Remie, LB and van Trijp, MP and Jansen, MG and Marques, JP and Claassen, JA and van de Rest, O and Vermeiren, Y and Smidt, N and Sikkes, SA and Deckers, K and Zwan, MD and van der Flier, WM and Köhler, S and Steegenga, WT and Oosterman, JM and Aarts, E},
title = {The Effects of a Multidomain Lifestyle Intervention on Brain Function and Its Relation With Immunometabolic Markers and Intestinal Health in Older Adults at Risk of Cognitive Decline: Study Design and Baseline Characteristics of the HELI Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e69814},
doi = {10.2196/69814},
pmid = {41252227},
issn = {1929-0748},
mesh = {Humans ; Aged ; *Cognitive Dysfunction/prevention & control/physiopathology ; *Brain/physiology/physiopathology ; Male ; Female ; *Life Style ; Biomarkers/blood ; Netherlands ; Exercise/physiology ; Magnetic Resonance Imaging ; Middle Aged ; },
abstract = {BACKGROUND: Studies of multidomain lifestyle interventions show mixed results on preventing or delaying cognitive decline in aging. A better understanding of central and peripheral mechanisms underlying these interventions could help explain these mixed findings.

OBJECTIVE: The HELI (Hersenfuncties na LeefstijlInterventie) study aims to investigate the brain and peripheral mechanisms of a multidomain lifestyle intervention in older adults at risk of cognitive decline.

METHODS: The HELI study is a 6-month multicenter, randomized, controlled multidomain lifestyle intervention trial powered to include 104 Dutch older adults at risk of cognitive decline. Individuals were deemed at risk when scoring ≥2 points on a lifestyle-modifiable risk factor scale (eg, overweight, physical inactivity, hypertension, and hypercholesterolemia). The intervention consisted of 5 domains (diet, physical activity, stress management and mindfulness, cognitive training, and sleep) and participants were randomized to one of two groups: (1) a high-intensity coaching group with weekly supervised online and on-site group meetings, exercises, and lifestyle-specific course materials, and (2) a low-intensity coaching group receiving general lifestyle health information sent through email every 2 weeks. The primary study outcomes are changes between baseline and 6-month follow-up in (1) brain activation in dorsolateral prefrontal cortex (dlPFC) and hippocampus and task accuracy during a functional magnetic resonance imaging (fMRI) working memory task, (2) arterial spin labeling-quantified cerebral blood flow in dlPFC and hippocampus, (3) systemic inflammation from blood plasma (interleukin-6, tumor necrosis factor-α, high-sensitivity C-reactive protein) and (4) microbiota profile from feces (gut microbiome diversity [Shannon and phylogenetic diversity] and richness [Chao1]). In addition, we will investigate intervention-induced gut-immune-brain links by assessing relations between effects in primary brain and gut outcomes. Secondary study outcomes include (1) structural and neurochemical magnetic resonance imaging (MRI), (2) anthropometric measurements, (3) neuropsychological test battery scores, (4) lifestyle-related questionnaire and smartwatch measures, and peripheral measures from (5) fecal, (6) blood, and (7) breath analyses.

RESULTS: This work was supported by a Crossover grant (Maintaining Optimal Cognitive Functioning In Aging [MOCIA] 17611) of the Dutch Research Council (NWO), granted in December 2019. The MOCIA program is a public-private partnership. Between April 2022 and October 2023, we successfully included 102 older Dutch adults (mean age 66.6, SD 4.3 years; 67/102, 65.7% female) with ≥2 lifestyle-modifiable risk factors of cognitive aging (median risk 3, IQR 2-3). The most common self-reported lifestyle-modifiable risk factors at baseline were overweight or obesity (76/102, 74.5%), followed by hypertension (58/102, 56.9%), hypercholesterolemia (57/102, 55.9%), and physical inactivity (57/102, 55.9%).

CONCLUSIONS: The HELI study aims to enhance our understanding of the working mechanisms of multidomain lifestyle interventions through its comprehensive characterization of central and peripheral markers. We intend to achieve this aim by assessing lifestyle intervention-induced changes in functional and structural MRI brain measures, as well as peripheral measures of the gut-immune-brain axis involved in cognitive aging.},
}

Humans
Aged
*Cognitive Dysfunction/prevention & control/physiopathology
*Brain/physiology/physiopathology
Male
Female
*Life Style
Biomarkers/blood
Netherlands
Exercise/physiology
Magnetic Resonance Imaging
Middle Aged

@article {pmid41252206,
year = {2025},
author = {Moreau, GB and Tian, J and Natale, NR and Naz, F and Young, MK and Nayak, U and Tanyüksel, M and Rigo, I and Madden, GR and Abhyankar, MM and Hagspiel, N and Brovero, S and Worthington, M and Behm, B and Marie, C and Petri, WA and Ramakrishnan, G},
title = {FMT promotes type 2 mucosal immune responses with colonic epithelium proliferation in recurrent CDI patients.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.195678},
pmid = {41252206},
issn = {2379-3708},
abstract = {BACKGROUND: Fecal Microbiota Transplantation (FMT) is the most effective therapy for recurrent Clostridioides difficile infection (rCDI), yet its mechanism of action remains poorly understood.

METHODS: We report the results of a clinical trial of subjects undergoing FMT therapy for rCDI (n=16), analyzing colon biopsies, plasma, peripheral blood mononuclear cells, and stool at the time of FMT and two-month follow-up. Plasma and colon biopsy samples were also collected from healthy controls for comparison with rCDI patients. Microbiome composition, colonic gene expression, and immune changes were evaluated through high-throughput sequencing and immunoprofiling via flow cytometry.

RESULTS: No subjects experienced recurrence at follow-up. FMT significantly altered the intestinal microbiome but had no significant impact on the systemic immune system. In contrast, FMT promoted broad changes in colonic transcriptional profiles compared to both pre-FMT and healthy control biopsies, inhibiting genes associated with pro-inflammatory signaling and upregulating type 2 immunity and proliferative pathways (Myc and mTORC1). FMT increased expression of IL-33 and the type 2 immune EGFR family ligand amphiregulin, potentially explaining upregulation of Myc and mTORC1 pathways. Spatial transcriptomics demonstrated that these changes were localized to the colonic epithelium. Comparison of transcriptional profiles with available single cell gene sets determined that post-FMT biopsies were enriched in signatures associated with proliferative cell types while repressing signatures of differentiated colonocytes.

CONCLUSIONS: We conclude that FMT promotes proliferation of the colonic epithelium in rCDI patients, which may drive regeneration and protect against subsequent CDI.

CLINICALTRIALS: gov NCT02797288.

FUNDING: NIH grants R01 AI152477, R01 AI124214, and K23 AI163368.},
}

@article {pmid41252027,
year = {2026},
author = {Vaila, C and Nikou, V and Mataragka, A and Katsenios, N and Zafeiriou, I and Kounani, K and Efthimiadou, A and Papakonstantinou, E and Fountas, S and Vlachakis, D},
title = {Adaptation to Climatic Change and Epigenetic Modifications of Soil Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1489},
number = {},
pages = {419-430},
pmid = {41252027},
issn = {0065-2598},
mesh = {*Soil Microbiology ; *Climate Change ; *Epigenesis, Genetic ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Rhizosphere ; Plants/microbiology ; *Adaptation, Physiological ; },
abstract = {The rhizosphere microbiome, and especially bacteria, is essential for the plant's life and health, forming different mutual beneficial relationships. Throughout evolution, bacteria have adapted to various habitats by adjusting their genomes in order to fit the changing environmental conditions, resulting in the development of additional functional traits. Epigenetic modifications in their DNA play a crucial role in their ability to thrive in such conditions. Climate change is a serious phenomenon, challenging the plant's health and soil microbiome's assembly, and bacteria must enhance their stability by using resistance, resilience, and redundancy, mainly by stress-driven epigenetic modifications. In this review, recent studies have been investigated in order to record the most abundant bacterial genera in the soil's rhizosphere of 11 plants and at the same time to locate the role each one of them plays in plant's health, which has also been regulated by epigenetic mechanisms, leading to the inheritance of diverse phenotypes. As a result, we propose that this field needs further investigation, and future research should be focused on testing the alterations of the abundance and possible epigenetic modifications on the DNA of the main bacterial genera in soil microbiome, from areas affected by the climate change consequences, in order to conclude to potential solutions for assisting the soil microbiome and plants to survive after such catastrophic conditions.},
}

*Soil Microbiology
*Climate Change
*Epigenesis, Genetic
*Microbiota/genetics
*Bacteria/genetics/classification
Rhizosphere
Plants/microbiology
*Adaptation, Physiological

@article {pmid41251823,
year = {2025},
author = {Della Mónica, IF and Godeas, AM and Scervino, JM},
title = {Hyphosphere interactions: P-solubilizing fungi modulate AMF phosphatase activity and mycorrhizal symbiosis via exudate-mediated communication.},
journal = {Mycorrhiza},
volume = {35},
number = {6},
pages = {66},
pmid = {41251823},
issn = {1432-1890},
support = {UBACyT 20020220400300BA//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; PIBAA 28720210100694CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PICT 01283-2021//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación/ ; PINI 04/B253//Fundación de la Universidad Nacional del Comahue para el Desarrollo Regional/ ; },
mesh = {*Mycorrhizae/physiology/enzymology ; *Symbiosis ; Plant Roots/microbiology ; *Phosphorus/metabolism ; Acid Phosphatase/metabolism ; *Phosphoric Monoester Hydrolases/metabolism ; Daucus carota/microbiology ; *Glomeromycota/physiology/enzymology ; *Phosphates/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots, enhancing water and nutrient absorption. Phosphate-solubilizing fungi (PSF) can solubilize and mineralize phosphorus, an essential nutrient with low bioavailability, and eventually interact with AMF. However, the understanding of how they interact in the hyphosphere, where root influence is absent, remains limited. Furthermore, the effect of PSF on the phosphatase activity of AMF, related to the P efficiency in acquisition and utilization, within the hyphosphere and mycorrhizosphere zones, remains unclear. Therefore, this study aimed to assess the effect of three different PSF (Talaromyces flavus, T. helicus, and T. diversus) exudates on extracellular acid phosphatases and alkaline phosphatases associated with intra- and extraradical AMF structures in the hyphosphere and mycorrhizosphere, in vitro. To achieve this aim, the AMF Rhizophagus intraradices was cultured with Ri T-DNA transformed carrot roots in a system using Petri dishes that mimicked the hyphosphere (with 2 sections: (a) with roots and AMF, and (b) with only AMF) and the mycorrhizosphere (with roots and AMF in the same place). Different concentrations of PSF exudates were placed in either the hyphosphere or the mycorrhizosphere, and at the end of the experiment (8 weeks), the phosphatase activity of the AMF was measured. This research highlights that the enzymatic activity of AMF is modulated by PSF exudates, depending on whether these exudates are present in the hyphosphere or the mycorrhizosphere. Exudates in the hyphosphere, where PSF are directly associated with AMF hyphae, have a more pronounced effect on AMF extraradical alkaline phosphatases than acid phosphatases, and promote symbiosis efficiency. In contrast, PSF exudates in the mycorrhizosphere had a neutral or negative effect on symbiosis efficiency, improving the extraradical alkaline phosphatases of AMF and the acid phosphatases of the roots. Also, the effect depends on the fungal identity. AMF act as mediators in this context, improving communication between the roots and the hyphosphere microbiome. When exploring the soil, the hyphae encounter compounds produced by microorganisms, thus establishing a complex network of interactions. These interactions enhance the symbiotic efficiency of AMF, modulating the host plant without direct contact. These results show that microbial interactions not only influence the efficiency of phosphorus transfer to plants but also have broader implications for soil health and fertility management.},
}

*Mycorrhizae/physiology/enzymology
*Symbiosis
Plant Roots/microbiology
*Phosphorus/metabolism
Acid Phosphatase/metabolism
*Phosphoric Monoester Hydrolases/metabolism
Daucus carota/microbiology
*Glomeromycota/physiology/enzymology
*Phosphates/metabolism

@article {pmid41251489,
year = {2025},
author = {Ye, H and Šlipogor, V and Hanson, BT and Séneca, J and Hausmann, B and Herbold, CW and Pjevac, P and Bugnyar, T and Loy, A},
title = {Associations between gut microbiota and personality traits: insights from a captive common marmoset (Callithrix jacchus) colony.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0044325},
doi = {10.1128/spectrum.00443-25},
pmid = {41251489},
issn = {2165-0497},
abstract = {Recent studies have suggested associations between consistent inter-individual behavioral variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated associations between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status, and relatedness of 26 captive common marmosets (Callithrix jacchus), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genus Desulfovibrio were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene dsrB confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between identified microbial taxa and personality traits in captive common marmosets.IMPORTANCEThis study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential of the gut microbiome to reflect or be associated with personality differences. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.},
}

@article {pmid41251470,
year = {2025},
author = {Young, MG and Just, J and Lee, YJ and McMahon, T and Gonzalez, J and Fuentes, P and Noh, S and Angelini, DR},
title = {Seasonally increasing parasite load is associated with microbiota dysbiosis in wild bumblebees.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118425},
doi = {10.1128/msystems.01184-25},
pmid = {41251470},
issn = {2379-5077},
abstract = {UNLABELLED: Gut microbiota often influence host defense against infection, but this relationship is incompletely understood in wild bumblebees. These critical pollinators host a characteristic core gut microbiota, yet field studies have offered conflicting insights into its association with Crithidia bombi, a prevalent trypanosomid parasite. To address this gap in our knowledge, we conducted an 3 year field survey, profiling the gut microbiota of 638 bumblebees from 9 sympatric species across diverse sites in Maine using 16S rRNA amplicon sequencing and qPCR for C. bombi detection. We confirmed a robust core bumblebee microbiota, identifying novel host-specific phylogenetic associations of bacterial amplicon sequence variants even among closely related host species. C. bombi infection was common and showed significant seasonal increases. We also found spatial variation, with higher prevalence in coastal regions. Crucially, increasing C. bombi infection load was consistently associated with microbiome dysbiosis. This dysbiosis was characterized by a depletion of core bumblebee-associated microbial taxa, notably Apibacter and Gilliamella (previously shown to be protective), and a corresponding increase in opportunistic, environmentally derived microbes like Entomomonas. While the core microbiota's association with initial pathogen transmission appears minor, its depletion in severe infections strongly supports a correlation to host health in wild bumblebees.

IMPORTANCE: The community of microorganisms in close association with an animal, its microbiota, can be important to its health. Understanding how microbiota composition relates to health and disease is an important goal with broad potential implications. Like most animals, bumblebees have a characteristic core gut microbiota. We have conducted a broad survey of bumblebees over 3 years to examine the interactions of microbiota composition with infection by an endemic trypanosomatid parasite. We found that the relative abundances of core microbes were inversely related to infection load, and that increased pathogen load was associated with the prevalence of novel microbes. These results are evidence of strong associations between bumblebees and their core microbiota and suggest a role in providing resistance to severe parasitism.},
}

@article {pmid41250828,
year = {2025},
author = {Zhao, C and Lao, J and Cao, J and Yang, Y and Liu, C and Tang, F},
title = {Advances in Gut Microbiome and Metabolomics Research in the Comorbidity of Inflammatory Bowel Disease and Depressive Disorder.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70173},
pmid = {41250828},
issn = {1440-1746},
support = {202328057//Science and Technology Plan Project of Jinan/ ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic autoimmune disorder characterized by persistent inflammation of the gastrointestinal tract, with a substantial proportion of patients experiencing comorbid depressive disorders. This comorbidity profoundly affects patients' long-term prognosis and quality of life. Emerging evidence suggests that the interplay between IBD and depression may be mediated by disruptions in the gut microbiome and metabolome. Notably, alterations in gut microbial composition and metabolic profiles observed in both IBD and depression indicate potential shared pathophysiological mechanisms, which could inform novel therapeutic strategies. This review aims to summarize recent advances in gut microbiome and metabolomics research related to IBD comorbid with depression, highlighting their implications for disease management and treatment. First, we provide an overview of the epidemiological features of IBD comorbid with depressive disorder, as well as the underlying pathophysiological mechanisms that may contribute to their bidirectional relationship. Subsequently, we highlight key microbiome and metabolite alterations observed in comorbid patients, which may contribute to disease onset and progression. At last, we also discuss emerging microbiota- and metabolite-based therapeutic approaches that hold promise for improving both gastrointestinal and psychological outcomes. In conclusion, integrating microbiome and metabolomics perspectives provides novel insights into the shared pathophysiology of IBD and depressive disorders and may inform the development of more effective and personalized interventions.},
}

@article {pmid41250628,
year = {2025},
author = {Yathindra, MR and Badugu, R and Singh, SK and Paluri, S and Poudala, H and Swathi, NL},
title = {The role of the urinary microbiome in diabetes-associated UTIs: current understanding and future directions.},
journal = {Journal of basic and clinical physiology and pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41250628},
issn = {2191-0286},
abstract = {This review explores the interplay between type 2 diabetes mellitus (T2DM) and urinary microbiome dysbiosis, focusing on its role in urinary tract infections (UTIs). Once considered sterile, the urinary tract hosts a diverse microbiota that supports mucosal immunity and pathogen resistance. In T2DM, chronic hyperglycemia and glycosuria disrupt microbial balance, impair immune responses, and increase UTI susceptibility. Glycosuria promotes pathogenic colonization, biofilm formation, and microbial shifts, with studies reporting a threefold rise in Escherichia coli and a 56 % reduction in Lactobacillus spp. in diabetic women with recurrent UTIs. Diabetic urine shows reduced diversity, higher abundance of Klebsiella, Pseudomonas, and Enterococcus, and elevated IL-8. Microbiota-targeted interventions, including probiotics (Lactobacillus crispatus, Lactobacillus rhamnosus GR-1), prebiotics (astaxanthin), and phytotherapeutics (cranberry), demonstrate potential via lactic acid, hydrogen peroxide production, competitive exclusion, and NF-κB modulation. A 12-month RCT showed significant UTI recurrence reduction with probiotics. Advances in 16 S rRNA sequencing and metagenomics reveal microbial signatures associated with diabetic UTIs, though methodological heterogeneity limits comparability. A review of 1,200 publications (2000-2024) highlights the need for longitudinal studies and precision microbiota therapeutics to translate findings into clinical practice.},
}

@article {pmid41250602,
year = {2025},
author = {Cosic, A and Halwachs, B and Schild-Prüfert, K and Zechner, EL and Kienesberger, S},
title = {Refining microbiome resolution: KoSCAPEbio identifies Klebsiella oxytoca complex species in16S rRNA amplicon data and uncovers associations with NEC.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2582900},
doi = {10.1080/19490976.2025.2582900},
pmid = {41250602},
issn = {1949-0984},
mesh = {*Klebsiella oxytoca/genetics/classification/isolation & purification ; Humans ; RNA, Ribosomal, 16S/genetics ; Klebsiella Infections/microbiology ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Infant ; },
abstract = {Klebsiella are early colonizers and commensals of human hosts but are also opportunistic pathogens. Research has focused on Klebsiella pneumoniae due to its global contribution to nosocomial infection and antibiotic resistance. Yet Klebsiella oxytoca and several closely related species are increasingly recognized as clinically significant bacteria underlying enteric and respiratory disorders. Inadequate interspecies discrimination inhibits advancement of our understanding of these diseases including necrotizing enterocolitis (NEC) in infants. Here we leverage the taxonomic potential of the amplified V3 and V4 regions of the K. oxytoca species complex (KoSC) 16S rRNA genes. We developed a curated database of all 16S rRNA gene sequences available for KoSC genomes and the automated pipeline KoSCAPEbio for efficient interspecies discrimination. Sequence polymorphism in the V3-V4 area revealed 41 signature sequences unique to individual species. Six amplicon variants are unique to the KoSC but shared by two to three species within the complex. Genetic linkage of the specific variants to the clinically relevant tiI gene cluster provided a predictive marker for risk of enterotoxin exposure. Reiteration of the workflow with K. aerogenes complex genomes and phylogroups of the K. pneumoniae species complex (KpSC) added K. aerogenes-specific variant typing. We then applied KoSCAPEbio to interrogate publicly available datasets. Analyses resolved and quantified coresident Klebsiella in patient samples including species belonging to KoSC, K. aerogenes and the KpSC. The population structure thus delineated in this proof of principle research differs significantly in disease versus controls. NEC cases associate positively with exclusive presence of the KoSC and negatively with cooccurrence of both KoSC and KpSC, suggesting conflict within the Klebsiella may promote pathogenesis. Thus, KoSCAPEbio has potential to contribute to a better understanding of factors involved in the etiology of NEC and other Klebsiella spp. associated diseases.},
}

*Klebsiella oxytoca/genetics/classification/isolation & purification
Humans
RNA, Ribosomal, 16S/genetics
Klebsiella Infections/microbiology
Phylogeny
*Gastrointestinal Microbiome/genetics
DNA, Bacterial/genetics
Infant

@article {pmid41250148,
year = {2025},
author = {Lam, AY and Lau, CH and Tam, WY and Chan, CT and Lok, TM and Suen, LK and Lee, LK and Yeung, EY and Lam, TK and Cheung, WK and Chui, MW and Soong, HS and Chow, FW and Lam, SC and So, SN and Yuen, SK and Siu, GK},
title = {Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {143},
pmid = {41250148},
issn = {2524-6372},
support = {2023-00-51 CRG230402//Tung Wah College/ ; 1-ZVZL//The Hong Kong Polytechnic University/ ; },
abstract = {BACKGROUND: Public washrooms (toilets) are potential hubs for pathogen transmission, yet the risk of microbial re-contamination via post-handwashing surfaces remains understudied. We characterized the prevalence and distribution of multidrug-resistant organisms (MDROs) and antimicrobial resistance genes (ARGs) in post-handwashing areas by sampling four high-contact sites, including faucets, paper dispensers, hand dryers, and exit door handles, in public washrooms across healthcare, commercial, and recreational facilities.

RESULTS: From the 232 post-handwashing surface samples collected, we isolated 17 MDROs (7.33% prevalence) from cultures, including extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E, n = 10), carbapenem-resistant Pseudomonas aeruginosa (CRPA, n = 5), and methicillin-resistant Staphylococcus aureus (MRSA, n = 2). Additionally, we novelly employed targeted probe capture metagenomics (TCM), which utilizes oligonucleotide probes to enrich and detect low-abundance microbial species and ARG sequences. TCM revealed the detection of human pathogenic taxa in 65.2% of samples, including P. aeruginosa (78.4%), Acinetobacter baumannii (77.9%), and S. aureus (71.1%). Clinically critical ARGs, such as blaCTX-M (2.0%), blaNDM (2.9%), blaSHV (3.4%), and mecA (62.3%), were detected in 63.7% of samples, indicating a potential transmission within the post-handwashing area.

CONCLUSIONS: Our findings highlight the role of post-handwashing areas as underrecognized reservoirs for MDROs, particularly MRSA. Furthermore, this study demonstrates the utility of TCM in public health surveillance by enabling a sensitive detection of rare but high-risk microbial species and drug resistance determinants in low-biomass environmental samples. This study offers a comprehensive and nuanced view of the microbial and resistome landscape of washroom environments, offering a revolutionary approach for future environmental surveillance.},
}

@article {pmid41250096,
year = {2025},
author = {Zhang, Y and Le Guennec, A and Pussinen, P and Proctor, G and Niazi, SA},
title = {Successful endodontic treatment improves glucose and lipid metabolism: a longitudinal metabolomic study.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1195},
pmid = {41250096},
issn = {1479-5876},
support = {FDS Pump Priming Grant 2022//Royal College of Surgeons of England/ ; },
mesh = {Humans ; Longitudinal Studies ; Male ; Female ; *Metabolomics ; *Lipid Metabolism ; *Glucose/metabolism ; Middle Aged ; Adult ; Biomarkers/blood ; *Root Canal Therapy ; Metabolome ; Periapical Periodontitis/metabolism/blood/therapy ; },
abstract = {BACKGROUND: Apical periodontitis (AP) is one of the most prevalent dental diseases. Its presence can increase systemic inflammatory burden and is associated with cardiometabolic disorders including higher cardiovascular risks and impaired glycaemic control. There is currently a paucity of knowledge showing whether successful endodontic treatment is associated with systemic metabolic improvements. This study aims to identify the potential impact of successful endodontic treatment on patients' serum metabolomic profiles, and to evaluate how these impacts are associated with the metabolic syndrome (MetS) indicators, inflammatory biomarkers, as well as blood and intracanal microbiomes.

METHODS: This self-controlled two-year longitudinal cohort study investigated the metabolic improvements associated with successful endodontic treatment in 65 AP patients using nuclear magnetic resonance (NMR) spectroscopy on serum samples. The samples were collected at 5 time points including pre-operative baseline and 3 month, 6 month, 1 year, and 2 year reviews.

RESULTS: Significant postoperative changes were observed in 24 (54.5%) metabolites. The results suggested improved glucose and lipid metabolism as well as reduced inflammatory burdens, as evidenced by a significant reduction in branched-chain amino acids at the 3 month review, a significant decrease in glucose and pyruvate at the 2 year review, a short-term reduction in cholesterol, choline, and fatty acid levels, and a progressive increase in tryptophan. In addition, strong associations were found between metabolic profile and clinical metabolic syndrome indicators, inflammatory markers, and pre-operative blood and intracanal microbiome, underscoring the systemic impact of AP and its treatment. A dynamic Bayesian model identified that metabolites associated with the tricarboxylic acid (TCA) cycle are the key regulators in the longitudinal alterations of the metabolic profiles.

CONCLUSIONS: Successful endodontic treatment in AP patients is associated with improved glucose and lipid metabolic profiles, and a reduction in systemic inflammation, suggesting a potential role in mitigating cardiometabolic disease risk.},
}

Humans
Longitudinal Studies
Male
Female
*Metabolomics
*Lipid Metabolism
*Glucose/metabolism
Middle Aged
Adult
Biomarkers/blood
*Root Canal Therapy
Metabolome
Periapical Periodontitis/metabolism/blood/therapy

@article {pmid41250081,
year = {2025},
author = {Xu, J and Song, J and Fu, Z and Zhou, H and Zhang, Y and Shi, C},
title = {Unraveling gut microbiome interferences in cancer immunotherapy: a meta-analysis of diverse drug effects.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {1776},
pmid = {41250081},
issn = {1471-2407},
support = {2023YFF1205000//National Key Research and Development Program of China/ ; Z-2018-35-2004//China International Medical Foundation/ ; 2023HT035//Industry, University and Research Projects of the Ministry of Education/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Immunotherapy/methods/adverse effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/microbiology/drug therapy/therapy ; Proton Pump Inhibitors/therapeutic use ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Probiotics/therapeutic use ; },
abstract = {Recent advancements in tumor therapy have centered on novel treatments, particularly immune checkpoint inhibitors (ICIs), which have transformed cancer treatment since their global approval in 2011. ICIs have demonstrated remarkable and substantial efficacy across a range of malignancies, including malignant melanoma, non-small cell lung cancer (NSCLC), head and neck cancers, renal carcinoma, and selected gastrointestinal cancers. Despite these promising outcomes, the challenges that during the clinical application, such as relatively low response rates and the occurrence of immune-related adverse events, can limit therapeutic benefits. Accumulating evidence highlights the gut microbiome as a critical modulator of cancer immunotherapy efficacy. Notably, alterations in gut microbiota composition observed in response to ICI therapy, and specific bacterial populations (such as an increased Clostridiales/ Baceroidales ratio, etc.) have been associated with improved responses in patients with NSCLC and renal cell carcinoma. However, the composition and function of the gut microbiome are influenced by a variety of factors, among which concomitant drug use plays a particularly prominent role. Medications commonly prescribed to cancer patients, such as antibiotics, proton pump inhibitors (PPIs), and probiotics, can significantly alter microbial communities, potentially impacting immunotherapy outcomes. Thus, there is a compelling need for rigorous research to elucidate how such drug-induced shifts in gut microbiota affect patient responses to ICIs. Thus, we conducted a meta-analysis which included 69 studies, 102 cohorts (22,568 patients were included) to systematically investigate the influence of drug interventions, including PPIs, antibiotics and probiotics on gut microbiome dynamics and ICI effectiveness. Progression-free survival (PFS), Overall survival (OS) and Objective response rate (ORR) were utilized as the main meta notions, while a subgroup analysis was determined based on: (1) tumor type; (2) exposure time window; (3) Treatment scheme as well. The total HR and 95% CI for PFS and OS are calculated separately for each intervention (probiotics, antibiotics, and PPIs) to compare their impact on ICI immunotherapy. Our research showed that the concurrent use of antibiotics or PPIs with ICIs was associated with significantly OS, PFS, and ORR. In contrast, probiotic supplementation demonstrated promising results with improved efficacy metrics. Besides, in subgroup analysis, patients using antibiotics within three months before or after the initiation of ICI therapy, OS, PFS, and ORR were significantly lower compared to those who did not receive antibiotics; the timing of antibiotic or PPI administration consistently resulted in poorer outcomes; a negative correlation between PPI use and OS, PFS, and ORR across treatment modalities was also exhibited. By elucidating the interplay between these factors, this study aims to provide robust evidence for optimizing ICI therapy, and to enlighten cancer treatment strategies more personalized, effective and safer, ultimately advancing patient care in oncology.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Immunotherapy/methods/adverse effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Neoplasms/immunology/microbiology/drug therapy/therapy
Proton Pump Inhibitors/therapeutic use
Anti-Bacterial Agents/therapeutic use/pharmacology
Probiotics/therapeutic use

@article {pmid41249904,
year = {2025},
author = {Zárate, A and Barrientos, L and Florez, JZ and Buschmann, AH and Pérez-Santos, I and Abanto, M and Bruna, P and Leyton, B and Vásquez, C and Inostroza, PA and Lundin, D and Borrego, CM and Balcázar, JL and Vila-Costa, M},
title = {Capturing the spatial structure of the benthic microbiome under an intensive aquaculture scenario in Chilean Patagonia.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {752},
pmid = {41249904},
issn = {1471-2180},
mesh = {Chile ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Aquaculture ; *Seawater/microbiology/chemistry ; Ecosystem ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; },
abstract = {BACKGROUND: Identifying the microbial taxa that structure assemblages in response to local disturbances along the Chilean Patagonian coast is critical for understanding community reorganization and ecological risk in this vulnerable marine environment. Here, we examined benthic microbial interactions across sixteen sites spanning 42-44°S in the Inner Sea of Chiloé and adjacent fjord systems. Using co-occurrence network analysis, we characterized spatial interaction patterns and identified keystone taxa whose relationships with environmental variables may serve as ecological indicators. The presence of keystone taxa supports the concept of microbial "seed banks," which sustain community stability and ecosystem functionality under stress. Networks revealed structured communities dominated by niche-specialist taxa, consistent with ecological processes of niche differentiation and environmental filtering.

RESULTS: The benthic environment was found to harbor niche-specialist taxa, including Flavobacteriaceae, Gemmataceae, Humimicrobiaceae, Clostridiaceae, and Sulfurovaceae, typically associated with organic enrichment and anthropogenic influence. These microbial families showed strong correlations with environmental gradients such as nitrate, phosphate, silicate, pH, salinity, and phaeopigments. Alpha-diversity analyses revealed greater microbial richness in FZ compared to the ISC, likely reflecting higher environmental heterogeneity and long-term adaptation to dynamic and fluctuating conditions. Beta-diversity analyses further supported the presence of distinct microbial assemblages between the two zones. Multivariate statistics and co-occurrence network analyses demonstrated that FZ communities display enhanced taxonomic interactions and greater network complexity, suggesting increased ecological stability. In contrast, microbial networks in the ISC exhibited reduced connectivity, potentially indicative of environmental stressors disrupting microbial spatial organization and network resilience. Moreover, the identification of indigenous bacterial isolates provided evidence for the presence of opportunistic host-associated pathogens, highlighting the utility of microbial biomarkers in detecting early ecological responses to human impacts.

CONCLUSION: Microbial co-occurrence patterns in northern Patagonian sediments reveal shifts in community assembly and increased network complexity that may enhance resilience to perturbations. The detection of strains harboring opportunistic pathogen biomarkers highlights risks under intense anthropogenic pressures. Monitoring keystone taxa thus offers early warning of functional decline. Broader spatio-temporal assessments remain essential to clarify microbial dynamics and their implications for ecosystem health and antimicrobial resistance.},
}

Chile
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Aquaculture
*Seawater/microbiology/chemistry
Ecosystem
Biodiversity
RNA, Ribosomal, 16S/genetics
*Geologic Sediments/microbiology

@article {pmid41249836,
year = {2025},
author = {Huang, Y and Sun, Y and Ronda, C and Mavros, CF and Li, J and Jacobse, J and Huang, LH and Resnick, SJ and Giddins, M and Freedberg, DE and Chavez, A and Goettel, JA and Wang, HH},
title = {Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41249836},
issn = {1546-1696},
support = {MCB-2025515//National Science Foundation (NSF)/ ; 1R01DK118044//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21AI146817//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R01CA272898//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5U19AI067773//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R03DK123489//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; N00014-17-1-2353//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; HR00111920009//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; S-168-4X5-001//United States Department of Defense | United States Air Force | AFMC | Air Force Research Laboratory (AFRL)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; 1061046//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; 1513935//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; IRIS Award//Columbia University/ ; },
abstract = {Metagenomic sequencing and metabolomics of fecal matter have revealed the impact of the gut microbiome on health and disease. In addition to microbiota, feces also contain shed or exfoliated host epithelial, secretory and immune cells, but RNA profiling of these cells is challenging owing to degradation and cross-contamination. Here we introduce exfoliome sequencing (Foli-seq) to profile fecal exfoliated eukaryotic messenger RNAs (feRNAs) originating from the upper and lower gastrointestinal regions and show that this 'fecal exfoliome' harbors stable RNAs that reflect intestinal and immune function. By selectively amplifying targeted transcripts, Foli-seq demonstrates robust, accurate, sensitive and quantitative measurement of feRNAs. In murine colitis models, feRNA reveals temporal processes of epithelial damage, immune response and intestinal recovery specific to different types of gut inflammation. Simultaneous exfoliome and microbiome profiling uncovers a dense host-microbe interaction network. Moreover, we demonstrate stratification of patients with inflammatory bowel disease into subgroups that correlate with disease severity. Fecal Foli-seq is a noninvasive strategy to longitudinally study the gut and profile its health.},
}

@article {pmid41249780,
year = {2025},
author = {Kou, R and Li, A and Yu, M and Wang, J and Hu, Y and Zhang, B and Liu, J and Wang, S},
title = {Bifidobacterium bifidum FB3-12 attenuates ovalbumin-induced allergic diseases by enhancing intestinal barrier function and regulating gut microbiota.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {227},
pmid = {41249780},
issn = {2396-8370},
support = {32302096//the National Natural Science Foundation of China/ ; },
abstract = {The escalating environmental changes have exacerbated the physiological suffering and economic burden caused by allergic diseases worldwide. Bifidobacterium bifidum (B. bifidum), due to its positive regulatory effects on the gut microenvironment, is considered a promising strategy for the prevention and treatment of allergies. Our study utilized the ovalbumin (OVA)-induced allergy mouse model to explore the anti-allergic potential of the self-screened strain B. bifidum FB3-12 (FB3-12) via intestinal intervention. The results demonstrated that a three-week FB3-12 treatment effectively suppressed the levels of immune markers, including OVA-specific immunoglobulin E (OVA-sIgE), mast cell protease-1 (Mcpt-1), and histamine (HIS) in the serum of allergic mice, and restored the Th2/Th1 immune response imbalance in the spleen. Furthermore, compared to the OVA group, FB3-12 intervention ameliorated intestinal damage and inflammation, significantly increasing the relative expression of Mucin-2 and tight junction proteins. Analysis of the gut microbiota profile revealed a distinct shift in the enterotype of OVA-challenged mice, characterized by a decreased Firmicutes/Bacteroidetes (F/B) ratio and a marked increase in the relative abundance of Akkermansia. FB3-12 intervention significantly enriched beneficial genera such as Lactobacillus and Colidextribacter, and upregulated the levels of short-chain fatty acids (SCFAs) and associated G protein-coupled receptors (GPRs) in the intestine. These findings underscore the therapeutic potential and application value of FB3-12 in alleviating allergic diseases through modulation of the gut microbiome.},
}

@article {pmid41249722,
year = {2025},
author = {Xu, N and He, Y and Yang, G and Huang, X},
title = {Exploring the Role of Gut Microbiota in Chronic Spontaneous Urticaria: Mechanisms and Potential Therapeutic Implications.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41249722},
issn = {1867-1314},
support = {no. 82103751//National Natural Science Foundation of China/ ; },
abstract = {Gut microbiota dysbiosis has emerged as a significant factor in the pathogenesis of chronic spontaneous urticaria (CSU), a condition characterized by immune dysregulation and skin inflammation. This review summarizes the current understanding of the role of gut microbiota in CSU pathogenesis, highlighting the alterations in microbial composition and function, the mechanisms by which dysbiosis triggers systemic inflammation and skin mast cell activation, and the impact of microbial metabolites. We critically evaluate the potential of gut microbiota-targeted therapies, such as probiotics, prebiotics, and fecal microbiota transplantation (FMT), as novel treatment strategies for CSU. Despite the evident promise of these approaches, significant challenges persist, including the necessity for personalized interventions, the collection of long-term efficacy and safety data, and a more profound understanding of the complex interplay between the gut and skin. Future research endeavors must prioritize the execution of clinical trials that evaluate the efficacy of gut microbiota modulation in CSU patients and the identification of biomarkers that can effectively predict treatment response.},
}

@article {pmid41249638,
year = {2025},
author = {Tinning, Z and Kaestli, M and Nowland, SJ and Siboni, N and Seymour, JR and Gibb, KS and Padovan, AC},
title = {Dynamics of Bacterial and Vibrio Communities in Blacklip Rock Oysters in the Seasonal Tropics.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {125},
pmid = {41249638},
issn = {1432-184X},
support = {2020-043//Fisheries Research and Development Corporation/ ; Discovery Project DP240100370//Australian Research Council/ ; },
mesh = {Animals ; *Vibrio/isolation & purification/genetics/classification ; *Ostreidae/microbiology ; Seasons ; Aquaculture ; Seawater/microbiology ; *Microbiota ; Australia ; Tropical Climate ; Shellfish/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Humans ; },
abstract = {Cultivation of the tropical Blacklip Rock Oyster (BRO) (Saccostrea spathulata) is an emerging Indigenous-led aquaculture industry in the seasonal tropics of northern Australia. However, little is currently known about the potential for pathogen outbreaks in this species. We conducted a year-long study to establish a microbial baseline to identify potential oyster and human health risks to inform future food safety decision making in this nascent industry. In healthy oysters, we identified both the core microbiome of this oyster species and the presence of potential oyster and human pathogens. The core bacteriome comprised nine bacterial families, while the core vibriome comprised the animal pathogens Vibrio harveyi and V. owensii. The potential human pathogen V. parahaemolyticus was detected in some oysters during the wet season, during periods of increased rainfall, turbidity and total nitrogen. The bacteriome and vibriome of oysters were significantly different to the adjacent seawater and therefore we concluded that seawater is not an appropriate surrogate for pathogen risk surveillance in this developing industry. These results provide new knowledge on the microbiology of a previously understudied oyster species and will inform monitoring methods, harvesting and shellfish quality compliance in this emerging Indigenous-led industry.},
}

Animals
*Vibrio/isolation & purification/genetics/classification
*Ostreidae/microbiology
Seasons
Aquaculture
Seawater/microbiology
*Microbiota
Australia
Tropical Climate
Shellfish/microbiology
*Bacteria/classification/genetics/isolation & purification
Humans

@article {pmid41249613,
year = {2025},
author = {Zhang, X and Jia, L and Lin, X and Zhou, L},
title = {The gut-bone axis in ankylosing spondylitis: mechanistic insights and the translational gap.},
journal = {Clinical and experimental medicine},
volume = {26},
number = {1},
pages = {12},
pmid = {41249613},
issn = {1591-9528},
support = {No. 202101//Wuxi Taihu Lake Talent Plan, Supports for Leading Talents in Medical and Health Profession/ ; },
mesh = {*Spondylitis, Ankylosing/drug therapy/immunology/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Bone and Bones/pathology/immunology ; Dysbiosis ; Interleukin-23/antagonists & inhibitors ; },
abstract = {The gut-bone axis is pivotal in the pathogenesis of ankylosing spondylitis (AS), with gut dysbiosis and mucosal immune activation driving skeletal pathology. However, translating these mechanistic insights into effective therapies remains challenging. This review critically analyzes this translational gap, arguing that the therapeutic paradoxes seen with cytokine inhibitors and microbiome-targeted therapies are a direct consequence of the disease's significant variability. We focus on the unexpected failure of IL-23 inhibitors and the dual effects of IL-17 blockade to illustrate the need for a nuanced understanding of tissue-specific immunity. We then propose a biomarker-driven, AI-assisted therapeutic framework that integrates multi-omic data to personalize AS treatment, aiming to bridge the gap between mechanistic insights and clinical success and offer a path toward progression-free remission.},
}

*Spondylitis, Ankylosing/drug therapy/immunology/microbiology/pathology
Humans
*Gastrointestinal Microbiome/drug effects
*Bone and Bones/pathology/immunology
Dysbiosis
Interleukin-23/antagonists & inhibitors

@article {pmid41249586,
year = {2025},
author = {Zhou, S and Bi, J and Zhou, S and Luo, L and Yan, X and Zou, J and Ji, Y and Zhao, S and Qiu, J and Liu, Z and Jiang, J and Wang, B and Liu, X},
title = {Community Assembly Mechanisms Underlying Divergent Responses of Indica and Japonica Rice Rhizosphere Microbiota to Drought Stress.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {126},
pmid = {41249586},
issn = {1432-184X},
support = {2022YFD2300302//National Key Research and Development Program of China/ ; 42277304//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; XUEKEN2022003//Fundamental Research Funds for the Central Universities/ ; BX20240168//National Postdoctoral Program for Innovative Talents/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {*Oryza/microbiology/growth & development/physiology/genetics/classification ; *Rhizosphere ; *Droughts ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; Agricultural Irrigation ; },
abstract = {Drought stress markedly reduces rice yield, with notable genotypic variation in drought tolerance. While the rhizosphere microbiome is regarded as the second genome of plants, how the indica and japonica rice rhizosphere microbial communities respond to deficit irrigation and their relationship with yield remain to be elucidated. Here, we conducted field experiments using 12 indica and 12 japonica rice varieties under full and deficit irrigation regimes. Yield-related traits, including filled grain number, seed setting rate, two-plant yield, and thousand grain weight, were measured, and the rhizosphere microbial communities were characterized by 16S rRNA gene sequencing. In line with previous studies, japonica varieties showed superior drought resistance in terms of yield performance. Both rice genotype and irrigation regime significantly influenced the composition and functional potential of the rhizosphere microbiome. Compared to indica rice, the japonica rice rhizosphere was enriched with more beneficial microorganisms. Enrichment of nitrogen‑metabolism‑related groups, such as Microvirga and Nitrososphaeraceae, may contribute to rhizosphere nitrogen cycling and support nitrogen availability for the rice. Similarly, higher abundance of Streptomyces in japonica varieties under drought conditions may be associated with improved drought tolerance. These microbial genera were closely associated with rice yield. Moreover, the japonica rhizosphere microbiome was less disturbed by water limitation, showing higher stability. Overall, the rhizosphere microbiome of japonica rice exhibited functional optimization under drought stress by promoting the enrichment of beneficial and nitrogen-cycling microbes, thereby enhancing drought resistance and yield stability. This study demonstrated a significant correlation between rhizosphere microbial communities and rice yield, providing fundamental insights that may contribute to future strategies for optimizing crop productivity through microbiome management in sustainable agriculture.},
}

*Oryza/microbiology/growth & development/physiology/genetics/classification
*Rhizosphere
*Droughts
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
Stress, Physiological
Agricultural Irrigation

@article {pmid41249582,
year = {2025},
author = {Qu, W and Wang, Z and Zhu, T and Cui, H and Bing, Z and Shen, S and Shen, Y and Yu, S and Zhuang, H and Wang, T},
title = {Aspergillus fumigatus promotes tumor angiogenesis via SLC7A11 on myeloid-derived suppressor cells.},
journal = {EMBO reports},
volume = {},
number = {},
pages = {},
pmid = {41249582},
issn = {1469-3178},
support = {BK20211508//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; 82273011//MOST | National Natural Science Foundation of China (NSFC)/ ; 021414380472//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; },
abstract = {The microbiome is increasingly recognized as playing a critical role in lung cancer prevention, diagnosis, and treatment. While bacteria are essential for tumor angiogenesis, the impact of fungi on this process remains largely unexplored. In this study, we investigate effects of Aspergillus fumigatus (A. fumigatus) on lung cancer. We show that inhalation of A. fumigatus increases tumor burden and angiogenesis in mouse models. Interestingly, A. fumigatus does not directly affect the proangiogenic abilities of tumor cells or endothelial cells. Instead, A. fumigatus promotes the accumulation of myeloid-derived suppressor cells (MDSCs), particularly G-MDSCs, in tumor tissues. A. fumigatus increases VEGF-A secretion from tumor-associated MDSCs, promoting tumor angiogenesis. Furthermore, we identify solute carrier family 7 member 11 (SLC7A11) as a key player in regulating this proangiogenic function through an interaction with High Mobility Group Box 1 (HMGB1) in MDSCs. Our results shed light on the mechanisms by which A. fumigatus influences MDSCs to promote angiogenesis and demonstrate that commensal fungi influence host immunity and support tumor progression.},
}

@article {pmid41249559,
year = {2025},
author = {Liu, B and Sondervorst, K and Nesporova, K and Faust, K and Govers, SK},
title = {Growth stage and interspecies interactions shape the cell biology and cell cycle characteristics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1580},
pmid = {41249559},
issn = {2399-3642},
support = {STG/21/068//KU Leuven (Katholieke Universiteit Leuven)/ ; 101040800//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 1110925N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 1251624N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 101105027//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteroides thetaiotaomicron/growth & development/genetics/cytology/physiology/metabolism ; *Cell Cycle ; *Clostridiales/growth & development/genetics/physiology ; Peptidoglycan/biosynthesis ; },
abstract = {The human gut is a densely populated environment where microbial cells face frequent nutrient fluctuations. While previous studies have identified changes in gene expression, protein concentrations, and metabolite levels, less is known about how gut bacteria respond to nutrient fluctuations at the cellular level. Here, we compared cell biological properties of B. thetaiotaomicron and R. intestinalis, two prevalent human gut microbiome members. Our comparison revealed distinct cellular properties of both bacteria during exponential growth in vitro, including a unique zonal peptidoglycan synthesis pattern in R. intestinalis. Upon nutrient depletion in stationary phase, we observed different cell morphological alterations, with B. thetaiotaomicron cells becoming wider and R. intestinalis cells shorter, accompanied by distinct intracellular changes. These alterations extended to other B. thetaiotaomicron strains, but not Roseburia species. By re-analyzing an existing RNA-seq dataset, we could link the cell biological response of both species to different alterations in gene expression in stationary phase. Finally, coculture experiments revealed a significant impact of interspecies interactions on cell morphological and transcriptomic properties of both bacteria. Together, our work provides insight into the unexplored cell biology of representative human gut microbiome members and how this is shaped by nutrient fluctuations and the presence of other species.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bacteroides thetaiotaomicron/growth & development/genetics/cytology/physiology/metabolism
*Cell Cycle
*Clostridiales/growth & development/genetics/physiology
Peptidoglycan/biosynthesis

@article {pmid41249313,
year = {2025},
author = {Kok, PJR and Wisse, BB and Kapuściak, M and Lampo, M},
title = {Amphibian supercooling capacity is not limited to sub-zero thermal environments.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40311},
pmid = {41249313},
issn = {2045-2322},
support = {2020/39/D/NZ8/02399//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Freezing ; *Amphibians/physiology ; Skin/microbiology ; Cold Temperature ; Acclimatization ; Microbiota ; },
abstract = {Freeze-tolerant amphibians initiate controlled freezing using ice nucleators and survive internal ice formation by accumulating cryoprotectants. In contrast, freeze-avoidant (supercooling) species rely on the inhibition of ice nucleators to prevent freezing altogether. All confirmed supercooling species are native to the Northern Hemisphere and regularly endure negative temperatures. The occurrence, ecological role, and underlying mechanisms of supercooling in amphibians remain poorly understood. Here, we demonstrate for the first time that amphibian supercooling capacity may be present even if not expressed (i.e., latent) and not limited to freezing thermal environments. Exploratory metagenomic data allow us to evaluate whether skin-associated bacteria could contribute to freeze avoidance. In addition, using field experiments, we assess cold and dehydration tolerance limits in two syntopic amphibian species from a high tepui summit (Roraima-tepui in Venezuela) and explore the potential role of cryoprotective dehydration in facilitating supercooling. Despite being syntopic, these species showed striking differences in thermal and dehydration tolerance. Physiological freeze avoidance in tropical montane amphibians is shown to be associated with low critical thermal minima, high dehydration tolerance and possibly antifreeze-producing skin microbiota, although the latter needs further investigation. These traits may determine species persistence under shifting climatic regimes, particularly in thermally variable montane systems.},
}

Animals
Freezing
*Amphibians/physiology
Skin/microbiology
Cold Temperature
Acclimatization
Microbiota

@article {pmid41249223,
year = {2025},
author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL},
title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40115},
pmid = {41249223},
issn = {2045-2322},
support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; },
mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth & development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention & control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; },
abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.},
}

Animals
*Soil Microbiology
*Cucumis sativus/parasitology/growth & development
*Microbiota/drug effects
*Nitrification/drug effects
Plant Roots/parasitology
*Tylenchoidea
Soil/chemistry
*Plant Diseases/parasitology/prevention & control
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
*Brachyura/chemistry

@article {pmid41249215,
year = {2025},
author = {Oliva-Arancibia, B and Villanueva, P and Ugalde, JA},
title = {Profiling of vaginal microbial communities in Chilean women via self-sampling and nanopore sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40093},
pmid = {41249215},
issn = {2045-2322},
support = {National Doctorate Scholarship 21240354//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt Regular 1221209//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; Chile ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Adult ; *Nanopore Sequencing/methods ; Young Adult ; Lactobacillus/genetics/isolation & purification/classification ; },
abstract = {The vaginal microbiota is a dynamic ecosystem that plays a central role in women's reproductive health, with Lactobacillus species typically dominating in healthy individuals. Disruptions to this microbiota can lead to dysbiosis, increasing susceptibility to infections such as bacterial vaginosis and contributing to adverse reproductive outcomes. Despite growing global interest in vaginal microbiome research, studies in Latin American populations remain limited, particularly in Chile. In this exploratory study, we aimed to characterize the vaginal microbiota of Chilean women using a combination of self-sampling and full-length 16S rRNA gene sequencing with Oxford Nanopore Technologies (ONT). We implemented a customized bioinformatic pipeline using the Emu classifier to achieve species-level taxonomic resolution. Our analysis revealed that most participants had microbiota dominated by Lactobacillus species, while a subset exhibited diverse microbial communities consistent with Community State Type (CST) IV. Alpha and beta diversity metrics supported these classifications and demonstrated that species-level resolution enhances the ability to distinguish CSTs. These findings provide the first species-level characterization of vaginal microbiota in Chilean women and demonstrate the utility of ONT sequencing and self-sampling in underrepresented populations. This work contributes essential baseline data for the region and highlights the importance of inclusive microbial profiling in advancing personalized approaches to women's health.},
}

Female
Humans
*Vagina/microbiology
Chile
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Adult
*Nanopore Sequencing/methods
Young Adult
Lactobacillus/genetics/isolation & purification/classification

@article {pmid41249202,
year = {2025},
author = {Gómez-Repollés, A and Villa-Rodríguez, E and Blahovska, Z and Ferguson, S and Radutoiu, S},
title = {High-quality genome assemblies of 152 root commensal bacteria from the model legume Lotus japonicus.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1793},
pmid = {41249202},
issn = {2052-4463},
support = {NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
mesh = {*Lotus/microbiology ; *Genome, Bacterial ; *Plant Roots/microbiology ; *Microbiota ; *Bacteria/genetics ; Symbiosis ; },
abstract = {Bacterial culture collections represent a valuable tool for mechanistic understanding of microbiome assemblies and are increasingly used to assemble tailored synthetic communities to characterize their microbe-microbe interactions and those with the environment. Given the size of these collections, short-read sequencing is primarily used to capture the encoded genetic information. Whilst sufficient for many microbiome studies, this approach is not amenable for understanding bacterial genome evolution or detailed genetic analyses at the entire genome level. Here we report the assembly of 152 full bacterial genomes from the Lj-SPHERE, the Lotus japonicus collection of root commensals. We performed long-read sequencing using Oxford Nanopore Technology and used this together with pre-existing Illumina sequences to de novo assemble these into high quality genomes with improved contiguity and quality. These genomes now provide a solid platform for detailed, mechanistic understanding of microbiome assembly, dynamics, and evolution in plants.},
}

*Lotus/microbiology
*Genome, Bacterial
*Plant Roots/microbiology
*Microbiota
*Bacteria/genetics
Symbiosis

@article {pmid41249178,
year = {2025},
author = {Zhang, J and Yu, D and Zhang, L and Wang, T and Zhang, L and Yan, J},
title = {Quantifying the relative contributions of bacterial and fungal communities to carcass decomposition using a quantitative microbiome profiling approach.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {210},
pmid = {41249178},
issn = {2055-5008},
support = {82101977//the National Natural Science Foundation of China/ ; 82030058//the National Natural Science Foundation of China/ ; },
mesh = {*Bacteria/classification/metabolism/genetics/isolation & purification ; *Fungi/classification/metabolism/isolation & purification/genetics ; Soil Microbiology ; *Microbiota ; Animals ; Metabolomics/methods ; *Mycobiome ; Postmortem Changes ; },
abstract = {Carcass microbial decomposition plays a vital role in global elemental cycling. However, bacterial and fungal absolute abundance dynamics, as well as their contributions to carcass decomposition, remain unclear. Here, the questions were investigated through quantitative microbiome profiling (QMP) and metabolomics. Within the first 14 days postmortem, microbial copies in grave soil and tissue increased by several orders of magnitude. Comparison of QMP with relative microbiome profiling (RMP) revealed strikingly different, even opposing successional trends for major phyla. Bacteria drove more metabolite variation than fungi in the decomposition. Co-occurrence networks revealed that key bacterial and fungal decomposers formed two distinct modules that were highly interconnected and significantly associated with carcass-derived metabolites, suggesting a synergistic relationship in the breakdown of organic matter. Notably, using QMP did not substantially enhance the accuracy of postmortem interval estimation. Collectively, our findings provide critical insights into microbial ecological dynamics during carcass decomposition.},
}

*Bacteria/classification/metabolism/genetics/isolation & purification
*Fungi/classification/metabolism/isolation & purification/genetics
Soil Microbiology
*Microbiota
Animals
Metabolomics/methods
*Mycobiome
Postmortem Changes

@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}

Animals
*Gastrointestinal Microbiome/genetics
Feces/microbiology/chemistry
Metagenomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
*Conservation of Natural Resources/methods
Metabolomics/methods
Metabolome
*Colobinae/microbiology
Endangered Species
Multiomics

@article {pmid41248758,
year = {2025},
author = {Habimana-Griffin, L and Prusa, J and Wang, B and Strong, L and Ning, J and Tovar, ESR and Toth, K and Butler, B and Reynoso, FJ and Markovina, S and Ciorba, MA and Dantas, G},
title = {A novel focal duodenal radiation injury model reveals dose-, time-, and spatially-dependent microbiome perturbations after radiation injury.},
journal = {International journal of radiation oncology, biology, physics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijrobp.2025.11.011},
pmid = {41248758},
issn = {1879-355X},
abstract = {PURPOSE: The duodenum is a key organ at risk during stereotactic ablative radiotherapy (SABR). Understanding mechanisms of radiation-induced intestinal injury (RIII) could reveal novel strategies to reduce SABR toxicities. The gut microbiome contributes to RIII, however existing preclinical models either require surgical manipulation or fail to recapitulate high-dose conformal treatment fields used during SABR, confounding microbiome studies. We developed a non-invasive focal bowel irradiation model to assess microbiome dynamics in both the duodenum and the stool after high-dose duodenal irradiation.

MATERIALS AND METHODS: C57BL/6J mice received sham treatment or focal irradiation (12 or 18 Gy) to the proximal duodenum using a small animal irradiator. Stool and duodenal tissue samples were collected at days 4, 14, and 91 post-treatment and processed for bacterial 16S rRNA gene V4 region amplicon sequencing (Illumina MiSeq platform). Microbiome diversity metrics were calculated and multivariable linear mixed modeling identified bacterial taxa associated with radiotherapy.

RESULTS: Oral iodine contrast enabled duodenum visualization and 100% of mice survived until sacrifice. Focal duodenal irradiation led to dose- and time-dependent changes in duodenal bacterial community composition that were not observed in stool. At days 4 and 14 post-treatment, 18 duodenal taxonomic groups were significantly perturbed, while only 2 taxa were significantly altered in the stool.

CONCLUSIONS: Our focal duodenal irradiation model is safe, well-tolerated, and easy to implement. It enables characterization of microbiome perturbations during both the acute and late phases of injury and serves as a platform for testing new RIII mitigation strategies. Our findings reveal that irradiation-induced changes in the duodenal microbiome are dose-, time-, and spatially-dependent and are not reflected in stool samples. These results underscore the imperative of directly assessing tissue-associated microbiota, as relying solely on stool samples risks overlooking critical, localized microbial dynamics that may drive injury and repair.},
}

@article {pmid41249173,
year = {2025},
author = {Cheng, Q and Lv, S and Yin, N and Wang, J},
title = {Microbial regulators of physiological and reproductive health in women of reproductive age: their local, proximal and distal regulatory roles.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {207},
pmid = {41249173},
issn = {2055-5008},
support = {2022YFA1304102//National Key Research and Development Program of China/ ; T2341010//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; *Reproductive Health ; Pregnancy ; *Gastrointestinal Microbiome ; Fertility ; *Microbiota ; Homeostasis ; Reproduction ; },
abstract = {The female microbiome is emerging as a key regulator of gynecological and reproductive health. This review summarizes how local and gut microbes affect gynecological outcomes, fertility, and pregnancy through metabolic, immune, and hormonal pathways. We highlight underlying mechanisms and intervention strategies, emphasizing the restoration of microbial homeostasis as a promising avenue for advancing understanding, prevention, and management of women's physiological and reproductive health conditions.},
}

Female
Humans
*Reproductive Health
Pregnancy
*Gastrointestinal Microbiome
Fertility
*Microbiota
Homeostasis
Reproduction

@article {pmid41248824,
year = {2025},
author = {Desouky, MA and Eldahshan, W and Atawia, RT},
title = {Exploring the gut-lung-brain axis: Focus on endothelial dysfunction, impaired bioenergetics and strategies to mitigate lung and cognitive disorders.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124089},
doi = {10.1016/j.lfs.2025.124089},
pmid = {41248824},
issn = {1879-0631},
abstract = {Dysbiosis has emerged as a major determinant in the pathogenesis of many human disorders and is a continuously expanding area of research. Identification of several microbial populations and their derived products marks an important milestone in microbiome research. Interestingly, there is evidence that gut microbiota-derived products affect distant organs such as the brain and lungs. Although the effect of gut dysbiosis on several lung- and brain-related disorders has been demonstrated, our knowledge of the mechanisms and consequences of individual metabolites and products on specific cell types such as endothelial cells is still evolving. Endothelial dysfunction is a prominent feature in vascular dementia and several lung disorders. Specifically, alteration in endothelial bioenergetics is an emerging area of research. In this review, the evidence on the interconnection between dysbiosis in the gut and three lung disorders- asthma, COPD and ARDS is discussed. Additionally, the association between these respiratory disorders and cognitive impairment is examined with mechanistic insights. Moreover, data involving the direct impact of key microbial metabolites and products on endothelial cells is synthesized and potential therapeutic modalities are highlighted. We identify the impact of microbial metabolites on endothelial dysfunction and bioenergetics as a potential gap in knowledge and a plausible avenue for future research.},
}

@article {pmid41248397,
year = {2025},
author = {Korenblik, V and Korosi, A and Brul, S and Bockting, C and Nieuwdorp, M and Lok, A},
title = {Feasibility and acceptability of 8-week oral tributyrin supplementation as add on to antidepressant medication in patients with depression: a study protocol paper for a pilot, randomised controlled trial.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e108423},
doi = {10.1136/bmjopen-2025-108423},
pmid = {41248397},
issn = {2044-6055},
mesh = {Humans ; *Antidepressive Agents/therapeutic use/administration & dosage ; Pilot Projects ; Adult ; Feasibility Studies ; Double-Blind Method ; *Depressive Disorder, Major/drug therapy ; *Triglycerides/administration & dosage/therapeutic use ; Middle Aged ; Male ; *Dietary Supplements ; Female ; Young Adult ; Adolescent ; Administration, Oral ; Drug Therapy, Combination ; Aged ; Randomized Controlled Trials as Topic ; Gastrointestinal Microbiome ; Treatment Outcome ; },
abstract = {BACKGROUND: Major depressive disorder (MDD) is a severe mental health condition that profoundly affects both psychological and physical well-being. Growing evidence indicates that targeting the gut-brain axis could present new therapeutic opportunities for MDD, given the role of gut microbiota and their metabolites in its pathophysiology. One promising approach involves supplementation with butyrate, a short-chain fatty acid that has demonstrated antidepressant potential in preclinical models of depression. However, clinical research exploring the effects of butyrate supplementation in individuals with MDD remains lacking.

METHODS: This study is a double-blind, parallel, 1:1 randomised placebo-controlled trial. The primary aim of this pilot study is to assess the feasibility and acceptability of an 8-week oral supplementation with tributyrin, a triglyceride form of butyrate (4 g/day), added to usual treatment with antidepressant medication in 24 patients with mild-to-severe MDD aged 18-65 years. Secondary outcomes include changes in depressive symptoms, assessed weekly throughout the supplementation period and at 16 weeks post-supplementation during follow-up, as well as changes in anhedonia and affect, measured multiple times per day via a smartphone application throughout the supplementation period. Additional outcomes include changes in gastrointestinal symptoms, changes in faecal microbiome, metabolites in blood and faeces, inflammation, epigenetic markers, stress and intestinal permeability.

ETHICS AND DISSEMINATION: The study has been approved by the Medical Research Ethics Committee of the Amsterdam University Medical Centre, the Netherlands.

DISCUSSION: Should the pilot demonstrate feasibility and acceptability, a larger-scale study will be warranted to evaluate the efficacy of tributyrin supplementation in alleviating depressive symptoms. This pilot will provide valuable insights to guide sample size calculations and refine study design for subsequent trials. Ultimately, this research could lead to novel adjunctive treatments for MDD targeting gut-brain signalling, offering new therapeutic avenues for patients with MDD.

TRIAL REGISTRATION NUMBER: This trial has been registered in the International Clinical Trials Registry Platform (registry number: NL-OMON57116).},
}

Humans
*Antidepressive Agents/therapeutic use/administration & dosage
Pilot Projects
Adult
Feasibility Studies
Double-Blind Method
*Depressive Disorder, Major/drug therapy
*Triglycerides/administration & dosage/therapeutic use
Middle Aged
Male
*Dietary Supplements
Female
Young Adult
Adolescent
Administration, Oral
Drug Therapy, Combination
Aged
Randomized Controlled Trials as Topic
Gastrointestinal Microbiome
Treatment Outcome

@article {pmid41248372,
year = {2025},
author = {Fernando, SM and Muscedere, J and Rochwerg, B and Johnstone, J and Daneman, N and Marshall, JC and Lauzier, F and Rudkowski, JC and Arabi, YM and Heels-Ansdell, D and Sligl, W and Kristof, AS and Duan, E and Dionne, JC and St-Arnaud, C and Reynolds, S and Khwaja, K and Cook, DJ and , },
title = {Frailty and the risk of ICU-acquired infections in a randomised trial: a protocol and statistical analysis plan.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e105227},
doi = {10.1136/bmjopen-2025-105227},
pmid = {41248372},
issn = {2044-6055},
mesh = {Humans ; *Frailty/complications ; *Intensive Care Units ; *Pneumonia, Ventilator-Associated/epidemiology/prevention & control ; *Cross Infection/epidemiology ; Length of Stay/statistics & numerical data ; Randomized Controlled Trials as Topic ; Risk Factors ; Aged ; Proportional Hazards Models ; Male ; Respiration, Artificial/adverse effects ; Female ; Research Design ; },
abstract = {INTRODUCTION: Dysregulated immunity may account for an increased risk of infection and other adverse outcomes among frail hospitalised persons. The primary objective of this study is to examine whether baseline frailty is associated with the risk of developing ventilator-associated pneumonia (VAP) or other intensive care unit (ICU)-acquired infections among invasively ventilated adults. Additional objectives are to examine the relationship between frailty and hospital length of stay, discharge to a long-term care facility and vital status. We hypothesise that persons with frailty compared with others would have an increased risk of VAP and other infections, a longer hospital stay, higher probability of discharge to a long-term care facility and higher mortality.

METHODS AND ANALYSIS: This is a preplanned secondary analysis of the PROSPECT trial (Probiotics to Prevent Severe Pneumonia and Endotracheal Colonization Trial) which enrolled patients across 44 ICUs in three countries. We will use Cox proportional hazards regression analysis to assess the association of frailty with the clinical outcomes of interest, adjusting for other baseline variables. Baseline demographic and descriptive outcome data will be reported using descriptive statistics. Regression results will be presented as adjusted HRs or ORs with 95% CIs for the associations of each independent variable with the primary, secondary and tertiary outcomes.

ETHICS AND DISSEMINATION: Participating hospital research ethics board approved the PROSPECT trial and data collection. The protocol for this study was approved by the Hamilton Integrated Research Ethics Board on 20 August 2015 (Project ID:19128). This study will identify whether frailty is associated with risk of VAP and other healthcare-associated infections in invasively ventilated patients, adjusted for other baseline factors. Results may be useful to patients, their caregivers, clinicians and the design of future research. Findings will be disseminated to investigators at a meeting of the Canadian Critical Care Trials Group. We will present study results at an international conference in the fields of critical care and infectious diseases, to coincide with or precede open-access peer-review publication. To aid knowledge dissemination, we will use a variety of formats. For example, for traditional and social media, we will create two different visual abstracts and infographics of our results suitable to share on clinician-facing and public-facing platforms.

TRIAL REGISTRATION NUMBER: NCT02462590.},
}

Humans
*Frailty/complications
*Intensive Care Units
*Pneumonia, Ventilator-Associated/epidemiology/prevention & control
*Cross Infection/epidemiology
Length of Stay/statistics & numerical data
Randomized Controlled Trials as Topic
Risk Factors
Aged
Proportional Hazards Models
Male
Respiration, Artificial/adverse effects
Female
Research Design

@article {pmid41248126,
year = {2025},
author = {Jefferson, J and Reigate, C and Giacomini, A and Rivero, MJ and Hitchings, M and Webster, TU and Wells, K},
title = {Triadic relationships between pasture exposure, gastrointestinal parasites, and hindgut microbiomes in grazing lambs.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0337086},
doi = {10.1371/journal.pone.0337086},
pmid = {41248126},
issn = {1932-6203},
mesh = {Animals ; Sheep/microbiology/parasitology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology/parasitology ; Bacteria/genetics/classification ; *Sheep Diseases/parasitology/microbiology ; Lolium ; },
abstract = {Livestock grazing in confined pastures often means grazing on a less diverse diet than under more natural conditions and increased exposure to gastrointestinal parasites prevailing in these pastures. However, how sward composition influences gut microbiome (GM) diversity and its relationship with parasite burden remains poorly understood. In this study, we analysed the faecal GM of weaned lambs grazing on two distinct sward types (perennial ryegrass and a mixed-species sward) over three consecutive months using 16S rRNA sequencing, in order to assess how microbial diversity and composition are related to environmental conditions and the gastrointestinal nematode (GIN) burden in naturally infected lambs. Sward type and sampling time explained some of the variation in GM alpha diversity and community composition (beta diversity), whereas individual lamb identity accounted for considerably more variation in microbial assemblages. Shifts in the relative abundance of bacterial genera such as Saccharofermentans, Anaerosporobacter, Butyrivibrio in relation to sward type and sampling time suggest mostly adaptive fluctuations in response to diet and pasture condition. Abundance shifts of Negativibacillus, and Candidatus Saccharimonas were also associated with GIN burden, which, in turn, was higher in lambs grazing on mixed swards compared to ryegrass. Our findings add to the growing understanding of how sheep microbiomes vary with pasture management and changes in parasite burden. We highlight that individual identity may shape gut microbiota, and that potential triadic interactions among gastrointestinal parasites, sward exposure, and the gut microbiome underscore the importance of considering host, parasite, and environmental factors collectively when evaluating microbiome dynamics in grazing livestock.},
}

Animals
Sheep/microbiology/parasitology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Feces/microbiology/parasitology
Bacteria/genetics/classification
*Sheep Diseases/parasitology/microbiology
Lolium

@article {pmid41247816,
year = {2025},
author = {Gao, Y and Wang, X and Wang, Q and Jiang, L and Wu, C and Guo, Y and Cui, N and Tang, H and Tang, L},
title = {Global impact of pelvic inflammatory diseases attributable to sexually transmitted infections in women of childbearing age: a comprehensive analysis based on GBD 2021 data and bibliometric analysis.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004066},
pmid = {41247816},
issn = {1743-9159},
abstract = {BACKGROUND: Pelvic inflammatory disease (PID), often caused by sexually transmitted infections (STIs), poses significant health threat to women of childbearing age (WCBA). This study assessed the global prevalence trends and research landscape of STIs-related PID.

METHODS: This study integrated GBD 2021 data and bibliometric analysis. Joinpoint regression calculated Average annual percentage change (AAPC) for age-standardized prevalence rate (ASPR) from 1990 to 2021. Decomposition analyses assessed the contributions of population growth, aging, and epidemiological changes to the prevalence trends for last 32 years. The Bayesian age-period-cohort (BAPC) model projected ASPR from 2022 to 2040, and the Nordpred model conducted a sensitivity analysis of the prediction results, which validated the findings' reliability. 1726 related publications were retrieved from the WOS Core Collection database. Bibliometric information was extracted with VOSviewer software for visualization.

RESULTS: In 2021, an estimated 1,009,957.64 cases of PID due to STIs occurred among WCBA globally, with chlamydial infection accounting for approximately 23%, gonococcal infection (4.98%), and other STIs (72.03%). From 1990 to 2021, the global ASPR of STIs-related PID increased by AAPC of 0.13%, with the largest increase observed among women in the 20-24 years age group. Regionally, the highest ASPR was observed in low SDI regions in 2021, while the fastest increase occurred in middle SDI regions over the last 32 years. Decomposition analyses highlighted the population growth as a key driver of global prevalence rise, accounting for 78.5 %. The global ASPR of STIs-related PID is projected to continue rising from 2022 to 2040. Bibliometric analysis showed stable research on STIs and PID, with an increased citation rate. The United States was the leading contributor. Research focused on chlamydia trachomatis, with recent studies exploring the vaginal microbiome, resistance and protective immunity.

CONCLUSIONS: This study performed an epidemiological assessment and bibliometric analysis of the PID attributable to STIs burden globally, informing policy-making and research directions.},
}

@article {pmid41247642,
year = {2025},
author = {Li, J and Hu, J and Yang, Y and Zhang, H and Liu, Y and Fang, Y and Qu, L and Lin, A and Luo, P and Jiang, A and Wang, L},
title = {Drug resistance in cancer: molecular mechanisms and emerging treatment strategies.},
journal = {Molecular biomedicine},
volume = {6},
number = {1},
pages = {111},
pmid = {41247642},
issn = {2662-8651},
support = {81772740//National Natural Science Foundation of China/ ; 82173345//National Natural Science Foundation of China/ ; 81972333//National Natural Science Foundation of China/ ; 82372883//National Natural Science Foundation of China/ ; 2022YFB4700904//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; *Neoplasms/drug therapy/genetics/metabolism/pathology/therapy ; Tumor Microenvironment/drug effects ; Animals ; Immunotherapy ; Antineoplastic Agents/therapeutic use/pharmacology ; Epigenesis, Genetic ; },
abstract = {Therapeutic resistance remains a defining challenge in oncology, limiting the durability of current therapies and contributing to disease relapse and poor patient outcomes. This review systematically integrates recent progress in understanding the molecular, cellular, and ecological foundations of drug resistance across chemotherapy, targeted therapy, and immunotherapy. We delineate how genetic alterations, epigenetic reprogramming, post-translational modifications, and non-coding RNA networks cooperate with metabolic reprogramming and tumor microenvironment remodeling to sustain resistant phenotypes. The influence of the microbiome is highlighted as an emerging determinant of therapeutic response through immune modulation and metabolic cross-talk. By summarizing key regulatory circuits, We establishe a unified framework linking clonal evolution, metabolic adaptability, and tumor ecological dynamics. We further synthesizes novel therapeutic strategies that convert resistance mechanisms into therapeutic vulnerabilities, including synthetic lethality approaches, metabolic targeting, and disruption of stem cell and stromal niches. Advances in single-cell and spatial omics, liquid biopsy, and artificial intelligence are emphasized as transformative tools for early detection and real-time prediction of resistance evolution. This review also identifies major translational gaps in preclinical modeling and proposes precision oncology frameworks guided by evolutionary principles. By bridging mechanistic understanding with adaptive clinical design, this work provides an integrated roadmap for overcoming therapeutic resistance and achieving sustained, long-term cancer control.},
}

Humans
*Drug Resistance, Neoplasm/genetics
*Neoplasms/drug therapy/genetics/metabolism/pathology/therapy
Tumor Microenvironment/drug effects
Animals
Immunotherapy
Antineoplastic Agents/therapeutic use/pharmacology
Epigenesis, Genetic

@article {pmid41247431,
year = {2025},
author = {Dhungana, P and Dam, A and Kiang, TKL},
title = {Clinical Pharmacokinetic-Pharmacodynamic Relationships of Pharmacological Strategies for Attenuating p-Cresyl Sulfate in Patients with Kidney Disease.},
journal = {Clinical pharmacokinetics},
volume = {},
number = {},
pages = {},
pmid = {41247431},
issn = {1179-1926},
abstract = {p-Cresyl sulfate (pCS) is a highly toxic uremic compound that is produced from tyrosine and phenylalanine in the gut and primarily excreted renally. In patients with kidney dysfunction, the accumulation of pCS can lead to the worsening of kidney disease and manifestation of organ toxicities. Various pharmacological strategies have been proposed to reduce pCS in patients with chronic kidney disease (CKD), but systematic pharmacokinetic-pharmacodynamic assessments have not been conducted to our knowledge. The objectives of this scoping review were to comprehensively and critically summarize the available literature using a newly devised, pharmacokinetic-pharmacodynamic assessment method. We searched PubMed, Embase, and Scopus for primary research articles in patients with CKD and devised the following novel approach to systematically evaluate each study: (i) positive reduction or null reduction of pCS; (ii) dose dependency; (iii) time dependency; (iv) effects on free versus total pCS; and (v) relationships to diet regimens (e.g., protein intake), microbiome composition, blood biochemistry, and clinical outcomes (i.e., progression of renal disease measured by initiation of dialysis or renal transplant; cardiovascular outcomes such as incidence of myocardial infarction, heart failure, cardiovascular death; and changes in qualityof- life instruments). Fifty-nine studies were identified with a total of 2593 study participants (pre-dialysis CKD: n = 1060; CKD on dialysis: n = 1499; and post-transplant CKD: n = 34). The studies included AST-120 (n = 3), sevelamer (n = 9), sucroferric Noxyhydroxide (n = 1 [+ 1 overlapping with sevelamer]), prebiotics (n = 15), probiotics (n = 9), synbiotics (n = 13), antibiotics (n = 3), ketoanalogs (n=3), and curcumin (n = 3). Only AST-120 and synbiotics consistently demonstrated significant pCS reductions, and the percentage (%) reductions by AST-120 were 40.9-75.6% for free and 28.8-42.8% for total pCS; whereas the percentage reduction by synbiotics were 6.4-78.1% for total and 16.7% for free pCS, the latter only evident in a subgroup with antibiotic-free regimen. Although sevelamer was also associated with a pCS reduction, the percentage reduction was modest and only based on the total concentration. In contrast, the majority of sucroferric oxyhydroxide, prebiotics, probiotics, ketoanalogs, and curcumin studies did not demonstrate consistent pCS reductions. Furthermore, dose dependency was not established in the majority of studies, and although some temporal relationships were evident, the data were very limited. Only a few of the analyzed studies measured both bound and unbound forms of pCS, and inconsistencies have been reported in a few studies. In Ngeneral, it was also difficult to establish associations with outcomes in most studies because of limitations in experimental design, and in instances where potential pharmacokinetic-pharmacodynamic relationships were observed, they were generally weak and only with surrogate markers of commonly measured biochemistry, oxidative stress, lipid profiles, and inflammatory markers, with only a handful of studies capturing clinical outcomes. In conclusion, we have identified potential pharmacological interventions that may be further developed for the purpose of reducing pCS in patients with CKD.},
}

@article {pmid41247319,
year = {2025},
author = {Wang, Z and Guo, X and Zhang, H and Zheng, T and Liu, Y and Dai, L and Xie, Y and Shang, X and Zhang, L and Yang, L and Yuan, L and Hou, X},
title = {Rotation-driven changes in physicochemical properties modulate soil microbial diversity and community complexity in tobacco-woad soils.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0301624},
doi = {10.1128/spectrum.03016-24},
pmid = {41247319},
issn = {2165-0497},
abstract = {Continuous tobacco monocropping leads to soil degradation and yield reduction. To address this, we evaluated the effects of tobacco (Nicotiana tabacum L.)-woad (Isatis tinctoria L.) rotation (A2, A4) compared to tobacco monoculture (A1) and woad monoculture (A3) on soil health and crop quality over a multi-year period. Methods involved comparative analysis of soil nutrients, enzyme activities, microbial community structure, and crop chemical composition and economic value. Key results demonstrated that tobacco-woad rotation significantly improved soil fertility. The tobacco-woad rotation could increase the content of organic matter, alkaline available nitrogen, available phosphorus, and available potassium in the soil, which were increased by 1.44%, 17.96%, 4.61%, and 16.20%, respectively, compared to tobacco monoculture. Soil urease and catalase activities, particularly urease (increased by 2.31 times), were significantly enhanced during the tobacco pre-growth period under rotation. Soil microbial communities were significantly restructured under tobacco-woad rotation versus monocropping. Bacterial phyla Acidobacteria, Gemmatimonadota, and Methylomirabilota were enriched in tobacco-woad rotation (A2) relative to tobacco monoculture (A1), while Chloroflexi, Methylomirabilota, and Verrucomicrobiota increased in woad-tobacco rotation (A4) versus woad monoculture (A3). Fungal shifts featured decreased Ascomycota and Basidiomycota with increased Mortierellomycota in both rotations, alongside reduced Chytridiomycota in A4. Rotation enriched key bacterial genera (MND1, Nitrospira, Subgroup-10, and RB41) and fungal taxa (Mortierella, Saccharomyces, and Saitozyma). Crucially, rotation harmoniously improved the chemical composition of both tobacco and woad leaves, increasing reducing sugars, total sugars, nicotine, potassium, and the sugar ratio in tobacco. The proportion of high-quality tobacco leaves post-curing increased by 10.24% (A2), contributing to a significantly higher total crop production value. In conclusion, tobacco-woad rotation effectively alleviates soil degradation associated with continuous tobacco cropping by enhancing soil nutrient availability, boosting key enzyme activities, and optimizing the structure and interactions of the soil microbial community. These soil improvements collectively drive superior crop quality and economic returns, supporting their adoption as a sustainable agricultural practice.IMPORTANCE(i) The effects of rotation of tobacco with woad on the quality of tobacco production were clarified using physiological and biochemical analyses. (ii) The effects of rotating tobacco with woad on soil microorganisms were revealed by microbiome sequencing of tobacco soils. Tobacco-woad rotation significantly improved the relative abundance of soil-dominant bacteria and decreased the relative abundance of harmful fungi. (iii) An efficient cultivation model of tobacco and woad suitable for Shandong was established by combining soil microbiomics with tobacco plant growth and development. Rotation of tobacco to woad gave the best results.},
}

@article {pmid41247142,
year = {2025},
author = {Wang, Y and Hou, Q and Wei, F and Liu, B and Feng, Q},
title = {MNetClass: a control-free microbial network clustering framework for identifying central subcommunities across ecological niches.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0098925},
doi = {10.1128/msystems.00989-25},
pmid = {41247142},
issn = {2379-5077},
abstract = {Investigating microbiome subnetworks and identifying central microbes in specific ecological niches is a critical issue in human microbiome studies. Traditional methods typically require control samples, limiting the ability to study microbiomes at distinct body sites without matched controls. Moreover, some clustering methods are not well-suited for microbial data and fail to identify central subcommunities across ecological niches after clustering. In this study, we present MNetClass, a novel microbial network clustering analysis framework. It utilizes a random walk algorithm and a rank-sum ratio-entropy weight evaluation model to classify key subnetworks and identify central microbes at any body site, without the need for control samples. We demonstrate its capabilities on both simulated and real microbiome data sets. Simulation results indicate that MNetClass outperforms current unsupervised microbial clustering methods. In applied case studies, the analysis of microbiome data from five distinct oral sites revealed site-specific microbial communities. Furthermore, MNetClass demonstrated superior predictive performance on cross-cohort Autism Spectrum Disorder data and identified age-related microbial communities across different oral sites, underscoring its broad applicability in microbiome research.IMPORTANCEMNetClass provides a valuable tool for microbiome network analysis, enabling the identification of key microbial subcommunities across diverse ecological niches. Implemented as an R package (https://github.com/YihuaWWW/MNetClass), it offers broad accessibility for researchers. Here, we systematically benchmarked MNetClass against existing microbial clustering methods on synthetic data using various performance metrics, demonstrating its superior efficacy. Notably, MNetClass operates without the need for control groups and effectively identifies central microbes, highlighting its potential as a robust framework for advancing microbiome research.},
}

@article {pmid41247019,
year = {2025},
author = {Du, H and Jiang, X and Liu, Y and Hou, J and Li, C and Wu, R and Li, SC and Dai, W},
title = {One-year restoration of vaginal health: synergistic dynamics of microbiome and metabolome following the elimination of high-grade cervical intraepithelial neoplasia.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0119025},
doi = {10.1128/msystems.01190-25},
pmid = {41247019},
issn = {2379-5077},
abstract = {Therapeutic elimination of high-grade cervical intraepithelial neoplasia (CIN) is widely implemented for cervical cancer prevention. Despite the demonstrated dysbiosis of vaginal microenvironment in high-grade CIN, its post-therapy restorations remain to be poorly understood, especially in functional aspects. This study aimed to characterize temporal changes in both vaginal microbiota (VM) and metabolome (VMeta) following therapeutic elimination of high-grade CIN. We conducted a longitudinal study of 32 HPV-positive women with high-grade CIN who underwent therapeutic procedures. Vaginal swabs were collected at baseline (pre-therapy) and at 6- and 12-month follow-up visits for integrated VM and VMeta analysis. We observed a gradual restoration of Lactobacillus crispatus levels from baseline to 12 months (P < 0.05). Concurrently, we detected significant decreases in dysbiosis-associated bacteria, including Prevotella bivia, Ureaplasma parvum, and Peptoniphilus sp. 6 months post-therapy compared to the baseline. VMeta analysis revealed distinct metabolic shifts across the follow-up periods. The early post-therapy phase (baseline to 6 months) was characterized by enrichment of glycerophospholipids and depletion of nucleotide metabolites, while the later phase (6-12 months) showed increases in flavonoids, lysophospholipids, bioactive amides, and amino acid metabolism. Integration of correlation and dynamic Bayesian network analysis indicated potential regulatory relationships and time-lag effects involving HPV infection, L. crispatus, Bifidobacterium sp., Streptococcus anginosus, Megasphaera sp., U. parvum, and those metabolites. This study enhances our understanding of a sequential restoration process post-therapy in the vaginal microenvironment.IMPORTANCETherapeutic elimination of high-grade CIN is routine, yet functional recovery of the vaginal ecosystem is poorly defined. In a 12-month longitudinal multi-omics study of 32 women, we show stepwise restoration: progressive L. crispatus dominance with sustained decreases in dysbiosis-associated taxa (P. bivia, U. parvum, Peptoniphilus). Metabolically, an early rise in glycerophospholipids and fall in nucleotide metabolites is followed by later enrichment of flavonoids, lysophospholipids, bioactive amides, and amino acid derivatives. Correlation and dynamic Bayesian network analyses reveal putative regulatory links, time-lag effects, and downstream impacts of HPV clearance. These findings deliver a functional roadmap of post-therapy recovery, nominate measurable microbial-metabolite milestones and candidate biomarkers for monitoring, and suggest targets for adjunct interventions to accelerate re-establishment of protective states. This work informs precision follow-up in cervical cancer prevention programs.},
}

@article {pmid41247018,
year = {2025},
author = {Xiong, M and Kuang, W and Liu, Z and Tong, R and Deng, X and Wang, N and Wan, X and Feng, M and Luo, Y and Zhang, B and Zhang, Z and Zheng, F},
title = {Quercetin alleviates ulcerative colitis via regulating gut microbiota and tryptophan metabolism.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0070325},
doi = {10.1128/msystems.00703-25},
pmid = {41247018},
issn = {2379-5077},
abstract = {UNLABELLED: Quercetin, a natural flavonoid in traditional Chinese medicinal plants, has shown promise in alleviating ulcerative colitis symptoms despite uncertainties about its exact mode of action. This study explored how quercetin influences tryptophan breakdown and gut bacterial populations in mice with chemically induced colitis. The treatment demonstrated measurable improvements-normalizing body weight, reducing spleen enlargement, lowering clinical severity scores, preserving colon structure, and healing tissue damage. Through advanced microbiome profiling and metabolic analysis, researchers observed increased populations of helpful gut microbes alongside higher concentrations of tryptophan byproducts. These biochemical shifts stimulated the aryl hydrocarbon receptor system, which plays a key role in restoring gut lining integrity. The collective evidence points to quercetin's therapeutic potential through its dual action on microbial ecology and tryptophan-derived signaling pathways.

IMPORTANCE: Ulcerative colitis is a chronic inflammatory disease with limited effective therapeutic options. In this study, quercetin-a flavonoid commonly found in traditional Chinese medicinal herbs-was shown to relieve colitis symptoms by reshaping gut microbiota and restoring tryptophan metabolism. Notably, the increase in indolelactic acid, a key microbial metabolite, led to activation of the aryl hydrocarbon receptor, which supports intestinal barrier integrity and dampens inflammation. These findings reveal a gut microbiota-derived metabolite-host signaling axis as a central mechanism of action, highlighting the potential of quercetin as a microbiota-targeted therapeutic approach for UC.},
}

@article {pmid41247017,
year = {2025},
author = {Carpentier, J and Derocles, SA and Chéreau, S and Marquer, B and Linglin, J and Lebreton, L and Legeai, F and Vannier, N and Cortesero, A and Mougel, C},
title = {Contrasting glucosinolate profiles in rapeseed genotypes shape the rhizosphere-insect continuum and microbial detoxification potential in a root herbivore.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0126925},
doi = {10.1128/msystems.01269-25},
pmid = {41247017},
issn = {2379-5077},
abstract = {Plant secondary metabolites are key mediators of plant-insect-microbiome interactions, yet their role in structuring functionally relevant insect-associated microbial communities remains poorly understood. Here, we combined a factorial experiment using Brassica napus genotypes differing in glucosinolate (GLS) content with distinct succession to investigate the eco-evolutionary dynamics of the microbiota of the root herbivore Delia radicum. Amplicon sequencing and microbial culturing revealed that both rhizospheric and gut microbial communities are shaped by plant genotype and soil legacy, with a subset of bacterial taxa shared across compartments. Notably, Pseudomonas brassicacearum, harboring the isothiocyanates (ITC) detoxifying gene saxA, was consistently recovered from both plant and insect habitats. Functional assays confirmed its capacity to degrade 2-phenylethyl isothiocyanate (PEITC), a major toxic GLS hydrolysis product. Other gut-derived microbial isolates exhibited heterogeneous responses to PEITC, ranging from growth inhibition, promotion, or growth recovery after a prolonged lag phase. Despite the toxicity of ITC, insect fitness proxies were enhanced on GLS +plants, suggesting microbiota-mediated adaptation to host chemical defenses. Our findings reveal a plant genotype-specific filtering of environmentally acquired microbes and highlight the role of detoxifying symbionts in Delia radicum performance.IMPORTANCEUnderstanding how herbivorous insects adapt to plant chemical defenses is important in the context of new agricultural practices. This study highlights that the host plant genotype shapes not only rhizospheric and gut microbial communities but also promotes the acquisition of symbiotic bacteria capable of detoxifying harmful isothiocyanates. These findings reveal a functional microbial pathway for insect adaptation to plant defenses, with potential implications for pest management strategies. By uncovering the role of plant-associated microbiota, the acquisition of beneficial microbes, and their functional contributions to host fitness, this work provides a foundation for innovative agroecological approaches that leverage plant-microbe-insect interactions.},
}

@article {pmid41247016,
year = {2025},
author = {Beilinson, V and Chen, GY and Hargadon, AC and Ruby, EG and McFall-Ngai, MJ},
title = {Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0049825},
doi = {10.1128/msystems.00498-25},
pmid = {41247016},
issn = {2379-5077},
abstract = {UNLABELLED: Understanding the cause and consequences of bacterial strain variation remains a challenge in the study of symbioses. While the diverse reactions of the host immune system to strain variants have been well studied in pathogenesis, much less is known about how strain variation influences beneficial associations. From the complex vertebrate gut microbiome to the more tractable invertebrate models of symbiosis, the host's cellular and molecular responses to this diversity remain largely a mystery. Here, we explore strain diversity in Vibrio fischeri, the bioluminescent bacterial symbiont of the Hawaiian bobtail squid, Euprymna scolopes. Phylogenetic analyses of the genomes of 62 V. fischeri strains, including 50 light organ-associated and 12 planktonic isolates, revealed several genes that were absent in planktonic strains, but uniformly present in symbiotic ones. To better understand the consequences of this diversity to the host, we selected five light-organ associated strains: three from E. scolopes but having different combinations of colonization factors, one from a congeneric squid host, and one from a marine fish. We colonized juvenile E. scolopes with these strains and, using RNAseq, found that (i) the most similar host transcriptomic responses occurred among the native E. scolopes strains, (ii) intermediate was the strain from the related squid, and (iii) least similar was the fish strain. Importantly, native strains downregulated immune-related genes more than non-native ones. Finally, host development was atypical or delayed when colonized by non-native strains. These experiments point the way to more targeted studies of the mechanisms underlying host responses to symbiont strain diversity.

IMPORTANCE: Variation among strains of a bacterial species is a powerful factor underlying the intensity of host responses during pathogenic infections. Less is known about the cellular and molecular responses of host tissues to differences between the strains present in an animal's normal microbiome. We use a natural, species-specific, symbiosis to explore the influence of strain-level differences on host gene expression and morphogenesis. Analysis of symbiotic strains from squids and fishes, as well as free-living strains, shows that the carriage of colonization determinants, while critical to competitive success among strains of a species, has a minimal effect on the transcriptional response of the host. We provide evidence that a more important driver of normal gene expression during the development of symbiosis is the history of a strain's co-diversification with its host species. Such studies, using simple invertebrate models, allow the recognition of otherwise obscured interactions underlying the more complex microbiomes of vertebrates.},
}

@article {pmid41246976,
year = {2025},
author = {Hoefle, D and Ramakrishnan, DK and Holländer, MA and Kiplimo, D and Konzag, W and Schena, L and Malacrinò, A and Tack, AJM and Abdelfattah, A},
title = {Fruit function beyond dispersal: effect of fruit decomposition on the plant microbiome assembly.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70698},
pmid = {41246976},
issn = {1469-8137},
abstract = {The evolutionary role of fruits has primarily been linked to seed dispersal. However, their influence on the soil and plant microbiomes subsequent to their decomposition has received no attention. We hypothesized that fruit decomposition alters the soil microbiome, and consequently the plant microbiome and performance. We used amplicon sequencing to analyze the bacterial communities in the soil, rhizosphere, and phyllosphere of tomato and chili plants grown with and without their fruit. Fruit decomposition affected soil chemistry, increased bacterial diversity and influenced bacterial community composition. Blrii41 and Sandaracinaceae and functions related to methanol oxidation and nitrification, mammalian and human gut metabolism were enriched. It also decreased germination rates and affected shoot but not root length. Fruit decomposition decreased phyllosphere microbial diversity and strongly shifted the rhizosphere and phyllosphere community composition. The plant microbiome showed increased functions related to ligninolysis, methanol oxidation, methylotrophy, and xylanolysis, among others. These results provide evidence that fruits exert a postdispersal influence on the seedling environment and the early plant microbiome assembly. This study expands the classical ecological view of fruit function and opens new directions for understanding microbial inheritance and leveraging fruit-derived microbiomes.},
}

@article {pmid41246908,
year = {2025},
author = {Miyake, K and Watanabe, D and Otawa, S and Kushima, M and Yui, H and Shinohara, R and Sakurai, D and Yamagata, Z},
title = {Gut Microbiome Alterations by Allergen Sensitisation and Symptom Severity in Paediatric Allergic Rhinitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70163},
pmid = {41246908},
issn = {1398-9995},
support = {20H03928//Scientific Research conferred by the Japanese Ministry of Education, Culture, Sports, Science, and Technology/ ; 24K13437//Scientific Research conferred by the Japanese Ministry of Education, Culture, Sports, Science, and Technology/ ; 23-iii5024//TERUMO LIFE SCIENCE FOUNDATION/ ; },
}

@article {pmid41246810,
year = {2025},
author = {Tan, H and Chen, M and Yao, H and Li, S and Nie, S},
title = {Dominant Gut Commensals Enriched by Pectin with Low Esterification Degree Orchestrate the Amelioration of Acute Ulcerative Colitis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09097},
pmid = {41246810},
issn = {1520-5118},
abstract = {Dietary fiber's health benefits are increasingly recognized as microbiota-dependent, with effects influenced by fiber structure. We previously observed that low-esterified pectin provides superior protection against DSS-induced colitis compared to its high-esterified form, but the mechanism was unknown. This study investigated the microbiota-dependent pathway underlying low-esterified pectin's anticolitic effect using FMT. By evaluating three pectin-induced bacteria (Bifidobacterium longum NSP002, Bacteroides xylanisolvens NSP003, Enterococcus faecium NSP004) individually and in a consortium, we found that the consortium exerted a significantly stronger protective effect, suggesting synergistic interactions and highlighting its potential as an FMT alternative. Mechanistically, this protection may involve three axes: (1) Gut microbiome remodeling (reduced Akkermansia, increased Bacteroides, elevated propionic acid). (2) Intestinal homeostasis modulation (reduced mme/calprotectin expression, activated PI3K/calcium signaling). and (3) Systemic metabolic reprogramming (increased serum phenylethylamine, enriched phenylalanine metabolism). These findings support the clinical potential of pectin for optimizing enteral nutrition and using pectin-enriched microbiota consortia to target IBD pathogenesis.},
}

@article {pmid41246777,
year = {2025},
author = {Wang, Z and Xu, J and Xu, G and Sha, Y and Wang, K and Chen, G},
title = {Decoding Hypercarotenemia: Integrating Pathophysiology, Clinical Recognition, and Precision Management.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94519},
doi = {10.7759/cureus.94519},
pmid = {41246777},
issn = {2168-8184},
abstract = {Hypercarotenemia represents a complex metabolic phenotype characterized by supraphysiological circulating carotenoid concentrations exceeding 300 μg/dL for β-carotene, manifesting as distinctive cutaneous xanthochromia with preserved scleral clarity - a critical differentiating feature from hepatobiliary dysfunction. The contemporary surge in detection rates, which has increased over the past decade, correlates with global dietary paradigm shifts, including the growth in plant-based diet adoption and the concurrent rise in metabolic dysfunction. This comprehensive review synthesizes current understanding of hypercarotenemia pathophysiology through systematic literature analysis encompassing molecular mechanisms, epidemiological trends, clinical phenotypes, and therapeutic interventions, with particular emphasis on genetic discoveries and precision management approaches. Hypercarotenemia pathogenesis involves sophisticated interactions among three key mechanistic pathways: (1) intestinal absorption via SR-B1 receptors, (2) enzymatic conversion through β-carotene oxygenase 1 and 2 (Beta-carotene oxygenase 1 (BCO1)/BCO2) systems, and (3) genetic susceptibility primarily mediated by BCO1 variants (rs6564851, rs12934922, rs7501331). The condition demonstrates remarkable clinical heterogeneity influenced by individual metabolic capacity, intestinal microbiome composition, and concurrent endocrinopathies, particularly thyroid dysfunction and diabetes mellitus. The management paradigms have evolved from simple dietary restriction to precision nutrition approaches, integrating genetic profiling with individualized tolerance thresholds while preserving established health benefits of carotenoid-rich diets. Standard diagnostic criteria incorporate both biochemical thresholds and functional assessments, including the retinol:β-carotene molar ratio as a functional measure of BCO1 activity. Although traditionally considered benign, hypercarotenemia serves as a valuable biomarker for underlying metabolic dysfunction and genetic variants affecting fat-soluble vitamin homeostasis, warranting clinical attention for risk stratification and personalized dietary counseling.},
}

@article {pmid41246705,
year = {2025},
author = {Chohan, PK and Brunhammer, E},
title = {Self-Directed Recovery of Gu Syndrome: Reversal of Multisystem Dysfunction via Microbiome Restoration and Subconscious-Guided Protocols.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94595},
doi = {10.7759/cureus.94595},
pmid = {41246705},
issn = {2168-8184},
abstract = {This case report documents a self-directed recovery from a complex, chronic multisystem condition consistent with Gu syndrome, involving Candida overgrowth, dysbiotic flora consistent with small intestinal bacterial overgrowth (SIBO), mold toxicity, intestinal hyperpermeability (leaky gut), and significant microbiome disruption. A 38-year-old male developed multiple symptoms after a trip to a developing country. His initial symptoms included excessive fatigue and weight gain, followed by multisystem involvement. Laboratory testing was positive for Candida albicans, dysbiotic flora consistent with SIBO, leaky gut, and mold toxicity. Management included dietary interventions, targeted supplementation, and intuitive subconscious guidance. The patient had a marked improvement in the clinical symptoms, physical and metabolic performance markers through a phased terrain-based recovery protocol and minimal pharmaceutical intervention. This case illustrates a novel integration of intuitive recovery and functional medicine with application for microbiome-centered therapeutic models.},
}

@article {pmid41246557,
year = {2026},
author = {Zhou, X and An, R and Li, X},
title = {Cervical cancer immune microenvironment: Mechanisms of HPV-mediated immune evasion and advances in immunotherapy (Review).},
journal = {Oncology letters},
volume = {31},
number = {1},
pages = {22},
doi = {10.3892/ol.2025.15375},
pmid = {41246557},
issn = {1792-1082},
abstract = {Cervical cancer, strongly associated with persistent infection by high-risk human papillomaviruses 16/18 (HPV 16/18), remains a major global health burden. The tumor immune microenvironment (TIME) of cervical cancer plays a decisive role in tumor progression and therapeutic outcomes, where HPV oncoproteins E5, E6 and E7 disrupt antigen presentation, interfere with interferon signaling, activate immune checkpoints and induce metabolic reprogramming, thereby establishing an immunosuppressive TIME. Therapeutic advances, including immune checkpoint inhibitors (e.g., pembrolizumab in KEYNOTE-826, nivolumab in CheckMate 358), therapeutic vaccines and adoptive cell therapies, have shown promise but face challenges such as low response rates, resistance, stromal barriers and microbiome-related influences. The aim of the present review is to summarize the current understanding of the cervical cancer TIME, elucidate HPV-mediated immune evasion mechanisms, and to highlight recent advances and ongoing challenges in immunotherapy. Future directions include combination strategies, novel immune targets, and precision approaches integrating spatial multi-omics and microbiota modulation, which may improve immunotherapy efficacy and support personalized treatments for cervical cancer.},
}

@article {pmid41246320,
year = {2025},
author = {Dey, P},
title = {Genes, guts, and microbes: decoding host-driven microbial regulation using intestine-specific conditional knockouts.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1674913},
doi = {10.3389/fimmu.2025.1674913},
pmid = {41246320},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Humans ; Dysbiosis ; Mice, Knockout ; *Intestines/microbiology/immunology ; *Intestinal Mucosa/metabolism/microbiology/immunology ; *Host Microbial Interactions/genetics ; Mice ; },
abstract = {This narrative review underscores the influence of host genetics in actively regulating gut microbiota composition and function, highlighting the distinctive advantages of intestine-specific conditional knockout (cKO) models in gut microbiome research. In contrast to whole-body knockouts or germ-free animals, these precision models, enabled by Cre-loxP technology, eliminate confounding systemic effects to elucidate how localized host genes within intestinal cells regulate the gut microbial ecology. The review identifies three fundamental host-driven regulatory mechanisms through the analysis of specific gene deletions: (1) barrier integrity (e.g., mucus and junction proteins), (2) immune defenses (e.g., antimicrobial peptides and glycan synthesis), and (3) metabolic signaling (e.g., bile acid receptors and glucose transporter). These pathways jointly impose microbial symbiosis, and their disruption leads to dysbiosis characterized by increased abundance of pathobionts (e.g., Escherichia, Proteobacteria), directly connecting host genetics to inflammatory and metabolic disorders. This host-centric viewpoint emphasizes the gut as an active regulator, rather than a passive microenvironment for the microbiota, providing significant insights for creating tailored therapeutics that focus on host pathways to restore microbial balance in disorders such as inflammatory bowel diseases.},
}

Animals
*Gastrointestinal Microbiome/immunology/genetics
Humans
Dysbiosis
Mice, Knockout
*Intestines/microbiology/immunology
*Intestinal Mucosa/metabolism/microbiology/immunology
*Host Microbial Interactions/genetics
Mice

@article {pmid41246313,
year = {2025},
author = {Xiong, J and Li, J and Xu, H and Li, Y and Lu, L and Yang, S},
title = {Microbiome and metabolomics analyses of the effect of heat-sensitive moxibustion on allergic rhinitis in rats.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1656060},
doi = {10.3389/fimmu.2025.1656060},
pmid = {41246313},
issn = {1664-3224},
mesh = {Animals ; *Moxibustion/methods ; *Rhinitis, Allergic/therapy/metabolism/microbiology/immunology ; Rats ; Rats, Sprague-Dawley ; *Metabolomics/methods ; *Gastrointestinal Microbiome ; Male ; Disease Models, Animal ; Hot Temperature ; Acupuncture Points ; },
abstract = {BACKGROUND: The original concept of acupoint sensitization theory was put forward in Huangdi Neijing, which believed that acupoints, as the reflecting parts of the body surface, are personalized, changeable, and sensitive. Heat-sensitive moxibustion has a good therapeutic effect on allergic rhinitis, but the mechanism is still unclear. Notably, acupoint sensitization in allergic rhinitis (AR) rats was accompanied by a distal thermal effect, with an increase in tail temperature (TTI) after 40 min of moxibustion.

OBJECTIVE: The objective was to utilize multi-omics techniques and correlation analysis to explore the unique mechanisms of heat-sensitive moxibustion in intervening in AR compared with traditional moxibustion from the perspectives of gut microbiota and metabolites.

METHODS: Thirty-six Sprague-Dawley (SD) rats were randomly divided into two groups: the ovalbumin (OVA) group (n = 27) and the control group (Con) (n = 9). The rat model of AR induced by standardized OVA was established through intranasal infusion after intraperitoneal OVA injection. Through behavioral scoring, nasal symptoms were evaluated, including nasal scratching, runny nose, and sneezing, to ensure the success of the modeling. The OVA group was randomly divided into the moxibustion group (n = 17) and the AR group (n = 8). Then, through suspended moxibustion for 40 min, they were divided into TTI, namely, the heat-sensitive moxibustion group (HM) (n = 8) and the non-TTI group (OM) (n = 8), and one subject was excluded. The levels of serum IL-4 and IgE were quantified by enzyme-linked immunosorbent assay (ELISA), and the histological characteristics of nasal tissues were evaluated by hematoxylin and eosin (H&E) staining to determine the reliability of the AR rat model and the effectiveness of thermal sensitization. The V3 and V4 regions of the 16S ribosomal DNA (rDNA) gene were analyzed from rat feces using 16S rDNA sequencing technology. In addition, non-targeted metabolomics was used to identify the differential metabolites in rat urine. Finally, through the comparison and correlation analysis of different bacterial microbiota and metabolites, we aimed to clarify the unique material basis of heat-sensitive moxibustion in the context of AR.

RESULTS: After the OVA modeling was completed, through behavioral score evaluation, we found that there were differences between the OVA group and the control group. After the intervention treatment, it was found that the levels of IgE and IL-4 in the AR group were significantly higher than those in the control group. Staining showed that moxibustion relieved nasal symptoms, and the thermal sensitization effect was satisfactory. We noticed that significant changes occurred in the flora under heat-sensitive moxibustion treatment. We investigated the mechanism of HM in treating AR using an integrated 16S rRNA sequencing technology and untargeted metabolomics. Our results showed that HM treatment ameliorated AR in rats. The high-throughput sequencing results indicate that HM significantly increased the relative abundance of species, such as Patescibacteria, Saccharimonadaceae, UCG-010, Butyrivibrio, Turicibacter, Lactobacillus murinus, and Adlercreutzia, while decreasing the relative abundance of Prevotellaceae. This shift in microbial composition is conducive to improving the gut microbiota of AR rats. Untargeted metabolomics results showed that HM treatment regulated the metabolites such as 1-methylhistidine, xi-3-hydroxy-5-phenylpentanoic acid O-beta-d-glucopyranoside, cladosporin, cuminaldehyde, daidzein, Pe(18:0/15:0), N-nervonoyl asparagine, edulitine, N-arachidonoyl glycine, 9alpha-(3-methyl-2E-pentenoyloxy)-4S-hydroxy-10(14)-oplopen-3-one, quisqualic acid, ethyl glucuronide, zileuton O-glucuronide, trichloroethanol glucuronide, Asp Leu Ser Glu, quinolinic acid, and norvaline. We finally identified six crossing pathways by pin-to-pair comparison of three groups: glutamatergic synapse, dopaminergic synapse, Kaposi sarcoma-associated herpesvirus infection, cocaine addiction, melanin production, alcoholism, and histidine metabolism. Subsequently, we focused on studying the histidine metabolism. To clarify the changes in the activity of this pathway, we measured the histamine content using an enzyme-linked immunosorbent assay. Compared with the OM group, we found that HM had a trend toward superior efficacy in reducing tissue histamine compared to OM. The histamine content in the HM group was significantly lower than that in the OM group. This finding suggests that HM is more effective in reducing histamine, and its effect may be related to a more efficient regulation of the histidine metabolic pathway.

CONCLUSIONS: This study demonstrates that heat-sensitive moxibustion alleviates allergic rhinitis through a multi-targeted mechanism involving both the modulation of specific gut microbiota (notably L. murinus, Patescibacteria, Butyrivibrio, and Turicibacter)-which is closely associated with alterations in key metabolites (cuminaldehyde and 1-methylhistidine)-and the regulation of histidine metabolism. To our knowledge, this represents the first investigation to establish comprehensive correlations between gut microbiota and urinary metabolomics profiles in an AR model. Our findings confirm the therapeutic role of heat-sensitive moxibustion in AR recovery and provide mechanistic insights supporting its clinical application, thereby proposing a novel strategic approach for AR treatment.},
}

Animals
*Moxibustion/methods
*Rhinitis, Allergic/therapy/metabolism/microbiology/immunology
Rats
Rats, Sprague-Dawley
*Metabolomics/methods
*Gastrointestinal Microbiome
Male
Disease Models, Animal
Hot Temperature
Acupuncture Points

@article {pmid41246300,
year = {2025},
author = {Liu, J and Fu, R and Su, Y and Li, Z and Huang, X and Wang, Q and Shi, Z and Wei, S},
title = {Applications of artificial intelligence in cancer immunotherapy: a frontier review on enhancing treatment efficacy and safety.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1676112},
doi = {10.3389/fimmu.2025.1676112},
pmid = {41246300},
issn = {1664-3224},
mesh = {Humans ; *Artificial Intelligence ; *Neoplasms/therapy/immunology ; *Immunotherapy/methods/adverse effects ; Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; Animals ; Treatment Outcome ; },
abstract = {Cancer immunotherapy represents a major breakthrough in oncology, particularly with immune checkpoint inhibitors (ICIs) and CAR-T cell therapies. Despite improved outcomes, challenges such as immune-related adverse events (irAEs) and treatment resistance limit clinical use. Artificial intelligence (AI) offers new opportunities to address these barriers, including target identification, efficacy prediction, toxicity monitoring, and personalized treatment design. This review highlights recent advances in AI applications for biomarker discovery, safety evaluation, gene editing, nanotechnology, and microbiome modulation, integrating evidence from clinical and preclinical studies. We also discuss future directions and challenges in applying AI to cancer immunotherapy, aiming to support further research and clinical translation.},
}

Humans
*Artificial Intelligence
*Neoplasms/therapy/immunology
*Immunotherapy/methods/adverse effects
Immune Checkpoint Inhibitors/therapeutic use/adverse effects
Animals
Treatment Outcome

@article {pmid41246295,
year = {2025},
author = {Yartey, SN and Awere-Duodu, A and Asantewaa, AA and Donkor, ES},
title = {Antibiotic impact on human microecology in low- and middle-income countries: a systematic age-stratified review of gut and respiratory microbiome and resistome.},
journal = {Therapeutic advances in infectious disease},
volume = {12},
number = {},
pages = {20499361251389738},
doi = {10.1177/20499361251389738},
pmid = {41246295},
issn = {2049-9361},
abstract = {BACKGROUND: Antibiotic exposure disrupts microbial communities in the gut and respiratory tract, causing functional changes that may have lasting health impacts and contribute to the spread of antibiotic resistance genes (ARGs) throughout life. However, age-stratified evidence of these effects, particularly in low- and middle-income countries (LMICs), remains limited.

OBJECTIVE: This systematic review assessed the impact of antibiotics on gut and respiratory microbiomes and resistomes in LMICs, with separate analyses for adults and children.

DATA SOURCES: PubMed, Scopus, Web of Science, & ScienceDirect.

METHODS: A comprehensive literature search was conducted using a predefined search strategy and eligibility criteria to identify relevant studies from LMICs. Twenty-five studies met the inclusion criteria: 23 examined the gut microbiome, and 2 focused on the respiratory microbiome. Key outcomes included microbial diversity (alpha/beta/gamma), taxonomic shifts, resistome profiles, functional changes, and recovery potentials, stratified by age group and body site.

RESULTS: Antibiotic exposure was generally associated with reductions in microbial diversity and altered taxonomic composition, with children showing more pronounced and prolonged disruptions than adults. Analysis of resistome changes revealed a critical finding: while antibiotics consistently selected for ARGs matching the drug class administered, a substantial reservoir of non-matching, background ARGs, conferring resistance to beta-lactams, aminoglycosides, vancomycin, tetracyclines, was also highly prevalent across studies. This indicates a silent pre-existing resistome that is enriched by antibiotic pressure. ARGs were more abundant in adult resistomes, though functional changes occurred across age groups. Microbiome recovery was observed over time, but resistome recovery was limited.

CONCLUSION: Antibiotic use significantly disturbs the gut and respiratory microbiomes and promotes ARG enrichment, especially in children, who demonstrate greater susceptibility and lower recovery potential. These findings emphasise the need for targeted antibiotic stewardship, improved microbiome recovery research, and enhanced resistome monitoring in LMICs.

TRAIL REGISTRATION: International Prospective Register of Systematic Reviews (PROSPERO), ID: CRD420250641394.},
}

@article {pmid41246285,
year = {2025},
author = {Ahmed, N and Gaur, V and Kamle, M and Chauhan, A and Chauhan, R and Kumar, P and Singh, NA},
title = {Microbiome-based therapeutics for metabolic disorders: harnessing microbial intrusions for treatment.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1695329},
doi = {10.3389/fmedt.2025.1695329},
pmid = {41246285},
issn = {2673-3129},
abstract = {The rising global rates of metabolic disorders, such as obesity, type 2 diabetes, non-alcoholic fatty liver disease, and metabolic syndrome, call for new treatment methods beyond traditional drugs. The human gut microbiota, made up of trillions of microorganisms that plays a crucial role in maintaining metabolic balance through complex biochemical processes and interactions between hosts and microbes. Dysbiosis, which involves changes in microbial composition and a decrease in diversity, has become a major factor in metabolic problems. This disruption impacts the production of short-chain fatty acid, increase in permeability of intestine, and causes enduring low-grade inflammation. This review features into the potential of treatments based on microbiome for metabolic syndromes, focusing on probiotics, prebiotics, synbiotics, and postbiotics. It also encompasses innovative methods such as engineered microbial consortium, fecal microbiota transplantation (FMT), and vaginal microbiota transplantation (VMT). Probiotics show significant promise in improving blood sugar control and enhancing lipid levels. Prebiotics help bring about positive changes in microbial composition and the production of beneficial metabolites. Synbiotic combinations provide added benefits by helping good microbes thrive while supplying nutrients they can ferment. Postbiotics have recent research focus because they are safer, more stable, easier to store, and less likely to contribute to antibiotic resistance comparative to live probiotics. Even now there are substantial complications in translating microbiome research into standardized therapeutics despite of promising pre-clinical outcomes and some initial clinical data. These comprises individual variances, strain-specificity, dosage problems, regulation issues, and the necessity for personalised treatment strategies. Future success will depend upon personalized medicine, technological developments, and the incorporation of multi-omics strategy to generate metabolic health therapeutics depending on targeted microbiomes.},
}

@article {pmid41246281,
year = {2025},
author = {Jeong, M and Park, S and Jeong, S and Park, S and Yeo, S and Ryu, B and Shin, JH and Lee, S},
title = {Multi-omics insights into plant-microbe dysbiosis caused by cyanobacterial bloom-affected water.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100500},
doi = {10.1016/j.crmicr.2025.100500},
pmid = {41246281},
issn = {2666-5174},
abstract = {The use of untreated, cyanobacterial bloom-affected river water as a readily available source for crop production is a realistic scenario in many regions, yet its systemic impact on crop health remains poorly defined. Here, we investigate the multifaceted effects of this practice by cultivating lettuce (Lactuca sativa) with bloom-season water from the eutrophic Nakdong River and comparing it to lettuce grown in a nutrient-optimized hydroponic solution. We found that exposure to bloom-affected water severely inhibited plant growth and led to the accumulation of microcystins in edible tissues, with estimated daily intakes exceeding WHO safety thresholds. Multi-omics analyses revealed that this phenotype was driven by a synergistic failure of internal and external support systems: key mitochondrial genes for energy production were downregulated, protective antioxidant flavonoids were depleted, and the aquatic microbiome shifted to a dysbiotic state that favored stress-tolerant taxa while reducing beneficial ones. Together, these results establish how bloom-affected water initiates a vicious cycle of physiological stress and microbial dysbiosis that undermines crop health. This study provides an integrative framework for assessing risks in real-world hydroponic systems and for guiding future investigations into more complex soil-based agriculture.},
}

@article {pmid41246271,
year = {2025},
author = {Liu, M and Wen, X and Feng, M and Sun, Y and Feng, X and Jin, T and Liu, B and Muhammad, S and Liu, K and Cheng, J and Li, J},
title = {Evaluation of Lactiplantibacillus plantarum CRS 33 to therapeutic effects on a murine model of Escherichia coli-induced endometritis.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1608791},
doi = {10.3389/fvets.2025.1608791},
pmid = {41246271},
issn = {2297-1769},
abstract = {INTRODUCTION: Bovine endometritis is a common postpartum uterine disease in dairy cows that is traditionally treated with antibiotics. However, excessive antibiotic use can lead to antimicrobial resistance and treatment failure. Lactiplantibacillus plantarum CRS33, a novel probiotic strain isolated from the uterus of a healthy cow, exhibits strong antibacterial potential. This study aimed to investigate the probiotic characteristics of Lactiplantibacillus plantarum CRS33 through whole-genome sequencing and to evaluate its anti-inflammatory effects in a mouse model of Escherichia coli-induced endometritis.

METHODS: Whole-genome sequencing was performed to identify genes related to antibacterial, anti-inflammatory, and immune-regulatory activities, and to confirm the absence of antibiotic resistance and virulence genes. Female mice were induced with Escherichia coli endometritis and treated with Lactiplantibacillus plantarum CRS33 at a dose of 1 × 10[⁹] CFU/mL. Uterine morphology, wet weight index, inflammatory cell infiltration, cytokine levels (IL-6, IL-1β, IL-8, TNF-α), and uterine microbiota composition were analyzed.

RESULTS: Genomic analysis revealed that Lactiplantibacillus plantarum CRS33 contains multiple functional genes related to antimicrobial, anti-inflammatory, and immune-modulatory pathways and lacks antibiotic resistance or pathogenic determinants. Treatment with Lactiplantibacillus plantarum CRS33 significantly alleviated uterine inflammation, reduced the wet weight index (p < 0.05), and improved histopathological lesions. It also decreased pro-inflammatory cytokine levels and inflammatory cell infiltration, while enhancing microbial diversity and increasing the abundance of beneficial bacterial taxa.

DISCUSSION: Lactiplantibacillus plantarum CRS33 demonstrates strong anti-inflammatory and microbiota-regulating properties in Escherichia coli-induced endometritis, highlighting its potential as a safe and effective probiotic alternative to antibiotics. Further validation in dairy cows is warranted to confirm its therapeutic potential under practical conditions.},
}

@article {pmid41246144,
year = {2025},
author = {Kayashima, A and Fukuhara, S and Miyamoto, K and Iwasaki, E and Kato, M and Sujino, T},
title = {Biliary stents reshape the bile microbiome in the absence of cholangitis.},
journal = {Endoscopy international open},
volume = {13},
number = {},
pages = {a27333468},
doi = {10.1055/a-2733-3468},
pmid = {41246144},
issn = {2364-3722},
abstract = {BACKGROUND AND STUDY AIMS: Biliary stents are widely used in endoscopic retrograde cholangiopancreatography (ERCP), yet their impact on the native bile microbiome under non-infectious conditions remains unclear. We aimed to characterize stent-associated alterations in the biliary microbiome using 16S rRNA gene sequencing.

PATIENTS AND METHODS: We analyzed bile samples collected during ERCP from 35 patients without clinical or laboratory evidence of acute cholangitis. Patients were categorized into a control group (n = 25; naïve papillae) and an endoscopic biliary stenting (EBS) group (n = 10; previously stented). Microbial composition was assessed using high-throughput 16S rRNA sequencing after propensity score matching to balance background characteristics.

RESULTS: Beta diversity differed significantly between groups (PERMANOVA, P < 0.01), despite no significant differences in alpha diversity. The EBS group demonstrated increased relative abundance of Firmicutes and Fusobacteriota , and depletion of Proteobacteria . Notably, Enterococcus was significantly enriched in the EBS group (log fold change 6.74; q < 0.01), whereas Sphingomonas was reduced.

CONCLUSIONS: Endoscopic biliary stenting is associated with distinct bile microbiome alterations, characterized by enrichment of Enterococcus species in clinically stable patients. These findings suggest that stents may predispose to opportunistic colonization, providing a potential mechanistic link to future cholangitis. Recognizing such preclinical dysbiosis may inform tailored antimicrobial strategies and future stent design.},
}

@article {pmid41246092,
year = {2025},
author = {Jia, B and Wu, X and He, G and Wang, Q and Guan, L and Ren, J and Li, G and Zheng, X and Yang, S},
title = {Oral microbiome dysbiosis is associated with chronic respiratory diseases: evidence from a population-based study and a hospital cohort.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1696041},
doi = {10.3389/fpubh.2025.1696041},
pmid = {41246092},
issn = {2296-2565},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Microbiota ; *Dysbiosis/microbiology/epidemiology ; Adult ; *Mouth/microbiology ; RNA, Ribosomal, 16S ; Aged ; Cohort Studies ; Nutrition Surveys ; Chronic Disease ; *Respiratory Tract Diseases/microbiology/epidemiology ; },
abstract = {BACKGROUND: The oral microbiome has been increasingly recognized for its role in systemic health through the oral-lung axis. However, population-level evidence linking oral microbial diversity and composition with chronic respiratory diseases (CRD) remains limited.

METHODS: We analyzed data from 4,384 adults in the 2009-2012 National Health and Nutrition Examination Survey (NHANES), defining CRD by self-reported chronic obstructive pulmonary disease (COPD), asthma, emphysema, or chronic bronchitis. Oral rinse samples underwent 16S ribosomal RNA (16S rRNA) V1-V3 sequencing. Alpha diversity, including observed amplicon sequence variants (ASVs), Faith's phylogenetic diversity (Faith's PD), Shannon-Weiner index, and Simpson index, and beta diversity, including Bray-Curtis, weighted UniFrac, and unweighted UniFrac distances, were assessed. Associations with CRD were examined using weighted logistic regression and restricted cubic splines (RCS). Differential genus abundance was identified by Wilcoxon tests with false discovery rate correction. A random forest model integrated microbial and clinical features. An independent hospital cohort was additionally profiled by 16S rRNA sequencing, and genus-level differences were assessed with linear discriminant analysis effect size (LEfSe) to validate NHANES findings.

RESULTS: Higher alpha diversity was inversely associated with CRD risk; each standard deviation increase in observed ASVs and Faith's PD reduced CRD odds by 19 and 17%, respectively (p < 0.05). Beta diversity showed significant community-level separation by CRD status (p = 0.01). Several genera, including Rothia and Veillonella, were enriched in CRD, whereas Prevotella, Haemophilus, and Neisseria were more abundant in non-CRD individuals. The random forest model achieved an area under the curve (AUC) of 0.65. In the hospital cohort, compositional shifts were consistent with NHANES findings, and LEfSe confirmed the depletion of Alloprevotella and Peptostreptococcus in CRD patients.

CONCLUSION: Oral microbial diversity and composition were significantly associated with CRD across both a representative U. S. population and a hospital cohort. Select genera and diversity indices may serve as non-invasive biomarkers for respiratory health, warranting further validation in longitudinal and mechanistic studies.},
}

Humans
Male
Female
Middle Aged
*Microbiota
*Dysbiosis/microbiology/epidemiology
Adult
*Mouth/microbiology
RNA, Ribosomal, 16S
Aged
Cohort Studies
Nutrition Surveys
Chronic Disease
*Respiratory Tract Diseases/microbiology/epidemiology

@article {pmid41245977,
year = {2025},
author = {Humińska-Lisowska, K and Łabaj, PP and Zielińska, K},
title = {Unique Athletic Gut Microbiomes and Their Role in Sports Performance: A Narrative Review.},
journal = {Journal of human kinetics},
volume = {99},
number = {},
pages = {79-97},
doi = {10.5114/jhk/202642},
pmid = {41245977},
issn = {1640-5544},
abstract = {The human gut microbiome, a diverse community of microorganisms, plays a crucial role in digestion, metabolism, immune function, and brain health. Key metabolites produced by the gut microbiota, such as short-chain fatty acids (SCFAs) and bile acids, are essential for energy production, metabolic regulation, and immune system modulation. The gut microbiome's composition is influenced by factors including diet, exercise, sleep, and age, and disruptions are linked to various health conditions. Elite athletes exhibit unique gut microbiota profiles that contribute to their exceptional performance and recovery. Their microbiomes are not only richer, but also possess unique microorganisms and functional capabilities, alongside distinct genetic landscapes that support their high-level physiological demands. This review focuses specifically on the athletic gut microbiome, exploring how it differs from that of an active or a sedentary individual, adapts to different training phases, extreme conditions like heat and hypoxia, and prolonged exertion. It highlights the dual role of the gut microbiome in both enhancing athletic performance and potentially contributing to disease development, particularly due to the prolonged exertion and stress associated with years of intense competition. The review also explores the implications of microbiome changes following periods of intense physical activity and their impact on the athlete's overall health. Finally, it evaluates athlete-specific interventions, including prebiotics, probiotics, and synbiotics, aimed at mitigating negative effects on the gut microbiome while supporting health and optimizing performance.},
}

@article {pmid41245891,
year = {2025},
author = {Yang, Q and Cai, Y and Guan, Y and Wang, Z and Guo, S and Qiu, S and Zhang, A},
title = {Metabolic phenotypes: Molecular bridges between health homeostasis and disease imbalance.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {4710-4719},
doi = {10.1016/j.csbj.2025.10.057},
pmid = {41245891},
issn = {2001-0370},
abstract = {Metabolic phenotypes represent the overall characterization of an individual's metabolites at a specific point in time. They precisely reflect the complex interactions among genetic background, environmental factors, lifestyle, and gut microbiome, thereby serving as a key molecular link between healthy homeostasis and disease-related metabolic disruption. In recent years, high-throughput metabolomics strategies have enabled the systematic analysis of small molecule metabolites in physiological and pathological processes. These metabolites not only serve as biomarkers for disease diagnosis, prognosis assessment, and treatment response prediction, but also elucidate novel mechanistic pathways in disease progression. The high-coverage, high-sensitivity detection of metabolites afforded by mass spectrometry and NMR-based metabolomics enables advances in precision medicine, facilitating biomarker discovery, pharmacokinetic studies, and the assessment of nutritional interventions. This review uses several common metabolic diseases, such as obesity, diabetes, cardiovascular diseases, and cancer, to explore the key role of metabolic phenotypes in disease risk stratification and precise prediction. Future phenotypic research will shift toward integrating artificial intelligence, big data mining, and multi-omics with the goal of revealing the complete network through which metabolic phenotypes regulate diseases. This research is expected to advance early diagnosis, precise prevention, and targeted treatment, contributing to a medical paradigm shift from disease treatment to health maintenance.},
}

@article {pmid41245847,
year = {2025},
author = {Sopirala, MM and Weber, D and Sood, G and Yassin, M and Palmieri, TL and Narasimhan, S and Sheckter, C and Caffrey, J and Mandell, S and Pisney, L and Kandiah, S and Somani, J and Mackow, N and Brust, K and Karaba, S and Doll, M and Chen, D and Abbo, L and Bischoff, W},
title = {A research agenda for burn infection prevention: identifying knowledge gaps and prioritizing future directions.},
journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE},
volume = {5},
number = {1},
pages = {e293},
doi = {10.1017/ash.2025.10213},
pmid = {41245847},
issn = {2732-494X},
abstract = {OBJECTIVE: Burn injuries result in loss of skin barrier and altered immune responses that in turn make patients especially vulnerable to healthcare-associated infections. Despite prolonged exposures of these patients to hospital environments, burn-specific infection prevention strategies are understudied. We present a research agenda identifying key research gaps and organizing them into priority areas to guide future investigations in this high-risk population.

DESIGN: Members of the Society for Healthcare Epidemiology of America (SHEA) Burn Infection Prevention and Control Special Interest Group and the American Burn Association (ABA) collaborated to develop this research agenda, combining expertise in infection prevention, antimicrobial stewardship, and burn care.

RESULTS: We identified five priority areas: (1) improving surveillance and epidemiologic data on burn infections; (2) better understanding of microbiology, including biofilms and the microbiome; (3) evaluating wound healing strategies; (4) refining infection prevention and control practices unique to burn units; and (5) building burn patient specific risk assessment and predictive models. The agenda highlights the need for standardized definitions and shared data platforms. It calls for evaluation of practical strategies for infection prevention, stewardship, and environmental control.

CONCLUSIONS: This research agenda intends to help guide future studies aimed at furthering knowledge and improving outcomes in burn care.},
}

@article {pmid41245833,
year = {2025},
author = {Ilie, OD and Văcărean-Trandafir, IC and Amărandi, RM and Nita, IB and Dobrin, PR and Doroftei, M and Ivanov, IC and Savuta, G and Kirov, B and Doroftei, B},
title = {Exploring gut microbiota alterations in Parkinson's disease: insights from a 16S amplicon sequencing Eastern European pilot study.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1654995},
doi = {10.3389/fnins.2025.1654995},
pmid = {41245833},
issn = {1662-4548},
abstract = {INTRODUCTION: Parkinson's disease (PD) is a neurodegenerative disorder increasingly associated with alterations in gut microbiota through the gut-brain axis (GBA). Despite growing global interest, studies examining microbiota composition in Eastern European populations remain limited.

METHODS: We profiled the gut microbiota of 59 Romanian individuals using 16S rRNA gene sequencing targeting the V3-V4 region. After quality filtering, 39 subjects (19 PD patients and 20 healthy controls [HC]) were retained for downstream analysis. Clinical metadata were collected to assess potential confounders, including age, sex, metabolic parameters, lifestyle, and comorbidities.

RESULTS: PD patients differed significantly from HCs in glycemia (p = 0.02), cholesterol (p = 0.027), and LDL levels (p = 0.047), and more frequently presented with restrictive diets and comorbidities such as cardiovascular disease and diabetes. While α-diversity metrics did not differ significantly between groups, principal coordinate analysis (PCoA) based on Aitchison distance showed moderate compositional separation. Permutational multivariate analysis of variance (PERMANOVA) confirmed that disease status was a significant driver of gut microbiota composition (R [2] = 5.3%, p = 0.002), independent of clinical and lifestyle covariates. Sparse partial least square linear discriminant (sPLS-DA) identified several genera distinguishing PD from HC, with Mogibacterium and RikenellaceaeRC9 gut group enriched in PD, and several known short-chain fatty acid (SCFA)-producing genera (Fusicatenibacter, Lachnospiraceae UCG-001, Butyricicoccus, Anaerostipes) enriched in HCs. Linear discriminant analysis (LDA) Effect Size (LEfSe) corroborated these findings, confirming the differential abundance of several SCFA-producing genera in the HC group.

DISCUSSION: Our results reveal distinct microbial signatures associated with PD in this Romanian cohort, marked by a consistent depletion of SCFA-producing bacteria in patients. These findings support the role of gut microbiota in PD pathophysiology and underscore the need for further studies in Eastern European populations.},
}

@article {pmid41245385,
year = {2025},
author = {Lee, C and Feuerstadt, P and Louie, T and Bancke, L and Guthmueller, B and Harvey, A and Hoeyer, F and Orenstein, R and Dubberke, ER and Khanna, S},
title = {Integrated analysis of the safety of fecal microbiota, live-jslm in adults with recurrent Clostridioides difficile infection from five prospective clinical trials: an update.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251395566},
doi = {10.1177/17562848251395566},
pmid = {41245385},
issn = {1756-283X},
abstract = {BACKGROUND: Fecal microbiota, live-jslm (RBL) is approved in the United States and Canada for prevention of recurrent Clostridioides difficile infection (rCDI) in adults following standard-of-care (SOC) antibiotic treatment.

OBJECTIVES: Provide an updated integrated safety analysis, incorporating final safety data from Punch CD3-OLS.

DESIGN: Safety data were combined from five RBL trials: three phase II and two phase III trials.

METHODS: Adult participants had documented rCDI and completed SOC therapy before receiving one or two doses of RBL or placebo, rectally administered as one treatment course. Treatment-emergent adverse events (TEAEs) were recorded for ⩽6 months.

RESULTS: TEAEs were reported in 70.9% (845/1192) of RBL recipients; most TEAEs were mild to moderate and gastrointestinal in nature. Most serious TEAEs were related to preexisting conditions or CDI. There was no clustering of serious TEAEs. Most TEAEs leading to death were related to preexisting conditions.

CONCLUSION: Overall, data demonstrate RBL has a favorable 6-month safety profile.

TRIAL REGISTRATION: ClinicalTrials.gov: NCT01925417; NCT02299570; NCT02589847; NCT03244644; NCT03931941.},
}

@article {pmid41245267,
year = {2025},
author = {Makkar, SK and Bishnupuri, KS},
title = {The gut microbiome and gastrointestinal cancers: mechanisms, biomarkers and therapeutic opportunities.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1676796},
doi = {10.3389/fphys.2025.1676796},
pmid = {41245267},
issn = {1664-042X},
abstract = {Gastrointestinal (GI) cancers remain a leading global cause of cancer-related mortality, significantly impacting public health and healthcare systems worldwide. Emerging evidence underscores the critical role of gut microbiome dysbiosis-characterized by disrupted microbial diversity and function-in GI carcinogenesis. Utilizing recent advancements in multi-omics technologies and sophisticated computational biology, researchers have elucidated distinct microbial signatures associated with colorectal, gastric, hepatobiliary, pancreatic, and esophageal cancers. This review comprehensively analyzes the primary mechanisms through which gut microbes contribute to cancer development and progression, encompassing genotoxicity, chronic inflammation, metabolic dysregulation, epigenetic modifications, and immunomodulation. Moreover, we explore innovative microbiome-derived biomarkers for potential clinical applications, including early diagnosis, prognosis assessment, and therapeutic response prediction. The intricate interactions between microbiota and standard cancer therapies-chemotherapy, immunotherapy, and radiation therapy-are discussed, highlighting microbiome influences on therapeutic efficacy and adverse effect profiles. We also critically assess the impact of modifiable factors such as diet, medications, lifestyle, and environmental exposures on microbiome composition and cancer risk. The review evaluates emerging therapeutic interventions, including dietary modifications, probiotics, prebiotics, fecal microbiota transplantation (FMT), and engineered live biotherapeutics. Despite notable advancements, significant hurdles remain, including clarifying causality, methodological standardization, and equitable global research representation. Addressing these challenges, we propose a strategic research agenda aimed at harnessing microbiome insights to advance precision oncology and improve GI cancer outcomes globally.},
}

@article {pmid41245018,
year = {2025},
author = {Sun, T and Kenyon, V and Valitutti, F and Fasano, A and Martin, V and Leonard, MM},
title = {Rates of parent-reported allergic conditions in children at-risk of celiac disease.},
journal = {JPGN reports},
volume = {6},
number = {4},
pages = {480-484},
doi = {10.1002/jpr3.70079},
pmid = {41245018},
issn = {2691-171X},
abstract = {Allergies and other chronic immune mediated conditions are becoming increasingly common. Here we utilized a prospective birth cohort called the Celiac Disease Genomic Environmental Microbiome and Metabolomic (CDGEMM) study to examine the frequency of parent reported allergic conditions and their association with celiac disease (CeD). We examined 271 children at-risk of CeD from the United States and found a high frequency of allergic conditions. In our overall cohort, 19.8% reported food protein-induced allergic proctocolitis (FPIAP), 12.5% reported IgE-mediated food allergy, and 14.7% reported atopic dermatitis. Among the 23 children with CeD, 21.74% had FPIAP, 8.7% had an IgE-mediated food allergy, and 21.74% had atopic dermatitis. No significant association between allergic conditions and CeD was found (p > 0.35 for all). These results highlight the widespread occurrence of parent-reported allergic conditions in children but do not suggest an association between allergic conditions and CeD development.},
}

@article {pmid41244711,
year = {2025},
author = {Andac-Aktas, AB and Calibasi-Kocal, G},
title = {Immunological landscape of colorectal cancer: tumor microenvironment, cellular players and immunotherapeutic opportunities.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1687556},
doi = {10.3389/fmolb.2025.1687556},
pmid = {41244711},
issn = {2296-889X},
abstract = {Colorectal cancer (CRC) remains one of the most lethal malignancies worldwide, with outcomes shaped not only by genetic alterations but also by the complexity of the tumor microenvironment (TME). The TME encompasses stromal and endothelial cells, extracellular matrix components, gut microbiota, and a diverse array of immune cells that dynamically interact to influence tumor initiation, progression, and therapeutic response. This review delineates the immunological landscape of CRC, highlighting the dual functions of innate immune cells-including tumor-associated macrophages, natural killer cells, dendritic cells, neutrophils, and mast cells-and adaptive immune players such as cytotoxic T lymphocytes, helper T-cell subsets, and B/plasma cells. These cellular interactions contribute to the heterogeneity between immunologically "hot" microsatellite instability-high (MSI-H) tumors, which are highly responsive to immunotherapy, and "cold" microsatellite-stable (MSS) tumors, which remain resistant. Key mechanisms of immune evasion, such as cancer immunoediting, checkpoint signaling, and exosome-mediated communication, are examined alongside prognostic tools like the Immunoscore that serve as biomarkers of immune infiltration. Emerging immunotherapeutic strategies, including checkpoint blockade, macrophage reprogramming, natural killer cell agonists, and microbiome modulation, are discussed with emphasis on both their promise and limitations in CRC management. By integrating current insights into immune-tumor interactions, the review underscores opportunities for developing personalized, TME-targeted interventions to improve CRC outcomes.},
}

@article {pmid41244696,
year = {2025},
author = {Belanche, A and Belzecki, G and Hernandez-Sanabria, E and Martínez-Fernandez, G and Ramos-Morales, E and de la Fuente, G},
title = {Editorial: Unravelling the unknown of the rumen microbiome: implications for animal health, productivity, and beyond.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720795},
doi = {10.3389/fmicb.2025.1720795},
pmid = {41244696},
issn = {1664-302X},
}

@article {pmid41244691,
year = {2025},
author = {Popowski, W and Domanowska, D and Koseski, D and Ostrowski, R and Zalewska, M and Małecka-Giełdowska, M and Łasica, A and Popowska, M},
title = {Analysis of the oral microbiome composition of healthy individuals and the in vitro antibacterial activity of platelet-rich fibrin from these individuals against oral pathogenic bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1691046},
doi = {10.3389/fmicb.2025.1691046},
pmid = {41244691},
issn = {1664-302X},
abstract = {Platelet-rich fibrin (PRF) is a platelet concentrate widely applied in various medical fields and is considered a valuable adjunct in tissue regeneration during surgical procedures. However, infections caused by biofilm-forming bacteria at surgical sites, combined with increasing antibiotic resistance, present a major clinical concern. Current research is focused on identifying alternative therapeutic strategies to improve infection control and promote wound healing. This study aimed to characterize the oral microbiome of healthy individuals and evaluate the in vitro antimicrobial properties of two PRF formulations. The antibacterial activity, along with its temporal dynamics at different initial bacterial concentrations, was assessed against Gram-negative bacteria (Escherichia coli, Porphyromonas gingivalis) and Gram-positive bacteria exhibiting diverse morphologies (Bacillus subtilis, Micrococcus luteus, Staphylococcus lentus, Enterococcus casseliflavus, Streptococcus mutans). Our results fill gaps in knowledge concerning the spectrum of PRF's antimicrobial activity, demonstrating efficacy against a range of opportunistic and pathogenic bacteria. Key findings include the absence of significant differences in oral microbiome composition between male and female participants, a lack of inhibitory effect of A-PRF against S. mutans, and a transient inhibitory effect against P. gingivalis observed only at low initial OD600 and within 24 h. These findings indicate that A-PRF therapy alone may not provide a sufficiently effective antibacterial effect in patients with oral infections, and that alternative or adjunctive therapeutic approaches should be considered in such cases.},
}

@article {pmid41244672,
year = {2025},
author = {Dubois, B and Delitte, M and Bragard, C and Legrève, A and Chandelier, A and Debode, F},
title = {Improving the profiling of wheat bacterial and fungal endophytic communities-a PCR clamping approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1690976},
doi = {10.3389/fmicb.2025.1690976},
pmid = {41244672},
issn = {1664-302X},
abstract = {BACKGROUND: Plant-associated endophytic microbial communities are an important source of biological diversity. To study them, efficient, robust, and standardized characterization methods are necessary. These communities are usually profiled using amplicon high-throughput sequencing (metabarcoding), but the large amount of host DNA often leads to substantial co-amplification of organellar sequences, thereby hampering accurate characterization. A promising solution is the use of PCR clamps, modified oligomers that block non-target DNA amplification. However, no practical guidelines are currently available to support their development, and no sets of clamps enabling comprehensive characterization of endophytic bacterial and fungal communities associated with wheat (Triticum aestivum ssp. aestivum) have been reported.

RESULTS: We developed PCR clamps to block wheat DNA co-amplification while targeting bacterial or fungal populations. For bacteria, two clamping strategies [blocking primers and peptide nucleic acid (PNA)] were evaluated on the 16S V5V7 region. The PNA exhibited superior efficiency (99.8% bacterial reads), whereas blocking primers still performed well (67-98%) and offered a cheaper alternative. The PNA approach was retained for subsequent designs due to its higher efficiency, and two additional PNAs targeting the 16S V4 region were designed to block chloroplast and mitochondrial DNA, respectively. The best results were achieved using both PNAs simultaneously, with 80% of reads being of bacterial origin. For fungi, two PNA clamps were designed targeting ITS1 and ITS2, leading to a substantial reduction in wheat DNA co-amplification, with up to 94 and 75% fungal reads obtained using the ITS1- and ITS2-targeting PNA, respectively. The results also highlighted that profiling endophytic communities without clamps risks significantly underestimating microbial diversity. Furthermore, four bacterial and fungal mock communities were created as tools for standardization and internal control, confirming that our clamps do not inhibit microbial DNA amplification.

CONCLUSION: Whereas amplifications without clamps yielded almost exclusively plant reads, the clamps developed here significantly increased the proportion of microbial reads. This in turn enhanced microbial diversity recovery and the reliability of conclusions drawn from endophytic community analyses. The methodology described provides a framework for clamp development that can be reproduced and adapted to any other host species.},
}

@article {pmid41244669,
year = {2025},
author = {Yuan, T and Chen, J and Yang, J and Li, L and Lu, S and Pu, J and Sun, Y and Lin, W and Lu, Y and Zhu, Z and Zheng, H and Xu, J},
title = {Species-level enterosignatures predict clinical phenotypes in chronic hepatitis B and causal triangulation of gut-metabolite-CHB interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683451},
doi = {10.3389/fmicb.2025.1683451},
pmid = {41244669},
issn = {1664-302X},
abstract = {Chronic hepatitis B (CHB) remains a significant global health challenge, with research indicating the gut microbiota's influence on disease progression, although investigations have primarily been limited to the genus level. This study conducted species-level research using the Human Gut Microbiome Analysis Database (HGMAD) to examine differences in gut microbiota between CHB patients and healthy controls (HC), to investigate enterotype associations with CHB, to assess the predictive capacity of enterosignatures for CHB phenotypes, and to determine causal relationships among gut microbiota, metabolites, and CHB. The cross-sectional investigation included 129 CHB patients and 58 HC, with fecal samples analyzed by 16S rRNA gene sequencing of the V3-V4 region. Significant differences in α-diversity and β-diversity (P < 0.05) were observed between the CHB and HC groups. Taxonomic analysis revealed that the high prevalent bacteria group was lower in CHB patients (61.15%) than in HC (98.05%), indicating increased gut microbiota heterogeneity in CHB. Among known bacterial species, pathogens showed higher prevalence in CHB patients (22.80% vs. 11.49%), with several potential enteropathogenic bacteria (e.g., Bacteroides fragilis and Haemophilus parainfluenzae) enriched in CHB. Dimensionality reduction and clustering analysis of gut microbiota in CHB patients revealed two distinct enterotypes: ET-P dominated by Prevotella and ET-B dominated by Bacteroides. ET-P demonstrated a correlation with elevated levels of hepatitis B virus (HBV) DNA, hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), CD4[+]T-cell count and CD8[+]T-cell count, and alpha-fetoprotein (AFP). The enterosignatures of ET-P and ET-B effectively predicted key clinical indicators: the area under the curve (AUC) was 0.78 (95% confidence interval [CI]: 0.69-0.86) for HBeAg levels, 0.86 (95% CI: 0.79-0.93) for HBV DNA levels, 0.75 (95% CI: 0.65-0.84) for AFP status, and 0.85 (95% CI: 0.77-0.92) for CD4[+]T-cell count status. Mendelian randomization (MR) analysis, integrating two gut-microbiota databases, provided genetic evidence for causal relationships between 16 species-level gut microbes and CHB. An elevated abundance of Prevotella copri was associated with an increased risk of CHB (OR = 1.42, 95% CI: 1.01-2.00, P = 0.045). Additionally, mediation MR analyses revealed potential metabolite-mediated mechanisms underlying the role of gut microbiota in CHB. Two enterotypes were identified in CHB patients, ET-P demonstrated positive associations with HBV activity and viral load. The enterosignatures derived from both enterotypes effectively predicted key CHB clinical indicators, establishing causal links and potential underlying mechanisms between gut microbiota and CHB. These findings indicate that the gut microbiota maintains close connections to HBV infection, correlating with viral load, host immune status, and disease prognosis in hepatitis B.},
}

@article {pmid41244617,
year = {2025},
author = {Ma, ZS},
title = {Microbial Biomarkers of Breast Tumor and Mastitis: Deciphering the Delicate Balance between Potentially "Evil" and "Benign" Alliances in Mammary Microbiomes.},
journal = {Breast care (Basel, Switzerland)},
volume = {},
number = {},
pages = {},
doi = {10.1159/000548037},
pmid = {41244617},
issn = {1661-3791},
abstract = {INTRODUCTION: Breast cancer and mastitis significantly impact women's health and their infants' wellbeing. The advent of metagenomic sequencing technology has opened new avenues to explore the relationships between mammary microbiomes and these diseases. Despite recent extensive studies, detailed understanding of the mammary microbiome-disease relationships remains incomplete.

METHODS AND RESULTS: Here, we apply the Specificity and Specificity Diversity framework (Ma 2024, BMC Biology) to identify unique/enriched species (US/ES) associated with mastitis, breast cancer, or their healthy controls. The US/ES lists contain potential biomarkers and offer fresh insights into the intricacies of mastitis etiology and the relationship between breast tissue microbiomes and breast cancer.

CONCLUSIONS: (i) The dynamic balance between coexisting alliances of beneficial microbes and harmful microbes (including opportunistic pathogens) holds key to understanding mastitis etiology. (ii) Intra-tumor microbes may serve multiple roles - as oncogenic microbes, neutral bystanders, or tumor suppressors, and their dynamic balance can influence breast cancer onset and progression. (iii) Significant challenges remain in developing effective probiotics, prebiotics and infant formulas due to complex entanglements between beneficial and harmful microbes. This complexity suggests that broad-spectrum or one-size-fits-all probiotic approaches may prove inadequate, pointing instead to the need for personalized prebiotic/probiotic/infant-formula solutions to restore and maintain healthy mammary microbiomes.},
}

@article {pmid41244152,
year = {2025},
author = {Mizuno, M and Ogata, Y and Nishihara, Y and Nishio, M and Katano, H and Sekiya, I},
title = {Microbiome-based profiles of airborne bacteria to support microbial risk assessment in cleanroom environments.},
journal = {Regenerative therapy},
volume = {30},
number = {},
pages = {991-998},
doi = {10.1016/j.reth.2025.10.019},
pmid = {41244152},
issn = {2352-3204},
abstract = {INTRODUCTION: Maintaining aseptic conditions is essential for cell product processing, as sterilization cannot be applied to living cells. Conventional environmental monitoring relies on particle counts and culture-based colony-forming unit measurements. These indicators fail to capture much of the diversity and provenance of airborne microbes because many taxa are nonculturable or require growth conditions not supported by standard culture media. Therefore, comprehensive DNA-based microbiome analysis is critical for evaluating microbial risks that conventional methods may overlook; however, such studies remain limited in cleanroom settings. This study aimed to comprehensively visualize the structure of airborne microbial communities in cleanroom environments and clarify microbial risks that cannot be fully captured by particle counts or culture-based methods.

METHODS: We collected airborne bacterial DNA from cleanrooms with environmental Grades B, C, and D using a high-volume air sampler. The DNA was extracted and analyzed via 16S rRNA gene amplicon sequencing targeting the V3-V4 regions. Bioinformatic analysis was performed using the QIIME2 pipeline, and microbial diversity was assessed using alpha and beta diversity indices. Abundant taxa were categorized based on their likely origin (environment- or skin-derived), and their distributions were examined in relation to facility management practices.

RESULTS: Analysis revealed the consistent detection of skin-associated bacteria, such as Cutibacterium and Corynebacterium, and environmental bacteria, including Bacillus and Paracoccus, across all cleanroom grades. Alpha- and beta-diversities exhibited no significant differences among the grades. However, temporary and irregular increases in skin-derived bacteria indicated operator-related non-persistent contamination. This interpretation was supported by skewness and kurtosis analyses, which indicated occasional but noticeable shifts in microbial abundance, particularly in high-grade cleanroom environments.

CONCLUSIONS: This study demonstrates the limitations of conventional culture-based monitoring and underscores the value of DNA-based approaches for characterizing airborne microbial communities in cleanrooms. The detection of temporary increases in skin-associated bacteria indicates that operator-related contamination can occur even under stringent environmental conditions. These findings support the development of integrated monitoring strategies that can capture both the composition and temporal fluctuations of airborne microbiota to enhance microbial risk assessment.},
}

@article {pmid41243980,
year = {2025},
author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N},
title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1083},
pmid = {41243980},
issn = {1362-4962},
support = {320237//Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI)/ ; //Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Autónoma de México/ ; },
abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.},
}

@article {pmid41243859,
year = {2025},
author = {Nami, Y and Barghi, A and Sadeghi, M and Farhadi, T and Babaei, S and Haghshenas, B},
title = {Probiotics in Women's Health: Mechanisms, Benefits, and Potential Applications for Preventing Bacterial Vaginosis and Sexually Transmitted Diseases in Sexual Health Products.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {11},
pages = {e70086},
doi = {10.1111/apm.70086},
pmid = {41243859},
issn = {1600-0463},
support = {50004407//Kermanshah University of Medical Sciences/ ; },
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Female ; *Vaginosis, Bacterial/prevention & control/microbiology ; *Sexually Transmitted Diseases/prevention & control/microbiology ; *Women's Health ; Vagina/microbiology ; Lactobacillus/physiology ; Microbiota ; },
abstract = {This review summarizes key clinical findings on probiotics in addressing bacterial vaginosis (BV) and sexually transmitted diseases (STDs) in women. Lactobacillus bacteria play a critical role in maintaining a balanced vaginal microbiome by supporting an acidic environment and helping combat conditions like BV, AIDS, maternal group B Streptococcus (GBS), and candidiasis. Probiotics, either alone or combined with antibiotics, have shown promise in promoting microbiome recovery and potentially reducing recovery time. However, their efficacy depends on the strains used and specific conditions, emphasizing the need for further research. Additionally, probiotics can mitigate risks associated with excessive antibiotic use, including antibiotic resistance. The increasing interest in probiotics for women's sexual health has led to the development of specialized products, though identifying superior strains and optimal dosages remains an ongoing challenge. In conclusion, probiotics offer a non-invasive and cost-effective approach to supporting women's health by promoting microbiota balance and enhancing immune function. They offer a promising strategy for managing BV and potentially reducing STD risks. However, further research is necessary to standardize strains, dosages, and application methods in order to achieve consistent and effective outcomes.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Female
*Vaginosis, Bacterial/prevention & control/microbiology
*Sexually Transmitted Diseases/prevention & control/microbiology
*Women's Health
Vagina/microbiology
Lactobacillus/physiology
Microbiota

@article {pmid41243640,
year = {2025},
author = {Zhang, M and Zhang, Y and Feng, G and Gao, W and Chen, Z and Lei, S and Wang, L and Li, S and Xiao, X and Long, Q},
title = {Neuroprotective Effects of Xanthoceras sorbifolia Bunge Oil on Tic Disorders Through Regulation of the Serotonergic Synaptic Pathway and the Gut Microbiome.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70317},
doi = {10.1002/mnfr.70317},
pmid = {41243640},
issn = {1613-4133},
support = {20254092//Research Project of Chinese Medicine in TCM Bureau of Guangdong Province/ ; 20244046//Research Project of Chinese Medicine in TCM Bureau of Guangdong Province/ ; KF2025A005//Open Funding Project of Jiyuan Neurohealth Industry Research Institute of Guangdong Pharmaceutical University/ ; A2024378//Research Foundation of Medical Science and Technology of Guangdong Province/ ; 2018B030322012//Guangdong Provincial Key laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases/ ; 2025KTSCX056//Characteristic Innovation Projects of Regular Higher Education Institutions in Guangdong Province/ ; },
abstract = {Xanthoceras sorbifolia Bunge Oil (XSBO), a type of edible oil derived from a Chinese oilseed crop, is rich in a variety of bioactive compounds and has been recognized for its neuroprotective properties. Tic disorders (TD), a common and complex neurological disorder, are characterized by a multifaceted etiology and a lack of effective therapeutic interventions. Our research pioneers the exploration of XSBO's ability to ameliorate both behavioral symptoms and pathological changes associated with TD. We found that XSBO can activate the BDNF/TrkB signaling pathway, protect dopaminergic neurons, and thereby exert neuroprotective effects. In addition, XSBO has demonstrated potent antioxidant and anti-inflammatory properties that contribute to the attenuation of neuroinflammatory processes. In addition, XSBO has been shown to modulate the balance of the gut microbiome, correcting dysbiosis and, in turn, influencing the serotonergic synaptic pathway, which is critical for the amelioration and management of TD. In essence, XSBO presents a therapeutic profile for TD through a multi-pronged approach that includes neuroprotection, anti-inflammatory activity, and modulation of the brain-gut axis. This study not only delineates the mechanisms by which XSBO exerts its effects in the treatment of TD but also provides critical evidence to further refine its clinical use.},
}

@article {pmid41243448,
year = {2025},
author = {Vliex, LMM and Barnett, D and Monzel, E and Nauta, A and Oudhuis, GJ and Fassarella, M and Holst, JJ and Zoetendal, EG and Penders, J and Blaak, EE},
title = {2'-Fucosyllactose supplementation results in a transient improvement in gut microbial resilience after vancomycin use in adults with overweight or obesity: a randomized, double-blind, placebo-controlled intervention.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2580693},
doi = {10.1080/19490976.2025.2580693},
pmid = {41243448},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Male ; *Vancomycin/adverse effects/therapeutic use/administration & dosage ; Female ; Adult ; *Trisaccharides/administration & dosage ; Middle Aged ; *Anti-Bacterial Agents/adverse effects/therapeutic use/administration & dosage ; Feces/chemistry/microbiology ; *Obesity/microbiology/drug therapy ; *Overweight/drug therapy/microbiology ; Bacteria/classification/genetics/isolation & purification/drug effects ; Dietary Supplements ; Fatty Acids, Volatile/analysis/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Antibiotic-induced perturbations of the gut microbiome can be long-lasting and potentially affect host metabolic health. Strategies supporting microbial resilience are needed to mitigate the negative impact of antibiotics. We investigated the potential of 2'-fucosyllactose (2'-FL) supplementation after vancomycin use in a double-blind placebo-controlled randomized intervention among adults with overweight/obesity. Participants received oral vancomycin for seven days followed by 2'-FL or placebo for eight weeks. At baseline, after vancomycin use and after supplementation, glucose tolerance, insulin sensitivity, plasma lipids, glucagon-like peptide 1, inflammatory cytokines, fecal short-chain fatty acids (SCFAs) and branched-chain fatty acids were analyzed. Gut microbial diversity, composition and resilience were analyzed using 16S rRNA gene sequencing. Vancomycin use decreased gut microbial richness and diversity and disrupted microbiota composition and fecal SCFA concentrations. 2'-FL improved gut microbial resilience compared to placebo (pTreatment*Time = 0.043) after two weeks of supplementation, but differences were no longer observed at the end of the intervention. Two-week 2'-FL supplementation also differentially impacted specific bacterial taxa. Eight-week 2'-FL supplementation decreased fasting plasma interleukin-6 (IL-6) concentrations (pTreatment*Time = 0.041). 2'-FL intake led to transient improvements in gut microbial resilience after vancomycin use, indicating its beneficial potential to limit antibiotic-induced perturbations. Subsequent effects on metabolic health were limited and require further study.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Double-Blind Method
Male
*Vancomycin/adverse effects/therapeutic use/administration & dosage
Female
Adult
*Trisaccharides/administration & dosage
Middle Aged
*Anti-Bacterial Agents/adverse effects/therapeutic use/administration & dosage
Feces/chemistry/microbiology
*Obesity/microbiology/drug therapy
*Overweight/drug therapy/microbiology
Bacteria/classification/genetics/isolation & purification/drug effects
Dietary Supplements
Fatty Acids, Volatile/analysis/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid41243094,
year = {2025},
author = {Andreani-Gerard, CM and Jiménez, NE and Palma, R and Muller, C and Hamon-Giraud, P and Le Cunff, Y and Cambiazo, V and González, M and Siegel, A and Frioux, C and Maass, A},
title = {Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {142},
pmid = {41243094},
issn = {2524-6372},
support = {Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Soil microbiomes harbor complex communities from which diverse ecological roles unfold, shaped by syntrophic interactions. Unraveling the mechanisms and consequences of such interactions and the underlying biochemical transformations remains challenging due to niche multidimensionality. The Atacama Desert is an extreme environment that includes unique combinations of stressful abiotic factors affecting microbial life. In particular, the Talabre Lejía transect is a natural laboratory for understanding microbiome composition, functioning, and adaptation.

RESULTS: We propose a computational framework for the simulation of the metabolic potential of microbiomes, as a proxy of how communities are prepared to respond to the environment. Through the coupling of taxonomic and functional profiling, community-wide and genome-resolved metabolic modeling, and regression analyses, we identify key metabolites and species from six contrasting soil samples across the Talabre Lejía transect. We highlight the functional redundancy of whole metagenomes, which act as a gene reservoir, from which site-specific adaptations emerge at the species level. We also link the physicochemistry from the puna and the lagoon samples to metabolic machineries that are likely crucial for sustaining microbial life in these unique environmental conditions. We further provide an abstraction of community composition and structure for each site that allowed us to describe microbiomes as resilient or sensitive to environmental shifts, through putative cooperation events.

CONCLUSION: Our results show that the study of multi-scale metabolic potential, together with targeted modeling, contributes to elucidating the role of metabolism in the adaptation of microbial communities. Our framework was designed to handle non-model microorganisms, making it suitable for any (meta)genomic dataset that includes high-quality environmental data for enough samples.},
}

@article {pmid41243049,
year = {2025},
author = {Elghannam, MT and Hassanien, MH and Ameen, YAR and Turky, EA and ELattar, GM and ELRay, AA and ELTalkawy, MD},
title = {New insights into the effects of microbiome and its derived metabolites on targeted immunotherapy.},
journal = {Journal of the Egyptian National Cancer Institute},
volume = {37},
number = {1},
pages = {74},
pmid = {41243049},
issn = {2589-0409},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Neoplasms/immunology/therapy/microbiology/metabolism/drug therapy ; *Immunotherapy/methods ; Tumor Microenvironment/immunology/drug effects ; Molecular Targeted Therapy/methods ; Bile Acids and Salts/metabolism ; Fatty Acids, Volatile/metabolism ; Methylamines/metabolism ; Indoles/metabolism ; },
abstract = {The significance of gut bacteria and their byproducts is gaining greater recognition, especially in the realm of immunotherapy. An imbalance in gut bacteria or their byproducts is intricately linked to the onset, progression, and treatment of cancer. Metabolites derived from gut microbiota, including short-chain fatty acids (SCFAs), secondary bile acids (SBAs), indole derivatives, and trimethylamine oxide (TMAO), engage with cellular targets to initiate intracellular signaling pathways. These signals are conveyed to the cell, influencing its growth. Targeted therapies encompass a complex and ever-evolving area that is crucial in cancer management. Nonetheless, it is vital to recognize that targeted therapy encounters a multitude of challenges. Factors influencing the success of targeted therapy include drug resistance resulting from prolonged use, side effects, and variations in genetic mutations, tumor diversity, and the complex nature of the tumor microenvironment. Recently, we have deepened our understanding of the relationship between the gut microbiome and anticancer targeted therapies. This is one face of the molecular pathologic epidemiology. This prompts us to investigate promising treatment strategies linked to these gut bacteria and their metabolites, thereby unlocking new possibilities for targeted anticancer therapies.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Neoplasms/immunology/therapy/microbiology/metabolism/drug therapy
*Immunotherapy/methods
Tumor Microenvironment/immunology/drug effects
Molecular Targeted Therapy/methods
Bile Acids and Salts/metabolism
Fatty Acids, Volatile/metabolism
Methylamines/metabolism
Indoles/metabolism

@article {pmid41242989,
year = {2025},
author = {Mullish, BH and Roberts, LA and Williams, HRT},
title = {Microbiota transplants: the concept of 'microbiome mismatching' explored.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {374},
pmid = {41242989},
issn = {2059-3635},
support = {MR/Z504002/1//RCUK | Medical Research Council (MRC)/ ; IS-BRC-1215-20013//DH | National Institute for Health Research (NIHR)/ ; IS-BRC-1215-20013//DH | National Institute for Health Research (NIHR)/ ; IS-BRC-1215-20013//DH | National Institute for Health Research (NIHR)/ ; },
}

@article {pmid41242981,
year = {2025},
author = {Andonotopo, W and Bachnas, MA and Dewantiningrum, J and Adi Pramono, MB and Bernolian, N and Yeni, CM and Putra Wiradnyana, AAG and Hariyasa Sanjaya, IN and Akbar, MIA and Darmawan, E and Sulistyowati, S and Stanojevic, M and Kurjak, A},
title = {The fetal exposome and Preterm Birth: a systematic synthesis of environmental exposures and multi-omics evidence.},
journal = {Journal of perinatal medicine},
volume = {},
number = {},
pages = {},
pmid = {41242981},
issn = {1619-3997},
abstract = {OBJECTIVES: Preterm birth (PTB), defined as delivery before 37 weeks of gestation, is a leading cause of neonatal mortality and long-term developmental impairment. Its complex etiology, spanning environmental, genetic, psychosocial, and socio-economic domains, limits effective prediction and prevention. We systematically synthesized evidence on how environmental exposures influence PTB risk through multi-omic disruptions within a fetal exposome framework.

METHODS: A comprehensive literature search was conducted in major biomedical databases, following PRISMA guidelines. Ninety-five human studies published through May 2025 were included, encompassing exposures such as ambient air pollution, endocrine-disrupting chemicals, maternal stress, nutrition, occupational hazards, climate variability, and microbiome alterations. Two reviewers independently extracted data (exposure type, omics platform, biospecimen, PTB subtype) with inter-rater reliability assessment, and study quality was evaluated using the Newcastle-Ottawa Scale. Findings were narratively stratified by exposure category, study design, and spontaneous vs. indicated PTB.

RESULTS: Environmental exposures were consistently associated with disruptions in oxidative stress, inflammation, immune regulation, hormonal signaling, placental aging, and microbial ecology, mediated by multi-omic signatures in maternal, placental, and fetal tissues. Candidate biomarkers show promise for early risk stratification but lack validation and population-level predictive performance due to heterogeneous exposure assessment and study design.

CONCLUSIONS: Integrating fetal exposome concepts with multi-omics enhances mechanistic insight into PTB risk and may support biomarker discovery and precision-guided prenatal interventions. Clinical translation requires standardized exposure measurement, biomarker validation, and equity-focused implementation.},
}

@article {pmid41242603,
year = {2025},
author = {Nouri, M and Chalmeh, A and Pourjafar, M and Pirbornatan, A and Amirian, A},
title = {Dose-dependent effects of a multicomponent toxin binder on the gut-liver-mammary axis and metabolic resilience in early-lactation dairy cows.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106489},
doi = {10.1016/j.tvjl.2025.106489},
pmid = {41242603},
issn = {1532-2971},
abstract = {The transition period in dairy cows' entails coordinated endocrine, metabolic, and immunological reprogramming that increases susceptibility to physiological endotoxemia, oxidative stress, hepatic strain, and insulin resistance. We conducted a randomized, blocked, four-arm longitudinal trial to evaluate dose-dependent effects of a multicomponent yeast-clay-probiotic toxin binder (Magnotox®) on systemic endotoxin load, redox balance, hepatic-lipid metabolism, insulin sensitivity, and performance in multiparous Holstein cows (n = 20) from -21 to +80 days in milk (DIM). Cows received a basal diet (Ctrl) or basal diet supplemented with 50g·d[-][1] (TB-Low), 75g·d[-][1] (TB-Med), or 100g·d[-][1] (TB-High) Magnotox. Blood and milk were sampled at six time points for lipopolysaccharide (LPS), malondialdehyde (MDA), total antioxidant capacity (TAC), fibrinogen, biochemical liver and lipid indices, and insulin-resistance metrics (HOMA-IR, QUICKI, RQUICKI). Linear mixed-effects and Bayesian hierarchical models were applied. TB-High elicited a sustained within-group post-calving decline in serum LPS (≈ 0.4 loge pg·mL[-][1] from immediate postpartum to ≈ Day +50), whereas the time-averaged between-group difference versus Ctrl was small (estimated EMM Δ TB-High - Ctrl ≈ -0.05 loge pg·mL[-][1]). Milk LPS did not differ among groups on the time-averaged scale (p = 0.48). TB-High showed higher HDL (+8.13mg·dL[-][1], p = 0.004) and increased total protein (+0.59g·dL[-][1], p < 0.0001) and albumin (+0.23g·dL[-][1], p = 0.0128) compared with Ctrl, with no significant changes in NEFA, glucose, or LDL. Oxidative stress was attenuated across binder groups (e.g., MDA reduction in TB-High = -0.241 ± 0.060, p < 0.001); TAC was better preserved over time in TB-High (Time × Group p = 0.034) with a similar trend in TB-Med (p = 0.059). Fibrinogen showed a non-significant downward trend in TB-High. Body condition score exhibited an overall group effect (p = 0.002), with the largest increases observed in TB-High and TB-Low; milk yield and component percentages were numerically higher in TB-High and TB-Med but did not differ significantly among groups. In summary, high-dose (100g·d[-][1]) multicomponent binder supplementation modulated the gut-liver-mammary axis during the transition period by mitigating endotoxemia and oxidative stress and supporting hepatic protein indices and body-reserve preservation, without adverse shifts in key energy metabolites. Larger, multi-herd trials with integrated rumen-intestinal microbiome profiling and mechanistic omics are warranted to confirm efficacy, refine dosing, and assess long-term productive and reproductive outcomes.},
}

@article {pmid41242569,
year = {2025},
author = {Yang, XL and Li, XH and Dong, BB and Zheng, PG and Liu, Q},
title = {Oral Microbiota Dysbiosis Contributes to Occurrence of Pneumonia in Patients Admitted to Intensive Care Unit with Spontaneous Intracerebral Hemorrhage.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108166},
doi = {10.1016/j.micpath.2025.108166},
pmid = {41242569},
issn = {1096-1208},
abstract = {Post-stroke pneumonia (PSP) is a major contributor to the high mortality rate among patients with spontaneous intracerebral hemorrhage. Dysbiosis of oral microbiota contributes to various pulmonary diseases through the oral-lung axis. This study aimed to explore the association between PSP and microbiota dysbiosis and to construct an early prediction model for PSP. A total of 139 patients admitted to the emergency intensive care unit between October 2022 and April 2024 were enrolled; 82 developed PSP. Oral microecological characteristics were analyzed to establish a PSP prediction model incorporating clinical characteristics. The relative abundance of oral microbiome was higher in patients with PSP according to abundance-based coverage estimator (z= -2.08, P=0.03707) and Chao index (z= -2.09, P=0.03673). A predictive model for PSP was built based on eight microbiomes and four clinical characteristics with an area under the curve of 0.837 (confidence interval: 0.757-0.917). The model was verified with area under the curve of 0.786 (95% confidence interval: 0.643-0.929). Porphyromonas were the oral bacteria with the greatest difference in relative abundance between the two groups, and were therefore selected as the exposed bacterial species. Sprague-Dawley rats exposed to Porphyromonas gingivalis exhibited oral microbiota dysbiosis and developed pneumonia, which could be eliminated by metronidazole, confirming its causative role. In conclusion, oral microbiota dysbiosis contributes to PSP occurrence, representing a novel pathogenic mechanism that has promoted the establishment of an early prediction model for PSP, facilitated early diagnosis, and provided new insights into preventing PSP.},
}

@article {pmid41242566,
year = {2025},
author = {Yousefi-Hashemabad, MJ and Hosseini Kakroudi, M and Pourashory, M and Forouzan, K and Yazdanpanah, N and Saleki, K and Rezaei, N},
title = {Intratumoral Bacterial Microbiota in Gastrointestinal Adenocarcinoma: From Computational Insights to Clinical Practice.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108174},
doi = {10.1016/j.micpath.2025.108174},
pmid = {41242566},
issn = {1096-1208},
abstract = {Intratumoral microbiota refers to bacteria and other organisms residing within the tumor microenvironment and are intriguingly found throughout the TME, including in cancer cells, immune cells, and stromal components. Among these microbiota, bacteria have gained attention due to their emerging roles in tumor biology. Recent research has uncovered new pathophysiological and therapeutic roles for targeting intratumoral bacterial microbiota. Emerging evidence pointed out that certain taxa, including Fusobacterium nucleatum and Porphyromonas gingivalis, can drive tumorigenic activity, whereas taxa such as Lactobacillus spp. may act as a protective agent. Overall, bacteria can influence cancer progression through mechanisms including immune modulation, metabolic reprogramming, and genomic instability. Furthermore, advances in artificial intelligence (AI) and microbiome profiling have identified prognostic microbial signatures and markers of treatment response. In addition, the mediation of the tumor microbiota via probiotics, antibiotics, engineered microbes, and fecal transplants exhibits novel approaches in targeted cancer therapy. The present review captures the role of intratumoral bacterial microbiota in adenocarcinomas and their significance in cancer development and progression as evidenced by experimental and clinical research.},
}

@article {pmid41242446,
year = {2025},
author = {Hu, X and Meng, P and Han, P and Li, L and Sun, B and Zhang, X and Song, X},
title = {Targeted blockade of IL-23 receptor by engineered IgY antibody attenuates bacterial enteritis via reprogramming gut microbiota-immune axis in grass carp (Ctenopharyngodon idella).},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148967},
doi = {10.1016/j.ijbiomac.2025.148967},
pmid = {41242446},
issn = {1879-0003},
abstract = {Grass carp (Ctenopharyngodon idella), a key aquaculture species in China, is severely impacted by bacterial and viral infections, particularly A. hydrophila-induced enteritis, gill necrosis, and septicemia, necessitating sustainable alternatives to antibiotic-dependent disease management. In this study, an orally delivered anti-IL-23R IgY antibody (IgYIL-23R) was developed to attenuate bacterial enteritis in grass carp through dual modulation of gut immunity and microbiota. Microencapsulated IgYIL-23R (>1:8000 titer) was produced by immunizing hens with recombinant grass carp IL-23R and incorporated into fish diets (0.1-0.6 %). Optimal growth performance was observed in the 0.3 % IgYIL-23R group, with a 28.7 % increase in final weight and a 1.8-fold elevation in specific growth rate (P < 0.01). Concurrently, key pro-inflammatory genes (IL23R, IL-17, TNF-α) were suppressed by 60-75 %, and intestinal histoarchitecture was restored. IgYIL-23R administration significantly altered gut microbiota composition, reducing pathogenic Proteobacteria (68 %) and Aeromonas (82 %) while enriching beneficial Bacteroidetes (3.2-fold) and Akkermansia (4.1-fold) (P < 0.001). Upon challenge with A. hydrophila, fish fed 0.3 % IgYIL-23R exhibited a 55 % higher survival rate, minimal tissue damage, and enhanced metabolic functions, including antibiotic biosynthesis and α-linolenic acid metabolism. These findings demonstrate that targeted IL-23R blockade via oral IgY reprograms the microbiota-immune axis, providing a sustainable, antibiotic-free strategy for controlling enteritis in aquaculture.},
}

@article {pmid41242238,
year = {2025},
author = {Li, Y and Hou, J and Liu, M and Du, Z and Chen, H and Liu, G and Wang, Y and Yao, Y and Sun, P and Zhao, L and An, Y},
title = {Multiomics and machine learning unveil root exudate-microbiota interactions for cadmium control in rice.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127960},
doi = {10.1016/j.jenvman.2025.127960},
pmid = {41242238},
issn = {1095-8630},
abstract = {Human health and the safety of rice are threatened by cadmium (Cd) contamination in paddy soils. Although root exudates affect Cd bioavailability, the impact of complex mixtures of exudates and their interactions with rhizosphere bacteria on Cd speciation remain poorly understood. This study pioneers the "metabolome - microbiome - Cd speciation" coupling mechanism using a machine learning-assisted multi-omics analysis. Specifically, we characterized root-exudate composition, microbiome, and Cd speciation in rhizosphere soils of seven rice genotypes spanning low-to high-Cd accumulation. Of the 2659 root exudates identified, XGBoost-SHAP pinpointed ten key exudates that significantly influenced acid-extractable Cd (ACD-Cd; R[2] = 0.72 with grain Cd). Mantel testing revealed strong relationships (P < 0.01) between these key exudates and specific microbial taxa, including Candidatus Sulfobium mesophilum, Geotalea uraniireducens, and Hypericibacter terrae. Key exudates exhibited direct detrimental effects on ACD-Cd (λ = -0.727 to -0.486) and indirect effects through microbial recruitment (e.g., λ = -0.282 for hydroxysuberic acid via Candidatus Sulfobium mesophilum), as determined by partial least squares-structural equation modeling (PLS-SEM) quantification of interaction pathways. Overall regulation was primarily influenced by direct effects, primarily through chelation or precipitation with Cd ions, thereby reducing their bioavailability. Additionally, certain exudates such as L-theanine and Pimelic acid attracted Candidatus Sulfobium mesophilum, which participates in the sulfur cycle and forms insoluble metal sulfide precipitates, reducing the solubility and bioavailability of Cd in soils. This insight offers new targets for rhizosphere engineering to reduce Cd accumulation in rice grains.},
}

@article {pmid41242205,
year = {2025},
author = {Li, X and Gao, X and Yu, S and Du, F and Liu, J and Kan, X and Liu, X and Yao, D},
title = {Rhizosphere microbiota diversity and salt stress-alleviating functional genes in coastal wild salt-tolerant plants.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128397},
doi = {10.1016/j.micres.2025.128397},
pmid = {41242205},
issn = {1618-0623},
abstract = {Saline-alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt-alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth-promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline-alkali land reclamation.},
}

@article {pmid41241915,
year = {2025},
author = {Preetham, K and Chatterjee, J},
title = {Research trend on the emerging role of the microbiome in idiopathic male infertility.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {193},
pmid = {41241915},
issn = {1572-9699},
mesh = {Male ; Humans ; *Infertility, Male/microbiology/etiology ; *Microbiota ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Oxidative Stress ; },
abstract = {Idiopathic male infertility remains a major challenge in reproductive medicine despite extensive diagnostic workups, prompting research into novel etiologies and interventions. Emerging evidence highlights the microbiome's role in modulating male reproductive health. This study analyzes global research trends on idiopathic male infertility and associated microbial health over the past two decades using a structured bibliometric approach. Data extracted from Scopus were examined through Biblioshiny and VOSviewer. The analysis reveals a clear transition from traditional genetic and oxidative stress-based studies to microbiome-centered and multi-omics investigations. Increased Research output and citation rates in recent years, underscoring the growing relevance of microbiome studies. Key contributors like Agarwal A, Wang X, Zhang H, and Lundy SD advanced understanding from genetic and oxidative causes to gut-testis and semen microbiome interactions. Leading contributors and countries, particularly China and the USA dominate collaborative networks. Key themes link microbial dysbiosis, oxidative stress, inflammation, and hormonal imbalance with impaired spermatogenesis. Environmental and lifestyle factors, including diet, alcohol, antibiotics, endocrine disruptors, and microplastics, were increasingly recognized as influencing microbiome-mediated fertility. Mechanistic insights into the gut-testis axis, endotoxemia, immune modulation, and nutrient metabolism suggest avenues for diagnostics and microbiome-based interventions, including probiotics, nutritional modulation, and fecal microbiota transplantation.},
}

Male
Humans
*Infertility, Male/microbiology/etiology
*Microbiota
Dysbiosis/microbiology
*Gastrointestinal Microbiome
Oxidative Stress

@article {pmid41040223,
year = {2025},
author = {Keller, A and Adeniyi, A and Akkaya-Colak, KB and Festing, M and Schwieters, A and Kumar, R and Sledziona, J and Gupta, K and Stevens, P and Pietrzak, M and Coppola, V and Ranganathan, P and Ahmer, B and Forero, A and Knoblaugh, SE and Mihaylova, MM},
title = {Gasdermin C links nutrient and immune signaling to protist-induced type 2 immunity and intestinal repair.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41040223},
issn = {2692-8205},
support = {T32 CA229110/CA/NCI NIH HHS/United States ; T32 CA229114/CA/NCI NIH HHS/United States ; R00 AG054760/AG/NIA NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; T32 GM141955/GM/NIGMS NIH HHS/United States ; },
abstract = {The Gasdermin family of proteins has recently been implicated in tissue repair and homeostasis through their effector function in type 2 immunity and pyroptosis. Yet the role of Gasdermin C proteins has not been fully characterized in the mammalian intestine, where environmental factors can influence epithelial regeneration and repair. Here we report that Gsdmc2-4 genes are regulated in a nutrient-dependent manner and are suppressed with aging. We uncover that commensal protists in the gut regulate Gsdmc2-4 expression through activation of type 2 immune responses. In intestinal organoid experiments, we find that STAT6 is necessary for Gsdmc2-4 induction in response to type 2 cytokines; however, basal expression of Gsdmc2-4 in vivo is only partially diminished in Stat6 knockout animals. Finally, in protist-colonized animals, loss of Gsdmc1-4 exacerbated mucosal erosion and inflammation in response to Dextran sodium sulfate (DSS) exposure, implicating these proteins in coordinating epithelial responses to injury.},
}

@article {pmid41241730,
year = {2025},
author = {Hrala, M and Deissová, T and Andrla, P and Radová, L and Zahornacká, S and Bohošová, J and Macháčková, T and Křen, L and Hrunka, M and Pinkasová, T and Ambrozová, M and Bosák, J and Slabý, O and Šmajs, D and Jabandžiev, P},
title = {Tissue and stool microbiome in pediatric inflammatory bowel disease patients: diversity differs in patients with relapsing and non-relapsing Crohn's disease.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {90},
doi = {10.1186/s13099-025-00766-5},
pmid = {41241730},
issn = {1757-4749},
support = {LX22NPO5103//NextGenerationEU/ ; LX22NPO5103//NextGenerationEU/ ; LX22NPO5103//NextGenerationEU/ ; LX22NPO5103//NextGenerationEU/ ; LX22NPO5103//NextGenerationEU/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; },
abstract = {BACKGROUND: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are chronic conditions characterized by periods of clinical remission and relapse. Pediatric cases (pIBD) often have a more complicated disease course, where approximately 30% will develop a relapse within a year of diagnosis. Identifying prognostic markers for pIBD is important to optimize treatment and improve long-term outcomes. Our aim was to analyze the tissue microbiome, identify microbial prognostic markers, and validate their predictive power in non-invasive fecal samples.

RESULTS: Tissue and fecal microbiome were characterized from a prospective cohort comprising 33 therapeutically naïve pCD and 23 pUC patients, and 26 non-IBD pediatric controls, using amplicon 16S rRNA gene sequencing. Disease relapse was monitored for one year. At diagnosis, relapsing pCD patients exhibited a significantly decreased alpha diversity and altered beta diversity in tissue compared to non-relapsing pCD patients. Specific taxa were differentially abundant in relapsing pCD, with Barnesiella being the most depleted genus in tissue samples. Receiver Operating Characteristic (ROC) analysis identified Barnesiella (AUC = 0.818), Butyricimonas, and Collinsella as individual microbial tissue markers discriminating pCD relapse. Combining Barnesiella with the weighted Pediatric Crohn's Disease Activity Index (wPCDAI) further enhanced the specificity and sensitivity of the ROC analysis (AUC = 0.872 in tissue, 0.852 in feces), suggesting potential for non-invasive prognostic markers from stool.

CONCLUSIONS: Tissue and fecal microbial markers can predict relapse in pCD patients with high prognostic power, providing a basis for precision medicine and personalized treatment strategies in pIBD.},
}

@article {pmid41241723,
year = {2025},
author = {Carolin, E and Kathrin, T and Benoît, Q and Jean-Yves, G},
title = {Veterinary medicine in reintroduction and reinforcement of the European pond turtle Emys orbicularis: a review.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {668},
pmid = {41241723},
issn = {1746-6148},
mesh = {Animals ; *Turtles/physiology/microbiology ; *Conservation of Natural Resources/methods ; *Endangered Species ; *Veterinary Medicine ; Europe ; },
abstract = {The European pond turtle Emys orbicularis is among the most endangered reptile species in Europe, facing severe population decline due to habitat loss and environmental degradation. Conservation efforts increasingly rely on translocation-based strategies, including species reintroduction and reinforcement. Veterinary medicine plays a crucial role in ensuring the health and survival of captive-bred and translocated individuals, yet standardized health assessment protocols remain scarce. This review based on 418 publications synthesizes current veterinary practices related to freshwater turtle conservation, focusing on health monitoring before, during, and after translocation. We evaluate key medical concerns across different life stages, including prevention of zootechnical issues, pathogen screening, microbiome health, and adaptation challenges in captive and wild populations. Additionally, we propose standardized health assessment guidelines to improve diagnostic accuracy and long-term monitoring, and provide a global overview of the common health issues as well as normal blood reference values. By fostering transdisciplinary collaboration between veterinarians, researchers and conservationists, this study aims to refine best practices and ensure sustainable, evidence-based conservation efforts for E. orbicularis and other freshwater turtle species.},
}

Animals
*Turtles/physiology/microbiology
*Conservation of Natural Resources/methods
*Endangered Species
*Veterinary Medicine
Europe

@article {pmid41241720,
year = {2025},
author = {Patavoukas, E and Tong, B and Guðnadóttir, U and Charalampous, K and Brusselaers, N and Schuppe-Koistinen, I and Engstrand, L and Fransson, E and Wiberg-Itzel, E and Hugerth, L},
title = {Differences in the faecal microbiome of obese and non-obese pregnant women: a matched cohort study in Sweden.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {750},
pmid = {41241720},
issn = {1471-2180},
}

@article {pmid41241418,
year = {2026},
author = {Mustafa, SS and Schmale, I and Man, LX},
title = {Pathophysiology of Chronic Rhinitis and Chronic Sinusitis With and Without Nasal Polyposis.},
journal = {Immunology and allergy clinics of North America},
volume = {46},
number = {1},
pages = {1-11},
doi = {10.1016/j.iac.2025.09.001},
pmid = {41241418},
issn = {1557-8607},
mesh = {Humans ; *Sinusitis/etiology/immunology/physiopathology ; *Nasal Polyps/immunology/etiology ; Chronic Disease ; *Rhinitis/etiology/physiopathology/immunology ; Microbiota ; },
abstract = {This article covers the pathophysiology of chronic rhinitis and chronic rhinosinusitis (CRS), focusing on both phenotypic and endotypic distinctions. It highlights how genetic and environmental factors contribute to disease development, emphasizing the roles of epithelial barrier dysfunction and microbiome disruption. The article categorizes CRS into forms with and without nasal polyps, each involving unique immune responses and inflammation types. Specific endotypes are also discussed, highlighting the complexity and heterogeneity of these conditions.},
}

Humans
*Sinusitis/etiology/immunology/physiopathology
*Nasal Polyps/immunology/etiology
Chronic Disease
*Rhinitis/etiology/physiopathology/immunology
Microbiota